3 rd INTERNATIONAL BAU-DRUG DESIGN CONGRESS

Transcription

1 3 rd INTERNATIONAL BAU-DRUG DESIGN CONGRESS Novel Methods and Emerging Targets in Drug Discovery & Patented Drug Development Bahçeşehir University Istanbul, Turkey October

2 Coordinator of Congress Assoc. Prof. Dr. Serdar DURDAĞI Department of Biophysics School of Medicine, Bahcesehir University Istanbul, Turkey Scientific Organization Committe Prof. Dr. Ayhan ÇELİK Prof. Dr. Burak ERMAN Prof. Dr. Canan ATILGAN Prof. Dr. Claudiu SUPURAN Prof. Dr. Esin Akı YALÇIN Prof. Dr. İsmail YALÇIN Prof. Dr. Yavuz ERGÜN Assist. Prof. Dr. Abdulillah ECE Assist. Prof. Dr. Yasemin KESKİN Assoc. Prof. Dr. Elif ÖZKIRIMLI Assist. Prof. Dr. Mustafa GÜZEL Assoc. Prof. Dr. Serdar DURDAĞI Assist. Prof. Dr. Ümit AKBEY 2

3 Dear Colleagues, It is my pleasure and honor to host the 3rd International Bahçeşehir University (BAU) Drug Design Congress at the Bahcesehir University, School of Medicine, in Istanbul. It will bring together renowned industrial and academic experts to further discuss the recent developments and advances in the drug design field. The main theme of the BAU-Drug Design 2015 Congress will be Recent Developments in Structure- and Ligandbased Drug Design Methodologies, which will cover a wide range of critically important topics such as Molecular Simulations, Molecular Modeling, Docking, De Novo Drug Design, Analysis of Protein/Protein and Drug/Protein Interactions, High Throughput Screening Methods, Pharmacophore Modeling, Structural Bioinformatics, Fragment-based Design, ADME/Tox, Protein Flexibility and Dynamics, and High Performance Computing. The congress aims to serve as a platform for interaction among leading experimental and computational scientists from academia and industry to discuss the latest developments in methodology, application and approaches in the drug design field and to accelerate scientific discovery as well as reflect the key goals of the strategic priorities of the university: Integration, inter-disciplinary research on basic health sciences. I look forward to welcoming the participants to this exciting congress in the magical city of Istanbul in October Sincerely Yours, Turker KILIC, MD, Ph.D Professor of Neurosurgery Bahcesehir University (BAU) Faculty of Medicine, Dean Department of Neurosurgery, Chairman Istanbul Turkey 3

4 3rd INTERNATIONAL BAU DRUG DESIGN CONGRESS PROGRAM 1 OCTOBER 2015, THURSDAY - FAZIL SAY HALL 08:30-09:30 Registration 09:30-10:00 Opening Ceremony 10:00-10:45 BURAK ERMAN - CL1 Department of Chemical and Biological Engineering, Koc University Dynamic Aspects of Ligand-Protein Recognition and of Allosteric Activity 10:45-11:15 Coffee Break NANOBIOTECHNOLOGY Chairs: BURAK ERMAN 11:15-11:45 ENGIN UMUT AKKAYA - CL 2 Department of Chemistry Bilkent University Autonomous Switching Between Therapeutic and Diagnostic Modes: Theranostics via Molecular Logic 11:50-12:20 OZGUR SAHIN - CL 3 Bilkent University, Department of Molecular Biology and Genetics Biomarker-guided Sequential Targeted Therapy: A Novel Approach to Overcome Resistance in Rapidly Evolving Tumors 12:25-12:40 DIDEM SEN KARAMAN OP 1 Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering Shape and Surface Engineering as a Tool to Enhance the Antibacterial Activity of Mesoporous Silica Nanoparticles 12:40-13:30 Lunch PEPTIDE-BASED DRUGS Chairs: : CLAUDIU SUPURAN, ELIF OZKIRIMLI 13:30-14:00 ERDOGAN GULARI CL 4 University of Michigan, Department of Chemical Engineering Antimicrobial Peptides: Promising Alternatives to Antibiotics 4

5 14:05-14:35 HENRY DAVID HERCE CL 5 Technische Universität Darmstadt, Germany and Rensselaer Polytechnic Institute Drug Design and Delivery Using Cell-Penetrating Peptides: A Journey From Precise Molecular Mechanisms to in-vivo Applications 14:40-15:10 SYMA KHALID CL 6 University of Southampton,Systems and Synthetic Biology Modelling Group Computer Simulations to Inform the Future, Rational Development of Antibiotics 15:15-15:45 ELIF OZKIRIMLI CL 7 Bogazici University, Department of Chemical Engineering A Novel Approach in the Design of Cell Penetrating Peptides with Intracellular Activity 15:45-16:15 Coffee Break NOVEL DRUG DISCOVERY Chairs: AYKUT UREN, AYHAN CELIK 16:15-16:45 MUSTAFA GUZEL CL 8 Istanbul Medipol University,International School of Medicine, Department of Medical Pharmacology Beyond Warburg Effect: Treatment for Cancer as a Metabolic Disease 16:50-17:20 CLAUDIU SUPURAN CL 9 University of Florence, Neurofarba Department, Section of Pharmaceutical Sciences and Department of Chemistry Carbonic Anhydrase IX: A Drug Target for Anticancer and Antimetastatic Agents 17:25-17:45 OZGE SENSOY- OP 2 Medipol University Understanding G-Protein-Coupled-Receptor (GPCR) Signaling From Atomistic Molecular Dynamics Simulations 17:45-18:15 LEE LANCASHIRE (THOMSON REUTERS SPEAKER)- OP 3 Practical Applications of Systems Biology Bioinformatics in Translational Science and Drug Discovery POSTER PREVIEWS: 18:20-19:00 Mehmet Varol Mehlika Dilek Altıntop Bahar Demir Aylin Kalfa Ecem Kalemoglu 5

6 19:15-20:45 POSTER PRESENTATIONS 20:45-22:00 OPENING COCKTAIL 2 OCTOBER 2015, FRIDAY - FAZIL SAY HALL TARGETED THERAPY FOR ANTICANCER AGENTS Chairs: ISMAIL YALCIN, ILHAMI GULCIN 09:00-09:30 AYKUT UREN CL 10 Georgetown University, Lombardi Comprehensive Cancer Center Targeted Therapy for Prevention of Metastasis in Osteosarcoma 09:35-10:05 CEYDA ACILAN AYHAN CL 11 TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Instititute Evaluation of Metal Based Agents as a Platform in Cancer Therapy 10:10-10:25 MINE ERGUVEN OP 4 Istanbul Aydın University, Faculty of Engineering Celecoxib-Loaded Solid Lipid Nanoparticles Show Promising Effects for the Treatment of Breast cancer in vitro 10:30-10:50 MURAT KIZIL OP 5 University of Dicle, Faculty of Science, Department of Chemistry DNA-damaging Small Molecules as Anticancer Agents: Analogues of the Cytotoxic Antibiotic Leinamycin and Duocarmycin SA and Bisacridines with Aromatic Linking Chains 10:50 11:15 Coffee Break DRUG ENZYME INTERACTIONS Chairs: RAHIME SIMSEK, ANDREW BARRON 11:15-11:45 AYHAN CELIK CL 12 Gebze Technical University, Department of Chemistry Enzyme/Prodrug Therapy- Repurposing of Existing Drugs in the form of Prodrugs 11:50-12:20 ILHAMI GULCIN CL 13 Ataturk University, Department of Chemistry The Inhibition Effects of Antioxidant Compounds on Carbonic Anhydrase Isoenzymes 6

7 12:25-12:40 SEBNEM GOKHAN ESSIZ- OP 6 Kadir Has University, Bioinformatics and Genetics Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations 12:40-13:30 Lunch STRUCTURE ACTIVITY RELATIONSHIP STUDIES Chairs: OZLEM KESKIN, CEYDA ACILAN AYHAN 13:30 14:00 ISMAIL YALCIN CL 14 Ankara University, Department of Pharmaceutical Chemistry Binding Site Description of Benzothiazoles as the RND Efflux Pump AcrB Inhibitors 14:05-14:35 KEMAL YELEKCI CL 15 Kadir Has University, Faculty of Engineering and Natural Sciences Department of Bioinformatics and Genetics De Novo Drug Design for Human Dopamine Transporter 14:40-15:10 GULACTI TOPCU CL 16 Bezmiâlem Vakif University, Faculty of Pharmacy, Department of Pharmacognosy & Phytochemistry Some Bioactive Triterpenoids as Potential Anti- Alzheimer Agents 15:15-15:30 SHAHER BANO- OP 7 Bahcesehir University In-Silico Discovery of Novel Inhibitors Against Dengue Virus Protease Enzyme 15:30-16:00 Coffee Break DRUG DESIGN STUDIES Chairs: MALCOLM WAKINSHAW, OZLEM DILEK 16:00-16:30 ANDREW BARRON CL - 17 Rice University,Department of Chemistry Fullerene Based Amino Acid and Peptides: Designing Drug Delivery and Interactions 16:35-17:05 OZLEM KESKIN CL 18 Koc University, Department Chemical and Biological Engineering Interface Structures as Templates for Modeling Protein Interactions 17:10-17:30 SERDAR DURDAGI CL 19 Bahcesehir University, School of Medicine Discovering Novel Drug Candidates Using Virtual Screening Methods 7

8 17:35-17:50 GULSAH ÇIFCI-OP 8 Bogazici University, Chemistry Department Assessing the Ligand-protein Binding Modes with Computational Tools 17:55-18:10 EBRU DEMET AKTEN-OP 9 Department of Bioinformatics and Genetics, Faculty of Natural Sciences and Engineering, Kadir Has University Classification of Distinct Conformers of β 2 - Adrenergic Receptor (β 2 AR) Based on Binding Affinity of Ligands Through Docking Studies 18:15-18:30 SELVI DURMUS OP 10 Bilkent University, Department of Molecular Biology and Genetics, Faculty of Sciences Predicting Efficacy of a Novel Snticancer Drug Candidate in the Scope of ABC and OATP Drug Transporters 16:55-17:20 S.SIBEL ERDEM-OP 14 Istanbul Medipol University, International School of Medicine Department of Medical Biochemisrty, Regenerative and Restorative Medical Research Center Near-IR Fluorophores and Their Use in Photodynamic Therapy POSTER PREVIEWS: 18:50-19:20 Eda Candoken Burak Kuzu Ersoy Colak Ebru Gokdemir Mert Mestanoglu Gizem Ergun 19:30-21:00 POSTER PRESENTATIONS 3 OCTOBER 2015, SATURDAY - FAZIL SAY HALL COMPUTER AIDED DRUG DESIGN Chairs: MATTHIAS STEIN, FATIH SEN 09:00-09:30 CANAN ATILGAN - CL 20 Sabancı University Computational Analysis of Trimethoprim Resistance in Dihydrofolate Reductase 09:35-10:05 OSMAN UGUR SEZERMAN CL 21 Acibadem University Identification and Verification of Mutations Impacting Protein Stability and Function 10:10-10:40 ESIN AKI YALCIN CL 22 Ankara University, Faculty of Pharmacy, Pharmaceutical Chemistry Department Mechanism of Action of Neurokinin-1 Receptors as an Anticancer Target 8

9 10:45-11:15 Coffee Break MOLECULAR SIGNALING AND NETWORKS Chairs: ILKAY YILDIZ, GULACTI TOPCU 11:15-11:45 MATTHIAS STEIN - CL 23 Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems The Molecular Systems Biology of Signaling and Metabolic Networks 11:50-11:10 FATIH KOCABAS-OP 11 Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University Development of Fluorometric CCHFV OTU Protease Assay and Identification of Potent Inhibitors 12:25-12:40 NUR BASAK SURMELI- OP 12 Izmir Institute of Technology Mechanisms of Activation and Regulation of the Nitric Oxide Receptor Soluble Guanylate Cyclase 12:40-13:30 Lunch CHEMICAL BIOLOGY Chairs: SULEYMAN GOKSU, MUSTAFA CULHA 13:30-14:00 MALCOLM WALKINSHAW CL 24 The Centre for Translational and Chemical Biology, The University of Edinburgh Allosteric Enzymes in the Glycolytic Pathway as Antiparasitic Drug Targets 14:05-14:35 OZLEM DILEK CL 25 Istanbul Kemerburgaz University, School of Medicine Highly Efficient Phosphate-catalyzed Bioorthogonal Reaction with Improved Biocompatibility for Click Chemistry 14:40-15:00 RAMIN E. SALMAS-OP 13 Bahcesehir University School of Medicine Department of Biophysics Combination of in-silico Approaches on G Proteincoupled Receptors (GPCRs) 15:15-15:30 Coffe Break 9

10 NAONOMATERIALS- DRUG DELIVERY Chairs: ENGIN UMUT AKKAYA, OZGUR SAHIN 15:30-16:00 MUSTAFA CULHA CL 26 Department of Genetics and Bioengineering, Yeditepe University Influence of Surface Chemistry of Nanomaterials on Their Toxicity 16:05-16:35 FATIH SEN- CL 27 Dumlupinar University, Department of Biochemistry In Vivo Biosensing Via Near-Infrared Fluorescent Single-Walled Carbon Nanotubes 16:40-16:55 OLCAY BOYACIOGLU OP 15 Adnan Menderes University Faculty of Engineering Department of Food Engineering Doxorubicin Delivered to Target Prostate Cells without Collateral Damage to Non-Targeted Prostate Cells In Vitro 17:00-17:15 BEGUM ALAYBEYOGLU-OP 16 Bogazici University, Department of Chemical Engineering A Novel Approach to Deliver Peptides That Target Intracellular Enzymes 17:20-17:35 FABIENNE DUMOULIN-OP 23 Gebze Technical University Optimization of Photosensiting Tetrapyrroles Efficacy: Targeting Strategies and / or Combination of Therapeutic Effects 17:35-17:50 CLOSING CEREMONY AND POSTER AWARDS 3 OCTOBER 2015, SATURDAY D CONFERENCES HALL MOLECULER MODELING STUDIES Chairs: MALCOLM WAKINSHAW, TIZIANO TUCCINARDI 09:00-09:30 ILKAY YILDIZ CL 28 Ankara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry Moleculer Modeling Studies Topoisomerase I Inhibitors 09:35-09:50 ANDLEEB ZAHRA- OP 17 COMSATS Institute of Information Technology Molecular Dynamics Simulations Analysis of Hybrid Region of MiRNA-mRNA Involved In Chronic Kidney Diseases 10

11 09:55-10:10 CEMAL KOPRULUOGLU- OP 18 Institute of Organic Chemistry and Biochemistry AS CR Quantum Mechanical Scoring Function For Virtual Screening 10:15-10:30 HALEH ABDIZADEH - OP 19 Sabanci University, Faculty of Engineering and Natural Sciences Perturbation Response Scanning Highlights the Role of Electrostatics in Remote Control of Proteinprotein Disassociation 10:45-11:15 Coffe Break NEW LEAD COMPOUNDS Chairs: SYMA KHALID, H.DAVID HERCE 11:15-11:45 TIZIANO TUCCINARDI CL 29 Department of Pharmacy, University of Pisa Consensus Docking as a Tool for the Identification and Optimization of New Lead Compounds 11:50-12:10 NIL ERGE AKKAYA-OP 20 Istanbul Technical University, Faculty of Science and Letters Improving the Water Solubility of Curcumin By Ultrasonically Prepared Alginate - Curcumin Complexes And Alginate Nano-Beads 12:15-12:30 OZGE BAYRAKTAR OP 21 Bogazici University,Department of Computational Science and Engineering Computer-aided Discovery of Sphingosine Kinase 1 (Sphk1) Inhibitors 12:40-13:30 Lunch PROTEIN-PROTEIN INTERACTIONS Chairs: UGUR SEZERMAN, CANAN ATILGAN 13:30-14:00 DEVRIM GOZUACIK CL 30 Sabancı University, Molecular Biology, Genetics and Bioengineering Program Autophagy Modulation as a Treatment Approach 14:05-14:30 UMIT AKBEY CL 31 Aarhus University Structural Biology of Functional Amyloids from Bacterial Biofilms 14:30-15:15 WORKSHOP ( UMIT AKBEY ) NMR Supported Structural Biology and Drug Design 11

12 15:15-15:30 Coffee Break SYNTHESIS OF ACTIVE INGREDIENTS AND DRUG-RECEPTOR INTERACTIONS Chairs: ESIN AKI YALCIN, MUSTAFA GUZEL 15:30-16:00 RAHIME SIMSEK - CL 32 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University Condensed 1,4-DHP Derivatives as Acetylcholine Esterase Inhibitors 16:05-16:35 SULEYMAN GOKSU- CL 33 Ataturk University, Faculty of Science, Department of Chemistry The Synthesis of Novel Dopamine, Rotigotine and Rivastigmine Analogues as Biologically Active Compounds 16:40:16:55 BELGIN SEVER-OP 22 Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry Synthesis and Evaluation of Some Benzodioxolebased Thiosemicarbazone Derivatives as Novel Anticancer Agents 17:00-17:15 HATICE TOHMA-OP 24 Erzincan University, Faculty of Art and Sciences, Department of Chemistry Evaluation of Protein Thiol Oxidation in Ageing Heart of Mice with Catalase Over Expression or Exercise 17:20-17:35 AYSE EREN-OP 25 Bogazici University, Chemical Engineering Department Comparative Analysis of Arylsulfatase A and Its Mutants 12

13 CONGRESS LECTURE 13

14 CL-1 Dynamic Aspects of Ligand-Protein Recognition and of Allosteric Activity Burak Erman Chemical and Biological Engineering, Koc University, Istanbul, Turkey Before binding to a specific location on the protein in a stable manner, a ligand probes a large area on the surface of the protein. During the trial and error type attempts for finding a comfortable position on the surface, the ligand has translational, rotational and vibrational energy. Successful docking of the ligand on the protein, i.e., recognition of the specific site on the protein by the ligand, requires the absorption of this energy by the protein. The first requirement of binding is the availability of a thermal and mechanical reservoir, the protein, into which the ligand can dump its energy. The only mode of interaction at this point is the vibrations of the ligand on the surface where it is held by favorable interactions with the protein. The ligand with its intrinsic vibrations applies pseudo-periodic forces to the protein, which may be viewed as a forcing function on the protein, or as a 'pump'. Forced vibrations of an object has several interesting features. When the characteristic frequencies of the protein are matched with the characteristic frequencies of the forcing function, resonance may occur at which, a large amount of energy may be transferred to the protein. Thus, the ligand-protein problem may be viewed, in its simplest form, as a forced-vibrations problem, with the ligand applying the forcing function and the protein being subject to forced vibrations. The solution of this problem in the absence of noise is well known in the field of structural dynamics. In the first part of this talk, we will discuss simple solutions for the dynamics of ligand-protein interactions. The second aspect of of the ligand binding problem is centered on the question 'How does the dynamics of the protein change after ligand binding?' In a closely related issue, 'How does the dynamics of the protein change following the mutation of a residue?. These changes are of special significance in the presence of allosteric activity. In the second part of the talk, we will discuss the dynamics of allosteric activity in signal transduction from the binding or mutation site to other sites of functional importance. The emphasis is on changes in the dynamic correlation functions which require input from molecular dynamics simulations. At the present, the problem of estimating the changes in protein dynamics appears not to be generalizable, and every special case has to be treated separately. This imposes a special emphasis on high precision molecular dynamics simulations, which will be discussed in the second part of the talk. 14

15 CL- 2 Autonomous Switching Between Therapeutic and Diagnostic Modes: Theranostics via Molecular Logic Engin Umut Akkaya Department of Chemistry and UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey Photodynamic therapy of cancer is based on the sensitization of dissolved molecular oxygen in tumors to generate singlet oxygen. In recent years, highly elaborate schemes have been developed to deliver these sensitizers to the target regions, or control their photosensitization capability by cancer related parameters. Differences in ph1 and glutathione (GSH) concentrations2 have been exploited in such activatable photosensitizers. In an earlier study,3 we proposed a molecular 1:2 demultiplexer which is also a proof of principle for a unimolecular theranostic agent which can switch between therapeutic and imaging (diagnostic) modes. However, due to the acknowledged limitations of the system, there was room for significant improvement. Now, we are reporting a new design with different switching mechanisms. Our new target compound is capable of switching from an effective singlet oxygen generator to an apoptosis sensor, reversibly. This has been possible with an understanding of demultiplexer operation. We will discuss operation of this information processing agent, which may indeed be the elusive Killer App for molecular logic gates. 15

16 References: [1] S. Ozlem, E. U. Akkaya, J. Am. Chem. Soc., 2009, 131, 48. [2] S. Erbas-Cakmak, O. A. Bozdemir, Y. Cakmak, E. U. Akkaya, Chem. Sci., 2013, 4, [3] S. Kolemen, M. Isik, G. M. Kim, D. Kim, H. Geng, M. Buyuktemiz, T. Karatas, X. F. Zhang, Y. Dede, J. Yoon, E. U. Akkaya, Angew. Chem. Int. Ed., 2015, 54,

17 CL 3 Biomarker-guided Sequential Targeted Therapy: A Novel Approach to Overcome Resistance in Rapidly Evolving Tumors Özgür Şahin Bilkent University Combinatorial targeted therapies are more effective in treating cancer by blocking by-pass mechanisms or inducing synthetic lethality. However, their clinical application is hampered by resistance and toxicity. To meet this important challenge, we developed and tested a novel concept of biomarkerguided sequential applications of various targeted therapies using ErbB2-overexpressing/PTEN-low, highly aggressive breast cancer as our model. We found that sustained activation of ErbB2 and downstream pathways drives trastuzumab resistance in both PTEN low/trastuzumab resistant breast cancers from patients and mammary tumors from genetically engineered mice. Although lapatinib initially inhibited trastuzumab resistant mouse tumors, tumors by-passed the inhibition by activating the PI3K/mTOR signaling network which was also observed in neo-adjuvant lapatinib-treated patients manifesting lapatinib-resistance. Trastuzumab+lapatinib resistance was effectively overcome by sequential application of a PI3K/mTOR dual kinase inhibitor (BEZ235) with no significant toxicity: however, BEZ235 treatment led to increased ErbB2 expression and phosphorylation in mouse tumors and in 3-D culture leading to BEZ235 resistance. Mechanistically, we identified ErbB2 protein stabilization and activation as a novel mechanism of BEZ235 resistance which was reversed by subsequent lapatinib+bez235 combination. Remarkably, this sequential application of targeted therapies guided by biomarker changes in the rapidly evolving resistant tumors doubled the life-span of mice bearing exceedingly aggressive tumors. This fundamentally novel approach of using targeted therapies in a sequential order can effectively target and reprogram the evolving resistant cancer signaling networks during treatment. 17

18 CL-4 Antimicrobial Peptides: Promising Alternatives to Antibiotics Saadet Albayrak Guralp, Kaitlyn Minchella, Erdogan Gulari Chemical Engineering Department University of Michigan Ann arbor, MI The rapid increase in antibiotic-resistant pathogenic bacteria is one of the major health problems that we currently face due to excessive and often inappropriate use of antibiotics in human and animal health care. Methicillin-resistant Staphylococcus aureus (MRSA), Vancomycin-resistant Enterococcus faecium (VRE), and multi-drug resistant Pseudomonas aeruginosa are the most common pathogens in healthcare facilities in the USA causing ~23000 deaths and two million infections per year. With an estimated 9 million TB new cases diagnosed and 1.5 million deaths in 2013 alone 1 TB remains as one of the most challenging diseases to treat. Rapid emergence of multidrug resistant (MDR-TB), and extensively drug resistant (XDR-TB) indicate the urgent need to develop new therapeutics which are more robust than the current generation of antibiotics. Inspired from nature s own defense mechanisms in fighting infections, our research focuses on natural microbicidal molecules called antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs). AMPs are short peptide sequences with a broad range of antimicrobial activities and present great potential as alternative drugs to conventional antibiotics due to their lower propensity for inducing drug resistance. Having similar morphologies with AMPs, (CPPs) are also capable of targeted cell-binding and disruption, and have shown very promising activities against a variety of other microbes. These ribosomally-synthesized peptides can easily be engineered by sequence alterations to improve their activity, specificity and stability. By generating libraries of peptide derivatives, one can study a large number of candidates simultaneously in a timely manner. Our lab specializes in a novel methodology where in silico custom designed peptide-encoding oligonucleotide libraries are cloned and expressed in a cellular host for rapid screening of active molecules. The combination of parallel oligonucleotide synthesis with microbial expression systems not only offers complete flexibility for sequence design but also allows for economical construction of very large peptide libraries. We have applied this approach to discovery of novel AMPs by constructing and screening a custom library of twelve thousand plantaricin-423 mutants in Escherichia coli where we identified many novel derivatives with enhanced specific activities against Listeria and Enterococcus species. In a smaller study, we have explored the anti-mycobacterial activity of a well-known CPP pvec and its derivatives and an AMP-mimic CSA-13 against several Mycobacterium species. Our preliminary data showed that at least two novel pvec mutants have an improved activity profile and display synergism with a common anti-mycobacterial antibiotic rifampicin against M. bovis BCG. 18

19 CL-5 Drugs Design And Delivery Using Cell-Penetrating Peptides: A Journey From Precise Molecular Mechanisms To In-Vivo Applications Henry David Herce Technische Universität Darmstadt, Biology Department, Germany Rensselaer polytechnic institute, Physics Department and Center for Biotechnology and Interdisciplinary Studies, US Guanidinium-rich molecules, such as cell-penetrating peptides, efficiently enter into living cells in a non-endocytotic energy-independent manner transporting a wide range of cargoes, including drugs and biomarkers. 1 The mechanism by which these highly cationic molecules efficiently cross the hydrophobic barrier imposed by the plasma membrane has remained, until now, as a fundamental open question. I will present a central mechanism based on a combination of computational, in vitro and in vivo experimental evidence that reveals an efficient energy-independent cellular translocation mechanism for arginine-rich molecules. 2-4 I will show how to apply these principles, which appear to be universal across cells from different species and kingdoms, to design, visualize and deliver drugs and biomarkers into living cells. 5- References: 1) Herce H.D.; Garcia A.E., J Biol Phys. 2007, 5, ) Herce H.D., Garcia A.E., Cardoso M.C., J Am Chem Soc., 2014, 136, ) Herce H.D., Garcia A.E., Proc Natl Acad Sci U S A, 2007,104, ) Herce H.D., Garcia A.E., Litt J, Kane RS, Martin P, Enrique N, Rebolledo A, Milesi V., Biophys J., 2009, 97, ) Herce H.D., Rajan M, Lättig-Tünnemann G., Fillies M,. Cardoso M.C.., Nucleus. 2014, 5, ) Nischan N., Herce H.D., Natale F., Bohlke N., Budisa N., Cardoso M.C., Hackenberger C.P.., Angew Chem Int Ed Engl. 2015, 54, ) Herce H.D., Deng W., Helma J., Leonhardt H., Cardoso M.C.. Nat Commun., 2013, 4,

20 CL 6 Computer Simulations To Inform The Future, Rational Development Of Antibiotics Syma Khalid University of Southampton, UK. All cells, whether prokaryotic or eukaryotic, are separated from the external environment by at least one membrane. These membranes provide a physical barrier to the entry of unwanted or toxic substances including drugs, into the interior of the cell. To enter the cell, drugs must either permeate through the lipid component of the bilayers, or through the proteins that are embedded within the membranes. The native membrane proteins are estimated to be the targets of > 50% of drugs. Some drugs, including many antibiotics work by causing cell lysis through direct disruption of the cell membrane, rather than entry into the cell. Thus it is clear, that understanding the cell membranes of bacteria are imperative for the future, rational design of novel drugs, in particular antibiotics. I will present results of our recent efforts to simulate the interaction of antimicrobial peptides with the membranes of Gram-negative bacteria. I will first describe how we constructed realistic, complex models of the membranes at two different levels of resolution, followed by a discussion of how the models are being used to understand the action of antibiotics. I will conclude with a discussion of future directions and possibilities for collaboration with experimental colleagues. 20

21 CL 7 A Novel Approach İn The Design Of Cell Penetrating Peptides With İntracellular Activity Elif Özkırımlı Boğaziçi University, Chemical Engineering Department, Istanbul, Türkiye Cell penetrating peptides that can carry cargo into the cell are of intense research interest in the field of drug delivery especially for their ability to transport hydrophilic or large molecules 1,2. These peptides can act as inert carriers to transport the bioactive drug into the cell. On the other hand, a cell penetrating peptide that harbors intrinsic bioactivity holds an even greater promise as a more efficient drug. In this talk, I will present our recent efforts toward the design of a chimeric peptide that posseses cell penetration and enzyme inhibition capabilities. The peptide comprises the hydrophobic region of pvec, a cell penetrating peptide 3, and different beta-lactamase inhibitory peptides 4,5. Our computational and in vitro and in vivo experimental results suggest that the peptide is able to cross the membrane, inhibit intracellular beta-lactamase and kill beta-lactamase producing antimicrobial resistant cells 6. Our ultimate goal is to devise a strategy that can be applied to the design of peptides that target other intracellular enzymes. Funding by TUBITAK (114M179) and Bogazici University Research Grant 09HA504P is gratefully acknowledged. Resources: 1. Copolovici DM, Langel K, Eriste E, Langel Ü. Cell-penetrating peptides: design, synthesis, and applications. ACS Nano Mar 25;8(3): Reissmann S. Cell penetration: scope and limitations by the application of cell-penetrating peptides. J Pept Sci Aug Elmquist A, Hansen M, Langel U Ü. Structure-activity relationship study of the cellpenetrating peptide pvec. Biochim Biophys Acta Jun 1;1758(6): Rudgers GW, Huang W, Palzkill. Binding properties of a peptide derived from betalactamase inhibitory protein. Antimicrob Agents Chemother Dec 1;45(12): Huang W, Beharry Z, Zhang Z, Palzkill. A broad-spectrum peptide inhibitor of betalactamase identified using phage display and peptide arrays. Protein Eng Nov 1;16(11): Alaybeyoglu B, Sariyar Akbulut B, Ozkirimli E. A novel chimeric peptide with antimicrobial activity. J Pept Sci Jan 19;21(4):

22 CL 8 Beyond Warburg Effect: Treatment For Cancer As A Metabolic Disease Mustafa Güzel Medipol University, Faculty of Medicine, Istanbul, Turkey Cancer still remains the second leading cause of death in the world after heart disease and cardiovascular complications. Moreover, survivors of cancer still continue to suffer from symptoms of pain, fatigue, and depression despite existing treatment advances for cancer treatment. Even though numerous pharmacological therapies have been developed in the past decade, the advantage of new treatment options remains important in the fight against this deadly disease. It is now well understood that protein kinases play key roles in the growth and survival of cancer cells by regulating their onset of DNA synthesis, their response to DNA damage and their entry, progression, and exit from mitosis. Clinical validations prove that protein kinases are an attractive class of therapeutic drug targets for cancer as demonstrated with the recent approval of six protein kinase inhibitors. The Warburg effect describes the particular reliance of cancer cells on glycolysis for energy. Increased glycolysis and acid resistance have been postulated to be an essential part of carcinogenesis, conferring a significant growth advantage as well as promoting typical tumor progression. Targeting accelerated glycolysis in cancer cells is a new promising modality for treatment of cancer. Inhibition of glycolysis can be done without significant side effects, and such treatment will be additive to most known cancer therapies. Recent studies show that Methyl Jasmonate reveals promising results for treatment of cancer. During the presentation the role of Aerobic Glycolysis for tumor growth and small molecule drug discovery and development efforts as well as their therapeutic applications for oncological indications will be highlighted. References: 1. "Substituted Fused Oxazoline Derivatives Useful as Antitumor Agents"; Mustafa Guzel, Devi Reddy, Rongyuan Xie, Dharma R. Polisetti, Soumya Sahoo, Stephen Davis, Mohan Rao, Kalpathy Santhosh, and Adnan M. M. Mjalli; High Point Pharmaceuticals Inc., High Point, NC, Patent #US 62/060,087, Novel Anticancer agents for hexokinase inhibition-substituted cyclic-3-indole derivatives ; Mustafa Guzel, Rongyuan Xie, Dharma R. Polisetti, Robert C. Andrews, Adnan M. M. Mjalli, and Stephen Davis; High Point Pharmaceuticals Inc., High Point, NC, PCT-Application No: US2014/

23 3. "Substituted Indole Derivatives Useful as Antitumor Agents"; Mustafa Guzel, Devi Reddy, Rongyuan Xie, Dharma R. Polisetti, Soumya Sahoo, Stephen Davis, Mohan Rao, Kalpathy Santhosh, and Adnan M. M. Mjalli; High Point Pharmaceuticals Inc., High Point, NC,, PCT- Application No: US2014/ Coller A. H.; İs cancer a Metabolic Disease ; The American Journal of Pathology, (2014), vol:184, No:1, p: Mathupala S. P., Ko Y. K, Pedersen P. L.; Hexokinase-II: Cancer s double-edged sword acting as both facilitator and gatekeeper of malignancy when bound to mitochondria ; Oncogene, (2006), vol:25, p: Lu W., Logsdon C. D., Abbruzzese J. L.; Cancer Metabolism and Its Therapeutic Implications ; Journal of Cell Science & Therapy, (2013), vol: 2, No: 2, p: Heiden M. G. V. ; Targeting Cancer Metabolism: a Therapeutic Window Opens ; Nature Reviews: Drug Discovery, (2011), vol: 10, p: Cohen S., Flescher E.; Methyl jasmonate: A plant stress hormone as an anti-cancer drug ; Phytochemistry, (2009), vol: 70, p: Goldin, N. et al.; Methyl jasmonate binds to and detaches mitochondria-bound hexokinase ; Oncogene, (2008), vol: 27, p: Flescher, E.; Jasmonates in cancer therapy ; Cancer Letters, (2007), vol: 245, p: Pathania, D., Millard, M., Neamati, N.; Opportunities in discovery and delivery of anticancer drugs targeting mitochondria and cancer cell metabolism ; Advanced Drug Delivery Reviews, (2009), vol: 61, p: Rotem, R. et al.; Jasmonates: Novel anticancer agents acting directly and selectively on human cancer cell mitochondria ; Cancer Research, (2005), vol: 65, No:5, p:

24 CL 9 Carbonic Anhydrase IX: A Drug Target For Anticancer and Antimetastatic Agents Claudiu T. Supuran University of Florence, Neurofarba Department, Section of Pharmaceutical Sciences and Department of Chemistry, Via della Lastruccia 3, 5019 Sesto Fiorentino, Firenze, Italy. Carbonic anhydrase IX (CA IX) is a membrane-bound, hypoxia-inducible enzyme that is highly expressed in many types of solid tumors, but shows very restricted expression in normal tissues [1]. The X-ray crystal structure of this enzyme in adduct with sulfonamide inhibitors was resolved by my group, affording for structure-based drug design campains [2-6]. Many new classes of CA IX inhibitors were reported in the last years, among which sulfonamides, sulfamates, coumarins, sulfocoumarins, polyamines, etc. [1-6]. CA IX plays an important functional role in processes critical for tumor growth and metastasis, including ph regulation, survival, adhesion and migration [1, 2]. The tumor-specific expression of CA IX and its association with cancer progression and poor treatment outcome has led to interest in targeting this enzyme for cancer therapy. The development of pharmacologic inhibitors that selectively target this isoform without off-target inhibition of cytosolic CAs is critical for their use as cancer therapeutics [1,2]. We described a series of novel ureido-substituted benzene-sulfonamides and coumarins/sulfocoumarins that selectively and potently inhibited CA IX activity in vitro, and reduced tumor growth and metastasis in vivo [3-5]. These compounds suppressed the drop in extracellular ph in a cell-based CA IX activity assay. Inhibition of invasion and/or induction of cell death were also observed when highly metastatic MDA-MB-231 LM2-4 breast cancer cells were cultured in hypoxia. Preclinical evaluation of selected ureidosulfonamide inhibitors demonstrated a correlation between the amount of intratumoral CA IX expressed in vivo and the degree of inhibition of tumor growth. Treatment of animals harboring highly CA IX-positive MDA-MB-231 LM2-4 or T4 orthotopic breast tumors resulted in significant inhibition of tumor growth and increased survival times. Furthermore, treatment of mice harboring human orthotopic breast tumors with ureido-sulfonamides in combination with paclitaxel resulted in significantly reduced tumor growth compared to either treatment administered alone. Bioluminescence imaging of lungs resected from treated mice revealed that lung metastases were virtually absent from animals treated with the combination therapy. Collectively, these studies provided strong proof of principle data for the therapeutic inhibition of CA IX activity for primary tumor growth and metastasis formation, especially when used in combination with conventional chemotherapy. One of these ureidosulfonamides possessing such properties, SLC-0111, entered in Phase I clinical trials for the treatment of solid metastatic tumors in October 2014 [7]. 24

25 1. Supuran, C.T. Nature Reviews Drug Discovery, 2008, 7, Neri, D., Supuran C.T. Nature Reviews Drug Discovery, 2011, 10, Touisni, N., et al, J. Med. Chem. 2011, 54, Pacchiano, F., et al, J. Med. Chem. 2011, 54, Lou, Y., et al, Cancer Res. 2011, 71, Alterio et al., Chem. Rev. 2012, 112, ClinicalTrails.gov: Safety Study of SLC-0111 in Subjects With Advanced Solid Tumours - ClinicalTrials_gov.mht. 25

26 CL - 10 Targeted Therapy For Prevention Of Metastasis in Osteosarcoma Aykut Üren Georgetown University, Washington DC, USA Osteosarcoma (OS) is the most common type of primary bone cancer in children and adolescents. Respiratory failure due to pulmonary metastasis remains the main cause of mortality in patients suffering from OS. There is strong evidence to suggest that Ezrin is a critical factor in the metastasis of OS cells, and high ezrin expression is associated with malignant progression and poor survival in osteosarcoma. Ezrin is a membrane-cytoskeleton linker protein that is involved in several dynamic cellular functions including cell-cell adhesion, cell shape and motility, membrane trafficking, cellular proliferation and apoptosis. Thus, targeting proteinprotein interactions involving ezrin with small molecules is a promising approach for managing lung metastasis. In an effort to achieve this goal, our earlier studies have established that NSC can directly interact with ezrin and inhibits its function in multiple assays. Our initial findings are expanded to include a transgenic mouse model of osteosarcoma that develops spontaneous lung metastasis and testing the ezrin inhibition in dog and human OS cell lines. NSC inhibited lung metastasis in the transgenic mouse model and blocked ezrin-mediated motility of both dog and human OS cells in culture and their invasion of Human Umbilical Vein Endothelial Cells (HUVEC) monolayer. As part of ongoing studies addressing the probable mechanisms underlying NSC action, we performed affinity-binding assays utilizing ezrin-coated sepharose beads in order to identify which putative protein interactions with ezrin are disrupted by our small molecule. Our results discovered novel ezrin binding proteins that are involved in transcription and translation suggesting a completely new molecular function of ezrin that is independent from its conventional role at the plasma membrane. Our results suggest that NSC can modulate ezrin function and may prevent tumor metastasis in vivo. Thus,targeting ezrin function with small molecules could be a novel approach to prevent tumor metastasis in OS and other tumors with elevated ezrin in their metastatic subclones. Furthermore, our findings highlight a novel molecular mechanism for ezrin in cancer metastasis. 26

27 CL 11 Evaluation Of Metal Based Agents As A Platform in Cancer Therapy Ceyda Açılan Ayhan TUBITAK Marmara Research Center Genetic Engineering and Biotechnology Instititute Gebze, Turkey Since the discovery of cisplatin, metal based agents have gained significant interest of researchers as potential anticancer drugs. Several drugs have been rationally synthesized to overcome the hurdles of cisplatin, with improved pharmacological properties and different mechanisms of action. Search for less toxic, but still potent anti-cancer agents revealed several compounds complexed different metals, such as platinum, palladium or copper complexes. Here, we describe several families of transition metal complexes, aiming to obtain stable, efficient and selective compounds, with different activity mechanisms. The complexes under study was evaluated for their electronic absorption spectra, thermal behavior, viscosity, fluorometric titration and agarose gel migration of plasmid DNA following drug exposure. Cell viability was compared in different types of cancers, in comparison to normal cells. The mean of cell death was assessed using live cell imaging, DNA morphology, and TUNEL. The effect of the agents on cellular DNA was investigated through gh2ax and 8-oxo-G staining. The agents were able to induce oxidative stress based on DCFDA analysis. Lastly, the cell cycle specificity was studied and the complexes were not found to cell cycle specific to exert their toxic effect. In summary, the agents under study grant premise for further studies. 27

28 CL- 12 Enzyme/Prodrug Therapy- Repurposing Of Existing Drugs In The Form Of Prodrugs Ayhan Çelik a, Gülden Yetiş a, Tuğba Güngör b, Meymet Ay b. a Gebze Technical University, Department of Chemistry-Biochemistry, Kocaeli, Turkey b Çanakkale 18 Mart University, Department of Chemistry, Çanakkale, Turkey Conversion of an inactive drug (prodrug) into an active drug (or its metabolites) is the starting point of the Enzyme Prodrug Therapy (EPT), one of the novel strategies attracted attention increasingly over 20 years with entering clinical trials in the last 6 years for cancer therapy, in particular [1]. It usually consist of a three component system; a prodrug, and an activating enzyme (or encoding gene) and a carrier. The advantages of the system over the traditional therapies are enhanced efficacy and reduced toxicity. Among the most studied strategies (an enzyme with a prodrug) are herpes simplex virus thymidine kinase (HSV-TK) with ganciclover (GCV), cytosine deaminase (CD) with 5-fluorocytosive (5-FC), cytochromes P450 with cyclophosphamide/ifosfamide (CPA/IFA) and nitroreductase with CB1954. Here, our works in this area are mainly focused on the nitroreductase system. Finding and characterisation of novel nitroreductases with enhanced activity and selectivity are of importance to the success of EPT together with novel small molecules as potential prodrug candidates [2]. We also discussed the use of existing, FDA approved drugs in the form of produgs not only for cancer therapy but for antimicrobial studies. By utilising EPT, we believe that, significant contribution will be possible for drug development by reducing costs and saving precious time. Key Words: Enzyme Prodrug Therapy, prodrugs, drug metabolites, nitroreductases, biotransformation. References 1. Rautio J, Kumpulainen H, Heimbach T, Oliyai R, Oh D, Järvinen T, Savolainen J. Prodrugs: design and clinical applications. Nat Rev Drug Discov Mar;7(3): Çelik A, Yetiş G. An unusually cold active nitroreductase for prodrug activations. Bioorg Med Chem Jun 1;20(11): This work was funded by The Scientific and Technological Research Council of Turkey (TUBITAK, Grant No. 110T754 and 113Z706) 28

29 CL 13 - The Inhibition Effects Of Antioxidant Compounds On Carbonic Anhydrase Isoenzymes İlhami Gülçin Atatürk University, Faculty of Sciences, Department of Chemistry,Erzurum-Turkey Antioxidant compounds can scavenge free radicals and increase shelf life by retarding the process of lipid peroxidation, which is one of the major reasons for deterioration of food, medicine and pharmaceutical products during processing and storage. An antioxidant molecule has been defined as any substance when found in low concentrations compared to that of an oxidizable substrate significantly delays or inhibits the oxidation. The major antioxidant compounds are especially phenolics and flavonoids, which are responsible for their health benefits. On the other hand, carbonic anhydrase (CA, EC ) is a ph regulatory enzyme in all life kingdoms, being found in organisms all over the phylogenetic tree. It catalyzes the hydration of carbon dioxide (CO 2 ) to bicarbonate (HCO - 3 ) and the corresponding dehydration of HCO - 3 in acidic medium with regeneration of CO 2. Also, CA isoforms are found in a variety of tissues. They participate in several crucial biological processes such as acid-base balance, respiration, CO 2 and ion transportation, bone resorption, ureagenesis, gluconeogenesis, lipogenesis and electrolyte secretion. On the other hand, the phenyl moiety of phenol was found to lay in the hydrophobic part of the CA active site, where CO 2, the physiologic substrate of the CAs, binds in the precatalytic complex, explaining thus the behavior of phenol as a unique CO 2 competitive inhibitor. This presentation consists of two main sections. The first section is devoted to main phenolic antioxidant compounds in the foodstuffs and beverages. The second general section is about some definitions of CA inhibitory effects of the main phenolic compounds used for antioxidant activity. The phenolic compounds and acids had marked especially CA I, and II inhibition effects and might be used as leads for generating CA isoenzyme inhibitors. This class of compounds may lead to isoform-selective inhibitors targeting just one or few of the medicinally relevant CAs. In addition, there are given some chemical and kinetic basis and technical details related to phenolic antioxidant compounds and CA isoenzymes. 29

30 CL 14 - Binding Site Description Of Benzothiazoles As the RND Efflux Pump Acrb Inhibitors Ismail Yalcin a, Serap Yilmaz a, Gulsen Altinkanat-Gelmez b, Kayhan Bolelli a, Deniz Guneser- Merdan b, M. Ufuk Over-Hasdemir b, Esin Aki-Yalcin a a Pharm. Chemistry Dept, Faculty of Pharmacy, Ankara University, Ankara, TR-06100, Turkey b Medical Microbiology Dept., Faculty of Medicine, Marmara University, Istanbul, Turkey Resistance-nodulation-division (RND) family is usually predominant in Gram-negative bacteria efflux systems and it is the most prevalent mechanism in multidrug resistant E. coli. Efflux pumps exemplify a unique phenomenon in drug resistances of bacteria that possess a single mechanism causing multidrug resistance (MDR) against several different classes of antibiotics. In E. coli, AcrAB-TolC serves as the major RND family tripartite efflux pump system that AcrB resides in the inner membrane and it is the energy transduction and substrate specificity determinant of the entire three-component pump assembly to extrude drugs out of the cell 1-3. The aim of this present study is (i) to evaluate novel lead compounds that are active as the RND AcrAB- TolC efflux pump inhibitors (EPIs) to reverse the antibacterial activity of antibiotics, particularly ciprofloxacin and/or chloramphenicol, in the AcrAB-TolC overexpressor E. coli clinical isolate; and (ii) to analyze the structure activity relationships by describing the protein binding site features of the lead compounds using docking protocols 4. References: 1) Higgins, C.F. Nature 2007, 446, ) Yilmaz,S., Altinkanat-Gelmez, G., Bolelli, K., Guneser-Merdan, D., Over-Hasdemir, M.U., Yildiz, I., Aki-Yalcin E,. and Yalcin, I., SAR and QSAR in Environmental Research, 2014, 25(7), ) Eicher, T., Cha, H.J., Seeger, M.A., Brandstätter, L. El-Delika, J., Bohnertd, J.A., Kernd, W.V., Verrey, F., Grütter, M.G., Diederichs, K., Pos, K.M., Proc Natl Acad. Sci. 2012, 109, ) Accelrys Inc. Discovery Studio 3.5., (2012). 30

31 CL 15 De Novo drug design for Human Dopamine Transporter Kemal Yelekci, Teodora Djikic Faculty of Engineering and Natural Sciences, Kadir Has University, Fatih 34083, Istanbul, Turkey Dopamine transporter (DAT) plays an important role in the termination of neurotransmission by rapid reuptake of dopamine (DA) from the synaptic cleft into presynaptic terminals where it will be degraded by monoamine oxidase. With the blockade of DAT, level of dopamine in synaptic cleft as well as dopaminergic neurotransmission will increase, followed by decreasing in intracellular degradation, as well as decreasing in production of reactive oxygen species (ROS) and oxidative stress. We have modelled the human DAT (hdat) based on a drosophila s DAT X-ray crystal structure, and minimized it in the environment of the lipid bilayer and solvent water. MD simulations on the empty transporter revealed small conformational changes of the backbone, but important changes of the amino acid sidechains, especially Asp79, Phe326 and Phe320 thus creating the partially closed state. The transporter was validated with known inhibitors downloaded from CHEMbl database, in Auto Dock 4.2. and GOLD 5 docking software both with rigid protein and with previously mentioned amino acids set to flexible. The obtained results correlated positively with the existing experimental results. The binding free energy for DA, according to pre-existent experiments, is ΔG experimental =-7,4 kcal/mol; while ΔG calculated =-6, 4 kcal/mol was obtained through our studies. The binding position of DA, also, coincides with previous literatures: interaction with Phe320, Asp79 and Thr156 amino acids. The binding energies of some of the de novo designed inhibitors were smaller than that of known inhibitors of hdat. 31

32 CL 16 Some Bioactive Triterpenoids as Potential anti-alzheimer Agents Gülaçtı Topçu Bezmiâlem Vakif University, Faculty of Pharmacy, Department of Pharmacognosy & Phytochemistry Fatih İstanbul, Turkey Lamiaceae (=Labiatae) family plants are represented by over 7500 species with about 240 genera in the world. Anatolia is a rich source of the Lamiaceae family plants, represented by 45 genera and 550 species with over 750 taxa and high endemism 1. Many Lamiaceae family plants extracts were investigated by our group and about 400 di- and triterpenoids were obtained from several genera 2-4 including Salvia, Sideritis, Teucrium, Micromeria, Nepeta and Lavandula species. However, among them, triterpenoids 4-6 isolated from Salvia species exhibited high antioxidant, anti-inflammatory, cytotoxic and anticholinesterase activities, particularly ursolic acid, oleanolic acid, and their derivatives. In this study, a series ursolic acid and oleanolic acid derivatives were semi-synthetically synthesized, and their anticholinesterase inhibitory activity against acetylcholinesterase and butyrylcholinesterase enzymes were investigated by Ellman 7 method as well as molecular docking and in silico studies, and some have been found more active than standard compound galantamine. Among highly active triterpenoids (Scheme 1), two of them were selected to test for their irritant, cytotoxicity and genotoxicity properties which were resulted in finding new lead drugs for the prevention and treatment of Alzheimer s Disease. (1) (2) R: OH Oleanolic acid (1) /Ursolic acid (2) and their derivatives (R: Hydroxy, Ether (Methoxy), Ester, Oxo, Oxime ) 32

33 CL 17 Fullerene Based Amino Acid and Peptides: Designing Drug Delivery and Interactions Andrew R. Barron 1 Department of Chemistry, Rice University, Houston, TX 77005, USA 2 Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA 3 Institute of Life Sciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK 4 ESRI, Swansea University, Bay Campus, Swansea SA1 8QQ, Wales, UK A series of [60]fullerene-substituted phenylalanine and lysine derivatives have been synthesized from which fullerene-substituted peptides may be prepared via solid phase peptide synthesis. The presence of the C 60 -substituted amino acid has a significant effect on the peptide s secondary structures and selfassembly properties. The fullerene substituted acts as a passport for intracellular delivery, enabling transport of a range of sequences into HEK-293, HepG2, and neuroblastoma cells where the peptides in the absence of the fullerene amino acid cannot enter the cell. Delivery of the fullerene species to either the cytoplasm or nucleus of the cell is demonstrated. Cellular studies show that the uptake for the anionic peptide is greatly reduced in comparison with the cationic fullerene peptides of the same concentration. A fullerene-based amino acid provides a route for the intra-cellular delivery of peptides and as a consequence the creation of a new class of cell penetrating peptides. The inhibition constant of a series of fullerene aspartic protease inhibitors we utilized fluorescence resonance energy transfer based assay to evaluate the enzyme kinetics of HIV-1 PR at various concentrations of inhibitors. Simulation of the docking is also presented. The experimental results show that C 60 -based amino acids are a good base structure in the design of protease inhibitors and that their inhibition can be improved upon by the addition of designer peptide sequences. Finally, porcine skin was fixed to a flexing device and topically dosed with an aqueous solution of fullerene substituted phenylalanine derivative of a nuclear localization peptide sequence. Confocal microscopy depicted dermal penetration of the nanoparticles in flexed skin. TEM analysis revealed fullerene peptide localization within the intercellular spaces of the stratum granulosum. 33

34 CL 18 Interface Structures as Templates for Modeling Protein Interactions Engin Cukuroglu, Attila Gursoy, Ruth Nussinov, Ozlem Keskin Koc University, Department Chemical and Biological Engineering Istanbul, Turkey Improvements in experimental techniques increasingly provide structural data relating to protein-protein interactions.classification of structural details of protein-protein interactions can provide valuable insights for modeling and abstracting design principles. Here, we aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. We find that there are unique fine-tuned interface structures in the PDB. These unique interfaces, which provide a rich resource of structural data of protein-protein interactions, can be used for template-based docking. We test the specificity of these non-redundant unique interface structures by finding protein pairs which have multiple binding sites. We suggest that residues with more than 40% relative accessible surface area should be considered as surface residues in template-based docking studies. This comprehensive study of protein interface structures can serve as a resource for the community. The dataset can be accessed at ccbb.ku.edu.tr/piface. 34

35 CL -19 Discovering Novel Drug Candidates Using Virtual Screening Methods Serdar Durdagi Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey It is possible to discover novel drug candidates using virtual drug screening methods with an integrated approach from small molecule databases (i.e., ZINC, Drugbank, ChEMBL, UniChem, etc.) which may include millions of compounds. In this talk, I will give successful examples 1-4 of studies on discovering of novel drug candidates using virtual screening methods carried in our lab. 1. Ramin Ekhteiari Salmas, Murat Senturk, Mine Yurtsever, Serdar Durdagi. Discovering Novel Carbonic Anhydrase Type IX (CA IX) Inhibitors from Seven Million Compounds Using Virtual Screening and In Vitro Analysis. Journal of Enzyme Inhibition and Medicinal Chemistry 2015; DOI: / Ramin Ekhteiari Salmas, Ayhan Unlu, Mine Yurtsever, Sergei Y Noskov, Serdar Durdagi. In- Silico investigation of PARP-1 catalytic domains in holo and apo states for the design of high affinity PARP-1 inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry 2015; doi: / Serdar Durdagi, Trevor Randall, Henry J Duff, Adam Chamberlin, Sergei Y Noskov. Rehabilitating drug-induced long-qt promoters: In-silico design of herg-neutral cisapride analogues with retained pharmacological activity. BMC Pharmacology and Toxicology 2014; 15(1):14. DOI: / Birce Buturak, Serdar Durdagi, Sergei Y Noskov, A Tugba Ozal Ildeniz. Designing of multitargeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches.. Journal of Molecular Graphics & Modelling 2014; 50C: DOI: /j.jmgm Keywords: Virtual screening methods, molecular docking, MD simulations, computer aided drug design 35

36 CL 20 Computational Analysis Of Trimethoprim Resistance in Dihydrofolate Reductase Haleh Abdizadeh, 1 Ömer Acar, 1 Yusuf Talha Tamer, 2 Tuğçe Altınuşak Batur, 1 Erdal Toprak, 2 Ali Rana Atılgan, 1 Canan Atılgan 1,* 1 Sabanci University, Faculty of Engineering and Natural Sciences 2 University of Texas Southwestern Medical Center, Green Center for Systems Biology Bacteria continuously adapt to their changing environment. It is a continuous endeavor to decipher how random mutations taking place at the gene level are taken up permanently through natural selection to sustain vitality at the organism level. We characterize the structural and dynamical changes induced on dihydrofolate reductase (DHFR), due to mutations occurring under the selection pressure induced by the antibiotic trimethoprim (TMP). Tetrahydrofolate (THF) is a precursor in the synthesis of DNA, RNA, and some proteins, and is obtained by reducing dihydrofolic acid (DHF) a process catalyzed by DHFR. TMP is a competitive inhibitor of folate, and binds to the same active site. Here, we investigate the structural features of DHFR that let it execute DHF THF reduction function while simultaneously casting out TMP. The resistance displayed by DHFR on TMP has been studied by a systematic experimental approach, and a series of permanent single/double/triple mutations have been observed. 1-3 Binding constant (thermodynamics) and catalytic activity (kinetics) measurements on different mutants provide conflicting results, implying that there are different routes towards conferring drug resistance. We carry out extensive molecular dynamics (MD) simulations for the most frequently observed mutants in their folate or TMP bound conformations. We evaluate the experimental findings regarding DHFR s drug resistance through structural changes in the enzyme. To understand if the molecules displaying competitive binding to the same region are discriminated by free energy changes that in turn affect binding probabilities, we perform thermodynamical analyses via the free energy perturbation approach 4 which has accuracy to within 0.2 kcal/mol. Another factor that is claimed to be effective in DHFR function is the dynamics of the Met20 loop that is in direct contact with folate binding region. These dynamics include an isomerization that is too slow to be directly observed by conventional MD. 5 We therefore employ the perturbation-response scanning method developed by our group 6 to quantify the interconversion propensity of the conformers. The competing (or synergistic) effects of dynamics and thermodynamics in the mutants are assessed through a combination of these computational approaches to rationalize the conflicting measurements of binding assays. 36

37 1. E. Toprak, A. Veres, J. B. Michel, R. Chait, D. L. Hartl and R. Kishony, Nature Genet. 44 (1), 101- U140 (2012). 2. T. Altinusak, Sabancı University, MS Thesis, (2014). 3. Y. T. Tamer, Sabancı University, MS Thesis, (2014) 4. A. Pohorille, C. Jarzynski and C. Chipot, J. Phys. Chem. B 114 (32), (2010). 5. J. R. Schnell, H. J. Dyson and P. E. Wright, Annu. Rev. Biophys. Biomol. Struct. 33, 119 (2004). 6. C. Atilgan and A. R. Atilgan, PLoS Computational Biology 5 (10), e (2009). 37

38 CL 21 Identification and Verification Of Mutations Impacting Protein Stability and Function Uğur Sezerman Sabancı University, Department of Biological Sciences and Bioengineering Istanbul, Turkey Mutations may have several impact on enzymes ranging from stability to substrate selectivity and specificity. There are several computational methods designed to study the impact of mutations. In this talk I will give a brief overview of these methods. Then I will talk about the Molecular Dynamics based methodology we employed to study the impact of mutations on stability and function of an enzyme. I will give several examples on cellulases and lipases. I will briefly describe the experimental methodology we used to verify the findings of computational studies. 38

39 CL 22 Mechanism Of Action Of Neurokinin-1 Receptors As An Anticancer Target Esin Aki-Yalcin a, Ozum Ozturk a, Kayhan Bolelli a, Tugba Ertan-Bolelli a, Andry Nur Hidayat b, Ozlem Bingol-Ozakpinar c, Filiz Ozdemir d, Ismail Yalcin a a Ankara University, Faculty of Pharmacy, Pharm. Chemistry Dept., Ankara, Turkey b Ankara University, Biotechnology Ins., Bioinformatics Dept, Ankara, Turkey c Marmara University, Faculty of Pharmacy, Biochemistry Dept, Istanbul, Turkey d Marmara University, Faculty of Pharmacy, Analytical Chemistry Dept, Istanbul, Turkey Neurokinin-1 receptor (NK1R) antagonists take attention as new and promising anticancer drugs recently. NK1R belongs to the family of G- protein coupled receptors and also known as tachykinin-1 receptor which selectively binds the neuropeptide substance P (SP) 1. It has been demonstrated that SP acts through NK1R as a mitogen in several human cancer cell lines; that NK1 receptors are present in a broad variety of tumors. It has been proved that non-peptide NK1R antagonists L-733,060, Aprepitant and L-732,138 inhibit tumor growth in several cancer cell lines 2. For the development of novel NK1R antagonists as antitumor agents, previously synthesized heterocyclic compounds by our group 3 were tested on various tumor cell lines comparing to the well known antagonist aprepitant. Molecular modeling studies such as molecular docking and pharmacophore generation were performed with known NK1R antagonists and BSN-009 by using Discovery Studio (DS) 3.5 by Accelrys to explain their binging modes to NK1R 4 (Figure 1-2). BSN-009 may be a good anticancer drug candidate as an NK1R antagonist and is worthy to carry on the anticancer in vivo studies. Figure 1 Figure 2 Key words: NK1 receptor antagonist, Anticancer, Pharmacophore, Docking 39

40 References: 1) Takeda, Y.; Chou, K.B.; Takeda, J.; Sachais, B.S.; Krause, J.E. Biochem. Biophys. Res. Commun. 1991, 179 (3), ) Meshki, J.; Douglas, S.D.; Lai, J.P.; Schwartz, L.; Kilpatrick, L.E.; Tuluc F. J. Biol. Chem. 2009, 284, ) Arisoy, M.; Temiz-Arpaci, O.; Yildiz, I.; Kaynak-Onurdag, F.; Aki, E.; Yalcin, I.; Abbasoglu, U. J. SAR and QSAR in Environmental Research 2008, 19:5, ) Accelrys Inc. Discovery Studio

41 CL - 23 The Molecular Systems Biology Of Signaling And Metabolic Networks Eileen Edler, Samira Yazdi, Matthias Stein Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, Magdeburg, Germany. Protein-substrate and protein-protein interactions are the basis for molecular recognition and high enzymatic turnover rates. Very often, Michaelis-Menten kinetic parameters are not available for a specific enzyme for a particular species but for a related one. These parameters are required for systems biology modeling of large networks1. A 3D structure-based estimate of enzyme kinetic parameters of metabolizing enzymes from a detailed analysis and comparison of moleculer interactions fields offers a fast and convenient approach to quantitatively describe interspecies differences in enzyme kinetics. The quantitative protein interaction property similarity analysis (qpipsa)2 allows to quantify differences and rationalize the effect of mutations on enzyme kinetics. The Rab family of proteins is a member of the Ras superfamily of monomeric G proteins. Approximately 70 types have now been identified in humans and analysis of the Rab superfamily allows to detect similarities and discover subtype-specificities3. The membrane-binding of early endosome Rab5 occurs via two post-translationally added geranylgeranyl anchors at two adjacent C-terminal cysteine residues. The orientational dependece of membrane-bound Rab5 on the membrane phospolipid composition is investigated at different levels of molecular representation using all-atom and coarse grained molecular dynamics simulations. References: 1) Stein, M.; Gabdoulline, R. R.; Wade, R. C. Curr. Op. Struct. Biol. 2007, 2, ) Gabdoulline, R.R.; Stein M.; Wade, R. C. BMC Bioinformatics 2007, 8, ) Stein, M.; Pilli, M.; Bernauer, S.; Habermann, B. H.; Zerial, M.; Wade, R.C. PLoS ONE 2012, 7, e

42 CL 24 Allosteric Enzymes in the Glycolytic Pathway As Antiparasitic Drug Targets Malcolm D. Walkinshaw The Centre for Translational and Chemical Biology, The University of Edinburgh, Michael Swann Building Edinburgh EH9 3BF The role of glycolysis in regulating cell proliferation makes the pathway a good potential drug target for a diverse range of diseases including cancer and parasite infection. Two key allosterically regulated enzymes in the pathway are phosphofructokinase (PFK) and pyruvate kinase (PYK). We have carried out structural and ligand binding studies on these proteins from both the TriTryps parasites (T.brucei, T.cruzi and L.mexicana) and mammals where they are potential targets against metabolic disorders, diabetes and cancer. By trapping the enzymes in different conformational states and solving their crystal structures it has been possible to understand how the enzyme activity is regulated by the binding of small molecule metabolites and nutrients in different allosteric pockets (1,2). The human, bacterial and trypanosomal PYK isoforms have distinctly different allosteric mechanisms for regulating enzyme activity and use a different selection of allosteric effectors and different ways for locking the protein conformation in an active (R-state) or inactive (T-state) form. A High Throughput Screen carried out by the NIH identified a number of promising hit molecules that kill both T.cruzi and T.brucei parasites. We are now developing some of these hits to drug like leads that could develop into the next generation of much needed drugs against the so-called neglected diseases like sleeping sickness (Human African Trypanomiasis) and Chagas disease. Our X-ray crystallographic studies of T.brucei PFK complexed with the inhibitors show that they bind in a pocket that is near the active site and block the transfer of a phosphate from ATP to the fructose-6p preventing formation of the product fructos-1,6-bisphosphate. Both the kinetica analysis of ligand binding and the X-ray structure show that the inhibitor does not bind competitively with ATP. This lack of competition with such an abundant substrate and the unique binding mode which differs from mammalian PFK makes this class of inhibitor an excellent starting point for further exploration by medicinal chemistry. 42

43 1.Morgan,H.P.,Zhong,W.,McNae,I.W.,Michels,P.A.M.,Fothergill-Gilmore,L.A., Walkinshaw,M.D.,(2014) Structures of pyruvate kinases display evolutionarily divergent allosteric strategies Royal Society Open Science 1 (1), Morgan, H. P., O'Reilly, F. J., Wear, M. A., O'Neill, J. R., Fothergill-Gilmore, L. A., Hupp, T., and Walkinshaw, M. D. (2013) M2 pyruvate kinase provides a mechanism for nutrient sensing and regulation of cell proliferation. Proc Natl Acad Sci U S A 110, Brimacombe, KR Walsh, MJ Liu, L Vásquez-Valdivieso, MG Morgan,HP., McNae, I., Fothergill- Gilmore, L.A.,Michels, P.A.M., Auld, D.A., Simenov A., Walkinshaw,M.D., Shen, M., Boxer, M.B., (2014), Identification of ML251, a Potent Inhibitor of T. brucei and T. cruzi Phosphofructokinase, ACS Med. Chem. Lett., 5 (1),

44 CL 25 Highly Efficient Phosphate-Catalyzed Bioorthogonal Reaction With Improved Biocompatibility For Click Chemistry Ozlem Dilek Istanbul Kemerburgaz University, School of Medicine Bioorthogonal reaction to label biomolecules in vitro and in living cells is one of the most powerful tools in chemical biology. An effective reactive pairs frequently used for chemical conjugation are aldehydes/ketones with hydrazines/hydrazides/oximes. Although the reaction is generally specific for the two components, even in a cellular environment, the reaction is very slow under physiological conditions. Additives or some catalyst based molecules such as 10 mm aniline are often used to increase the reaction rate, but these chemicals can be detrimental to the cells. We have found that adding an ortho-phosphate group to an aromatic aldehyde increases the reaction rate with a hydrazine or hydrazide by an order of magnitude. Another advantage is that phosphate group enhances the aqueous solubility of the reagent and its hydrazone product. We have synthesized phosphate-substituted aldehyde synthetic mimic models to study kinetics of their reactions with hydrazines and hydrazides that contain a fluorophore. Fluorescence properties of hydrazone products are also studied. Impacts of bioorthogonal reactions on future drug design (i.e., in situ combinatorial drug design), biomolecule labeling and detection (site-specific derivatization of proteins, DNA, lipids..etc) are also briefly highlighted. This rapid bioorthogonal reaction should therefore be potentially a very useful technique for routine site-specific chemical ligations to study and image complex cellular processes in biological systems. 44

45 C -26 Influence Of Surface Chemistry Of Nanomaterials On Their Toxicity Mustafa Culha, Mine Altunbek, Seda Demir, Manolya Hatipoglu Department of Genetics and Bioengineering, Yeditepe University, Istanbul 34755, Turkey There is a strong relationship between surface chemistry of nanomaterials (NMs) and their action in living systems. With proper surface modifications, biocompatibility of NMs can be increased for their use not only in medicine and biomedical applications but also in other consumer products. The use of NMs has long been considered and investigated for their use in drug targeting and delivery. It is now clear that not every NM can be used in medicine and nanostructures constructed from bio-friendly polymers and biomacromolecules are more proper for such applications. However, there are cases that NMs with proven toxicity such ZnO, silver nanoparticles (AgNPs) and quantum dots (QDs) should be a part of a formulation or consumer product. 1, 2 In such cases, it is necessary to find a way to reduce or eliminate their toxic effect. Among the strategies, surface modification with biocompatible ligand offers unique opportunities for the toxicity reduction. In this presentation, the relationship between the surface chemistry of mentioned NMs and their toxic effect would be the focus. A number of ligands and polymeric structures with biological origin are covalently attached to the NM surfaces and their cytotoxicity is evaluated. The potential difficulties with surface modifications are also discussed and solutions are offered. The authors acknowledge the financial support of European Commission through FP7 project NANOMICEX and Yeditepe University. References: 1- M Altunbek, A Baysal, M Çulha Colloids and Surfaces B: Biointerfaces, 2014, 121, MK Hatipoglu, S Keleştemur, M Altunbek, M Culha Nanotechnology, 2015, 26 (19),

46 CL -27 In Vivo Biosensing Via Near-Infrared Fluorescent Single-Walled Carbon Nanotubes Fatih Sen Dumlupinar University Department of Biochemistry Kutahya, Turkey Single-walled carbon nanotubes are particularly attractive for biomedical applications, because they exhibit a fluorescent signal in a spectral region where there is minimal interference from biological media. Although single-walled carbon nanotubes have been used as highly sensitive detectors for various compounds, their use as in vivo biomarkers requires the simultaneous optimization of various parameters, including biocompatibility, molecular recognition, high fluorescence quantum efficiency and signal transduction. Adrressed herein, a polyethylene glycol ligated copolymer stabilizes near infrared- fluorescent single-walled carbon nanotubes sensors in solution, enabling intravenous injection into mice and the selective detection of local nitric oxide concentration with a detection limit of 1 mm. The half-life for liver retention is 4 h, with sensors clearing the lungs within 2 h after injection, thus avoiding a dominant route of in vivo nanotoxicology. After localization within the liver, it is possible to follow the transient inflammation using nitric oxide as a marker and signalling molecule. Finally, we demonstrate that alginate-encapsulated single-walled carbon nanotubes can function as implantable inflammation sensors for nitric oxide detection, with no intrinsic immune reactivity or other adverse response for more than 400 days [1-5]. 1) Heller, D. A. et al. Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes. Nature Nanotech. 4, (2009). 2) Jin, H., Heller, D. A., Kim, J. H. & Strano, M. S. Stochastic analysis of stepwise fluorescence quenching reactions on single-walled carbon nanotubes: single molecule sensors. Nano Lett. 8, (2008). 3) Jin, H. et al. Detection of single-molecule H2O2 signalling from epidermal growth factor receptor using fluorescent single-walled carbon nanotubes. Nature Nanotech. 5, (2010). 4) Kim, J. H. et al. The rational design of nitric oxide selectivity in single-walled carbon nanotube near-infrared fluorescence sensors for biological detection. Nature Chem. 1, (2009). 5) Zhang, J. Q. et al. Single molecule detection of nitric oxide enabled by d(at)15 DNA adsorbed to near infrared fluorescent single-walled carbon nanotubes. J. Am. Chem. Soc. 133, (2011). 46

47 CL 28 Molecular Modeling Studies Topoisomerase I Inhibitors Ilkay Yildiz 1, Tugba Ertan-Bolelli 1, Sanaz Ataei 2, Serap Yilmaz 1, Egemen Foto 3, Nuran Diril 3, İsmail Yalçın 1 1 Ankara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 2 Ankara University, Biotechnology Institute, Tandogan Ankara, Turkey 3 Hacettepe University, Faculty of Science, Department of Molecular Biology, Beytepe 06532, Ankara, Turkey DNA topoisomerases, which catalyze the interconversion of various topological states of DNA, were originally discovered to change the superhelical structure of closed circular DNAs. Depending on the nature of the reactants and reaction conditions, topoisomerases can catalyze DNA relaxation/supercoiling, catenation/decatenation and knotting/unknotting reactions [1,2]. Based on their functional mechanisms, DNA topoisomerases have been classified into two types. Type I DNA topoisomerase breaks and rejoins only one of the two strands during catalysis, while type II DNA topoisomerase acts on both strands for each DNA strand-passing reaction and it requires ATP for full activity [3]. The mechanisms of intereference with Topoisomerase activity are quite different and can be divided into two classes; Topoisomerase poisons and Topoisomerase catalytic inhibitors. Investigation of the inhibitory activity of eukaryotic Topoisomerases is widely used in anticancer drug development. Recently, a new series of 2H-3,4-dihydro-1,4-benzoxazines, has been investigated for their inhibitory activity on eukaryotic DNA topoisomerase I in cell free system using relaxation method [4]. We had very interesting results. While some of the compounds showed Topo I poison activity, some of them indicated Topo I catalytic inhibitory activity. In here, we tried to explain activity differences between similar 2H-3,4-dihydro-1,4-benzoxazines using molecular modeling study such as generating 3Dcommon feature hypotheses and molecular docking in Discovery Studio 3.5. Key words: Benzoxazines; Topoisomerase I Inhibitors; Pharmacophore Analysis; Molecular docking 47

48 References: [1] Wang JC. DNA Topoisomerases. Ann Rev Biochem 1996; 65: [2] Ting CY, Hsu CT, Hsu HT, Su JS, Chen TY, Tarn WY, Kuo YH, Jacqueline WP, Liu LF, Hwang J. Biochem Pharm 2003;66: [3] Nitiss JL. Biochim Biophys Acta 1998;1400: [4]. Foto, E. Hacettepe University, Faculty of Science, Department of Molecular Biology, Master Thesis [5] Ataei S. Ankara University Biotechnology Institute, Master thesis

49 CL 29 Consensus Docking As A Tool For The Identification And Optimization Of New Lead Compounds Tiziano Tuccinardi Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy Ligand-protein docking is one of the most widely used techniques among in-silico approaches for both ligand binding pose predictions and identification of new hits in virtual screening (VS) campaigns. Many studies assessed the reliability of docking software through different approaches; however, only few studies reported the possibility of using different docking software at the same time (consensus docking, CD). [1] In this context we tested the reliability of applying a consensus docking approach, combining ten different docking procedures, as a strategy to improve the accuracy of docking studies in terms of qualitative prediction of the ligand binding disposition. The analysis was carried out in terms of consensus cross-docking on four different protein targets and the results highlighted that the CD protocol a) is able to predict the ligand binding pose better than the single docking programs, b) can be used to get hints about the reliability a of a docking pose. [2] By the use of the targeted enriched databases belonging from the Directory of Useful Decoys (DUD) [3] we also evaluated the performance of the CD approach in virtual screening. The results demonstrated that CD can be profitably used to identify new hit compounds by employing the consensus pose level as a parameter for compound selection. In order to further verify the reliability of the CD approach, we experimentally tested its application in a VS study aimed at identifying new non-covalent fatty acid amide hydrolase (FAAH) inhibitors, which can provide a valid pharmacological strategy for the treatment of various neurodegenerative and neuroinflammatory diseases. A pre-filtered library of commercial compounds was subjected to the CD analysis and the ten top ranked compounds were purchased and subjected to enzymatic assays. Eight out of the ten tested compounds showed FAAH inhibition activity, resulting to a hit ratio of 80%. Furthermore, the two most active compounds showed low micromolar IC 50 values and could be considered as promising leads for the development of potent FAAH inhibitors. [4] 49

50 References 1) Houston, D. R.; Walkinshaw, M. D. Consensus docking: improving the reliability of docking in a virtual screening context. J. Chem. Inf. Model. 2013, 53, ) Tuccinardi T, Poli G, Romboli V, Giordano A, Martinelli A. Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies. J. Chem. Inf. Model. 2014, 54, ) Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49, ) Poli G, Giuntini N, Martinelli A, Tuccinardi T. Application of a FLAP-consensus docking mixed strategy for the identification of new fatty acid amide hydrolase inhibitors. J Chem Inf Model. 2015, 55,

51 CL 30 Autophagy Modulation As A Treatment Approach Devrim Gözüaçık Sabancı University, Molecular Biology, Genetics and Bioengineering Program, Tuzla, Istanbul, Turkey. Autophagy is a cellular stress mechanism characterized by sequestration of bulk cytoplasm, proteins and organelles in double or multimembrane vesicles, and their delivery to and subsequent degradation by the cell's own lysosomal/vacuolar system. This biological phenomenon occurs at low basal levels in all cell types (from yeast to mammals) under non-deprived conditions, performing homeostatic functions like protein degradation and organelle turnover. Autophagy is rapidly upregulated under conditions leading to cellular stress like nutrient or growth factor deprivation, to provide an alternative source of intracellular building blocks and substrates for energy generation. Unbiased screens performed in our lab led us to discover novel players involved in autophagy regulation. Our protein screens resulted in the characterization of novel protein-protein interactions involving core autophagy machinery components (ATG proteins). Our microrna screens allowed us to discover new autophagy-regulating micrornas. As a result of these studies, unexpected direct links between autophagy and other important cellular pathways were revealed, and novel entry points for autophagy regulation and coordination were described. Autophagy dysregulations play a critical role in the pathogenesis and progress of several human health problems, including neurodegenerative disorders (i.e. Parkinson's and Huntington's diseases), and cancer. Autophagy modulation in these diseases might be used as a therapeutic approach, and in this sense, proteins and micrornas discovered and characterized in our studies constitute novel drug targets. In this speech, results from our recently published and unpublished studies will be presented and the importance of autophagy modulation for therapeutic purposes will be discussed. *This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) 1001 Grant number: 112T272 and Sabanci University. 51

52 References: 1) Arachiche A and Gozuacik D. Autophagy in health and disease. In the book: Toxicity and autophagy in neurodegenerative disorders. Jose Manuel Fuentes (Ed.). Springer Publishing ISBN: ) Tekirdag KA, Ozturk DG, Gozuacik D. Regulation of autophagy by mirnas. In the book: Autophagy: Cancer, Other Pathologies, Inflammation, Immunity, and Infection. Hayat MA (Ed.). Elsevier Academic Press ISBN: ) Karakas HE and Gozuacik D. Autophagy and cancer. Turkish Journal of Biology, 2014, 38, (2014), ) Tekirdag KA, Ozturk DG, Gozuacik D. Alterations in autophagic-lysosomal potential during ageing and neurological diseases: The mirna perspective. Current Pathobiology Reports, 2013 December 2013, Volume 1, Issue 4, pp ) Korkmaz G*, Tekirdag KA*, Ozturk DG, Kosar A, Sezerman OU and Gozuacik D. MIR376A is a regulator of starvation-induced autophagy. PLoS ONE, 2013, 8(12): e doi: /journal.pone ) Tekirdag AK*, Korkmaz G*, Ozturk DG, Agami R, Gozuacik D. mir-181a regulates starvation- and rapamycin-induced autophagy through targeting of ATG5. Autophagy, 2013 March; 9(3): ) Oral O*, Oz-Arslan D*, Itah Z, Naghavi A, Deveci R, Karacali S, Gozuacik D. Cleavage of Atg3 protein by caspase-8 regulates autophagy during receptor-activated cell death. Apoptosis, 2012 Aug; 17(8): ) Korkmaz G, le Sage C, Tekirdag AK, Agami R, Gozuacik D. mir-376b controls starvation and mtor inhibition-related autophagy by targeting ATG4C and BECN1. Autophagy, 2012 February; 8 (2):

53 CL 31 Structural Biology Of Functional Amyloids From Bacterial Biofilms Ümit Akbey Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus Interdisciplinary Nanoscience Center (inano), Aarhus University, Aarhus Structural biology relies on established techniques like X-ray crystallography, electron microscopy, solution NMR, and ssnmr spectroscopy. ssnmr is a powerful technique for studying structure and dynamics of large, non-crystalline, heterogeneous or insoluble biological systems. It does not require long-range order and it does not have an intrinsic size limitation. Moreover, solid and solution NMR can deliver valuable dynamics information in a site-specific manner at atomic resolution over a large timescale. My primary goal is to determine the atomic-resolution structures of biofilm forming functional fibrils from Gram positive and negative bacteria, by using advanced ssnmr. Starting from these structural insights, I aim to understand fibril formation in function and disease, the role of amyloids in biofilms, ways of controlling or preventing biofilm formation in the associated chronic diseases, and finally, the structural switch of proteins between soluble, oligomeric and fibrillar states. Moreover, the interactions of major-biofilm forming fibrils will be studied with their minor partners (in the context of protein - protein interactions), polysaccharides or DNA; the molecular details of potential chaperone-aided control of fibril formation will be investigated by studying the effect of the ClpC chaperone on isotope labeled TasA for B. subtilis. As a novel method, with the recent development in the filed of ssnmr, it is now possible to study functional amyloids in their complex, native and insoluble bacterial biofilms, without the need of purification, even at their live conditions via In-vivo structural biology. Preliminary results will be shown on several protein systems from different bacteria. 53

54 CL -22 Condensed 1,4-DHP Derivatives As Acetylcholine Esterase Inhibitors Rahime Şimşek 1, Miyase Gözde Gündüz 1, Cihat Şafak 1, Serdar Durdağı 2, Mert Mestanoğlu 2, Murat Şentürk 3 1 Hacettepe University, Faculty of Pharmacy, Ankara, Turkey 2 School of Medicine, Bahcesehir University, Istanbul, Turkey 3 Department of Chemistry, Agri Ibrahim Cecen University, Agri, Turkey In last decade, drug repurposing concept is fashionable. According to this term, research findings can be translate to new drugs by using data about molecular basis of diseases. Many drug molecules for their principal targets have already been tested in humans, thus we have detailed information about their pharmacological, toxicity and drugable properties. Thus, these drug molecules are ready for new usage after quick clinical trials. Alzheimer s disease (AD) is characterized by progressive memory loss, decline in language skills, and other cognitive impairments. Despite the ethiology of AD is not well-known, there are several factors such as amyloid-β (Aβ) deposits, -protein aggregation, oxidative stress, and low levels of acetylcholine (ACh) that are thought to play significant roles in AD. It is obvious that the selective loss of cholinergic neurons in AD results in a deficit of ACh in specific regions of the brain especially learning and memory center. The primary approach for treating AD has therefore focused on increasing the levels of ACh in the brain by using acetylcholinesterase inhibitors (AChEI) such as tacrine, donepezil, galantamine, and rivastigmine. It is well-known that Ca 2+ overload is the main factor initiating the processes leading to cell death. There are many evidence showing calcium dysfunction, involved in the pathogeny of AD, augments Aβ formation and hyperphosphorylation. Ca 2+ entry through L channels causes calcium overload and mitochondrial disruption, which lead to the activation of the apoptotic cascade and cell death. Hence, blocking the entrance of Ca 2+ through Ca 2+ channel could be a good strategy to prevent cell death. Because of 1,4-dihydropyridines (DHPs) selectively block L-type voltage-dependent Ca 2+ channels, new hybrid molecules having acetylcholine esterase inhibitory and calcium channel blockade properties can be new approach for the treatment of AD. Besides these biological activities, these type of compounds could prevent oxidative stress. Recent research has demonstrated that oxidative damage is an event that precedes the appearance of other pathological hallmarks of AD. 54

55 We have used structure-based design and virtual screening methods and investigated a new activity of condensed 1,4-DHP derivatives from a small molecule library with around 300 compounds (i.e., we have synthesized these compounds in recent years). In silico results showed that 9 of 300 compounds are potent inhibitors of AChE with moderate calcium channel blockade activity. These compounds are then tested in vitro and results showed that compounds have AChEI activity with between nm. We conclude that one compound which was the most potent AChEI, being 12-fold more potent than tacrine. The in vivo activity of the compounds should be further explored. 55

56 The Synthesis of Novel Dopamine, Rotigotine and Rivastigmine Analogues as Biologically Active Compounds Süleyman Göksu Ataturk University, Faculty of Science, Department of Chemistry, 25240, Erzurum, TURKEY Dopamine (1) is a hormone-like neurotransmitter that exhibits an important role in central nervous system (CNS) related disorders such as schizophrenia and Parkinson s disease. 1 It has been reported that many chemical compounds have dopamine like actions. 2 A drug Rotigotine (2), commercially known as neupro, is a dopmaninergic compound and used in the treatment of Parkinson s disease as transdermal patch. 3 Benzylamines are also beneficial organic compounds having important biological activities in CNS. 4 Rivastigmine (Exelon, 3) is a well known drug used in the treatment of neurodegenerative disorders such as dementia of Alzheimer s and Parkinson's diseases. 5 Rivastigmine (3) is cholinergic drug that inhibits AChE in an irreversible manner. In addition, sulfamides are important compounds in synthetic organic chemistry and medicinal chemistry. The sulfamide drug quinagolide (Norprolac, 4) is an anti hyperprolactinemia and a dopaminergic compound. 6 The recently developed sulfamide compound 5 (JNJ ) is a powerful anticonvulsant. The potential use of 5 in the treatment of inflammatory, neuropathic pains and depression has been reported. 7 HO HO NH 2 OH N S N O O N OH H N H O N S N H O S H N O S O NH Because of the important biological activities of dopamine, benzylamines and sulfamides in CNS, a series of dopamine related compounds and benzylamines were synthesized by our group. The synthesized amines were converted to their sulfamide derivatives and they were evaluated for their biological activities including acetylcholinesterase (AChE), butyrylcholinesterase (BuChE) and carbonic anhydrase (hca) inhibitory properties. Most of the synthesized compounds showed potent inhibition against these metabolic enzymes. Resources: 1) Haadsma-Svensson, S.R.; Svensson, K. A. CNS Drug Rev. 1998, 4, 42. 2) Cannon, J. G. Prog. Drug Res. 1985, 29, ) Giladi, N.; Boroojerdi, B.; Korcyn, A. D.; Burn, D. J.; Clarke, C. E.; Schapira, A. H. Mov. Disord. 2007, ) Youdim, M. B. H.; Fridkin, M.; Zheng, H. Mech Ageing Dev. 2005, 126, ) Rösler, M.; Retz, W.; Retz-Junginger, P.; Dennler, H. J. Behav Neurol. 1998, 11, ) Barlier, A.; Jaquet, P. Eur. J. Endocrinol. 2006, 154, ) Smith-Swintosky, V. L. U.S. Pat. Appl. Publ. (2007), US A ; Chem Abstr. 2007, 147,

57 ORAL PRESENTATION 57

58 OP 1 Shape And Surface Engineering As A Tool To Enhance The Antibacterial Activity Of Mesoporous Silica Nanoparticles Didem Şen Karaman a, Shamila Sarwar b, Diti Desai a, Soumyananda Chakraborti *d, Emma M. Björk c, Magnus Odén c Pinak Chakrabarti c, Jessica M. Rosenholm *a a Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland, b Department of Biochemistry, Bose Institute, Kolkata, India, c Nanostructured Materials Division, Department of Physics, Chemistry and Biology, Linköping University, Sweden, ddepartment of Chemistry Indiana University, Bloomington, Indiana, USA. For many years, antibiotics have been used to inhibit or kill pathogenic bacteria. However, antibacterial resistance has also developed over time, which is becoming a growing problem. The bacterial resistance to antibacterial drugs has been attempted to be overcome by discovering new antibiotics and chemically modifying existing antimicrobial drugs. Still, there is no assurance that the new drug developments can catch up to the pathogen's fast and frequent development of resistance in a timely manner. One of the most promising strategies to address this challenge is utilizing antibacterial nanomaterials to combat the resistance as well as nanocarriers for effective delivery of antibiotics to pathogenic bacteria. Among the developing applications of antibacterial nanostructured materials, mesoporous silica particles (MSPs) can be highly feasible. This is due to their flexible and versatile design options, which could in this context be beneficial to employ MSPs themselves as antibacterial agents for combating antibacterial resistance and induce synergetic effects together with existing antibiotics and/or utilize them as vehicles to carry antibiotics for delivery to bacteria. In the literature, very little insight regarding antibacterial properties of silica nanoparticles exist to date. Therefore, we aimed to consider a couple of the decisive properties of mesoporous silica nanoparticles: the shape (morphology) effect together with surface coating. As a special focus, we have investigated the effect of MSPs with different aspect ratios and surface coatings to enhance the antibacterial activity; and also aimed to impart synergistic effects to the already existing antibiotic kanamycin which is difficult to be taken up by bacteria. The thus produced antibacterial agents samples were targeted against several Gram positive and Gram negative bacteria. Our results revealed that the designed MSPs with the highest aspect ratio had the highest interference on the bacterial growth. In order to investigate the inhibition mechanism of the MSPs, the interaction of the nanoparticles with bacterial membranes and DNA has been assessed using various spectroscopic and imaging techniques. Furthermore, the synergistic antibacterial effect of nanoparticles at LD50 dosage in 58

59 combination with kanamycin against Vibrio Cholerae was also studied. Our experiments here convincingly showed that the bacterial growth can be inhibited by shape engineering of MSPs and further fine-tuning for reaching synergetic effects together with for kanamycin can be provided with the different aspect ratios, and this phenomenon has good antibacterial potential to be utilized in the future. Keywords: mesoporous silica nanoparticle, antibacterial nanoparticle, antibiotic 59

60 OP 2 Understanding G-Protein-Coupled-Receptor (Gpcr) Signaling From Atomistic Molecular Dynamics Simulations Özge Şensoy Medipol University, School of Engineering and Natural Sciences, Kavacık Campus, 34810, Beykoz/İstanbul The Nobel Prize award to Lefkowitz and Kobilka underscores the extraordinary progress achieved in understanding some of the most important molecular machines in cell function and signaling: G-proteincoupled-receptors (GPCRs), which are responsible for transmitting extracellular signals to the inside of the cell by coupling to heterotrimeric G-proteins. Elements of the complex signaling interaction network have become clearer from accumulating structural information at the molecular level. Based on such information, detailed attention was accorded to the function-related conformational changes in the TM bundle of GPCRs, but less so to the amphipathic helical motif, Helix-8 (Hx8), which is located immediately after the end of the seventh transmembrane domain. Yet the conservation of such a structure in nearly all GPCRs and its involvement in various cellular processes such as G-protein coupling, receptor expression, and internalization suggests a specific role for this domain in GPCR signaling. Furthermore, the discovery of G-protein-independent signaling, notably those mediated by Arrestins (Arrs) has changed the classical view of GPCR signaling where Arrs were previously thought to mediate exclusively desensitization and, in some cases, internalization processes. A key set of questions raised by the availability of multiple signaling pathways then is how the relative efficacy of engaging a certain signaling effector (G-protein or Arr) depends on the ligand that activates the receptor. This ligand-dependent-selectivity for coupling to a specific signaling pathway is known as functional selectivity, and is mediated by biased ligands. While rapid progress is being made in this field, we are still far from understanding of molecular mechanisms responsible for specific engagement of GPCRs with a certain signaling effector. In this talk, I will recapitulate strategies along with corresponding results- used to address the abovementioned open questions in the field. Correspondingly, in the first part of the talk, I will present recent results concerning the mechanistic role of Hx-8 in interactions of GPCRs with PDZ-domain containing proteins. In the second part, I will discuss the likelihood structural basis for intriguing functional selectivity displayed by the Arr family towards the phosphorylation state of the receptor with more emphasis on its relevance to functional complementation approaches. Finally, I will briefly discuss the concept of biased signaling in the context of targeted drug design strategies. 60

61 OP 3 Practical Applications of Systems Biology Bioinformatics in Translational Science and Drug Discovery Lee Lancashire Thomson Reuters Systems biology information and associated analytical approaches have greatly contributed to many scientific discoveries and drug development approaches. Nowadays, systems biology information combined with high-performance computing and big data information technologies is transforming scientific research and clinical applications to accelerate the discovery of new diagnostics, treatments and cures as well as further advance personalized and translational medicine. Computational modeling is central to this mission and its success relies on the quality and amounts of data and curated knowledge contributing to data analysis and predictive models. Unprecedented wealth of biological and patient data is being integrated today triggering development of new computational algorithms providing more robust reproducible outcomes. In this presentation, Thomson Reuters scientists will show examples of how they use databases of protein interactions, biological pathways, and disease biomarkers for various data analysis applications including constructing predictive models that identify molecular subtypes, biomarkers, associated disease and drug mechanisms as well as novel drug targets. 61

62 OP 4 Celecoxib-Loaded Solid Lipid Nanoparticles Show Promising Effects For The Treatment Of Breast Cancer İn Vitro Mine Ergüven a, Melike Üner b, Gülgün Yener b a İstanbul Aydın University, Faculty of Engineering, İstanbul, Turkey; b İstanbul University, Faculty of Pharmacy, Department of Pharmaceutical Technology, İstanbul, Turkey Many etiological factors and the complexity of breast cancers present challenges for prevention and treatment. The main challenge is the penetration of drug in the cell because of the drug efflux proteins restriction. 1 A non-steroidal anti-inflammatory drug Celecoxib (CEL) is a potent selective cyclooxygenase (COX)-2 inhibitor that is being commonly used to treat pain and inflammation, but it also exerts anti-cancer effects both COX-2 dependent and independent manner. Solid lipid nanoparticles (SLN), nanostructured lipid carriers (NYLT) and nanoemulsions (NE) are designed to overcome this disadvantages. 2 Our aims were to find out effective formulation(s) of CEL and shed light to possible underlying mechanism for breast cancer treatment. MCF-7 human breast cancer (ATCC HTB-22 TM) cells were used. After the design of three formulations of CEL by us as SLN, NYLT and NE, they were loaded with 10 µm CEL. Groups were determined as control group (untreated), positive control group (an estrogen receptor antagonist and a commonly used drug in clinic as Tamoxifen), CEL itself, SLN, NE and NYLT. The effects were evaluated by cell proliferation index, apoptotic index, the apoptotic protein levels [caspase-3, bax] and the survival/resistant protein levels [COX-2, protein kinase B (AKT), phospho (p)-akt, midkine (MK), B-cell lymphoma 2 (bcl-2), drug efflux proteins as ABCG2 and P-glycoprotein (P-gp)] for 48 h. CEL formulations decreased cell number and viability in comparison to the control group, the positive control group and celecoxib (p<0.05). The decrease rank from highest to lowest was SLN, NLC and NE respectively (p<0.05). In concordance with these results, SLN led to highest apoptotic index (p<0.001), it induced highest increase in caspase-3 and bax levels (p<0.05). Maximum decrease in COX-2 levels were determined at the SLN group (p<0.05). SLN took the last place for the inhibition of Bcl-2, MK, AKT and p-akt (p<0.05). SLN induced no change in ABCG2 and P-gp levels at the SLN group. Previous reports showed that CEL increased sensitivity to other drugs, however it increased the expression of ABCG2 in breast cancer. In this experiment, SLN formulation seems to accomplish highest drug accumulation in cell without any drug efflux protein challenge. 62

63 Our SLN formulation of CEL can be used effectively alone and in the combination therapies regardless of drug efflux protein concern. Consequently, this decreases toxicity resulting in good prognosis with higher life quality. In addition, the inhibitory effect of CEL on MK which is a newly pronounced growth factor in cancer era was also shown for the first time. Keywords Celecoxib, Solid lipid nanoparticle, Breast Cancer, MCF-7 References: 1) Vtorushin S.V.; Khristenko K.Y.; Zavyalova M.V.; Perelmuter V.M.; Litviakov N.V.; Denisov E.V.; Dulesova A.Y.; Cherdyntseva N.V. Exp Oncol. 2014,36, ) Uner M.;Yener G.; Ergüven M.; Karaman E. F.; Utku E.U. Curr Nanosci. 2014, 10,

64 OP 5 DNA-Damaging Small Molecules As Anticancer Agents: Analogues Of The Cytotoxic Antibiotic Leinamycin And Duocarmycin SA And Bisacridines With Aromatic Linking Chains Murat Kızıl, Bircan Çeken Toptancı, Hayrettin Dinç Dicle University, Faculty of Science, Chemistry Department, Diyarbakır Most of the anticancer chemotherapeutic drugs that are broadly and successfully used today are DNA damaging agents. Targeting of DNA has been proven to cause relatively potent and selective destruction of tumor cells. However, the clinical potential of DNA-damaging agents is limited by the adverse side effects and increased risk of secondary cancers that are consequences of the agents' genotoxicity. 1 Our aim was to synthesise analogues of the cytotoxic antibiotic leinamycin and duocarmycin SA and bisacridines with aromatic linking chains and to investigate their DNA cleavage activities. Analogues of the cytotoxic antibiotic leinamycin and duocarmycin SA and two bis-intercalation molecules of different chain lengths were synthesized and characterized. 2-4 The DNA cleavage activities of ligands ( M) were determined by agarose jel electrophoresis in the absence and presence of copper(ii). Overall, the results showed that synthesized ligands displayed high in vitro DNA-cleaving properties. Keywords: Anticancer agents, Duocarmycin SA, Bisacridines DNA binding We acknowledge TÜBİTAK for the financial support of the project KBAG-109T788 and DUBAP 08- FF-69 and 12-FF-106. Resources: 1) Gurova K. Future Oncol. 2009, 10, ) Tietze F.L.; Major F. Eur. J. Org. Chem., 2006, ) Lorente, A. Fernandez-Saiz, M., Espinoza, J.F., Jaime, C., Lehn, J.M., Vigneron, J.P., Tetrahedron,1995, 36, ) Chatterji, T., Kızıl, M., Keerthi, K., Chowdhury, G., Pospilis T and Gates, K. S., J. Am. Chem. Soc.,2003, 125,

65 OP 6 Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed By Molecular Dynamics Simulations Sebnem G. Essiz a, Brian J. Bennion b, Edmond Y. Lau b, Jean-Luc Fattebert b, Aiyana Emigh b, Felice C. Lightstone b a Kadir Has University, Bioinformatics and Genetics, Istanbul Turkey b Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory Permanent inhibition of acetylcholine esterase, AChE, results in runaway neurotransmission leading to cognitive deficiencies, seizures, paralysis, and eventually death depending on the exposure. We present data from quantum mechanics/molecular mechanics (QM/MM) and 100 ns (MD) simulations of the apo and soman-adducted forms of hache to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. By using correlation and principal component analysis of MD trajectories, the altered motions are detected and resulting structures provide alternative pathways into and out of the enzyme active site through the side-door in the soman-adducted protein. Resources: Bennion B.J.*, Essiz S.G.*, Lau E.Y, Fattebert,J.C., Emigh A., Lightstone, F.C, A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations, *contributed equally, PLoS ONE 10(4) (2015) 65

66 OP 7 In-Silico Discovery Of Novel İnhibitors Against Dengue Virus Protease Enzyme Shaher Bano Mirza a,b, Serdar Durdagi and M. Qaiser Fatmi a School of Medicine, Department of Biophysics, Bahcesehir University, Istanbul, Turkey b Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad, Pakistan Dengue virus is a major issue of tropical and sub-tropical regions. Dengue virus has been the cause behind the major alarming epidemics in the history with mass causalities from the decades. Unavailability of on-shelf drugs for the prevention of further proliferation of virus inside the human body results in immense number of deaths each year 1. This issue necessitates the design of novel antidengue drug. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of dengue virus 2. Therefore, approximately 18 million compounds from the ZINC database have been screened against the target (2VBC: resolution 3.15 Å) 3.On account of screening, we have used incremental construction algorithm of Glide docking program of Maestro molecular modeling package with its features High throughput virtual screening (HTVS), Standard precision (SP), Extra precision (XP) and in a combination of Prime, Induced fit docking (IFD) has also been applied 4, 5. Five top ranked compounds were selected from the IFD results with greater predicted binding energies with the catalytic triad residues that may act as potential inhibitors for the underlying target protease enzyme. The top ranked compound ZINC , ZINC , ZINC , ZINC , ZINC has shown the predicted binding energy of , , , , kcal/mole, respectively, making interaction with three catalytically important amino acids. In computational studies, our proposed compounds confirms promising results against all the four serotypes of dengue virus, strengthening the opportunity of these compounds work as potential on-shelf drugs against dengue virus. Further experimentation on the proposed compounds can result in development of strong inhibitors. Keywords: Dengue virus serotypes, Protease enzyme, NS3, in-silico drug discovery, ZINC database References: 1) Wichapong, K.; Nueangaudom, a.; Pianwanit, S.; Sippl, W.; Kokpol, S. Trop. Biomed. 2013, 30 (3), ) Mahy, B. W. J.; Regenmortel, M. H. V. Van. Desk Encyclopedia of Human and Medical Virology; ) Bas, D. C.; Rogers, D. M.; Jensen, J. H. Proteins Struct. Funct. Genet. 2008, 73 (3), ) Madhavi Sastry, G.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W. J. Comput. Aided. Mol. Des. 2013, 27 (3), ) Irwin, J. J.; Shoichet, B. K. J. Chem. Inf. Model. 2005, 45 (1),

67 OP 8 Assessing The Ligand-Protein Binding Modes With Computational Tools Gülşah Çifci Bağatır a, Viktorya Aviyente a, Gerald Monard b, Ebru Demet Akten c a. Bogazici University, Chemistry Department, Istanbul, Turkey b. Université de Lorraine, Theoretical Chemistry and Biochemistry Group SRSMC Nancy, France c. Kadir Has University, Bioinformatics and Genetic, Istanbul, Turkey Designing small molecules with desirable binding affinity and biological activity is one of the major goals in computational biology. 1-4 Molecular docking, is one of the most popular methods used to identify the orientations of molecules into the active site of a target protein structure. 2,3 An important goal of computational medicinal chemistry is to develop methods that accurately can estimate the free energy of binding, ΔG bind, which allows to predict the binding strength of any drug candidate without synthesizing it. Computational methods that combine molecular mechanics energy and implicit solvation models, such as Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), have been widely used in free energy calculations. 1-3 Compared with rigorous methods such as Free Energy Perturbation (FEP) and Thermodynamic Integration (TI) methods, 4 MM/PBSA and MM/GBSA are computationally more efficient. 5 The inhibition of phosphodiesterase (PDE) enzymes, which are responsible for the breakdown of adenosine 3',5'-monophosphate (camp) will be investigated. 6 The potentially clinical benefits of PDEIV inhibition require to design novel inhibitors for PDEIV enzyme with less side effects than known potent PDEIV inhibitors. For this purpose, we will consider the results of our previous work where we used pharmacophore modeling and docking process for the PDEIV-B enzyme to propose candidate inhibitors. 7 For PDEIV-ligand complex, the PDEIV selective inhibitor rolipram, whose X-ray structure is co-crystallized with PDEIV (pdb code: 1RO6) will be used. The experimental binding free energies of rolipram ( G exp = kj/mol) and Syntex 3 ( kj/mol) and a few other ligands that are known from the experimental IC 50 results of Dal Piaz et al. 8 will be tested for PDBIV (1RO6) and its complex. Then, the same procedure will be repeated for the complexes with ligands proposed in our earlier work 7 and the knowledge of calculating binding Gibbs Free energies will be extended to further studies. 67

68 References: 1) Kongsted, J.; Ryde, U. J.Comput. Aided Mol. Des. 2009, 23, ) Rastelli, G.; Degliesposti G.; Del Rio, A.; Sgobba, M. Chem. Biol. Drug Des. 2009, 73, ) Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. J. of Comp. Chem. 2010, 31(4), ) Genheden, S.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Ryde, U. J. Phys. Chem. B. 2010, 114, ) Hou, T.; Wang, J.; Li, Y.; Wang, W. J. Chem. Inf. Model. 2011, 51, ) Hughes, B.; Owens, R.; Perry, M.; Warrellow, G.; Allen, R. Drug Discovery Today. 1997, 2 (3), ) Çifci, G.; Aviyente, V.; Akten, E.D. Molecular Informatics 2012, 31(6-7), ) Dal Piaz, V.; Giovannoni, M. P.; Castellana, C.; Palacios, J. M.; Beleta, J.; Doménech, T.; Segarra, V. Eur. J. Med. Chem. 1998, 33,

69 OP 9 Classification Of Distinct Conformers Of Β 2 -Adrenergic Receptor (Β 2 ar) Based On Binding Affinity Of Ligands Through Docking Studies Ebru Demet Akten Department of Bioinformatics and Genetics, Faculty of Natural Sciences and Engineering, Kadir Has University, Cibali 34083, Istanbul, Turkey β 2 AR is a member of G-protein-coupled receptors (GPCRs), and is involved in the relaxation of pulmonary tissues through the binding of catecholamines, such as epinephrine. The lack of its activation leads to difficulty in breathing and in more severe cases to asthma attacks. The receptor activates itself through specific conformational changes in the ligand binding site and other conserved regions. Therefore, it is crucial to look into the dynamic character of the receptor, which will help to understand the distinctiveness in the binding mode of each ligand with a specific activity. In this study, a classification protocol was developed and used to classify receptor β 2 AR conformers based on the binding mode of selected ligands with known activities. First, distinct conformational states of the ligand s binding pocket were obtained from a 2.8 μs MD simulation conducted on the available crystal structure of β 2 AR (PDB is:2rh1) which represents the inactive state of the receptor, prior to this study [1,2]. A total of 2800 snapshots collected at every 1 ns were clustered based on the RMSD value of the five key residues at the binding site (Asp113, Val117, Ser203, Ser207 and Asn312) [2,3]. A total of 13 distinct snapshots were obtained when the cut-off value for the RMSD was set to 1.5 Å. Next, a total of 8 ligands were docked to each 13 conformers using AutoDock, GOLD and GLIDE softare tools. The best pose of each ligand in the conformer was selected and evaluated based on its vicinity to four critical residues (Asp113, Ser203, Ser207 and Asn312). The poses that were not in this neighbourhood were discarded and the remaining ones were sorted based on their score values. The conformers that are found in the top five were selected to be the most suitable conformational state for that ligand. If the ligand was an agonist that prefers an active state, then the selected conformer would most likely represent an active state. Previously, the same protocol was applied to 5 inactive and 7 active crystal structures and successfully distinguished the active structures from the inactive ones. Generating alternative conformations of the receptor and classifying them as active or inactive is an important practice in the drug design studies that are often limited to one snapshot obtained from x-ray studies. 69

70 Keywords: β 2 -Adrenergic Receptor, GPCR, conformational change, dynamic character, binding mode, docking/scoring, agonist, active state. References: 1) Ozcan, O., A. Uyar, P. Doruker and E. D. Akten, BMC Struc. Biol. 2013, 13(29), 2) Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Steven RC, Science 2007, 318: ) Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, Kobilka BK, Nature 2007, 450:

71 OP 10 Predicting Efficacy Of A Novel Anticancer Drug Candidate In The Scope Of ABC And OATP Drug Transporters Durmus S 1, Unal O 2, Khodadust R 2, Icsel C 3, Yilmaz VT 3, Yagci Acar F 2, Sahin O 1, Ulukaya E 4 1 Department of Molecular Biology and Genetics, Faculty of Sciences, Bilkent University, Cankaya, Ankara, Turkey 2 Department of Chemistry, Faculty of Sciences, Koc University, Sariyer, Istanbul, Turkey 3 Department of Chemistry, Faculty of Arts and Sciences, Uludag University, Bursa, Turkey 4 Department of Medical Biochemistry, Faculty of Medicine, Uludag University, Bursa, Turkey A newly-synthesized palladium (II) complex was shown to inhibit the growth of various cancer cell lines including from colon, lung, prostate and ovary. In vitro cytotoxic activity of this complex was substantially better in colon and ovarian cell lines compared to cisplatin and carboplatin. In vivo, this compound decreased the volume of colon tumors more effectively than oxaliplatin. These results suggest that the palladium (II) complex may be a good anti-cancer drug candidate. In this study, we investigated the interaction of this complex with pharmacologically important drug transporters as these transporters have key roles in the biodistribution of majority of anti-cancer drugs on the market, thus affecting their efficacy and toxicity. Using MDCKII cell lines expressing ABC transporters (MDR1, Bcrp1 and Mrp2) and HEK293 cell lines expressing OATP proteins (OATP1A2, OATP1B1 and OATP1B3), we performed growth inhibitory experiments and/or cellular uptake assays to evaluate which transporters are more likely than others to transport the palladium (II) complex and confer resistance/sensitivity to it. We found that MRP2 overexpression in MDCKII cells decreases its sensitivity to the palladium complex, suggesting this complex to be a transported substrate. The impact of P-gp and BCRP were not as evident as MRP2. Initial growth inhibition findings were suggestive for OATP1B1 and OATP1B3 to mediate the uptake of the palladium complex into the cells, thus increase the cellular sensitivity. To confirm these results more thoroughly, we have performed cellular uptake experiments using the same cell lines and developed and ICP-MS assay to determine the intracellular palladium levels. Results of these assays will also be presented in the conference. All in all, these results suggest that the novel palladium (II) complex can be transported by various drug transporters that can have substantial impact on the in vivo behavior of this drug candidate. Thus, we are currently testing these findings in vivo to evaluate the distribution, elimination and potential risks and benefits of this novel palladium complex treatment. 71

72 OP 11 Identification Of Small Molecule Binding Pocket And Potent Inhibitors Of CCHFV OTU Deubiquitinase Galip Servet Aslan, Fatih Kocabas Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey Crimean-Congo hemorrhagic fever virus (CCHFV) is a deadly tick-borne virus. CCHFV utilizes OTU deubiquitinase, which is expressed from L segment of CCHFV genome. CCHFV OTU involves in viral invasion through antagonizing of NF-κB signaling pathway. Inhibition of CCHFV OTU by small molecules could lead to development of anti-cchfv therapies. To this end, we utilized in silico and in vitro drug screening approaches and identified the pocket of Y89-W99 as the inhibition site of CCHFV OTU 1. In silico screening of over half-million compounds against this newly identified inhibition pocket revealed small molecules with high binding affinity. In addition, we utilized a florescent UB-AMC assay and demonstrated in vitro inhibition of CCHFV OTU by two small molecules 2. These findings indicate the pocket of Y89-W99 as a pharmaceutical target for optimization and identification of CCHFV OTU inhibitors that could serve as lead structures for discovering therapies against CCHFV. Keywords: CCHFV, OTU protease, fluorometric OTU assay, deubiquitinase, small molecules, Nairovirus, Bunyaviridae References: 1) Kocabas, F; Ergin, E. K. " Identification of small molecule binding pocket for inhibition of Crimean- Congo hemorrhagic fever virus OTU protease." Turk Journal of Biology. Under review. 2) Kocabas, F.; Aslan, G. S. "Fluorometric CCHFV OTU protease assay with potent inhibitors." Virus Genes (2015):

73 OP 12 Mechanisms Of Activation And Regulation Of The Nitric Oxide Receptor Soluble Guanylate Cyclase Nur Başak Sürmeli Izmir Institute of Technology and The Scripps Research Institute Keywords: nitric oxide, guanylate cyclase (guanylyl cyclase), cyclic GMP (cgmp), nucleotides, signal transduction, drug design, metalloenzymes, heme proteins Many important physiological processes, such as vasodilation, myocardial function, perfusion and neurotransmission, are mediated by nitric oxide (NO) signaling. Soluble guanylate cyclase (sgc) is the primary receptor for NO. NO binding to the ferrous (Fe 2+ ) heme cofactor activates sgc which leads to formation of second messenger cyclic guanosine monophosphate (cgmp). Under oxidative stress, sgc heme can be oxidized resulting in NO insensitivity; currently the fate of oxidized sgc is unknown. Cinaciguat is a therapeutic compound that has been developed to activate oxidized enzyme, but the mechanism of activation by cinaciguat remains elusive. Here, the stability of oxidized sgc was investigated by monitoring the rate of heme loss, and the mechanism of action of cinaciguat was investigated. In addition, sgc activity is tightly regulated by NO, ATP and GTP. The mechanistic details of sgc regulation by these molecules are not well understood. Since the dysregulation of NO/sGC/cGMP pathway can lead to a variety of diseases such as hypertension, coronary heart disease and other vascular disorders. Understanding regulation of sgc is vital for finding a cure for these diseases. The mechanistic details of sgc regulation by nucleotides and NO was also investigated. A new comprehensive model that gives a more accurate description of sgc regulation by NO and nucleotides was discovered. References: 1. Eric S. Underbakke, Nur Basak Surmeli, Brian C. Smith, Sarah L. Wynia-Smith, and Michael A. Marletta, Nitric Oxide Signaling. In: Comprehensive Inorganic Chemistry II, Vol 3. Oxford: Elsevier, , N. Basak Surmeli, Michael A. Marletta, Insight into the rescue of oxidized soluble guanylate cyclase by the activator cinaciguat., Chembiochem, 13, , N. Basak Sürmeli, Frederike M. Müskens, Michael A. Marletta, The Influence of Nitric Oxide on Soluble Guanylate Cyclase Regulation by Nucleotides: Role of the pseudosymmetric site., J. Biol. Chem., 290, ,

74 OP 13 Combination Of In-Silico Approaches On G Protein-Coupled Receptors (Gpcrs) Ramin E. Salmas, Serdar Durdagi School of Medicine, Department of Biophysics, Bahcesehir University, Istanbul, Turkey Since we mainly face with the lack of crystallographic knowledge of GPCRs, any researches based on experimental approaches on these critical membrane proteins undergo some challenges. So it would be so reasonable to employ new approaches of theoretical chemistry, which have been validated recently. Here we tried to address to main obscure problems of this area, despite of many obstacles. The main receptors which are focused in our studies including; Dopamine receptors (DR), C-C chemokine receptors (CCR) and opioid receptors. Comparative protocols, long atomistic molecular dynamic (MD) simulations, post-processing MD analysis, 3D-QSAR and other classical simulation techniques were used to predict non-solved structures, activation and inhibition mechanisms and also discover new drug potential compounds. 74

75 OP 14 Near-IR Fluorophores And Their Use In Photodynamic Therapy S. Sibel Erdem Istanbul Medipol University, International School of Medicine Department of Medical Biochemistry Photodynamic therapy (PDT) is a promising treatment modality for various diseases including several types of cancer, cardiovascular and dermatological diseases. Since PDT is a local treatment, it has possible advantages over current treatment alternatives. Briefly, PDT involves combination of light and a photosensitizer (PS), which is activated by absorption of specific wavelength light and creates local tissue damage through generation of reactive oxygen species (ROS) that induce a cascade of cellular and molecular events. Due to the very short life-time and travel limitation of generated ROS species, PDT offers localized treatment for the disease in interest. The most important component of PDT is the photosensitizer. Various types of photosensitizers have been developed, while some of them are approved and are being used in clinics, many of them are still in different stages of pre-clinical and clinical studies. Photosensitizers, generally have highly hydrophobic, water insoluble structures and they are prone to aggregation. Aggregation of PS leads to reduced ROS generation and thus lowers the PDT activity. Even though PDT is favorable treatment modality, it is still in need of improvement. Therefore, it is crucial to design and synthesize water-soluble photosensitizers and/or to conjugate them to drug delivery vehicles or biomolecules for efficient delivery to the target site. Photodynamic therapy, types of photosensitizers and conjugation strategies and photodynamic therapy applications will be briefly discussed. 75

76 OP 15 Doxorubicin Delivered To Target Prostate Cells Without Collateral Damage To Non-Targeted Prostate Cells In Vitro Olcay Boyacıoğlu a,b, Christopher H Stuart a, George Kulik a, William H Gmeiner a a Wake Forest School of Medicine, Department of Cancer Biology, Winston-Salem, NC, USA b Adnan Menderes University, Faculty of Engineering, Department of Food Engineering, Aydın, TURKEY Chemotherapeutic drugs cause inevitable collateral damage on healthy cells. The use of doxorubicin (Dox) may result in systemic toxicities and serious health issues for cancer patients in the long term. High dose of cytotoxic drugs are given to the patients to ensure the targeted cancer cells encounter an effective dose of the drug after it is diluted in the patient s body. The term targeted cancer cell is used quite loosely here. In fact, the drug is given to patients without taking any aim and simply affects all cells. Therefore, targeted delivery of cytotoxic drugs is an important objective to improve cancer chemotherapy. 1 Prostate-specific membrane antigen (PSMA) has elevated levels of expression on the apical plasma membrane 2 of prostate cancer cells; hence is of interest for targeted delivery of cytotoxic drugs for cancer treatment. PSMA is an exopeptidase 3 with folate hydrolase and NAALADase (N-acetylated α- linked acidic dipeptidase) activities. PSMA is present on the membrane in a dimer form, 4 and was shown to interact with dimerized ligands compared to monomeric ligands. 5 Our research group has developed a novel single-stranded DNA aptamer to PSMA through Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. The aptamer has specific sequences embedded to promote Dox binding, and can be dimerized to develop dimeric aptamer complexes (DACs) for specific delivery of Dox to PSMA-expressing (PSMA+) cancer cells. DACs are stable under physiological conditions and are internalized specifically into PSMA+ C4-2 cells with minimal uptake into PSMA-null PC3 cells. Cellular internalization of DAC was demonstrated by confocal microscopy and flow cytometry. Covalent modification of DAC with Dox (DAC-D) resulted in a complex with stoichiometry ~4:1. Dox was covalently bound in DAC-D using a reversible linker that promotes covalent attachment of Dox to genomic DNA following cell internalization. Dox was released from DAC-D under physiological conditions with a half-life of 8 hours, sufficient for in vivo targeting. DAC- D was used to selectively deliver Dox to C4-2 cells with endosomal release and nuclear localization of Dox. DAC-D was selectively cytotoxic to C4-2 cells with similar cytotoxicity as the molar equivalent of free-dox. In contrast, DAC-D displayed minimal cytotoxicity to PC3 cells, demonstrating the complex 76

77 displays a high degree of selectivity for PSMA+ cells. DAC-D displays specificity and stability features that may be useful for improved delivery of Dox selectively to malignant tissue in vivo. Keywords: aptamer, chemotherapy, prostate cancer, prostate-specific membrane antigen, targeted drug delivery. Resources: 1) Li, L, et al. Curr Med Chem 2013:20, ) Christiansen, JJ, et al. Mol Cancer Ther 2005:4, ) Denmeade, SR, et al. Sci Transl Med 2012:4, ) Schülke, N, et al. Proc Natl Acad Sci USA 2003:100, ) Aggarwal, S, et al. Cancer Res 2006:66,

78 OP 16 A Novel Approach to Deliver Peptides that Target Intracellular Enzymes Begum Alaybeyoglu, a Ece Altinisik, b Deniz Irvali, a Berna Sariyar Akbulut, b Elif Ozkirimli a a Department of Chemical Engineering, Bogazici University, 34342, Istanbul Turkey b Department of Bioengineering, Marmara University, 34722, Istanbul Turkey Antibiotic resistance, resulting from the misuse or underuse of antimicrobial drugs, has been acknowledged since the discovery penicillin. Among many resistance mechanisms bacteria have acquired, the production of the antibiotic-inactivating beta-lactamase enzymes is the most prominent. The co-administration of beta-lactam type antibiotics and beta-lactamase inhibitors has been used as a treatment strategy. Despite the success of these combination therapies, mutations of the beta-lactamase enzyme have led to resistance against available inhibitors emphasizing the novel inhibitor design in the field of antibiotic resistance. As an alternative to small molecule drugs, peptide-based drugs are favored due to their high efficacy and low toxicity, with a disadvantage of their larger size and hydrophobicity restricting their uptake. Along with the discovery of cell penetrating peptides (CPPs), which can translocate through the cell membrane without the need for a receptor, the studies on peptide-based drugs that target intracellular proteins have regained attention. In our previous studies, we have proposed a novel chimeric peptide that has a potential to translocate across the bacterial cell wall and inhibit intracellular beta-lactamase. This chimeric peptide combines a cell penetrating peptide region and a beta-lactamase inhibitory region and was found to have antimicrobial activity against beta-lactamase producing E. coli. In an effort to guide the development of chimeric peptides, we investigate this peptide and similar inhibitory peptides that are designed based on the same strategy. The peptides were characterized by determining their minimum inhibitory concentrations, by measuring the enzyme kinetics and their bacterial selectivity and by monitoring the effect on bacterial cells using microscopic methods. We believe expanding the knowledge base of antimicrobial action of peptide-based drugs will accelerate and advance peptide based drug discovery studies. We gratefully acknowledge TUBITAK (114M179) for funding the project. 78

79 OP 17 Molecular Dynamics Simulations Analysis Of Hybrid Region Of Mirna-Mrna Involved In Chronic Kidney Diseases Andleeb Zahra a, Amina khan a, Muhammad Jawad Khan a, Muhammad Qaiser Fatmi a, Burak Erman b a COMSATS Institute of Information Technology, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan b Koç University, Rumelifeneri, Sarıyer/İstanbul. MiRNAs are small, double stranded, non-coding RNAs that regulate gene expression by deregulating mrnas. MiRNAs play important roles in modifying various cellular processes such as cell growth, differentiation, apoptosis, and immune response. In addition, mirnas play important role in the pathogenesis of various renal diseases, including chronic kidney diseases (CKD). CKD refers to the gradual loss in kidney function with declining glomerular functional rate (GFR). The study focuses on regulatory mechanism of mirna-mrna interactions to control gene expression in CKD. Our results of homology studies of mirna-mrna hybrid highlighted the effect of partial complementary binding pattern on regulation of genes by mirna. Based on those studies, mirna-mrna complex was subjected for Molecular Dynamic simulations for 100 ns. In-silico mutation in mrna was introduced to check its role on complex formation. Mutant mirna-mrna complex was again subjected for 100ns MD simulations. We found that introduction of mutation in RNA-mRNA duplex and does not compromise the stability of the complex. RMSD and RMSF analysis of both wild type and mutant complexes suggested that effect on mutation varies from point to point in seed and non-seed regions of mirna. These results can be the best interpretation of involvement of mirna in controlling the downstream signaling and causing the disease. This phenomena will open up new horizon for HITS- CLIP experiments in CDK. References: Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M., Yefanov, A., Lee, H., Zhang, N., Robertson, C. L., Serova, N., Davis, S., Soboleva, A., Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M., Yefanov, A., Lee, H., Zhang, N., Robertson, C. L., Serova, N. & S. D. (2013). NCBI GEO: archive for functional genomics data sets update. Nucleic Acids Res, 41:

80 Chandrasekaran, K., Karolina, D. S., Sepramaniam, S., Armugam, A., Wintour, E. M., Bertram, J. F., & Jeyaseelan, K. (2012). Role of micrornas in kidney homeostasis and disease. Kidney international, 81(7), Ginawi, I. A., Elasbali, A. A., Ahmed, H. G., Ashankyty, I. M., Altamimi, T., Alhasan, S., & Al-hazimi, A. M. (2013). Population screening for chronic kidney disease and its associated risk factors: a survey in Hail region, KSA. Journal of Public Health, 5(7), Ho, J., Ng, K., Rosen, S., Dostal, A., Gregory, R. & Kreidberg, J. (2008). Podocyte-specific loss of functional micrornas leads to rapid glomerular and tubular injury, Journal of the American Society of Nephrology, 11(19). 80

81 OP 18 Quantum Mechanical Scoring Function For Virtual Screening Cemal Köprülüoğlu (a,b), Milan Dejmek (a), Haresh Ajani (a,b), Adam Pecina (a), Palanisamy Deepa (a), Jindřich Fanfrlík (a), Jan Rezac (a,b), Martin Lepšík (a), Pavel Šácha (a), Radim Nencka (a), Michal Šála (a), Hubert Hřebabecký (a), Vladimir Kryštof (c) and Pavel Hobza (a,b) (a) Institute of Organic Chemistry and Biochemistry v.v.i Academy of Sciences of the Czech Republic, Flemingovo nam. 2, , Prague6, the Czech Republic (b) Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, Olomouc, Olomouc, the Czech Republic (c) Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, the Czech Republic Reliable scoring of docking poses is the Holy Grail for the academic and industrial pharmaceutical research. It is well known that different docking/scoring approaches give different ranking of poses. 1 The scores are obtained via statistical, empirical or physics-based functions. 2 In the last category, we have undertaken a broad and careful development of semiempirical quantum mechanical (QM) method which was parametrized against high-level QM data. The resulting PM6-D3H4X method is fast and reliably describes a broad range of noncovalent interactions; accuracy of the method is very close to that of much more expensive methods like DFT-D. 3 We have developed a QM-based scoring function 4 which is constructed as a sum of physical terms, i.e. the interaction energy, the solvation free energy, the change of the conformation free energy of the ligand and protein and the interaction entropy. This scoring function was successfully applied to half-a dozen of targets. 5 In this study we have established a QM based virtual screening protocol and searched in-house database (>1000 compounds) for kinase inhibition. All the preparatory steps were done by using Schrödinger modules LigPrep, Epik, ConfGen, Macromodel and the docking was done using Schrödinger Glide module. 6 The scoring function is based on the above mentioned semi-empirical quantum chemical method applied to the results obtained from Glide docking. We chose the compounds with high score values for the experimental testing for CDK2 inhibition. We identified four hits with IC50 of 1-12 micromolar and by one round of structure optimization we obtained three compounds with submicromolar activity. In summary, the QM-based virtual protocol presented here is useful in fishing out the active compounds from libraries of compounds. 81

82 References 8) Leach, A.R.; Shoichet, B.K.; Peishoff, C.E. J. Med. Chem., 2006, 49, ) Gohlke, H.; Klebe, G. Curr. Opin. Struct. Biol. 2001, 11, ) Řezáč J.; Hobza, P. J. Chem Theory Comput. 2012, 8, ) Fanfrlík, J.;Bronowska, A.K.;Řezáč J.;Přenosil,O.;Konvalinka,J.; Hobza, P. J. Phys. Chem B 2010, 114, ) Lepšík, M.; Řezáč J.; Kolář, M; Pecina, A.; Hobza, P.; Fanfrlík, J. ChemPlusChem 2013, 78, ) Friesner, R.A.; Banks, J.L.; Murphy, R.B.; Halgren, T.A. et al. J. Med. Chem. 2004, 47,

83 OP 19 Perturbation Response Scanning Highlights The Role Of Electrostatics In Remote Control Of Protein-Protein Disassociation Haleh Abdizadeh, Ali Rana Atilgan, Canan Atilgan Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, Istanbul, Turkey We unify elastic network model with Perturbation Response Scanning (PRS) 1 as an efficient approach for predicting kinetically hot spots in a set of 27 protein complexes, using the three dimensional structures of the bound and free proteins as an input. PRS, a method based on the linear response theory, predicts the critical residues triggering the conformational transitions between bound and free forms of the proteins constructing the pair. In order to apply the technique, we need to construct a matrix holding the cross-correlations between residue pairs. Thus, we treat the proteins as elastic networks in a coarsegrained approach and use the inverse Laplacian. PRS reveals that while for a group of protein pairs, the residues promoting the disassociation of the bound proteins are mainly confined to regions with large motions, there are others where these residues are located on parts of the protein unaffected structurally during binding/unbinding processes. Strikingly, only one of the protein complexes displays hot residues from the interface of the complex. Other cases introduce residues from remote parts of the protein. We categorize the protein complexes based on hot residue location on protein complex structure. We find that electrostatic potential distribution of the free and bound proteins contribute to disassociation processes controlled via remote sites on the protein complexes. We validate the approach by illustrating the biological significance of hot residues selected by PRS. We find that the residues whose perturbation leads to the observed conformational changes usually correspond to either functionally important residues or are highly conserved. Keywords: Conformational transition, Perturbation response scanning, protein complex disassociation References: 1. Atilgan, C.; Atilgan, A. R., Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein. PLoS Comput. Biol. 2009, 5 (10), e

84 OP 20 Improving The Water Solubility Of Curcumin By Ultrasonically Prepared Alginate - Curcumin Complexes And Alginate Nano-Beads Nil Erge Akkaya, Sevim İşçi Turutoğlu, Ahmet Fatih Ertem, Huceste Giz ITU, Faculty of Science and Letters, 34469, Maslak, Istanbul, Turkey Key words: Curcumin, alginate, nano-beads Curcumin (bis-α,β-unsaturated β-diketone), is a major component of the yellow spice turmeric, derived from the rhizomes of curcuma longa. It is commonly used as flavouring and coluring agents in foods and well known for its antioxidant properties. It is used in India for centuries as a spice and medicinal agent. Curcumin has a wide variety of bioactivities, including chemopreventive, antienflamatory, antioxidant as well as antitumor properties1,2. Alginate is an anionic biopolymer, a natural polysaccharide, used for improving the bioavailability of curcumin and related substances in drug release and food supplement applications. It is of interest as a biopolymer to prepare nanocapsules owing to its good biocompatibility, biodegradability, non-toxicity, gelation and film formation properties3. Soluble sodium alginate can be cross-linked using calcium chloride, with formation of insoluble alginate particles with different diameters, depending on the concentrations of sodium alginate and calcium chloride4. Alginate is selected as the agent to increase the water solubility of curcumin. The studies are carried out in the ultrasound environment with different alginate concentrations and the water solubility of curcumin is observed with alginate addition. At 25 C, in neutral conditions, curcumin solubility was increased to 0,6035 ± 0,0861 mg/ml. In thesame samples, the amount of curcumin per mg of alginate was calculated, curcumin solubility increased with decreasing concentration of alginate in solution. Curcumin s highest solubility, in 0,05 % alginate solution was 0,2521 mg curcumin/mg alginate. Alginate - curcumin beads were prepared, after drying at room conditions, diameter of microspheres were around approximately 1 mm. When 1g of dried microspheres were consumed as food or medication, the amount of curcumin supplied is 2,92 mg. Viscosity measurements of curcumin - alginate solutions before and after sonication have shown that sonication has reduced the viscosity by half. Zeta-potential measurements have shown that samples exposed to ultrasound have more homogeneous charge distribution than the samples not-treated with ultrasound. 84

85 Bead containing solutions were subjected to freeze-drying and concentration of the microspheres in the solution was increased. From SEM images, data show that nano-sized alginate beads were efficiently formed with diameters as small as 9,77 nm. References: 1) Tapal, A. ve Tiku, P. K., (2011). Complexation of curcumin with soy protein isolate and its implications on solubility and stability of curcumin. 2) Guzman-Villanueva, D., El-Sherbiny, İ. M., Herrera-Ruiz, D. ve Smyth, H. D. C., (2013). Design and In Vitro Evaluation of a New Nano-Microparticulate System for Enhanced Aqueous-Phase Solubility of Curcumin. 3) Aggarwal, R. B., Sundaram, C., Malani, N. ve Ichikawa, H., (2006). Curcumin: the indian solid gold. 4) Shi, P., He, P., Teh, T. K. H., Morsi, Y. S. ve Goh, J. C. H., (2011). Parametric analysis of shape changes of alginate beads. 85

86 OP 21 Computer-Aided Discovery Of Sphingosine Kinase 1 (Sphk1) Inhibitors Ozge Bayraktar a, Elif O. Ozkirimli a,b, Kutlu O. Ulgen b a Department of Computational Science and Eng., Bogazici University, Bebek, Istanbul, Turkey, b Department of Chemical Eng., Bogazici University, Bebek, Istanbul, Turkey Sphingosine-1-phosphate (S1P) signaling pathway plays an important role in controlling cell survival, cell proliferation, lymphocyte trafficking, angiogenesis, and cell differentiation. Sphingosine kinases (SphKs) catalyze the phosphorylation of sphingosine to sphingosine-1-phosphate (S1P). Elevated expression of SphK1 is observed in breast, colon, and prostate cancers 1-2, and there is increased interest in developing SphK1 inhibitors as effective chemotherapeutic agents for cancer treatment. In the recently determined crystal structures of SphK1, there are binding pockets for ATP and sphingosine and, to date, these sites have been targets for inhibitor development. Inhibitors that target these sites are nonspecific and novel allosteric sites need to be identified for specific inhibitor design. In this work, we use computational docking and screening methods in Schrodinger platform to identify a pool of orthosteric and allosteric inhibitors. In this work, our first aim is to identify orthosteric inhibitors that target the sphingosine binding site. 500,000 compounds from the ZINC 3 database were screened using high throughput virtual screening (HTVS) in Glide and high scoring compounds were identified. Then, ligand based pharmachophore hypotheses were generated by QSAR studies from 28 heterocycle derivatives containing oxadiazole and 54 heterocycle derivatives containing thiazole. The compounds that match these pharmacophore hypotheses were ranked based on ligand efficiency metrics and docking score and the pharmacokinetic and druglikeness properties. As a result, a set of compounds that target the sphingosine binding site were proposed based on both structure based and ligand based docking studies. Our second aim was to identify allosteric inhibitors. Although it was reported that SphK1 is minimally a dimer, 4 the structure of the dimer is not known and the dimer interface may serve as an excellent candidate for allosteric inhibitor design studies. To that end, the dimer structure was predicted using PRISM 5-6 and high throughput virtual screening was performed to identify compounds that might bind to the dimer interface and possibly affect oligemerization of the kinase. This work will provide a guide for future development of inhibitors targeting SphK1. 86

87 Resources: 1) Alshaker, H.; Sauer, L.; Monteil, D.; Ottaviani, S.; Srivats, S.; Böhler, T.; Pchejetski, D. Adv. Cancer Res. 2013, 117, ) Heffernan-Stroud, L.A.; Obeid, L.M. Adv. Cancer Res. 2013, 117, ) Irwin, J.J.; Shoichet, B.K. J Chem Inf Model. 2005, 45(1), ) Lim, K.G.; Tonelli, F.; Li, Z.; Lu, X.; Bittman, R.; Pyne, S.; Pyne, N.J. J Biol Chem. 2011, 286, ) Baspinar, A.; Cukuroglu, E.; Nussinov, R.; Keskin, O.; Gursoy, A. Nucl. Acids Res. 2014, 42, ) Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O. Nat Protoc. 2011, 6(9), Key Words: SPHK1, Virtual Screening, Docking, Pharmacophore Modeling, 3D-QSAR 87

88 OP 22 Synthesis And Evaluation Of Some Benzodioxole-Based Thiosemicarbazone Derivatives As Novel Anticancer Agents Belgin Sever a, Mehlika Dilek Altıntop a, Gülşen Akalın Çiftçi b, Halide Edip Temel b, Zafer Asım Kaplancıklı a a Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Eskişehir, Turkey b Anadolu University, Faculty of Pharmacy, Department of Biochemistry, Eskişehir, Turkey Cancer is an important cause of death worldwide accounting for 7.9 million deaths in 2007 and with an estimated 13 million deaths in Up to now, many chemotherapeutic drugs have been developed as anticancer agents but most of them have remained insufficient for cancer treatment because of their lack of specificity to cancer cells and correspondingly their high risk of toxicity. Therefore, pharmaceutical research has focused on the discovery of more selective and less toxic anticancer agents. 1 Thiosemicarbazones have been widely used as anticancer agents associated with their capacity of iron coordination and complexation with most of the transition metal ions. Triapine, a thiosemicarbazone derivative, is a promising anticancer agent inhibiting ribonucleotide reductase enzyme which is important for cell proliferation. 2 On the other hand, 1,3-benzodioxole moiety is also found in a variety of antimitotic agents such as podophyllotoxin, steganacin, and combretastatin A-2. 3 In the current work, new benzodioxole-based thiosemicarbazone derivatives were synthesized via the reaction of 4-(1,3-benzodioxol-5-yl)thiosemicarbazide with aromatic aldehydes. The compounds were evaluated for their cytotoxic effects on A549 human lung adenocarcinoma and C6 rat glioma cell lines using MTT assay. Among these compounds, 4-(1,3-benzodioxol-5-yl)-1-([1,1'-biphenyl]-4- ylmethylene)thiosemicarbazide (5) can be identified as the most promising anticancer agent against C6 (IC 50 = 32.67±6.43 μg/ml) and A549 cell lines (IC 50 = 80±10 μg/ml) compared to cisplatin (IC 50 = 14.33±2.31 μg/ml; 18.33±4.16 μg/ml, respectively). Compound 5 increased early and late apoptosis in C6 cells (25%) more than cisplatin (16.3%), whereas the compound caused early and late apoptosis in A549 cells (12.11%) more than control (3.1%). Compound 5 also caused disturbance on mitochondrial membrane potential in C6 and A549 cell lines. Key words: Thiosemicarbazone, Benzodioxole, Cancer, Apoptosis, Mitochondrial membrane potential. 88

89 References: 1) Moorthy, N.S.; Cerqueira, N.M.; Ramos, M.J.; Fernandes, P.A. Mini Rev. Med. Chem. 2013, 13, ) Chapman, T.R.; Kinsella, T.J. Front. Oncol. 2012, 1, ) Wang, H.H.; Qiu, K.M.; Cui, H.E.; Yang, Y.S.; Luo, Y.; Xing, M.; Qiu, X.Y.; Bai, L.F.; Zhu, H.L. Bioorg. Med. Chem. 2013, 21,

90 OP 23 Optimization of Photosensiting Tetrapyrroles Efficacy: Targeting strategies and / or Combination of Therapeutic Effects Fabienne Dumoulin Gebze Technical University, Chemistry Department, PO Box 141, Gebze Kocaeli, Turkey The maximum absorption wavelength of phthalocyanine, generally centered at 680 nm but extendable up to 1000 nm, make them attractive photosensitisers for PDT, as NIR absoprtion allows a deeper tissue penetration and excitation in the therapeutic window. Efficient design of phthalocyanines can be achieved thanks to the versatility of the chemical functionalization possibilities. Rational appraoches based on a fine tuning of the desired properties together with SAR considereations will be presented, as well as dual action strategy developped for additional antivascular effect, and several targeting strategies, using aptamers, vitamins, carbohydrates and naoparticles.. Starting from three different subsitution pattern bases (glycerol, polyethylene glycol and octasulfanyl non peripheral), the results of ten years of research at the Gebze Technical University on the optimization of photosensitisers for photodynamic therapy will be presented. See more in: New. J. Chem 2015, 39, / PlosOne, 2014, 9(5): e97894 / Dalton Trans. 2014, 43, / Photochem. Photobiol. 2014, 90, / Arkivoc, 2014, (i) / Molecular Pharmaceutics 2013, 10, / J. Porphyrins Phthalocyanines 2013, 17, / J. Porphyrins Phthalocyanines 2013, 17, / Turkish J. Chem. 2013, 37, / Photodiagn. Photodyn. Ther. 2013, 10, / Tetrahedron Lett. 2012, 53, / Nanoscale 2012, 4, / Org. Biomol. Chem. 2012, 10, / Tetrahedron Lett. 2011, 52, / J. Porphyrins Phthalocyanines 2011, 15, / Dalton Trans. 2011, 40, / Tetrahedron Lett. 2010, 51, / Coord. Chem. Rev. 2010, 254, / Tetrahedron 2010, 66, / New. J. Chem. 2010, 34, / Langmuir 2010, 26(8), / Photochem. Photobiol. Sci. 2009, 8, / J. Porphyrins Phthalocyanines 2008, 12,

91 POSTER PRESENTATIONS 91

92 PP 1 Molecular Docking And Biological Evaluation Of Some Indole Derivatives As Inhibitors Of Gelatinases MMP-2 And MMP-9 Zühal Kilic-Kurt a, Filiz Bakar b and Süreyya Ölgen c a Department of Pharmaceutical Chemistry, b Department of Biochemistry, Faculty of Pharmacy, Ankara University, Tandoğan, Ankara, Turkey, c Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İstanbul Kemerburgaz University, Bağcılar, İstanbul, Turkey The matrix metalloproteinases (MMPs) are secreted from the cells as inactive proenzymes which are activated and regulated by many factors, such as steroid hormones, cytokines and growth factors. 1 They play important roles in many physiopathological processes such as degradation of extracellular matrix proteins, facilitating tumor metastasis and angiogenesis, resistance to apoptosis. 2 Abnormal MMPs activities have been shown to be linked in development and maintenance processes as well as in several diseases including cancer, diabetes and neurodegenerative diseases. 3 The human MMPs comprise more than 20 known members which are are classified as collagenases, gelatinases, stromelysins and matrilysin according to their substrate specificity. 4,5 Among all MMPs, MMP-2 and MMP-9 (gelatinases) are highly involved in tumor invasion and metastasis and have become an attractive target for the design of new therapeutic agents against cancer. 6 In this study, previously synthesized some indole compounds were evaluated for inhibitory activities against gelatinases MMP-2 and MMP-9 by enzyme-linked immunosorbent assay. The results showed that the compounds have inhibitory activities on MMP-2 and MMP-9 in a concentration dependent manner. In addition, to analyze the binding affinity of the compounds in active sites of MMP-2 and MMP-9, molecular docking studies were carried out using Autodock vina software. In general, the binding modes of the compounds into the active sites of MMP-2 and MMP-9 were correlated with their inhibitory activity. Keywords: MMP-2, MMP-9, activity, molecular docking, indole derivatives This study was supported by Turkish Research Council and Technology Grant SBAG-113S

93 References 1. Hashizume, K.; Takahashi, T.; Hirako, M.; Kohsaka, T.; Sato, T.; and Ito, A. Theriogenology, 1997, 47, Santos, M. A.; Marques, S. M.; Tuccinardi, T.; Carelli, P.; Panelli, L.; Rossello, A. Bioorg. Med. Chem. 2006, 14, Sjøli, S.; Solli, A. I.; Akselsen, Q.; Jiang, Y.; Berg, E.; Hansen, T. V.; Sylte, I.; Winberg, J. O. Biochimica et Biophysica Acta, 2014, 1840, Marcq, V.; Mirand, C.; Decarme, M.; Emonard, H.; Hornebeck, W. Bioorg. Med. Chem. Lett. 2003, 13, Kalvaa, S.; Singamb, E. R. A.; Rajapandianb, V.; Saleenaa, L. M.; Subramanian, V. J. Mol. Graphics Modell. 2014, 49, Cheng, X-C.; Wang, Q.; Fang, H.; Tang, W.; Xu, W-F. Bioorg. Med. Chem. 2008, 16,

94 PP 2 Distinguishing Active/Inactive States Of Β 2 -Adrenergic Receptor (Β 2 ar) Based On Binding Affinity Of Ligands Through Docking Studies Müberra Yilmaz a) ; Pemra Doruker b) ;Ebru Demet Akten c) a) Computational Science and Engineering Program and Polymer Research Center, Bogazici University, Istanbul, Turkey b) Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey c) Department of Bioinformatics and Genetics, Faculty of Natural Sciences and Engineering, Kadir Has University, Cibali 34083, Istanbul, Turkey β 2 AR is a member of G-protein-coupled receptors (GPCRs), and is involved in the relaxation of pulmonary tissues through the binding of catecholamines, such as epinephrine. The lack of its activation leads to difficulty in breathing and in more severe cases to asthma attacks. The receptor activates itself through specific conformational changes in the ligand binding site and other conserved regions. Therefore, it is crucial to look into the dynamic character of the receptor, which will help to understand the distinctiveness in the binding mode of each ligand with a specific activity. In this study, a classification protocol was developed and used to classify receptor β 2 AR conformers based on the binding mode of selected ligands with known activities. First, distinct conformational states of the ligand s binding pocket were obtained from a 2.8 μs MD simulation conducted on the available crystal structure of β 2 AR (PDB is:2rh1) prior to this study [1,2]. A total of 2800 snapshots collected at every 1 ns were clustered based on the RMSD value of the five key residues at the binding site (Asp113, Val117, Ser203, Ser207 and Asn312) [2,3]. A total of 13 distinct snapshots were obtained when the cut-off value for the RMSD was set to 1.5 Å. Next, a total of 8 ligands were docked to each 13 conformers using AutoDock, GOLD and GLIDE softare tools. The best pose of each ligand in the conformer was selected and evaluated based on its vicinity to four critical residues (Asp113, Ser203, Ser207 and Asn312). The poses that were not in this neighbourhood were discarded and the remaining ones were sorted based on their score values. The conformers that are found in the top five were selected to be the most suitable conformational state for that ligand. If the ligand was an agonist that prefers an active state, then the selected conformer would most likely represent an active state. Previously, the same protocol was applied to 5 inactive and 7 active crystal structures and successfully distinguished the active structures from the inactive ones. 94

95 Generation alternative conformations of the receptor and classifying them as active or inactive is an important practice in the drug design studies that are often limited to one snapshot obtained from x-ray studies. Keywords: β 2 -Adrenergic Receptor, GPCR, conformational change, dynamic character, binding mode, docking/scoring, agonist, active state. References: 1) Ozcan, O., A. Uyar, P. Doruker and E. D. Akten, BMC Struc. Biol. 2013, 13(29), 2) Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Steven RC, Science 2007, 318: ) Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, Kobilka BK, Nature 2007, 450:

96 PP 3 An Amperometric 2-Propanol Sensor Based On A New Nanomaterials Sinan Eriş [a], Handan Pamuk [a], Esma Erken [a], Fatih Şen [a] * [a] Dumlupinar University, Biochemistry Department, 43100, Kütahya, Turkey A new amperometric 2-propanol sensor has been developed by using new platinum nanomaterials. The detection of 2-propanol concentration is based on the response currents resulted from the electrocatalytic oxidation of 2-propanol. The characterization of nanomaterials was performed by X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), atomic force microscopy (AFM) and transmission electron microscopy (TEM), ICP-OES, electrochemical measurements (CV and CA) [1-2]. Their results show the formation of highly crystalline and colloidally stable new platinum nanosensors. In 0,5 M H 2 SO 4 solution containing different 2-propanol concentrations, the sensor shows a good sensitivity of anodic pick 0.56 volt (A/mg Pt). The results demonstrate that the Pt(0)@DPA electrodes are potential as the electrochemical integrated sensors for 2-propanol detection. The average particle sizes of the nanosensor are about 3.5 nm. [2-4]. Keywords: Atomic Force Microscopy (AFM), Electroless Platining; Electrocatalysis, Nanoparticles, X-ray Photoelectron Spectroscopy. References [1] N. Elfström, A.E. Karlström, J. Linnros Nano lett., 3 (2008), pp [2] S. Y. Shen, T. S. Zhao, J. B. Xu, Y. S. Li, J. Power Sources 2010, 195, [3] F. Şen, G. Gökağaç. J Appl Electrochem DOI /s [4] F. Şen, G. Gökağaç S. Şen. J Nanopart Res (2013) 15:1979 DOI /s

97 PP 4 Synthesis Of New Ureas Derived From Sulfonamides As Potential Anticancer Agents Sevda Türka, Fatih Toka, Hülya Çelikb, Sevgi Karakuşa, Hayrunnisa Nadaroğluc, Kaan Küçükoğlud, Bedia Koçyiğit-Kaymakçıoğlua amarmara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34668, Istanbul- Turkey bagri Ibrahim Cecen University, Faculty of Pharmacy, Department of Pharmaceutical Technology, 04000, Agri-Turkey cataturk University, Erzurum Vocational School, Department of Food Technology, 25240, Erzurum- Turkey dataturk University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 25240, Erzurum- Turkey Urea derivatives have attracted a great deal of interest owing to their anticancer1, antifungal, antibacterial, anti-inflammatory2 and HIV-protease inhibitory3 activities, depending on their substituents. Sulfonamides are also an important class of biologically active molecules. They have been used in the treatment for several years and they are known for their antibacterial, diuretic and antitumor activities4. In the current work, new urea derivatives were obtained by the reaction of sulfonamides with various isocyanates. Chemical structures of the compounds were elucidated by FT-IR, 1H-NMR, MS spectra and elemental analysis. The target compunds were screened for their ability to inhibit carbonic anhydrase isoenzymes. In this procedure; carbonic anhydrase (hca-1 and hca-2) isozymes were purified by using Sepharose 4B-L-Tyrosine sulfanilamide affinity chromatography from human erythrocytes. The inhibition/activation activity of synthesized molecules on hca-1 and hca-2 was also studied. With calculating IC50 and Kİ values; the types of inhibiton for drug derivatives which showed inhibition activity was determined5-6. Resources: 1) Luzina, L. E.; Popov, A. V. Eur. J. Med. Chem. 2012, 53, ) Keche, A. P.; Hatnapure, G. D.; Tale, R. H.; Rodge, A. H.; Birajdar, S. S.; Kamble, V. M. Bioorg. Med. Chem. Lett. 2012, 22, ) Stranix, B. R.; Sauve, G.; Bouzide, A.; Cote, A.; Sevigny, G.; Yelle, J.; Perron V. Bioorg. Med. Chem. Lett. 2004, 14,

98 4) Ghorab, M. M.; Ceruso, M.; Alsaid, M. S.; Nissan, Y. M.; Arafa, R. K.; Supuran, C. T. Eur. J. Med. Chem. 2014, 87, ) Demir Y.; Demir N.; Nadaroglu H.; Bakan E. Prep Biochem Biothech. 2000, 30: ) Demir Y.; Nadaroglu H.; Demir N. Biol Pharm Bull. 2004, 27:

99 PP 5 Electrochemically Synthesized Partially Rgo/Ppy-Pt/Zno Modified Glassy Carbon Electrode As Highly Selective And Sensitive Sensors For Detection Of Ascorbic Acid, Dopamine And Uric Acid Sait Bozkurt, Fatih Sen Biochemistry Department, Faculty of Arts and Science, Dumlupınar University, Sen Research Group Kütahya, Turkey. We report here an efficient and simple approach for the preparation of a partially reduced graphene oxide polypyrrole zinc oxide modified glassy carbon electrode (RGO-Ppy-Pt/GCE). The modification of the RGO-GCE consists of three steps. These include (i) chemical synthesis of graphite oxide by a modified Hummer's method, 1 (ii) exfoliation of graphite oxide to graphene oxide (GO) by ultrasonication and (iii) controlled partial electrochemical reduction in 0.1 M phosphate buffered medium (ph 3.0) via potentiodynamic cycling (2 cycles) to obtain a partially reduced graphene oxide modified glassy carbon electrodes (RGO-GCE). The behaviour of the RGO-GCE towards ascorbic acid (AA), dopamine (DA) and uric acid (UA) was investigated by differential pulse voltammetry, with an enrichment time of 3 minutes. 2 Morphological (SEM and TEM) and electrochemical characterization studies were also reported. Finally, the performance of the RGO-GCE based sensor was successfully tested for analysing UA and quantitative recoveries of AA and DA in serum samples. Resources: 14) Pamuk, H.; Aday, B.; Şen, F.;Kaya, M. RSC Adv.2015, 5, ) Hou, S.; Kasner, M. L.; Su, S.; Patel, K.; Cuellari, R. J. Phys. Chem. C. 2010, 114,

100 PP 6 Novel Alcohol Sensor Based On Nixpt100-X@Ppy Ternary Alloy Nanoparticles Coated Electrode Özlem Karatepe, Bahdişen Gezer, Fatih Şen 1. Dumlupınar University, Department of Biochemistry, Kütahya 2. Uşak University, Department of Chemical Engineering, Uşak A novel alcohol sensor was proposed in the present work, which was based on the pulsed electrodeposition of Ni x Pt 100-x binary alloy nanoparticles on polypyrrole. 1,2 The composition, morphology and catalytic activity of the obtained nanoparticles were characterized by X-ray diffraction, energy dispersive X-ray spectroscopy, scanning electron microscopy and voltammetry, respectively. The Ni 75 Pt coated glassy carbon electrode was proved to be suitable for detecting alcohol. For comparison, the electrodes with Ni 0 Pt Ni 25 Pt and Ni 50 Pt were also prepared and studied. Resources: 1) Cooper, J. S.; Jeon, M. K.; McGinn, P. J. Electrochem. Commun., 2008, 10, ) Jeon, M. K.; Lee, K. R.; Daimon, H.; Nakahara,A.; Woo, S. Catal. Today. 2008, 132,

101 PP 7 Dynamic Properties Of The ORC1 Wild Type And Mutant Proteins Derya AYTAN a, Cenk DENKTAŞ b, Nagehan Ersoy Tunalı a a Halic University, Department of Molecular Biology and Genetics, Istanbul, TURKEY b Yıldız Technical University, Department of Physics, Istanbul, TURKEY. Ornithine Transporter 1 (ORC1) protein, a mitochondrial ornithine transporter belonging to solute carrier family 25, is encoded by the SLC25A15 gene. It transports ornithine from the cytosol to the mitochondrial matrix. This protein has essential roles in the urea cycle 1. We have recently identified a novel SCL25A15 mutation, p.ala15val, which interferes with the transport ability of ORC1 protein 2. This mutation causes Hyperornithinemia-hyperammonemia-homoctrullinuria (HHH) syndrome, a rare autosomal recessive urea cycle disorder. In this study, we aimed to understand how ORC1 protein structure is altered by the mutation. For this purpose, we used molecular dynamic (MD) simulations, and compared the structures of wild type and mutant ORC1 proteins. We investigated the thermodynamic properties of the proteins via MD simulations for constant temperature (310 K). We also illustrated the alterations on ORC1 protein structure using a map of potential energy levels. We believe that this study will expand our knowledge for future drug discovery studies for Hyperornithinemia-hyperammonemia-homoctrullinuria (HHH) syndrome. Resources: 1. Tezcan K, Louie KT, Qu Y, Velasquez J, Zaldivar F, Rioseco-Camacho N, Camacho JA(2012).Adult-onset presentation of a hyperornithinemia-hyperammonemia-homocitrullinuria patient without prior history of neurological complications. JIMD Rep. 3: Ersoy Tunalı E, Marobbio CMT, Tiryakioğlu NO, Punzi G, Saygılı SK, Önal H, Palmieri N (2014). A novel mutation in the SCL25A15 gene in Turkish patient with HHH syndrome: Functional analysis of the mutant protein. Molecular Genetics and Metabolism. 112:1:

102 PP 8 Modeling Huntington s Disease Mutation Nagehan Ersoy Tunalı Halic University, Department of Molecular Biology and Genetics, İstanbul, TURKEY Huntington s Disease (HD) is one of the fatal neurodegenerative disorders of the central nervous system. The pathogenic mutation causing the disease is the abnormal expansion of the CAG repeats (polyq) in the first exon of the HD gene, which encodes a protein of 3144 aa, termed huntingtin (htt). The pathology of HD is restricted to the brain, and medium spiny GABA-ergic striatal neurons are selectively lost 1. Htt shows no homology to any other counterparts, therefore fold recognition method was utilized to determine the 3D structure of htt, using VMD. The protein was loaded as sequences of 400 aa. For each 400 aa sequence, five best models were retrieved. The best model for the polyqbearing first 400 aa sequence was identified to be 1WA5_B. In the second part of the study, htt mutation was modelled by creating polyq expansion by adding extra glutamine repeats to the first 400 aa part of the protein. Wild type htt contains 23Qs. In humans, CAGs show meiotic instability and repeats are considered to show incomplete penetrance. Repeats above 40 definitely cause HD. In order to represent these stages, polyq region of htt was made expanded with 10,13, 14, 15, 16, 20, 25 and 30 additional glutamines, which result in mutant proteins of 33, 36, 37, 38, 39, 43, 48 and 53Q. The mutant models were compared to the best wild type model, 1WA5_B. According to the results, 39 or more glutamines cause conformational changes. Especially turn and coil regions were found to be longer and increased in number, and α-helices were found to be shorter. As a second step, models of only the polyq regions of 36Q and 53Q proteins were constructed and compared to the polyq region of the 1WA5_B model. The turn and coil structures were increased in number and α-helices were shorter. In this situation, protein may gain non-covalent interactions within itself or with other proteins and aggregate in the form of twisted β-sheets. Lengthened turn and coil and shortened α-helix structures significantly change the conformation of the protein. In this new conformation, protein may become susceptible to proteolysis. On the other hand, conformational change may also cause deficiency in normal htt proteolysis, in that case toxicity comes into play due to inreased half life of the protein. It has been shown that aggregate-forming mutant htt is compatible with variable β-sheet/ β-turn model by using N- terminal htt in mammalian cell cultures and cortical neurons 2. This proves that the resulting mutant structure is toxic to the cells. On the other hand, these intercellular aggregates can protect the cells against toxicity by isolating the mutant proteins in the cell. The mechanisms leading to selective neurodegeneration can be explored via modeling the normal and mutant forms of the related proteins and analyzing their molecular structures. The findings of this very 102

103 first htt modeling study in the literature is consistent with the proposed model of toxic gain of function, and opens the way for efficient drug design for a yet incurable neurodegenerative disease. Resources: 1. Graveland, G. A., Williams, R. S. & DiFiglia, M. (1985). Evidence for degenerative and regenerative changes in neostriatal spiny neurons in Huntington's disease. Science, Vol. 227, No. 4688, pp Poirier, M.A., Jiang, H. & Ross, C.H. (2005). A structure-based analysis of huntingtin mutant polyglutamine aggregation and toxicity: evidence for a compact beta-sheet structure, Hum. Mol. Genet.,Vol.14, No.6, pp Rajagopalan, S. and Andersen, J.K. (2001). Alpha synuclein aggregation: Is it the toxic gain of function responsible for neurodegeneration in Parkinson s disease? Mechanisms of Ageing and Development, Vol.122, No.14, (30 Sep 2001), pp

104 PP 9 Monitoring Iron Binding Mechanism With A Microfluidic Continuous Flow Device Gökşin Liu*, Ali Rana Atılgan, Canan Atılgan, Ali Koşar, Alpay Taralp Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul Miniaturization of systems down to micro scale enables observavtion of fast reactions within small volumes. The purpose of this study is to build a micro-fluidic continuous-flow device to monitor the iron binding dynamics of ferric binding proteins under different environmental conditions on the time scale of milliseconds. A microfluidic chip, housing compartment of mixing chamber, where the reaction is detected, is designed and connected to a high-pressure syringe pump controlled by solenoid valves.diamond shape fins are placed in the mixing chamber to achieve an effective mixing, which provides better kinetic results within smaller volumes. The detection cell extends throughout the mixing chamber so as to capture the entire mixing process. The reaction is monitored with a high-resolution camera and analyzed by a program plotting color intensities at certain points. The advantage of this system over similar systems lies in its compactness, small scale, low cost and disposability 1. This design may also be used in drug binding tests by observing the ligand binding kinetics in an efficient and costeffective manner2. 104

105 PP 10 Synthesis Of Novel Biologically Active Acridine-Sulfonamide Hybrid Compounds Containing Tetrazole Ring İbrahim Esirden a, Muharrem Kaya b a Chemistry Department, Faculty of Arts and Science, Dumlupınar University, Evliya Çelebi Campus Kütahya, Turkey. b Biochemistry Department, Faculty of Arts and Science, Dumlupınar University, Evliya Çelebi Campus Kütahya, Turkey. Tetrazoles are synthetic compounds with the highest nitrogen ingredients among the stable heterocycles. The most significant use of tetrazoles is mostly found in medicinal chemistry. For instance, the tetrazole ring can be found in drugs or drug applicants with antiallergic, antihypertensive and antibiotic activity, 1 3 in AIDS treatments or in cancer. 4, 5 Acridines are known to be biologically versatile compounds possessing several biological activities. Some of the acridine derivatives bearing a heterocyclic/aromatic ring system as one of the substituents have been found to be associated with biological activities. Nitrogen-containing heterocycles are indispensable structural units for medicinal chemists. The discovery of acridines as DNA intercalating agents, anticancer, 6 analgesic, 7 hypertensive, anti-inflammatory 8 and carbonic anhydrase inhibitors 9 have attracted the attention of organic chemists and thus led to intensive interest in the synthesis of several drugs based on acridine. In this study, we report an effective and facile microwave irradiation method via one-pot a multicomponent reaction for the synthesis of biologically active acridine-sulfonamide hybrid compounds containing tetrazole ring in high yield and very short reaction times. Target molecules have been characterized by FT-IR, 1 H-NMR, 13 C-NMR (APT) and HRMS, respectively. 105

106 This study is supported by Dumlupınar University Research Fund (Grant Number: ). References: 1. Mavromoustakos, T.; Kolocouris, A.; Zervou, M.; Roumelioti, P.; Matsoukas, J.; Weisemann, R. J. Med. Chem. 1999, 42, Toney, J. H.; Fitzgerald, P. M. D.; Grover-Sharma, N.; Olson, S. H.; May, W. J.; Sundelof, J. G.; Vanderwall, D. E.; Cleary, K. A.; Grant, S. K.; Wu, J. K.; Kozarich, J. W.; Pompliano, D. L.; Hammond, G. G. Chem. Biol. 1998, 5, Hashimoto, Y.; Ohashi, R.; Kurosawa, Y.; Minami, K.; Kaji, H.; Hayashida, K.; Narita, H.; Murata, S. J. Card. Pharm. 1998, 31, Abell, A. D.; Foulds, G. J. J. Chem. Soc. Perkin Trans. 1997, 1, Tamura, Y.; Watanabe, F.; Nakatani, T.; Yasui, K.; Fuji, M.; Komurasaki, T.; Tsuzuki, H.; Maekawa, R.; Yoshioka, T.; Kawada, K.; Sugita, K.; Ohtani, M. J. Med. Chem. 1998, 41, Kimura, M.; Kato, A.; Okabayashi, I. J. Heterocycl. Chem. 1992, 29, Kumar, A.; Sharma, S.; Srivastave, V. K. Ind. J. Chem. 2003, 14B, Sondhi, S. M.; Bhattacharjee, G. Cent. Eur. J. Chem. 2004, 2, Kaya, M.; Basar, E.; Çakir, E.; Tunca, E.; Bulbul, M. J. Enzyme Inhib. Med. Chem. 2012, 27,

107 PP 11 An Integrated Computational Approach Of Virtual Screening, Molecular Docking And Molecular Dynamics Simulations For The Discovery Of Potent S1PL Inhibitors Against Inflammatory Neurodegenerative Disorders Utku Deniz, Elif Ozkirimli Olmez, Kutlu O. Ulgen Chemical Engineering Department, Bogazici University, Bebek Istanbul Turkey Sphingosine 1-phosphate (S1P), a significant polar sphingolipid metabolite, plays a major role in the regulation of cell migration, vascular stability and differentiation. 1 It carries out communication within the cell as a second messenger. 2 Multiple sclerosis (MS), one of the frequently encountered neurodegenerative diseases and a progressive inflammatory disorder of the central nervous system (CNS), is mediated by a decrease in concentration of intracellular S1P, which induces migration of pathogenic T cells to the blood stream and disrupts the CNS. 3 The microsomal enzyme sphingosine 1- phosphate lyase (S1PL) hydrolyzes intracellular S1P 4 and thus, S1PL has become a promising drug target against inflammatory neurodegenerative diseases such as MS and Alzheimer`s diseases (AD). In this study, the integrated strategy starts with virtual screening of ZINC database 5 of 500,000 compounds using either ligand-based or structure-based pharmacophore modeling to retrieve high scoring 10,000 hits followed by molecular docking of candidate molecules obtained from pharmacophore modeling to rigid or flexible protein conformations. Molecules obtained after substructure search of common scaffolds for scaffold hopping are also docked. After multistep docking and substructure search of common scaffolds, the compounds with high docking scores, fitness values to the hypothesis, binding efficiency index (BEI) and lipophilic ligand efficiency (LLE), low molecular weight and high percentage of human oral absorption (HOA) were selected and further analyzed via induced fit docking (IFD), molecular dynamic (MD) simulations and binding free energy calculations in order to gain an insight into the binding modes and the key residues in binding. As a final outcome, the molecules with drug-like properties were proposed as potential inhibitors of S1PL. Some of the proposed compounds have also proven effective against specific cancer cells and malarial parasites (antiviral action). These potential inhibitors can serve as leads in future medicinal chemistry efforts to find new compounds against destructive actions of pathogenic T cells. 107

108 Resources: 1) Bartke, N.; Hannun, Y. A. J. Lipid Res. 2009, 50(Suppl.), ) Hait, N. C.; Allegood, J.; Maceyka, M.; Strub, G. M.; Harikumar, K. B.; Singh, S. K.; Luo, C.; Marmorstein, R.; Kordula, T.; Milstien, S.; Spiegel, S. Science 2009, 325(5945), ) Matloubian, M.; Lo, C. G.; Cinamon, G.; Lesneski, M. J.; Xu, Y.; Brinkmann, V.; Allende, M. L.; Proia, R. L.; Cyster, J. G. Nature 2004, 427(6972), ) Serra, M.; Saba, J. D. Adv. Enzyme Regul. 2010, 50(1), ) ZINC Database, 108

109 PP - 12 Structure-Antimicrobial Activity Relationship Studies Of 3,4,5- Trisubstituted 4,5-Dihydro-1,2,4,5-Oxadiazaboroles Meryem Pir a, Merve Ilter a, Fatma Budak b, Hikmet Agirbas a a Kocaeli University, Faculty of Arts and Sciences, Department of Chemistry, 41380, Izmit, Turkey b Kocaeli University, Faculty of Medicine, Department of Microbiology, 41380, Izmit, Turkey On the basis of the biological activity displayed by other heterocyclic systems that contain B-N bonds, oxadiazaboroles should be interesting candidates for biological activity. 1 Some oxadiazaboroles were synthesized from amidoximes and phenyl boronic acid. 2-3 However, to our knowledge, no antimicrobial activity data of 3,4,5-trisubstituted 4,5-dihydro-1,2,4,5-oxadiazaboroles was reported. We synthesized a series of seventeen 3,4,5-trisubstituted 4,5-dihydro-1,2,4,5-oxadiazaboroles (4a-r). The synthesized compounds (4a-r) have been evaluated for their in vitro antimicrobial activity against a panel of microorganisms including S. aureus, E. faecalis, P. aeruginosa, E. coli, and C. albicans. The pmic values of the compounds were correlated with physicochemical descriptors: Hammett substituent constants (σ) and the lipophilic constant (π). Six statistical successful 2D-QSAR models were obtained with fair statistical fittings. The pmic values of 3,4,5-trisubstituted 4,5-dihydro-1,2,4,5-oxadiazaboroles were also correlated with five theoretical descriptors as independent variables and thirteen statistical successful 2D-QSAR models were obtained. The geometrical optimization of all the compounds has been done by ab initio (RHF/3-21G) method incorporated in the Hyperchem package. E HOMO and E LUMO were calculated by Gaussian 03W software using DFT (B3LYP) method with the 3-21G basis set. Application of training and test sets to 2D-QSAR models gave good results. Squared correlation matrix of the theoretical descriptors used in the QSAR study showed no correlation between the descriptors. 109

110 Resources: 1) Baker, S.J.; Zhang, Y-K.; Akama, T.; Lau, A.; Zhou, H.; Hernandez, V.; Mao, W.; Alley, M.R.K.; Sanders, V.; Plattner, J.J. J Medicinal Chemistry. 2006, 49, ) Dürüst, Y.; Dürüst, N. J Chem Eng Data. 2007, 52, ) Dürüst, Y.; Akcan, M.; Martiskainen, O.; Siirola, E.; Pihlaja, K. Polyhedron. 2008, 27,

111 PP 13 Microwave Assisted Synthesis And Biologycal Activity Studies Of Some New Derived From Antipyrine Neslihan Demirbas a, Serpil Demirci b, Arif Mermer a, Serdar Ulker c, Ahmet Demirbas a a) Karadeniz Technical University, Department of Chemistry, 61080, Trabzon, TURKEY b) Giresun University, school of Applied Science, Department of Crop Production and Technology, Giresun, TURKEY c) Recep Tayyip Erdoğan University, Department of Biology, 53100, Rize, TURKEY Antimicrobial resistance, infectious diseases became responsible for a significant proportion of deaths worldwide. Although World Health Organization defines the antimicrobial agents as miracle drugs leading weapons for the treatment of infectious diseases, a number of the current clinically efficacious antimicrobial agents are becoming less effective as a result of the development of antimicrobial resistance. 1, 2 Despite the continued threat of resistance, β-lactams remained the most important antibacterials in current clinical use. Another privileged scaffold thiazolidinone constitute a very attractive target for combinatorial synthesis due to its structure activity relationship, and it belongs an important class of N and S containing heterocycles, which are widely used as key building blocks in the field of drugs and pharmaceutical agents. 3 In this study, some new penicillin derivatives containing 1,3-thiazole moiety have been synthesized and screened for their antimicrobial activities. 111

112 Resources: 1) Raparti, V. Chitre, K., Bothara, V. Kumar, S. Dangre, C. Khachane, S. Gore, B. Deshmane, Eur. J. Med. Chem., ) Demirci S., Demirbas A., Ulker S., Bozdeveci A., Karaoglu S.A., Demirbas N., Arch. Pharm. Chem. Life Sci.,

113 PP 14 Investigation Of The Binding Behaviour Of HLA-B27 Alleles At Varying Ph Conditions Using Computational Methods Zeynep Kutlu Kabaş, Gülin Özcan, Onur Serçinoğlu, Pemra Ozbek Department of Bioengineering, Marmara University, Goztepe, Istanbul, Turkey The extremely polymorphic nature of Human MHCs, also known as Human Leukoycte Antigens (HLA), is associated with various diseases 1. Among them, Ankylosing Spondylitis (AS), which is an autoimmune disease affecting the axial skeleton, is associated with B*27 alleles of HLA. A single amino acid replacement (ASP116HIS), having a key role in pathogenesis pathway, distinguishes HLA B*27:05 and HLA-B*27:09 alleles as associated and non-associated with Ankylosing Spondylitis (AS), respectively2-5. Acidic ph conditions leading to elevated proton concentrations represent the effect of long-term exposure to the low ph conditions that can be related to the inflammation within joints and other affected tissues in AS 6. This ph effect can be described by the protonation/deprotonation states of Histidine. In this study, we aim to investigate the extent of the effect of the ph change (ph values 5.0, 6.0 and 7.0) on the peptide binding behavior of the two differentially autoimmune diseaseassociated HLA-B27-subtypes. A peptide library was constructed and computational molecular docking was performed via Autodock 4.0. Additionally, 50 ns parallel molecular dynamics simulations were conducted via NAMD2.9 simulation engine with the CHARMM27 force-field to estimate the success of docking by comparing binding stability of the docked peptide and the original peptide. The preferred amino acids for each position of pvipr are harmonious with experimental studies. MD simulation analyses shows that re-docked peptides are stable in their binding groove. References 1) Marsh, S. G.: Nomenclature for factors of the HLA system, update June European journal of immunogenetics : official journal of the British Society for Histocompatibility and Immunogenetics 2001, 28, ) Ramos, M.; Lopez de Castro, J. A.: HLA-B27 and the pathogenesis of spondyloarthritis. Tissue antigens 2002, 60, ) Ziegler, A.; Loll, B.; Misselwitz, R.; Uchanska-Ziegler, B.: Implications of structural and thermodynamic studies of HLA-B27 subtypes exhibiting differential association with ankylosing spondylitis. Advances in experimental medicine and biology 2009, 649, ) Uchanska-Ziegler, B.; Loll, B.; Fabian, H.; Hee, C. S.; Saenger, W.; Ziegler, A.: HLA class I-associated diseases with a suspected autoimmune etiology: HLA-B27 subtypes as a model system. European journal of cell biology 2012, 91,

114 5) Brewerton, D. A.; Hart, F. D.; Nicholls, A.; Caffrey, M.; James, D. C.; Sturrock, R. D.: Ankylosing spondylitis and HL-A 27. Lancet 1973, 1, ) Steen, K. H.; Steen, A. E.; Reeh, P. W.: A dominant role of acid ph in inflammatory excitation and sensitization of nociceptors in rat skin, in vitro. The Journal of neuroscience : the official journal of the Society for Neuroscience 1995, 15,

115 PP 15 The Establishment of Homeobox Family Inhibitor Library and Meis1 Reporter Assays Raife Dilek Turan 1, Enes K. Ergin 2, Fatih Kocabas 1* 1 Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey 2 Computer Science, North American University, Houston, USA One of the dilemmas of the cardiac regeneration research has always been the difficulty of studying modulators of cardiac regeneration, owing to the lack of the mammalian heart regeneration model. In contrast, we recently showed that the neonatal mammalian heart is capable of regeneration following myocardial infarction. This led us to uncover Meis1, which belongs to TALE-type class of homeobox proteins, as one of the key regulators of cardiomyocyte cell cycle arrest and a potential therapeutical target 1,2. Discovery of Meis1 as one of the key regulator of cardiomyocyte cell cycle arrest and transcriptional activator of two synergistic cyclin dependent kinase inhibitors p16 and p21 provided a new platform for the development of therapeutics targeting cardiomyocyte cell cycle. Goal of this study is to identify cardiogenic inhibitors of Meis1 that could reactivate this regenerative phenomenon in the adult heart. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening, luciferase reporter assays, ex vivo and in vivo cardiomyocyte proliferation assays to discover cardiogenic inhibitors of Meis1. Keywords: Meis1, cardiogenic inhibitors, cardiomyocytes, small molecules, cardiac regeneration Resources: 1) Fatih Kocabas (co-first author), Ahmed I Mahmoud, Shalini A. Muralidhar, Wataru Kimura, Ahmed S. Koura, Suwannee Thet, Enzo R. Porrello, and Hesham A. Sadek. Meis1 regulates postnatal cardiomyocyte cell cycle arrest. Nature 497, no (2013): ) Fatih Kocabas, Junke Zheng, Suwannee Thet, Neal G. Copeland, Nancy A. Jenkins, Ralph J. DeBerardinis, Chengcheng Zhang, and Hesham A. Sadek. "Meis1 regulates the metabolic phenotype and oxidant defense of hematopoietic stem cells." Blood (2012) 115

116 PP 16 Synthesis Of Some New Norfloxacine Derivatives And Investigation Of Their Antimicrobial Activities Serpil Demirci a, Meltem Mentese b, Arif Mermer b, Serdar Ulker c, Ahmet Demirbas b, Neslihan Demirbas b a Giresun University, school of Applied Science, Department of Crop Production and Technology, Giresun, TURKEY b Karadeniz Technical University, Department of Chemistry, 61080, Trabzon, TURKEY c Recep Tayyip Erdoğan University, Department of Biology, 53100, Rize, TURKEY During the past few years, the excessive use and maltreatment of commonly used antibiotics have caused to emerging resistant bacteria leading to diminish the efficiency of them. 1 This increase in the microbial infections and pathogenic resistance to the commonly used drugs has led the medicinal and organic chemists to develop novel antimicrobial agents with new mechanism of action, urgently. Another approach for the development of new antibiotics, which are not resistant, is to combine two or more pharmacophores into a single molecule. It is well known that more efficacious antibacterial compounds can be designed by joining two or more biologically active heterocyclic systems together in a single molecular framework. The hybrid compounds containing two or more pharmacophore in one structure are believed that these substances reduce the development of resistance and have broader action spectrum. 2 In the present study, new hybrid compounds derived from 1,2,4-triazole moiety have been synthesized by Mannich reactions, and screened for the antibacterial activity. O F COOH 1a: R'= N O 1b: R'= NH N O R' S N N N N N N 1c: R'= NH 1d: R'= 1e: R'= N N CH 3 1f: R'= N NH N N 1a-f 116

117 Resources: 16) T. Maruyama, Y. Kano, Y. Yamamoto, M. Kurazono, K. Iwamatsu, K. Atsumi, E. Shitara, Bioorg. Med. Chem., ) M. Yolal, S. Basoglu, H. Bektas, S. Demirci, S. Alpay-Karaoglu, A. Demirbas, Russian J. Bioorg. Chem.,

118 PP 17 Analysis Of TALE And İts Specific Target DNA İnteractions By Free Energy Perturbation Calculations And Perturbation-Response Scanning Sofia Piepoli*, Batu Erman, Canan Atılgan Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul Bacterial plant pathogens belonging to Xanthomonas genus infect cells by injecting Transcription Activator-Like effector(tale) proteins to modify plant gene expression1. Crystal structure of the PthXo1 TALE protein bound to its DNA target reveals specificity of interactions between the two molecules at the sequence level2. In this case, TALE DNA binding domain consists of ~22 repeats, each characterized by conserved amino acids. Alignment of the sequence of the repeats shows perfect homology except for the amino acids at positions (repeat variable diresidues- RVDs) which specifically bind to DNA bases3 according to the code: HD C, NG T, NI A and NN G in most cases, while there are some exceptions. Not all repeats have to perfectly contact DNA to bind and it is unclear how TALE pairs up with a target DNA sequence while avoiding off-target sites. By means of molecular dynamic simulation tools, we quantify specific intermolecular binding stability. We analyze selected point mutations introduced into the RVD region of the protein sequence and predict resulting free energy differences in the interacting complex using detailed free-energy perturbation calculations4. By systematically applying this method, we interpret the role of local interactions in contributing to the overall stability of the system. Additionally, we investigate the role of other residues along the repeat and their allosteric effect on the stability of the RVD by using the Perturbation-Response Scanning (PRS)5 statistical method. While directed forces are applied on a single target residue, the resulting relative changes in all other residues coordinates are recorded in magnitude and directionality. Identification of key residues for stability of binding at specific positions will allow computational design of TALEs that can be experimentally tested for binding affinity and off-target specificity. The analysis is aimed to contribute to the study of TALE-DNA binding mechanism regulation. 1) Kay S., Bonas U. How Xanthomonas type III effectors manipulate the host plant, Current Opinion in Microbiology, 2009, 12, 1. 2) Mak A. N., Bradley P., Cernadas R. A., Bogdanove A. J., Stoddard B. L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science, 2012, 335,

119 3) Moscou M. J., Bogdanove A. J. A simple cipher governs DNA recognition by TAL effectors. Science, 2009, 326, ) Pohorille A., Jarzynski C., Chipot C. Good practices in free-energy calculations. J. Phys. Chem., 2010, 114, 32. 5) Atilgan C., Atilgan A. R. Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein. PLoS Comput. Biol., 2009, 5, e

120 PP 18 Computational Study On The Binding Behaviour Of HLA-B44 Alleles Asuman Bunsuz, Onur Serçinoğlu, Pemra Ozbek Sarıca Department of Bioengineering, Marmara University, Goztepe, Istanbul, Turkey Understanding the characteristic dynamics of different Human Leukocyte Antigen (HLA) alleles may help explain the mechanism of initial steps in T-cell activation. Displaying a highly polymorphic nature, HLA proteins are associated with various diseases 1. HLA-B*44:05 differs from HLA-B*44:02 at position 116 (TYR116ASP) at the floor of the region that binds to the C terminus of the peptide and located distant from the suggested class I tapasin binding region. While HLA-B*44:02 loads peptide efficiently in the presence of tapasin, HLA-B*44:05 is relatively tapasin independent 2. Similarly, another single amino acid polymorphism (ASP156LEU), which has a key role in strong alloreactivity in vivo, distinguishes HLA-B*44:02 from HLA-B*44:03 3. These two alleles are associated with antitumor, antiviral and minor Ag-specific responses 4. In this study, in order to investigate the peptide binding behavior of these alleles displaying single residue polymorphisms, various computational techniques have been employed. Peptide binding stabilities of HLA-B*44 alleles were analyzed via ENCOM 5 by performing alanine scanning mutagenesis. Moreover, computational dockings were performed on the modeled peptides formed upon single point alanine mutations aiming to address the key peptide residues in binding using HADDOCK server 6. Additionally, 20 ns parallel molecular dynamics simulations were conducted via NAMD2.9 7 simulation engine with the CHARMM27 8 force-field. Stability of peptide binding and the factors contributing to this stability were investigated in detail since understanding the differences in binding behavior is of considerable interest both from structural and immunological points of view. References 1. Williams, T. M. Human leukocyte antigen gene polymorphism and the histocompatibility laboratory. J. Mol. Diagn. 3, (2001). 2. Sieker, F., Springer, S. & Zacharias, M. Comparative molecular dynamics analysis of tapasindependent and -independent MHC class I alleles. Protein Sci. 16, (2007). 3. Badrinath, S. Differential Impact of HLA-B*44 Allelic Mismaches at Position 156 on Peptide Binding Specificities and T-Cell Diversity. J. Stem Cell Res. Ther. 04, (2014). 4. Macdonald, W. A. et al. A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition. J. Exp. Med. 198, (2003). 120

121 5. Frappier, V., Chartier, M. & Najmanovich, R. J. ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Res. 43, (2015). 6. Dominguez, C., Boelens, R. & Bonvin, A. HADDOCK: a protein protein docking approach based on biochemical or biophysical Information. J. Am. Chem. Soc (2003). 7. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, (2005). 8. Brooks, B. R. et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, (1983). 121

122 PP 19 Synthesis And Aflatoxin B 1 Inhibitory Activities Of Novel Eugenol Derivatives Substituted Carbamate Belma Zengin Kurt a, Zuhal GUNESLI b, Isıl GAZIOGLU a, Fatih SONMEZ b a Bezmialem Vakif University, Faculty of Pharmacy, Deparment of Medicinal and Analitical Chemistry, 34093, Istanbul, TURKEY b Sakarya University, Pamukova Vocational High School, 54900, Sakarya, TURKEY Aflatoxins are known to be secondary metabolites produced by Aspergillus flavus, Aspergillus parasiticus, and Aspergillus nomius. The source of these fungi has been traced to a toxic contaminant in a groundnut meal used in feed. 1 Aflatoxin B 1 (AFB1) has toxic, carcinogenic, mutagenic and teratogenic effects in laboratory animals and is classified by the International Agency of Research on Cancer as Group 1 human carcinogen. 2 Eugenol is generally used as a food flavoring agent. In view of its non-mutagenic and noncarcinogenic properties, it is generally regarded as safe. Hence it is used for inhibition of aflatoxin B 1. 3 In this study, novel Eugenol derivatives substituted carbamate were synthesized by reacting with isocyanates. All synthesized carbamate derivatives showed higher inhibitory properties against Aflatoxin B 1 compared to Eugenol. Resources: 1) Lee J., Her JY., Lee KG., Food Chem. 2015, 189, ) Abdel-Wahhab MA., Hassan NS., El-Kady AA., Khadrawy YA., El-Nekeety AA., Mohamed SR., Sharaf HA., Mannaa FA., Food Chem. Toxicol., 2010, 48, ) Komala VV., Ratnavathi CV., Vijay Kumar BS., Das IK., Food Control, 2012, 26,

123 PP 20 Investigation Of Fenamic Acids At Density Functional Theory Level Boğaç Erçığ a,b, Rasmus Leth a, Lars Olsen a, Flemming Steen Jørgensen a a Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark. b Molecules Thérapeutiques in silico, Université Paris Diderot, 35 Rue Hélene Brion, Paris, France. Cytochrome P450 enzymes (P450s) are important by metabolizing many drugs, generating several different products, metabolites, by several different types of reaction. 1 For fenamic acids, we have investigated the following reactions: aliphatic hydroxylation, aromatic oxidation and N-hydroxylation. The possible mechanisms for these reactions, all mediated by P450s, are studied by density functional theory (DFT) for four different fenamic acids (mefenamic acid, meclofenamic acid, tolfenamic acid and diclofenac). The DFT results are compared to the experimental data and different spin state energies and structures are examined. Rate-determining step for N-hydroxylation of a secondary amine on the fenamic acids is investigated. Finally, the DFT results are used to improve the performance SMARTCyp method, which is a fast and efficient method for prediction of P450 mediated site-of-metabolism. 2 Resources: 1) Woolf, T. F., and Jordan, R. A. (1987) Basic concepts in drug metabolism: Part I, Journal of clinical pharmacology 27, ) Rydberg, P., Gloriam, D. E., Zaretzki, J., Breneman, C., & Olsen, L. (2010). SMARTCyp: A 2D method for prediction of cytochrome P450-mediated drug metabolism. ACS Medicinal Chemistry Letters, 1,

124 PP 21 Biochemical Kinetics And Molecular Docking Studies On Tyrosinase Inhibition By Some Novel 1,2,4 Triazole Derivative Compounds Elif Ayazoglu a, Aylin Kalfa a, Safak Akin a, Olcay Bekircan a, Ahmet Colak a, Ahmet Yasar b, Nagihan Saglam Ertunga a a Karadeniz Technical University, Faculty of Science, Department of Chemistry, Trabzon b Karadeniz Technical University, Faculty of Pharmacy, Department of Science of Basic Pharmacy Trabzon Tyrosinase (monophenol, o-diphenol:oxygen oxidoreductase; EC ) is a copper-containing enzyme responsible for biosynthesis of melanin pigment in skin, hair, and eyes. It catalyzes two reactions in the melanin biosynthetic pathway: hydroxylation and oxidation of monophenols to o- quinones (monophenolase activity), and oxidation of o-diphenols to o-quinones (o-diphenolase activity). The enzyme is widely distributed in mammals, plants, insects, fungi, and bacteria. Various dermatological disorders, such as melasma, age spots and sites of actinic damage, arise from the accumulation of an excessive level of epidermal pigmentation. In addition, unfavorable enzymatic browning of plant-derived foods by tyrosinase causes a decrease in nutritional quality and economic loss of food products. Tyrosinase has also been linked to Parkinson s and other neurodegenerative diseases. Therefore, identification of tyrosinase inhibitors has promising potential in the treatment of such ailments. Tyrosinase inhibitors have become increasingly important for cosmetic and medicinal products primarily in relation to hyperpigmentation of skin. In this study, four 5-methyl-2-hepthyl-2,4- dihydro-3h-1,2,4-triazol-3-one derivative compounds (Y1-Y4) were synthesized, characterized and then their potential for mushroom tyrosinase inhibition was evaulated. Structures of these novel products were determined by spectroscopic methods (IR, 1 H-NMR, 13 C-NMR and MS). All inhibiton studies were performed at ph 5.0, 25 C and 43.5 µg/ml enzyme concentration in the presence of L- Tyrosine substrate (at the concentration of its K m value, 140 µm). Kojic acid was used as a reference standard inhibitor. Among the tested compounds Y3 was found to be the most potent inhibitor in terms of its IC 50 values (at mm levels). This compound behaved as an uncompetitive inhibitor for mushroom tyrosinase activity. The kinetic parameter (K I ) characterizing this inhibition was calculated as 1,72 mm. Moreover, molecular docking studies are been performed by using auto dock vina and gaussian programmes to support experimental data. It is concluded that these compounds may be useful for development of new generation drugs and cosmetic products or prevention of undesirable browning in food due to strong tyrosinase inhibition activities. 124

125 Acknowledgement: This work was financially supported by The Scientific and Technological Research Council of Turkey (TÜBİTAK), Grand no:114z711. Resources: 1) Lerner, A. B.; Fitzpatrick, T. B., Physiol. Rev. 1950, 30, 91. 2) Fitzpatrick, T. B.; Miyamoto, M.; Ishikawa, K., Adv. Biol. Skin. 1967, 8, 1. 3) Raper, H. S., Physiol. Rev. 1928, 8, ) Mason, H. S., Annu. Rev. Biochem. 1965, 34, ) Kubo, I.; Kinst-Hori, I.; Yokokawa, Y. J., Nat. Prod. 1994, 57,

126 PP 22 In Vitro Inhibition Of Tyrosinase By Some 1,2,4 Triazole Derivative Compounds: Inhibition Mechanism And Molecular Docking Elif Ayazoglu a, Aylin Kalfa a, Ahmet Colak a, Ahmet Yasar b, Olcay Bekircan a, Melike Yıldırım Akatın a a Karadeniz Technical University, Faculty of Science, Department of Chemistry, Trabzon b Karadeniz Technical University, Faculty of Pharmacy, Department of Science of Basic Pharmacy Trabzon Polyphenol oxidase, or tyrosinase (EC ), is a copper enzyme, widely distributed throughout microorganism, plants and animals. This enzyme catalyzes two different reactions in the presence of oxygen: the hydoxylation of monophenols to o-diphenols (monophenolase activity ) and the oxidation of o-diphenols to o-quinones (diphenolase activity) which, in turn, are polymerized to brown, red or black pigments. So, tyrosinase is known to be a key enzyme in melanin biosynthesis, determining the color of mammalian skin and hair. Various dermatological disorders, such as melasma, age spots and sites of actinic damage, arise from the accumulation of an excessive level of epidermal pigmentation. In addition, unfavorable enzymatic browning of plant-derived foods by tyrosinase causes a decrease in nutritional quality and economic loss of food products. The clinical and industrial importance of prevention of undesirable tyrosinase activity encourages us to seek potent tyrosinase inhibitors. In this study, a series of 2-[3-(4-chlorophenyl)-5-(4-methoxybenzyl)-4H-1,2,4-triazol-4-yl]acetohydrazide and 4-amino-2-heptyl-5-(4-methoxybenzyl)-2,4-dihydro-3H-1,2,4-triazol-3-one derivative compounds were examined for their inhibitor efficiencies on mushroom tyrosinase activity (at ph 5.0, 25 C and 43.5 µg/ml enzyme concentration) in the presence of L-Tyrosine substrate (at the concentration of its K m value, 140 µm). Kojic acid was used as a reference standard inhibitor. The compound O2 was found the most potent inhibitor among examined molecules (O1-6, B1-2) in terms of their IC 50 values (at µm levels). This compound behaved as a classical uncompetitive inhibitor for mushroom tyrosinase activity. The kinetic parameter (K I ) characterizing this inhibition was calculated as 373 µm. Moreover, molecular docking studies are been performed by using auto dock vina and gaussian programmes to support experimental data. It is concluded that these compounds may be useful for development of new generation drugs and cosmetic products or prevention of undesirable browning in food due to strong tyrosinase inhibition activities., Acknowledgement: The authors are grateful to the Research Fund of the TUBITAK for their support with project No:114Z

127 Resources: 1) Vamos-Vigyazo, L., Crit. Rev. Food Sci. 1981;15: ) Mason, H. S., J. Bio. Chem. 1948, 72, ) Prota, G., Med. Res. Rev. 1988, 8, ) Bekircan, O.; Menteşe, E.; Ülker, S.; Kucuk,C., Arch. Pharm. Chem. Life Sci. 2014, 347, ) Bekircan, O.; Menteşe, E.; Ülker, S., Z. Naturforsch. 2014, 69b,

128 PP 23 Computational Investigation Of Protein Dynamics Based On Energy Dissipation Elif Naz Bingol, Onur Sercinoglu, Pemra Ozbek Sarıca Department of Bıoengineering, Marmara University, Goztepe, Istanbul, Turkey One of the major defense mechanism in higher organisms against microbial pathogens is T cellmediated immunity. T cells recognize foreign material from the fractions of the antigen, ceased or deficient proteins and peptides from viruses, which are presented with peptide-loaded major histocompatibility complex (pmhc) molecules and triggers an immune response. Many alleles and subtypes of these proteins are found to be associated with autoimmune diseases; hence the importance of understanding the mechanism of signal transduction within the complex is crucial. Proteins are open systems where external energy can be transferred with the help of intermolecular interactions since the residues of a protein are always fluctuating 1,2. Perturbation dynamics allows us to find a signaling pattern in proteins using external energy as an input and focuses on dispersion of this energy between residues in the overall structure. Perturbation of specific residues would give further details on the dynamical character of a protein such as peptide binding. In order to obtain further details on the stability of the peptide and to investigate the presence of a possible binding network in human leukocyte antigen (HLA) molecules, we applied an energy dissipation method. In this method, we performed molecular dynamics simulations with and without energy perturbation using NAMD 4 software with the CHARMM27 5 force field. Energy perturbation was applied by increasing the velocity of a chosen residue at the desired time step of the initial MD simulation. Energy change of each residue was calculated based on the total energy difference between the perturbed and the reference simulations. Afterwards, residue response times, corresponding to the time of the response of a residue after the perturbation of another chosen residue, are determined. Key residues determined through the response times enlighten both the similarities and the differences between the alleles and their binding properties. Resources: 1. Ma, C.-W., Xiu, Z.-L. & Zeng, A.-P. A new concept to reveal protein dynamics based on energy dissipation. PLoS One 6, e26453 (2011). 2. Ma, C.-W., Xiu, Z.-L. & Zeng, A.-P. Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation. PLoS One 7, e31529 (2012). 128

129 3. Gunasekaran, K., Ma, B. & Nussinov, R. Is allostery an intrinsic property of all dynamic proteins? Proteins 57, (2004). 4. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, (2005). 5. Brooks, B. R. et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, (1983). 129

130 PP 25 Synthesis Of New Acridine Sulfonate Esters Hybrid Compounds Including 5-Amino-1,3,4-Thiadiazole-2-Sulfonamide Burak Aday a, Muharrem Kaya b a Chemistry Department, Faculty of Arts and Science, Dumlupınar University, Evliya Çelebi Campus Kütahya, Turkey. b Biochemistry Department, Faculty of Arts and Science, Dumlupınar University, Evliya Çelebi Campus Kütahya, Turkey. 1,8-Dioxoacridine derivatives are compounds having interesting biological features which are similar to the structure of Nicotinamide Adenine Dinucleotide, an important co-enzyme found in cells. 1 They have a wide range of pharmacological properties such as antimicrobial, 2 antibacterial, 3 fungicidal, 4 antitumor 5 and anticancer, 6 and are also used for glaucoma treatment as carbonic anhydrase inhibitors. 7-9 Herein we wish to report an efficient for the synthesis of acridinedione derivatives via one-pot MCRs of 5-Amino-1,3,4-thiadiazole-2-sulfonamide containing new amine compound, dimedone and sulfonate ester compounds containing aromatic aldehydes in high yields and short reaction times by using assisted microwave method. Then, these compounds were characterized by IR, 1 H-NMR and 13 C-NMR data and high resolution mass spectral analyses, respectively. Scheme1. Synthesized novel 5-Amino-1,3,4-thiadiazole-2-sulfonamide containing acridine- sulfonate esters derivatives * This study is supported by a grant (Project Number: 114Z044) from TUBITAK. 130

131 Resources: 1) Singh, S.; Chhina, S.; Sharma, V. K.; Sachev, S. S. J. Chem Soc. Chem. Commun.1982, 8, ) Wainwright, M. J. Antimicrob. Chemother. 2001, 47, ) Palani, K.; Thirumalai, D.; Ambalavanan, P.; Ponnuswamy, M. N.; Ramakrishnan, V. T. J. Chem. Crystallogr. 2005, 35, ) Srivastava, A.; Nizamuddin, C. Indian J. Heterocycl. Chem. 2004, 13, ) Mikata, Y.; Yokoyama, M.; Mogami, K.; Kato, M.; Okura, I.; Chikira, M.; Yano, S. Inorg. Chim. Acta. 1998, 279, ) Pitta, M. G. R.; Souza, E. S.; Barros, F. W. A.; Filho, M. O. M.; Pessoa, O.; Hernandes, M. Z.; Lima, M. D. C. A. D.; Galdino, S. L.; Pitta, I. D. R. Med. Chem. Res. 2013, 22, ) Kaya, M.; Basar, E.; Çakir, E.; Tunca, E.; Bulbul, M. J. Enzyme Inhib. Med. Chem. 2012, 27, ) Ulus, R.; Yeşildağ, İ.; Tanc, M.; Bülbül, M.; Kaya, M.; Supuran, C. T. Bioorg. Med. Chem. 2013, 21, ) Yeşildağ, İ.; Ulus, R.; Basar, E.; Aslan, M.; Kaya, M.; Bülbül, M. Monatsh. Chem. 2014, 145,

132 PP 28 Manganese(II) Carboxylate / Nitrogenous Base Complexes: Structure And Catalase-Like Activities Yalçın KILIÇ a, İbrahim KANİ a 1 Department of Chemistry, AnadoluUniversity, Eskişehir It s known that there is a relationship between reactive oxygen types (hydroxy radicals, hydrojen peroxide and superoxide ion) which are results of aerobic respiration and chronic diseases and aging. Catalase is an enzyme causing disproportionation of hydrogen peroxide, one of the reactive oxygen compounds, to oxygen and water. The design and synthesis of oxygen or carboxylato bridged dinuclear manganese complexes have attracted much attention because of their biological relevance in different manganese containing enzymes [1]. A large number of dinuclear manganese complexes showing catalase activity have been studied in detail by various groups using several structural as well as functional model complexes [2] In this study, di-nuclear Mn(II) complexes with 4-chlorobenzoic acid/5-chloro-2- aminobenzoic acid and bipy ligands, [Mn 2 (µ-4-clc 6 H 4 COO) 2 (bipy) 4 ] 2(ClO 4 ) (1) and [Mn 2 (µ-5-cl-2- NH 2 C 6 H 3 COO) 2 (bipy) 4 ] 2(ClO 4 ) (2), were synthesized and characterized by X-ray crystallography, elemental analysis, IR and UV-vis spectroscopy. Activities for disproportionation of hydrogen peroxide were studied by changing parameters like different solvent and temperature. Also, addition of base and cycle of catalase activity were studied. Keywords: Catalase, complex, manganese, crystallography Resources: 1) Gelasco, A.; Pecoraro, J., J. Am. Chem. Soc., 1993, 115, ) Mathur, M.P.; Crowder, M.; Dismukes, G.C., J. Am. Chem. Soc., 1987, 109,

133 Cl 2+ 2(ClO 4 ) Cl 2+ 2(ClO 4 ) NH 2 N N N N Mn O O O O N N Mn N N N N N N Mn O O O N N Mn N O N H 2 N Cl Cl (1) (2) Figure 1. The molecular structures of [Mn 2 (µ-4-clc 6 H 4 COO) 2 (bipy) 4 ] 2(ClO 4 ) (1) and [Mn 2 (µ-5-cl-2- NH 2 C 6 H 3 COO) 2 (bipy) 4 ] 2(ClO 4 ) (2) complexes This work was supported by the Scientific Research Fund of TUBITAK Project Number: 113Z

134 PP 29 Colloid And Interface Science İn Nanopharmaceutical Research: The Use Of Langmuir-Blodgett Films And Black Lipid Membranes For Approaching Drug-Cell Interactions Erhan Süleymanoğlu Department Of Pharmaceutical Chemistry, Gazi University, Faculty Of Pharmacy Ankara-Turkey Since cell membranes are physical and functional interface between extracellular signals and intracellular genetic machinery governing cell functions, the dynamics of cell surface and its physical states upon recognition by drugs or drug delivery vehicles attracts research interest. Plasma membrane has been considered as the most important target, other than DNA and intracellular biomolecules, for many anticancer drugs. Developing drugs with improved properties requires understanding of how such vehicles interact with the firstly encountered cell membrane via their route to cell nuclei for further effects on gene expression. These events are size dependent and thus nanopharmaceutical surface chemistry becomes an essential issue to study. Following our previous models on interfacial recognitions of bilayer membranes with pharmacologically active molecules1, the work presented herein is focused on the role of phospholipids in normal and pathological assembly and organization of the membrane proteins, multimeric protein complexes, reconstituted receptors, and higher order supercomplexes, or hyperstructures upon their recognition by antineoplastic agents. Lipid monolayers at the liquid air interface are well-defined two-dimensional arrangements of amphiphilic molecules and are routinely used as models for biomembranes. These interfacial systems represent suitable model systems for following colloidal and interfacial interactions beyond the classical quantitative physicochemical reasoning. Surface parameters can be independently varied over a broad range and the structure can be analyzed with nanoscale precision. First, the initial recognition events between Taxol (Paclitaxel), Vinblastine, Vinorelbine and Vincristine and lipid moieties were studied by lipid monolayer measurements, where the surface recognition between drugs and phospholipid monolayers was approached. Either in bound and unbound state, lipids are both attractive objects for study in terms of supramolecular chemistry due to their thermodynamically and hydrophobically driven unique selfassemblying features. Their complexes can be approached either by employing phospholipid vesicles or if decrease in dimensions is needed, lipid bilayers, such as Black Lipid Membranes (BLMs) or monolayers, such as Langmuir-Blodgett (LB) films can be used (Fig. 1)2. The latter allow also the microfabrication of confined structures as lipid monolayer spreading and mixing and offers the opportunity for transfering Langmuir monolayers on to a solid support, the item being also of interest for materials science and bioelectronics. LB films composed of drug-lipid complexes can be prepared 134

135 either by cast-stretching method, in which the complex electrostatics is maintained by counter cations of phosphate anions being changed to cationic lipophilic amphiphiles or by LB method, where drugs are transferred with charged lipid monolayers at the air-water interface by vertical dipping of the drugs. The intrinsic control of the internal layer structure and the resulting film thickness at a molecular level employing a variety of phases and structures, as well as the possibility to couple this design to sophisticated measurement (ellipsometry, vibrational spectroscopy, fluorescence, Grazing-Incidence X- Ray diffraction, as well as TOF-SIMS, synchrotron radiation facilities, etc.) and microscopic units (such as atomic force-afm, Brewster Angle Microscopy-BAM and inverted fluorescence microscopes) makes LB film a preferred method of use2,3. Lipid monolayer experiments were performed with a computer controlled Langmuir film balance The surface pressure was measured by the Wilhelmy method using a filter paper plate using ultra pure water at 25 C. Dipalmitoylphosphatidyl choline (DPPC) films were obtained by spreading at the air/water interface. Then, after complete evaporation of the solvent, the ligand unbound and drug-bound lipid films were slowly compressed up to the defined lateral pressure. The forces responsible for the formation of drug-lipid complexes and the domains formed were followed by AFM combined with inverted fluorescence microscopy mounted beneath the LB trough. Figure 1. Schematic representations for the preparations of planar membranes via (A) thebimolecular black lipid membrane(blm) approach; (B) the Langmuir Blodgett(LB) technique and (C) vesicle spreading with additional osmotic shock treatment for opening the polymeorsome. Adaptedfrom3. Black lipid membranes (BLMs) are free-floating membranes with defined composition that are ideally suited for characterizing nanopharmaceutical carrier membrane interactions free of any potential perturbations. These bilayer lipid membranes (BLMs) were formed by the conventional Mueller-Rudin 135

136 technique in holes, 0.5^1 mm in diameter, of a diaphragm of a polytetrafluoroethylene (PTFE) chamber. The membrane-forming solution contained 20 mg DPPC, dissolved in 1 ml of n-decane. The bilayers surrounding solution contained typically 20 mm Tris, 20 mm MES, 20 mm CAPSO and 10 or 100 mm KCl, agitated by magnetic bars. Pore-spanning nano-blms were constructed by the painting method applying a drop of 2 μl of DPPC lipid molecules across the nanoporous membranes with plastic pipet. The excess solvent was blown away by a stream of N2 gas. Bilayer formation was proved by either employing measurements of gramicidin channel activity or by measurements of the BLM capacitance. These two alternative methods were correlated with the microscopy techniques to verify the formation of real bilayer regions rather than multilayers, liposomes, or some other nonbilayer lipid domains. Resources: 1) Süleymanoğlu E., Nucleic Acid-Phospholipid Self-Assemblies Approached by Black Lipid Membranes (BLM). B. Sc. Project, Dept. of Biophysics and Radiobiology, Institute of Biotechnology, The Sofia University, Sofia, Bulgaria, 1988, pp.: 1-78 (In Bulgarian). 2) Ovchinnikov Yu. A., Bioorganic Chemistry, Prosveshtenie Publishing House, Moscow, 1987, pp.: (In Russian). 3) van Rijn, P.; Tutus, M.; Kathrein, C.; Zhu, L.; Wessling, M.; Schwaneberg, U. and Böker, A. Chem. Soc. Rev., 2013, 42,

137 PP 30 Evaluation Of The Effect Of A New Substituent Of 1,2,5- Thiadiazolidine 1,1-Dioxide Compound On Cell Division Zülal Atlı Şekeroğlu*, Aliye GEDİZ Ertürk b, Vedat Şekeroğlu a, Seval KONTAŞ Yedier a A department Of Biology, Faculty Of Science And Letters, Ordu University, ORDU, TURKEY B department Of Chemistry, Faculty Of Science And Letters, Ordu University, ORDU, TURKEY Exploring and designing novel molecules capable of interacting with nucleic acids and triggering apoptosis is currently one of the most promising strategies for researchers to discover novel anticancer drugs for chemotherapy 1. Sulfonamides are an important group of organic compounds that possess several types of biological activities including anticancer activity 2. Schiff bases and their metal complexes are widely investigated due to their various biological activities such as antifungal, antibacterial, antiviral, antitumor, antiproliferative and antioxidant 3. In this study, 3-amino-4-[4-(dimethylamino)phenyl]-4,5-dihydro-1,2,5-thiadiazolidine 1,1-dioxide (DFTD) compound which is one of the substituent of 1,2,5- thiadiazolidine 1,1-dioxide compounds and contains both sulfamide and schiff base functional groups were examined. Two articles were published before about its synthesis and structurally characterization 4,5. The aim of this study is to investigate cytotoxic and cytostatic effects of DFTD in human lymphocyte cultures using nuclear division index (NDI) and mitotic index (MI). Cultures were treated with DFTD at three different concentrations (45, 90 and 180 µg/ml) for 48 h. Both solvent negative (Dimethyl sulfoxide) and positive control (Mytomycin- C) groups were also established. Furthermore, effect of DFTD was investigated when used in combination with Mytomycin-C. Dose-dependent decreases observed in the MI and NDI were found statistically significant at all DFTD concentrations tested compared with the solvent control. These results show that DFTD has cytotoxic and cytostatic potential. In addition, when DFTD and Mytomycin-C were used together more cytotoxic and cytostatic effects were detected. The first data about possible cytotoxic and cytostatic potential of DFTD were obtained with this preliminary study. We are planning to perform detailed studies to determine the inhibitory effect on cell division and genotoxicity of DFTD and to investigation whether DFTD displays a chemotherapeutic agent activity when it is used alone or combined with other chemotherapeutic drugs on different cancer cell lines. 137

138 Key words: 1,2,5- thiadiazolidine 1,1-dioxide, cell division, cytotoxicity, human lymphocyte cultures. Resources: 1) Letafat, B., Shakeri, R., Emami, S., Noushini, S., Mohammadhosseini, N., Shirkavand, N., Ardestani, S.K., Safavi, M., Samadizadeh, M., Letafat, A., Shafiee, A., Foroumadi, A. Synthesis and in vitro cytotoxic activity of novel chalcone-like agents. IJBMS. 2013, 16, ) Rodriguez, O.M., Maresca, A., Témpera, C.A., Bravo, R.D., Colinas, P.A., Supuran, C.T. N-β- Glycosyl sulfamides are selective inhibitors of the cancer associated carbonic anhydrase isoforms IX and XII. Bioorg. Med. Chem. Lett. 2011, 21, ) Osowole, A.A., Akpan, E.J. Synthesis, spectroscopic characterisation, ın-vitro anticancer and antimicrobial activities of some metal (II) complexes of 3-{4, 6-Dimethoxy Pyrimidinyl) iminomethyl naphthalen-2-ol. EJAS. 2012, 4, ) Arslan, N.B., Erturk, A.G., Kazak, C., Bekdemir, Y. 3-Amino-4-[4-(dimethylamino)phenyl]- 4,5-dihydro-1,2,5-thiadiazole 1,1-dioxide. Acta Crystallogr Sect E Struct Rep Online. 2011, 67, ) Erturk, A.G., Bekdemir, Y. Microwave-assisted synthesis of some substituted sulfamides. Phosphorus, Sulfur Silicon Relat. Elem. 2014, 189,

139 PP 31 Challenges In Soft Gel Capsulation Of Plant Oils Fatma Pınar Şenkon Bülent ZEBİL Dr. Zeliha ÜSTÜN ZADE VİTAL PHARMACEUTICALS &DRUG INC. Konya Organize Sanayi Bölgesi, Güzel Konak Sk. No:8-10, Selçuklu-Konya/Türkiye Soft gel capsule is an edible package made from gelatin or other suitable materials which is filled with active ingredients to produce a unit dosage mainly for oral use. It can be produced in a single step therefore this pharmaceutical form is more preferable in recent years. Soft gel capsules mainly used for encapsulation of the suspensions and emulsions. The mineral oils, liquid hydrocarbons and essential oils are especially used as filling materials. These medications are tasteless, unscented, smooth and can become very slippery when moist, so they can easily be swallowed. The most important advantage is that the active material can be released in the stomach rapidly because of easy disssolving of the gelatin in the stomach. In spite of having a lot of advantages, their manufacturing processes of soft gel capsules have some difficulties. Personal qualifications, machine settings or raw material properties can cause deviations. However the most important issue is the physical and chemical properties of the filling materials. The main goal of this study is to observe the production line parameters, determine the best conditions and make it standardized to produce zero defect products for shelf life. 139

140 PP 32 Development Of Fluorometric CCHFV OTU Protease Assay And Identification Of Potent Inhibitors Galip Servet Aslan 1, Fatih Kocabas 1* 1 Department Of Genetics And Bioengineering, Faculty Of Engineering, Yeditepe University, Istanbul 34755, Turkey Crimean-Congo hemorrhagic fever virus (CCHFV) is a deadly tick born virus with no currently existing therapies. In the L segment of CCHFV genome, CHFV OTU deubiquitinase is expressed and involve in viral invasion through antagonizing of NF-κB signaling pathway. Development of robust drug screening strategies and identification of small molecule inhibitors against CCHFV OTU promises for future anti-viral therapies. To this end, here we report our two successive studies regarding identification of small molecule binding site of CCHFV OTU protease and development of florescent UB-AMC assay, to identify potent inhibitors of CCHFV OTU protease and measure CCHFV OTU protease activity, respectively. We utilized in silico approaches and in vitro correlation analysis and revealed Y89-W99 as a pharmaceutical inhibition site on CCHFV OTU protease 1. Furthermore, depending on our flourometric assay, we successfully measured CCHFV OTU protease activity and reported in vitro inhibition of CCHFV OTU protease with two small molecules 2. These results suggested that flourometric analysis of CCHFV OTU activity could be integrated into small molecule inhibitor screening and Y89-W99 site can be used as pharmaceutical target. Keywords: CCHFV, Nairovirus, Bunyaviridae, OTU protease, deubiquitinase, drug screening, fluorometric OTU assay, small molecules Resources: 1) Kocabas, F; Ergin, E. K. " Identification of small molecule binding pocket for inhibition of Crimean- Congo hemorrhagic fever virus OTU protease." Turk Journal of Biology. DOI: /biy ) Kocabas, F.; Aslan, G. S. "Fluorometric CCHFV OTU protease assay with potent inhibitors." Virus Genes (2015):

141 PP 33 Synthesis, Characterization Of New Diflunisal 1,2,4-Triazole-3- Thiones* Göknil Pelin Coşkun a, Kemal Yelekçi b, Teodora Djikic b,ş. Güniz Küçükgüzel a A marmara University, Faculty Of Pharmacy, Department Of Pharmaceutical Chemistry, Haydarpaşa, 34668, İstanbul-TURKEY. B kadir Has University, Faculty Of Engineering And Natural Sciences, Deparment Of Bioinformatics And Genetic, İstanbul, Turkey. Non-steroidal anti-inflammatory drugs posses activity by inhibiting cyclooxygenes enzymes (COX-1 COX-2 and COX-3). Diflunisal is a non-steroidal anti-inflammatory drug which was reported to inhibit mostly COX-2 enzyme rather than COX-1 enzyme (1). The role of COX-2 enzyme in aspects of carcinogenesis like proliferation and apoptosis is also effective. 1,2,4-triazole-3-thiones were reported to possess different biological activities (2). In this study, we synthesized new 1,2,4-triazole-3-thiones and elucidate their structure by FT-IR and 1 H-NMR. Their purity were proven by TLC, HPLC and elemental analyses. These compounds will further be evaluated for their possible anticancer activities and moleculer binding of diflunisal 1,2,4-triazole-3-thiones on COX enzyme active site will be investigated. N H N N S A OH F F Resources 1) Lu X.; Xie W.; Reed D.; Bradshaw W.S.; Simmons D.L. Proc. Natl. Acad. Sci. 1995; 92(17): ) Küçükgüzel Ş.G.; Çıkla-Süzgün P. Eur J Med Chem. 2015, 97, * This research was supported by the The Scientific and Technical Research Council of Turkey (TÜBİTAK), Research Fund Project Number: 144S

142 PP 34 Synthesis, Anticancer Activity And Molecular Modeling Of Etodolac-Thioether Derivatives As Potent Methionine Aminopeptidase (Type Ii) Inhibitors Işıl Çoruh 1, Özge Çevik 2, Kemal Yelekçi 3, Teodora Djikic 3, Ş.Güniz Küçükgüzel 1 1 marmara University, Faculty Of Pharmacy, Department Of Pharmaceutical Chemistry, Haydarpaşa İstanbul, Turkey. 2 Cumhuriyet University, Faculty Of Pharmacy, Department Of Biochemistry, Sivas, Turkey. 3 kadir Has University, Faculty Of Engineering And Natural Sciences, Department Of Bioinformatics And Genetic, İstanbul, Turkey. In eukaryotes, there are two isoforms of methionine amino peptidase (MetAP), MetAP1 and MetAP2. MetAP2 appears to play a critical role in cell proliferation and tumor growth. In recent years, 1,2,4- triazole derivatives and thioethers are reported as potential MetAP2 inhibitors [1]. Etodolac, (R,S) 2- [1,8-diethyl-1,3,4-tetrahydrapyrano(3,4-b)indole-1-yl]acetic acid, is a non-steroidal anti-inflammatory drug which has anticancer activities reported in the literature [2,3]. In addition, Etodolac hydrazones and 1,2,4-triazole-3-thiones have been reported to have anticancer effect [4,5]. In the light of these literatures, etodolac was chosen as a starting substance to synthesize thioether compounds. The aim of this study is to synthesize novel thioether compounds starting from etodolac drug substance, evaluate and confirm their structures by FTIR, 1 H-NMR, 13 C-NMR and elemental analysis data. The synthesized compounds will be evaluated on the several cancer cell lines in the following studies. Our strategy opens up possibilities for the design and synthesis of new thioether moieties with anticancer activities. CH 3 CH 3 H N O N N N S R 1 R 2 R 1 : -CH 3, -C 2 H 5, -C 6 H 5 R 2 : -, -F, 2-Cl, 4-Cl, 2,6-diCl, -CH 3, -NO 2 142

143 In continuation to extend these research area on anticancer compounds with MetAP2 structure inhibitory activity, in the present work structure activity relationships of a series of etodolac-thioether derivatives derived from 1,2,4-triazole-5-thione have been studied. Our study may also allow the identification of key substrates by database mining. Acknowledgement: This study was supported by the Marmara University Research Committee. Project Number: SAG-C-DRP Resources: 1) Hou Ya-P, Sun J, Pang Zhong-H, Lv Peng-C, Li Dong-D, Yan L, Zhang Hong-J, Zheng Emily X, Zhao J, Zhu Hai-L. Bioorg Med Chem, 2011, 19: ) Kobayashi M., Nakamura S., Shibata K., Sahara N., Shigeno K., Shinjo K., Naito K., Ohnishi K. Eur J Haematol, 2005, 75(3): ) Murata S., Adachi M, Kioi M, Torigoe S, Ijichi K, Hasegawa Y, Ogawa T,. Bhayani M. K, Lai S.Y, Mitsudo K, Tohnai I. Anticancer Res, 2011, 31(9): ) Çıkla P, Özsavcı D, Bingöl-Özakpınar Ö, Şener A, Çevik Ö, Özbaş-Turan S, Akbuğa J, Şahin F, Küçükgüzel ŞG. Arch.Pharm, 2013, 346, ) Çıkla-Süzgün P, Kaushik-Basu N, Basu A, Arora P, Talele TT, Durmaz İ, Cetin-Atalay R, Kucukguzel ŞG. J Enzyme Inhib Med Chem, 2015, in press. 143

144 PP 36 Chemdp: A Natural Product-Based Chemical Database Of Pakistan For Computational Drug Discovery Studies Shaher Bano Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad, Pakistan. The Chemical Database of Pakistan (ChemDP; release 01) is a fully-referenced, evolving, web-based, virtual database which has been developed to introduce natural products (NPs) and their derivatives from the biodiversity of Pakistan to Global scientific communities. The prime aim is to provide quality structures of compounds with relevant information for computer-aided drug discovery studies. For this purpose, over 1000 NPs have been identified from more than 400 published articles, for which 2D and 3D molecular structures have been generated with a special focus on their stereochemistry, where applicable. The PM7 semi-empirical quantum chemistry method has been used to energy optimize the 3D structure of NPs, which can be downloaded as.mol2, sd, sybyl, pdb file a readable format by many chemoinformatics/bioinformatics software packages. Each entry in ChemDP contains over 100 data fields representing various molecular, biological, physico-chemical and pharmacological properties, which have been properly documented in the database for end users. These pieces of information have been either extracted from the literatures or computationally calculated using various computational tools. Cross referencing to major data repositories I.e ChemSpider is made available for overlaping compounds.an android app for ChemDP is available at its website.the ChemDP is freely accessible at 144

145 PP 37 Virtual Screening Of NS5 Protein Of Dengue Virus: A Ligand Based Pharmacophore Modeling Approach Shaher Bano Mirza Kamilia Tasleem and M. Qaiser Fatmi Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad, Pakistan. Dengue is one of the most prevailing diseases at the moment that is spreading around the Globe very rapidly with approximately 1 million people being affected to date. It is a chronic disease that may prove to be fatal if not treated on time. Immediate need for dengue drug is needed so that its hazardous effect can be controlled. Although some inhibitors are proposed for different dengue proteins through different procedures, no on-shelf drug is available for it to date1. The purpose of this research is to discover dengue drug using ligand-based pharmacophore modeling, virtual screening and docking. Perceiving a pharmacophore is the first essential step towards understanding the possible interactions between a receptor and a ligand2. A set of compounds can be screened against those models to find the hits which can be used later for docking purposes. NS5 dengue protein consists of 900 amino acids and RNA dependent RNA polymerase (RDRP) site of NS5 protein of dengue is considered as target site whose catalytic domain ranges from 270 to 900 residues. RDRP was chosen due to its major role in virus replication3. All the existing inhibitors proposed for this protein have been searched and their pharmacophore models have been generated on the basis of structural similarities. These models were generated primarily for biflavonoids that showed bioactivity against NS5 RNA dependent RNA polymerase (RDRP) protein. Screening of these models has been done initially for validation and then with ~80000 compounds from three libraries. Common compounds generated among all the models have been docked against NS5 RDRP and the top results have been considered as the potential inhibitor for NS5 dengue protein on the basis of binding energies and binding residues. Inhibitors with ID D , L , L of antiviral library, D of antibacterial, P of smart library were considered best because they bind to very important binding residues with less binding energies that acts as catalytic sites of NS5 protein and thus these inhibitors can affect the functioning of this protein and help us discover more effective on-shelf drugs. Keywords: Dengue virus, NS5 RNA dependent RNA polymerase (RDRP) protein, biflavonoids, ~80000 compounds, antiviral library, ligand-based pharmacophore modeling, virtual screening and docking, Chemdive. 145

146 Novelty: Pharmacophore generation and screening of antiviral, antibacterial, and SMART libraries from Chemdive data repository for antiviral drug discovery against NS5 RNA dependent RNA polymerase (RDRP) protein of Dengue virus. Resources: 1) Alen, M. M., & Schols, D. (2012). Dengue virus entry as target for antiviral therapy. Journal of tropical medicine, ) Wolber, G., & Langer, T. (2005). LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. Journal of chemical information and modeling, 45(1), ) Guzman, M. G., Halstead, S. B., Artsob, H., Buchy, P., Farrar, J., Gubler, D. J., & Peeling, R. W. (2010). Dengue: a continuing global threat. Nature Reviews Microbiology, 8, S7-S

147 PP -38 Benzotriazole Mediated Syntheses Of Peptidomimetics: Depsi- And Aminoxy- Peptides İlker Avan Anadolu University, Faculty of Science, Department of Chemistry, 26470, Eskisehir The therapeutic applications of peptides is of great importance in pharmacological sciences. Nevertheless, low bioavailability and fast enzymatic degradation of peptides in living organism limits the utilities of peptides for therapeutic applications. Therefore, peptide-like compounds (peptidomimetics) have been designed and synthesized to reduce the disadvantages of natural peptides and to improve pharmacokinetic properties of native analogs 1,2. Peptidomimetics benefit from conformational constraints and have better pharmacokinetic properties. In contrast to their natural analogues, peptidomimetics are usually characterized by; (i) good metabolic stability towards endogenous proteases, (ii) high affinity for specific receptors, (iii) greater oral bioavailability, (iv) more rapid excretion. Peptidomimetic compounds can be built up by coupling of unnatural amino acids (small peptidic scaffolds) as natural analogs 1,2. Free depsidipeptides (depsides), depsi di, tri-peptides, oligo esters and aminoxypeptides were -hydroxy- -aminoxy-carboxylic acids. Chemical structures of all synthesized compounds were elucidated by 1 H NMR, 13 C NMR and elemental analyses. Retention of original chiralities in reactions was determined by chiral HPLC analyses 3,4. References (1) Avan, I.; Hall, C. D.; Katritzky, A. R. Chem. Soc. Rev. 2014, 43, (2) Giannis, A.; Rübsam, F. In Advances in Drug Research; Bernard, T., Urs, A. M., Eds.; Academic Press: 1997; Vol. 29, p 1. (3) Avan, I.; Tala, S. R.; Steel, P. J.; Katritzky, A. R. J. Org. Chem. 2011, 76, (4) Katritzky, A. R.; Avan, I.; Tala, S. R. J. Org. Chem. 2009, 74,

148 PP 39 The Cytotoxic Effects of Turmeric-Black Pepper-Cinnamon Extracts Mix on Breast Cancer Cell Line MDA-MB-231 Duygu AYGÜNEŞa, Canfeza SEZGİNb, Buket KOSOVA CANa a. Ege University Medical Faculty Department of Medical Biology b. Ege University Medical Faculty Department of Medical Oncology In recent years, herbal therapies have been widely used to support the effects of chemicals applied in conventional cancer treatment. Aromatic plants are the source of many drugs used in cancer treatment and the most important ones for support therapy options. In the literature, there are various studies indicating that turmeric1 (Curcuma longa), black pepper2 (Piper nigrum), and cinnamon3 (Cinnamomum sp.) extracts have anti-bacterial, anti-inflammatory, anti-viral, anti-oxidant and anticancer activity. In our study, we aimed to investigate the cytotoxic effects of a mixture of extracts obtained from these three plants, on human breast cancer cell line MDA-MB-231. Turmeric-Black Pepper-Cinnamon extract mixture (ZKT) was supplied by FGC Consulting Natural and Herbal Products Ltd. Co. (Urla, Izmir, Turkey). WST-1 cell viability assay (Roche, Mannheim, Germany) was performed to determinate the cytotoxic effects of ZKT on breast cancer cells. The cells were plated at a cell density of 1 X 104 cells in 96-well plates and grown with Leibovitz's L-15 Medium containing various concentrations (1 /10-1/107) of ZKT, depending on the experiment. The cells were treated by different concentrations during 24, 48 and 72 hours. The absorbance values of WST-1 reagent added cells were measured at a microplate reader plate. GraphPAD 6.0 (La Jolla, California, USA) software was used. For graphs and statistical analysis. After the evaluation of cytotoxicity assay results, it is determined that ZKT has a significant cytotoxic effect on breast cancer cell line MDA-MB-231. IC50 value for 24 hours was determined as 1/50 dilution ratio. In our study, the cytotoxicity of the turmeric-black pepper-cinnamon extract mixture was determined using cell viability assays and it has been observed that components of ZKT may be promising in clinical breast cancer treatment as a support theraphy. As continuation of our study, the ZKT active ingredients, turmeric extract curcumin and black papper extract piperine which improves the bioavailability of curcumin, will be encapsulated 148

149 nanotechnologically. The cytotoxic activity on the breast cancer will be assessed as in vitro and in vivo with these nanoparticules and these experiments will continue by combining with the chemotherapeutics that used in breast cancer treatment. Resources: 1) Lin et al. Drug Deliv. 2015, Jul 23:1-6. 2) Greenshields et al. Cancer Lett. 2015, Feb 1;357(1): ) Lu et al. Carcinogenesis Mar;31(3):

150 PP 40 Synthesis Of Tetra-Substituted Pyrazole Molecules And Their SAR Studies On Cannabinoid Receptors Mehmet Servet Gümüş, Nurettin Menges Pharmacy Faculty, Yüzüncü Yil University, 65080, Van, Turkey Cannabinoid-1 receptor (CB1R) is one of the most abundant neuroregulatory receptors in the brain and involved mainly in regulating feeding and appetite. 1 In addition to the brain, this receptor is also expressed in the peripheral organs, such as adipose tissues, muscle, and liver. 2 Distinct from CB1R, cannabinoid-2 receptor (CB2R) is mostly expressed in the immune system and primarily associated with immune regulation and neurodegeneration. Clinically, a CB1R targeted antiobesity agent known as rimonabant or SR141716A was launched in Europe in 2006; however, it was soon withdrawn in 2008 due to severe central nervous system (CNS) adverse effects, including depression, anxiety, and stress disorders (Figure 1). Figure 1. Tetra-substitute pyrazole skeletons Consequently, antiobesity agents acting on brain CB1R, such as taranabant (MK-0364) and otenabant (CP ), were all terminated in the late stages of development. During the past decade, tremendous efforts have been dedicated to seeking antiobesity agents targeting CB1R in the literature. Hence, detailed description on the design, synthesis, structure activity relationships (SAR) of the newly developed compounds, and in vitro studies for the potential candidate will be presented in this study. To do this, we have designed many new pyrazole derivatives and calculated their theoretical parameters such as logp, PSA (polar surface area), logs, MR (molecular refractivity), HOMO, LUMO, and ESP (electronic surface potential). Second step will be synthesis of important candidates and evaluation of their biological activity on cannabinoid receptors. 150

151 Resources: We are grateful to Scientific Research Council of Yüzüncü Yil University (2014-ECZ-B170) for financial support 1) Wilson, R. I.; Nicoll, R. A. Science 2002, 296, ) Howleff, A. C.; Barth, F.; Bonner, T. I.; Cabral, G.; Casellas, P.; Devane, W. A.; Felder, C. C.; Herkenham, M.; Mackie, K.; Martin, B. R.; Mechoulam, R.; Pertwee, R. G. Pharmacol. Rev. 2002, 54,

152 PP 41 Elucidating Communication Pathways İn Macrolide Binding Region: Similarities And Differences Between Prokaryotic And Eukaryotic Ribosomes Pelin Guzel, Ozge Kurkcuoglu Istanbul Technical University, Department of Chemical Engineering, Maslak 34469, Istanbul Protein synthesis machine ribosomal complex is composed of small (30S: prokaryotes, 40S: eukaryotes) and large (50S: prokaryotes, 60S: eukaryotes) subunits, with numerous functional sites conserved over three kingdoms of life (bacteria, archaea and eukaryote). Nascent polypeptide chains synthesized in the peptidyl transferase center (ptc) on the large subunit, pass through the peptide exit tunnel (pet) and emerges at the solvent site 1. It was shown that the bacterial complex modulates an allosteric link between A2062 a peptide sensor on pet and ptc, in order to stall protein synthesis of specific polypeptides 2. In this study, allosteric communication pathways between A2062 (bacteria numbering) on pet and ptc functional residue A2451 (bacteria numbering) was elucidated and compared for ribosomal complexes of T. Thermophilus, S. Cerevisiae and H. Sapiens, to understand if this mechanism may be used in eukaryotes as well. Ribosome structures were described as graphs formed of nodes linked by edges, where nodes were placed at phosphor and alpha-carbon atoms. Length of edges were calculated based on atom-atom contacts. Then, Yen s algorithm was employed to calculate shortest paths between the two functional residues 3. Our results indicated that allosteric communication pathways between pet and ptc passed through conserved residues for both prokaryotes and eukaryotes, remarkably using mostly the same residues, implying a common allosteric mechanism of the ribosome employed in different organisms. Interestingly, macrolides, a group of antibacterial agents, travel through pet and target this allosteric region between ptc and pet, yet must discriminate bacterial and eukaryotic ribosomes. Recent ribosomal structures suggest that the size of pet is narrower in the eukaryotic ribosome and may prevent macrolides from reaching ptc 4. In this line, for T. Thermophilus 50S and H. Sapiens 60S subunits, we extracted ribosomal tunnel cavities and compared their structures. An additional loop on the ribosomal protein L4 protruding into the tunnel on 60S seems to give a physical constriction to the passage of macrolides, when compared to the ribosomal tunnel on 50S. This physical constraint of L4 in eukaryotes may be an important structural property to consider when designing new antibiotics that can discriminate bacteria and eukaryotes. 152

153 Resources: 1) Gabashvili I.S.; Gregory S.T.; Valle M.; Grassucci R.;, Worbs M.;, Wahl M.C.; Dahlberg A.E.; Frank J. Mol. Cell 2001, 56, ) Vazquez-Laslop N.; Thum C.; Mankin A. S. Mol. Cell 2008, 30, ) Guzel P.; Akdas B.; Kurkcuoglu O. Physical Biology (submitted) 4) Yusupov M., Recent Progress in Ribosome Structure Studies. In: Koreaki, I. Regulatory Nascent Polypeptide, Springer,

154 PP 42 Cytotoxicity Properties Of Novel Cylotriphosphazene Derivatives Containing Chalcones As Side Groups Against Human Prostate Cancer Cells Kenan Koran a, Eray Çalışkan c, Suat Tekin b, Süleyman Sandal b, Ahmet Orhan Görgülü a a Faculty of Science, Department of Chemistry, Firat University, Elazig, TURKEY b Faculty of Medicine, Department of Physiology, Inonu University, Malatya, TURKEY c Faculty of Science, Department of Chemistry, Bingol University, Bingol, TURKEY Cyclophosphazenes are molecules which contain a phosphorus-nitrogen double bond. Chalcones are an important class of natural compounds that can be prepared by the Claisen Schmidt condensation reaction. 1 New cyclophosphazene compounds (1 and 2) containing chalcones as side groups were designed and characterized by spectroscopic methods. ( 31 P NMR, 1 H NMR, 13 C NMR, FT-IR spectrum). New cyclophosphazene derivatives containing chalcones as side groups were investigated cytotoxicity properties by using human prostate cancer cell lines (PC-3). Varying concentrations of these compounds (1 and 2) (1, 5, 25, 50 and 100 μm) was treated with prostate cancer cells for 24 h. Antitumor activities of cyclophosphazenes (1 and 2) were evaluated by 3- (4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. 2,3 Cyclophosphazene derivatives (1 and 2) significantly reduced % cell viability comparative to the control (p<0.05). Compounds 1 and 2 have antitumor activity on human prostate cancer cell lines. The results indicated 154

155 that these compounds showed the highest anti-cancer activity against on human prostate cell lines. IC50 values of these compounds (1 and 2) were calculated that show activation effects against PC-3 cells. Keywords: Cyclotriphosphazene, Chalcone, PC-3, Anticancer. Acknowledgement: This Project is supported by The Scientific and Technological Research Council of Turkey (TUBITAK) Project No: KBAG-115Z101. Resources: 1) Funiss, B.S.; Hannford, A.J.; Smith, P.W.G.; Tatchell, A.R., Vogel s Textbook of Practical Organic Chemistry, 2004, 5th ed., Longman, pp , London. 2) Görgülü, A.O.; Koran, K.; Özen, F.; Tekin, S.; Sandal, S., Journal of Molecular Structure, 2015, ) Singh, N.K.; Singh, S.B., Synth. React. Inorganic and Metal-Org. Chem. 2002, 32,

156 PP 43 Preparation And Evaluation Of Doripenem Loaded Microparticles For Pulmonary Delivery Ozlem Akbal 1, S. Hande Tekarslan 1, Deniz Morina 1, Erdal Cevher 1, Ayca Yildiz-Pekoz 1 1 Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Technology Carbapenems are broad-spectrum β-lactams and, are used to treat infections due to Gram-negative bacteria 1,2. Doripenem is a carbapenem which has a broad-spectrum acitivity against gram-positive and gram negative including Pseudomonas aeruginosa for the treatment of pneumonia, urinary tract infections and intra-abdominal infections 3. Gram-negative pathogen P. aeruginosa is an important cause of pneumonia and also is recognized as a pathogen in COPD 4. Doripenem was proved as the most active carbapenem against Pseudomonas aeruginosa 5. The lungs are suitable for both local and systemic drug delivery. Controlled release formulations to pulmonary drug delivery may provide an effective adjunct approach to orally or parenteral delivered antibiotic for clearing persistent lung infections 6. Aim of the study is to optimize doripenem-loaded microparticles which were developed by ionotropic gelationspray drying techniques. The microparticles with different lactose, trehalose and leucine concentrations were produced and in vitro drug release properties, drug deposition modeling (NGI), antimicrobial susceptibility andcytotoxicity of doripenem loaded microparticles were evaluated. Resources: 1) Chen Y., Garber E., Zhao Q., Ge Y.,Wikler M.A., Kaniga K., Saiman L. In vitro activity of doripenem (S-4661) against multidrug-resistant Gram negative bacilli isolated from patients with cystic fibrosis. Antimicrob Agents Chemother,2005, 49, ) Fritsche TR, Stilwell MG, Jones RN.Antimicrobial activity of doripenem (S-4661): a global surveillance report (2003). Clin Microbiol Infect., 2005, 11, ) Jones RN, Huynh HK, Biedenbach DJ, Fritsche TR, Sader HS. Doripenem (S-4661), a novel carbapenem: comparative activity against contemporary pathogens including bactericidal action and preliminary in vitro methods evaluations. J Antimicrob Chemother, 2004, 54, ) Martinez-Solano L., Macia M.D., Fajardo A., Oliver A., Martinez J.L.Chronic Pseudomonas aeruginosa infection in chronic obstructive pulmonary disease. Clin Infect Dis., 2008, 47: ) Jones R.N., Sader H.S., Fritsche T.R. Comparative activity of doripenem and three other carbapenems tested against Gram-negative bacilli with various β-lactamase resistance mechanisms. Diagn Microbiol Infect Dis, 2005, 52, ) Taylor K.M.G. Pulmonary drug delivery Ed:Michael E.Aulton, Aulton s Pharmaceutics The Design and Manufacture of Medicine, Third edition,churchill Livingstone Elsevier.,

157 PP 44 Investigation Of Anticancer Properties Of New Phosphazene Compounds Against Human Prostate Cancer Cells Kenan Koran a, Suat Tekin b, Eray Çalışkan c, Süleyman Sandal b, Ahmet Orhan Görgülü a a Faculty of Science, Department of Chemistry, Firat University, Elazig, TURKEY b Faculty of Medicine, Department of Physiology, Inonu University, Malatya, TURKEY c Faculty of Science, Department of Chemistry, Bingol University, Bingol, TURKEY In this study, hydroxychalcone compounds were synthesized via the Claisen Schmidt condensation reaction. 1 After that new cyclophosphazene compounds (1 and 2) bearing chalcone as side groups were designed and characterized by 31 P NMR, 1 H NMR, 13 C NMR, FT-IR spectrum spectroscopic methods. O R N O P O P N N P O O O R R: -H for Phosphazene 1 O 3-Cl for Phosphazene 2 O R R New cyclophosphazene derivatives were investigated anti-cancer properties by using human prostate cancer cell lines (PC-3). Varying concentrations of compounds 1 and 2 (1, 5, 25, 50 and 100 μm) was treated with PC-3 cells for 24 h. Antitumor activities of cyclophosphazenes (1 and 2) were evaluated by 3-(4,5-dimethylthiazol-2- yl)-2,5-diphenyltetrazolium bromide (MTT) assay. 2,3 Cyclophosphazene compounds 1 and 2 significantly reduced % cell viability comparative to the control (p<0.05). The results indicated that these compounds showed the highest anti-cancer activity against on human prostate cell lines. IC50 values of these compounds (1 and 2) were calculated that show activation effects against PC-3 cells. 157

158 Keywords: Phosphazene, Hydroxychalcone, Human Prostate Cancer Cells, Antitumor. Acknowledgement: This Project is supported by The Scientific and Technological Research Council of Turkey (TUBITAK) Project No: KBAG-115Z101. Resources: 4) Funiss, B.S.; Hannford, A.J.; Smith, P.W.G.; Tatchell, A.R., Vogel s Textbook of Practical Organic Chemistry, 2004, 5th ed., Longman, pp , London. 5) Görgülü, A.O.; Koran, K.; Özen, F.; Tekin, S.; Sandal, S., Journal of Molecular Structure, 2015, ) Singh, N.K.; Singh, S.B., Synth. React. Inorganic and Metal-Org. Chem. 2002, 32,

159 PP 44 Determination of Cytotoxicity Properties of New Synthesized Phenylacrylonirile Derivatives on Human Ovarian Cancer Cells Furkan Özen a, Suat Tekin b, Kenan Koran a, Süleyman Sandal b, Ahmet Orhan Görgülü a a Faculty of Medicine, Department of Physiology, Inonu University, Malatya, TURKEY b Faculty of Science, Department of Chemistry, Firat University, Elazig, TURKEY 2-(2,3,4-Trimethoxyphenyl)-1-(substitutephenyl)acrylonitrile derivatives were synthesized according to the Knoevenagel condensations protocol. 1,3 The chemical structures of these compounds are show below. The anti-cancer activities of these compounds (1a-c) were determined in A2780 cancer cell lines by using MTT [3-(4,5- dimethylthiazol)-2-yl]-2,5- diphenyl-2h-tetrazolium bromide] assay method. 4,5 CH 3 CH 3 O CH 3 CH 3 CH 3 O CH 3 CH 3 CH 3 O CH 3 O O CN CH 3 O O CN Cl O O CN F F F ( 1a ) ( 1b ) Compound 1a, 1b and 1c significantly reduced % cell viability comparative to the control (p<0.05). Compound 1a, (1, 5, 25, 50 and 100 µm doses), 1b, (5, 25, 50 and 100 µm doses) and 1c, (5, 25, 50 and 100 µm doses) reduced cell viability of A2780 cells (p<0.05). The results indicated that these compounds showed highest anti-cancer activity against on human ovarian cell lines. IC50 values of these compounds (1a-c) were calculated that exhibit activation effect against A2780 cells. Acknowledgement: The authors are grateful to the Research Fund of the TUBITAK for their support with project No 110T652. Keywords: A2780, phenylacrylonitrile, ovarian cancer, MTT assay Resources: 1) Görgülü, A.O., Investigated of Synthesis, Characterization and Cytotoxic Proporties of New Coumarinoxycyclotriphosphazenes from Reactions of Dihydroxycoumarins with Cyclotriphosphazenes, 2014, TUBITAK (110T652 Latest project report), ) Buu-Hoi, By N. P.; Saint-Ruf, G.; Lobert, B. J. Chem. Soc. (c), 1969, ) Ismet, B.; Selma, S.; Umıt, C.; Mustafa, B.; Oktay, A.; Ozen, O. J. of Enzyme Inh. and Med. Chem. 2008, 23(1), ) Görgülü, A.O.; Koran, K.; Özen, F.; Tekin, S.; Sandal, S., Journal of Molecular Structure, 2015, ) Singh, N.K.; Singh, S.B., Synth. React. Inorganic and Metal-Org. Chem. 2002, 32, ( 1c ) 159

160 PP 46 Effect Of Intracellular Ionic Strength On Bacterial Trigger Factor Dynamics M.Tarık Can, G. Ezeroglu a, A. Uyar a, O. Kurkcuoglu b, P. Doruker a a Dept. of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkiye, b Dept. of Chemical Engineering, Istanbul Technical University, Istanbul, Turkiye Trigger factor (TF) protein, found in bacterial cells and chloroplasts, is the first chaperone welcoming the newly synthesized nascent polypeptide chains to facilitate their folding process 1. TF is composed of three domains, namely the binding, the core and the head domains. Here, we report several independent molecular dynamics (MD) simulations of TF protein performed at 29 mm and 150 mm ionic strengths, which sum up to a total duration of more than one microsecond. Root mean square deviations from the initial structure indicate high flexibility of TF at both concentrations. Radius of gyration distributions point to more extended conformers at 150 mm. Residue mean square fluctuations from the average structure present more mobility at 29 mm. Clusters obtained via overall and domain-wise alignments of MD snapshots elucidate the differences in TF s inter- and intra-domain conformational flexibility at mentioned concentrations. Principal component analysis of MD trajectories at both ionic strengths further reveal the collective dynamics of apo TF domains, such as the opening/closing and the twisting motions observed in the head domain. Overall, this study points to the importance of ionic strength in view of conformational dynamics especially for a protein like TF, which carries a large portion of charged, both acidic and basic, residues. Resources: 1) Blaha, G., Wilson, D., N., Stoller, G., Fischer, G., Willumeit, R., and Nierhaus, K., H., Localization of the Trigger Factor Binding Site on the Ribosomal 50S Subunit, Journal of Molecular Biology, 2003, Vol. 326, pp

161 PP 47 Investigation Of Urease Inhibition By Some 1,2,4 Triazol Derivatives Aylin Kalfa a, Elif Ayazoglu a, Ahmet Yasar b, Ahmet Colak a, Olcay Bekircan a, Yakup Kolcuoglu a a Karadeniz Technical University, Faculty of Science, Department of Chemistry, Trabzon b Karadeniz Technical University, Faculty of Pharmacy, Department of Science of Basic Pharmacy Trabzon Ureases (urea amidohydrolases, EC ) are a group of metalloenzymes widespread in nature among plants, bacteria, fungi, algae and invertebrates that, although with different protein structures, exercise a single catalytic function, that is the hydrolysis of urea, its final products being ammonia and carbonic acid. Urease is a virulence factor in infections of urinary and gastrointestinal tracts, possibly causing severe diseases such as peptic ulcers and stomach cancer as in the case of Helicobacter pylori, while the efficiency of soil nitrogen fertilization with urea (the most used fertilizer worldwide) decreases due to ammonia volatilization and root damage caused by soil ph increase. The control of the activity of urease through the use of inhibitors could counteract these negative effects. In this study, six 2-[3-(4- chlorophenyl)-5-(4-methoxybenzyl)-4h-1,2,4-triazol-4-yl] acetohydrazide derivative compounds (4a-f) were examined for their inhibitor efficiencies on Jack bean urease activity. All experiments were performed at optimum conditions (ph, temperature and enzyme concentration values, 7.5, 35 C, 120 µg/ml, respectively) in the presence of urea as substrate at the concentration of its Km value, 2,78 mm. Thiourea was used as a reference standard inhibitor. 4-Phenyl-2-[(4-methylpiperazin-1-yl)methyl]-5- {[3-(4-chlorophenyl)-5-(4-methoxybenzyl)-4H-1,2,4-triazol-4-yl]methyl}-2,4-dihydro-3H-1,2,4- triazole-3-thione (Compound 4e) was found the most potent inhibitor in terms of its IC 50 value (at µm levels). This compound behaved as a noncompetitive inhibitors for Jack bean urease activity. The kinetic parameter (K I ) characterizing this inhibition was calculated as 255 µm. Futhermore, molecular docking studies by using auto dock vina and gaussian programmes have been performing to support experimental data. It is concluded that these compounds may be useful for development of new generation drugs. This research was funded by The Scientific and Technological Research Council of Turkey (TUBITAK), Project no: 114Z711. Resources: 1) Krajewska, B., J. Mol. Cat. 2009, ) Benini, S.; Rypniewski, W. R; Wilson, K. S; Mangani, S.; Ciurli, S., J. Am. Chem. Soc. 2004, ) Bekircan, O.; Ülker, S.; Menteşe, E, J. Enz. Inh. Med. Chem. 2015, 1-161

162 PP 48 Replacing Some Parts Of Angiotensin Antagonists With Twenty Essential Aminoacids, And Their Docking Results With 4YAY Gizem Ergun School Of Medicine, Bahcesehir University, Istanbul, Turkey Considering the parts that don't interact well with the receptor protein, twenty essential amino acids were replaced with those parts or just added to angiotensin antagonists that are already used in antihypertensive drug industry. SP /XP/ IFD dockings were done with the recently discovered 4YAY. And it was seen that docking resutls were better compared to reference scores, the newly synthesized ligands have shown better acitivity with the receptor protein. Resources: 1. Zhang, H., Unal, H., Karnik, S., Cheerezov, V.. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography, Cell (2015). 162

163 PP - 49 Anticholinesterase Activity Of Novel 3-Hydroxyflavones Identified By Docking Studies Burcu Culhaoglu a,c, Atilla Akdemir b, Turan Ozturk c, Gulacti Topcu d a Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, 34093, Turkey b Department of Pharmacology, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, 34093, Turkey c Department of Organic Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul, 34469, Turkey d Department of Pharmacognosy/Phytochemistry, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, 34093, Turkey Dementia is one of the main syndrome in several neurological disorders including Alzheimer s, Parkinson s, and Huntington s diseases. Among them, Alzhemer s Disease (AD) is a progressive degenerative disorder of the brain and the most common cause of cognitive impairment in the elderly 1. It is characterized by the presence of amyloid deposits and neurofibrillary tangles in the brain in association with a loss of cholinergic neurons in the brain areas related to mainly memory and learning 2. The inhibition of cholinesterases is considered to be involved in increasing acetylcholine level in the brain and thus has been implicated in the treatment of Alzheimer's disease. Development of novel ligands as cholinesterase inhibitors can be accelerated using structure based approaches 3. In this study we report the identification of a novel class of flavonoids as ligands for acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors using their respective crystal structures as templates in docking studies. Firstly, we prepared a small library of synthetically accessible 3-hydroxyflavone derivatives. These compounds were subject to docking studies to identify compounds with high docking scores, which were then synthesized a series of 3-hydroxyflavone derivatives and screened for inhibition of AChE and BChE with Ellman method 4. Some structural derivatives exhibited very good inhibitory activity towards BChE selectively. 163

164 Figure: Structure of a derivative of 3-hydroxyflavone Resources: 1) Standridge, J.B. Clin. Ther. 2004, 26, ) Zheng W.H.; Bastianetto, S. ; Mennicken, F. ; Ma, W. ; Kar, S. Neuroscience, 2002, 115, ) Akdemir, Z., Rucktooa, P.,Jongejan, A., Elk, R., et al., Bioorg. Med. Chem., 2011, 19(20), ) Ellman, G.L.; Courtney, K.D.; Andres, V.; Featherston, R. M. Biochem. Pharmacol., 1961, 7,

165 PP 50 Synthesis And Spectroscopic Properties Of Azacoumarin Derivative As A Fluorescent Probe For Protein Labeling Hazel Erkan a, Özlem Dilek b a Istanbul Yeditepe University, Department of Biotechnology, Istanbul, TURKEY b Istanbul Kemerburgaz University, School of Medicine, Istanbul, TURKEY With the rapid development of chemical biology, many diagnostic fluorophore based tools were created and they were widely used to study and manipulate proteins in order to understand their complicated biological functions in cells. For example, in bioorthogonal chemistry1, aldehyde or ketone functional groups can be attached to peptides and proteins using chemical or biochemical methods at physiological conditions and temperature.2 The fluorophores react with the aldehyde functional group of protein at or near physiological conditions to form a stable conjugated product.3,4,5 The final product shows a significant increase in emission quantum yield upon covalent bond formation. In some cases, a red shift of the absorption and emission maxima is observed.3,4,5 In this study, we highlight the synthesis and spectroscopic properties of some azacoumarin fluorophores to study tubulin-tubulin tyrosine ligase (TTL) system in live cells. Salicylaldehyde is used as a convenient and cheap mimic model of formyl tyrosine on our modified tubulin system. The reaction between salicylaldehyde and azacoumarin hydrazine is monitored by UV-vis difference spectrum at room temperature. Hydrazone or imine formation also changes its spectroscopic property, which shows a red shift on both absorption and emission spectra or an increase on fluorescence. Newly synthesized fluorophores should therefore be very useful tools for understanding complex processes in live cells. References: 1. Zheng, M., et al., Development of Bioorthogonal Reactions and Their Applications in Bioconjugation. Molecules, (2): p Banerjee, A., et al., Site-Specific Orthogonal Labeling of the Carboxy Terminus of α-tubulin. ACS Chemical Biology, (8): p Dilek O.; Bane SL. Aromatic Hydrazine-Based Fluorophores: Synthesis, Spectroscopy and Bioapplications. Book Chapter, Nova Science Publishers 2013, Dilek O.; Bane SL, Journal of Fluorescence, Syntheses and spectroscopic characterization of boron dipyrromethene-derived hydrazones. 2011, 21, 1, Dilek O.; Bane SL, Tetrahedron Letters, 165

166 PP 51 Nitro-Substituted Perhalodienes As Precursors For Synthetically And Physiologically İnteresting Chemical Compounds Serdar Gökşin Aydınlı Istanbul University, Engineering Faculty, Department of Chemistry, Division of Organic Chemistry, 34320, Avcilar, Istanbul, Turkey Nitro-substituted perhalodienes, are valuable starting materials for the directed synthesis of highly functionalized heterocycles which became topic of recent investigations due to wide variety of synthetically and pharmacologically interesting properties as fungicidal, antibacterial, antitubercular, and anticonvulsant. Entering of a nitro substituent to these molecules enforces the biological activity 1. The easily accessible 2-Nitropentachloro-1,3-butadiene 2,3 being one of the most attractive and noticeable members of this new class of synthetic building units and often the starting material of choice, due to its stepped reactivity in S N Vin reactions. Applying selective and mild reactions, this diene enables click chemistry type synthesis to create of drug-like molecules and complexed organic structures based on quick, reliable and selective chemical reactions. The present work focuses on synthesis of biologically promising derivatives of highly functionalized heterocycles obtained by the reactions of some substituted polyhalogenated-1,3-nitrobutadienes with nucleophiles containing some heterocylic amine and thiol functional groups. The synthesis always start with the attack of a nucleophile at the activated terminal carbon atom of the nitrodichlorovinyl group within 2-Nitropentachloro-1,3-butadiene. The structures were evidenced by spectroscopic methods such as elemental analysis, NMR, FT-IR, MS and single crystal X-ray diffraction. Cl Cl Cl Cl Cl NO 2 Cl Cl Cl Cl Br NO 2 Cl Cl Cl Cl NO 2 NO 2 Cl Cl Cl NO 2 Cl Cl Cl Cl SR Cl Cl NO 2 Cl Cl SR N Cl NO 2 Some Nitro- and S,N-substituted perhalodienes 166

167 Resources: 1) Zapol'skii, V. A.; Namyslo, J. C.; Gjikaj, M.; Kaufmann, D.E. Beilstein J. Org. Chem. 2014, 10, ) Ol dekop, Yu. A.; Kaberdin, R. V. Zh.Org. Khim., 1976, 12 (9), ) Aydınlı, G., Sayil, C.; Ibis, C. Spectrosc Lett. 2010, 43 (1),

168 PP 52 New CACYP51 Homology Model Validated For Virtual Screening Suat Sarıa, Jóhannes Reynıssonb, Sevim Dalkaraa ahacettepe University, Faculty of Pharmacy, Dept. of Pharmaceutical Chemistry, Ankara, Turkey buniversity of Auckland, School of Chemical Sciences, Auckland, New Zealand Here we report the homology model of Candida albicans lanosterol 14α-demethylase (CACYP51) and its validation through a two-step docking study for future use for a virtual screen of azole antifungals. Using MODELLER1 we created a structure model for CACYP51 in holo form employing the crystal structure data of the same enzyme from Saccharomyces cerevisiae (PDB id: 4K0F) as a template and a pairwise alignment (identity: 65%, similarity: 78%). First we screened the library of La Regina et al.2 including 55 ligands with known minimum inhibitor concentration (MIC) values against C. albicans, using GOLD3 (with all scoring functions), AutoDock4, and AutoDock Vina5, applying heme binding parameters derived from CDS data for GoldScore6 and ChemScore7. 25 of these ligands had MIC values < 10 μg/ml2 and GoldScore was able to rank 18 of these most potent 25 compounds among the 25 top-scoring docked compounds (72% match). Later we screened seven azole antifungal drugs with known [Azole]0.5 values8 (Fig.). Regression analyses of the results with the experimental data revealed that GoldScore produced the best correlation (R2: 0.56) of the scoring functions used. Together these results lead us to the conclusion that GoldScore is the best tool to discern active compounds from inactive ones and the homology. 168

169 References 1) Šali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, ) La Regina, G. et al. J. Med. Chem. 2008, 51, ) Cole, J.C.; Nissink, W. M.; Taylor R., Protein-Ligand Docking and Virtual Screening with GOLD: Virtual Screening in Drug Discovery, Taylor & Francis CRC Press, Boca Raton, Florida, ) Morris, G.M. et al. J. Comput. Chem. 2009, 16, ) Trott, O.; Olson, A.J. J. Comput. Chem. 2010, 31, ) Jones, G. et al. J. Mol. Biol. 1997, 267, ) Eldridge, M.D. et al. J. Comp. Aid. Mol. Design, 1997, 11, ) Warrilow, A.G.S. et al. Antimicrob. Agents Chemother. 2010, 54,

170 PP 53 Synthesis And Evaluation Of New Thiazole Derivatives As Potential Antitumor Agents Ahmet Özdemir a, Mehlika Dilek Altıntop a, Gülşen Akalın Çiftçi b, Halide Edip Temel b a Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey b Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey Cancer is one of the leading causes of morbidity and mortality worldwide and extensive efforts have been devoted to the discovery of new anticancer agents. The clinical efficacy of tiazofurin and its analogues, dasatinib and bleomycins (BLMs) pointed out the importance of thiazole moiety in the field of cancer treatment. 1 In the current work, new thiazole derivatives were synthesized via the reaction of 4-(1H-imidazol-1- yl/1h-1,2,4-triazol-1-yl)benzaldehyde thiosemicarbazone with substituted phenacyl bromides. MTT assay was carried out to determine the cytotoxic effects of the compounds on A549 human lung adenocarcinoma and C6 rat glioma cell lines. The most effective compounds were also investigated for their effects on apoptosis and mitochondrial membrane potential. The compounds showed more potent inhibitory effects on C6 cells than A549 cells. Among these derivatives, 2-[2-(4-(1H-1,2,4-triazol-1- yl)benzylidene)hydrazinyl]-4-(4-nitrophenyl)thiazole (2) was the most promising agent due to its notable inhibitory effect on C6 cells with an IC 50 value of 13.00±1.00 µg/ml when compared with cisplatin (IC 50 = 12.67±3.06 µg/ml). Compound 2 increased early and late apoptotic cell population (18.3%) more than cisplatin (16.3%). Furthermore, this compound caused disturbance on mitochondrial membrane potential (40.2%) in C6 cells, which was similar to cisplatin (42.3%). This outcome pointed out that compound 2 exhibited potent and selective anticancer activity against C6 cells and induced apoptosis. Key words: Thiazole, Imidazole, Triazole, Cancer, Apoptosis, Mitochondrial membrane potential. 170

171 Resources: 1) Ayati, A.; Emami, S.; Asadipour, A.; Shafiee, A.; Foroumadi, A. Eur. J. Med. Chem. 2015, 97,

172 PP -54 Synthesis And Pharmacological Evaluation Of New Thiadiazole Derivatives As Potential Antinociceptive Agents Mehlika Dilek Altıntop a, Özgür Devrim Can b, Ümide Demir-Özkay b, Zafer Asım Kaplancıklı a a Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey b Department of Pharmacology, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey Thiadiazole has received considerable attention as a privileged scaffold due to its significant therapeutic potential. The sulfur atom of thiadiazole ring imparts improved liposolubility, which is crucial for the delivery of CNS drugs to their site of action. The mesoionic nature of 1,3,4-thiadiazoles allows these compounds to cross cellular membranes and interact with biological targets with distinct affinities. 1,2 In the current work, new thiadiazole derivatives were obtained via the reaction of 5-(4- nitrophenyl)amino-1,3,4-thiadiazole-2(3h)-thione with N-(alkyl/aryl)-2-chloroacetamide/4- (chloroacetyl)morpholine. The synthesized compounds were investigated for their potential analgesic activity against thermal, mechanical and chemical nociceptive stimuli using hot-plate, tail-clip and acetic acid-induced writhing tests, respectively. The assessment of motor coordination was carried out using Rota-Rod test. In hot-plate and tail-clip tests, compounds 2, 3, 4, 5, 7 and 8 caused centrally mediated antinociceptive activity prolonging the reaction time significantly in mice. According to acetic acid-induced writhing test, compounds 1, 3, 5 and 6 significantly reduced acetic acid-induced writhing response in mice (peripherally mediated antinociceptive activity). Compounds 1, 3 and 6 significantly decreased both horizontal and vertical locomotor activity in mice. This outcome indicated that the antinociceptive effects of these compounds are not specific. On the other hand, other compounds did not affect the motor performance in mice. Key words: Thiadiazole, Antinociceptive activity, Locomotor activity, Hot-plate test, Tail-clip test, Acetic acid-induced writhing test 172

173 Resources: 1) Li, Y.; Geng, J.; Liu, Y.; Yu, S.; Zhao, G. ChemMedChem 2013, 8, ) Haider, S.; Alam, M. S.; Hamid, H. Eur. J. Med. Chem. 2015, 92,

174 PP 55 A New BODIPY/Ni Complex For Binding Of Cytochrome C On Magnetic Nanoparticle Esra Maltas a,b, Ahmed Nuri Kursunlu a, Gulsin Arslan b, Mustafa Ozmen a a Selcuk University, Faculty of Science, Department of Chemistry, Konya, Turkey b Selcuk University, Faculty of Science, Department of Biochemistry, Konya, Turkey Fluorescent sensors were also designed for metal cations as chromium, zinc, aluminum, copper, nickel, etc. due to a lot of biomedical applications 1-4. Among them, BODIPY s were studied extensively for applications of optic, sensor, and dye owing to their unique photo physical properties as sharp absorption pro- file, high fluorescence quantum yields, good photo-stability and large extinction coefficients in recent years. In this study, 3,5-{Bis[4,4-difluoro, 8-(2,6-diethyl, 1,3,5,7-tetramethyl-4-bora-3a,4a-diazasindacene)]}benzoylchloride (BODIPY) was synthesized for the improving of a new immobilized metal affinity supporting material. Firstly, the synthesized BODIPY was immobilized on iron oxide superparamagnetic nanoparticles (SPIONs) and then, Ni(II) ions were chelated with the active terminals of BODIPY on nanoparticles surfaces to prepare an immobilized metal affinity (IMA) adsorbent for protein adsorption. The amount of BODIPY coated on SPIONs was about 29.7 M at 10 mg nanoparticles. 738 mol of Ni(II) ions were loaded to 10 mg of the SPIONs/BODIPY. The binding amount of cytochrome c was found to be 170 g to the SPIONs/BODIPY/Ni at ph 7.4. The binding amount of the molecules on SPIONs was analyzed by using UV vis, fluorescence and atomic absorption spectroscopy. The characterization of the prepared surfaces was performed by FT-IR, SEM and TEM. Resources: 1) Kostereli, Z.: Ozdemir, T.: Buyukcakir, O.: Akkaya, E.U. Org. Lett. 2012, 14, ) Kolemen, S.: Bozdemir, O.A.: Cakmak, Y.: Akkaya, E.U. Chem. Sci. 2011, 2, ) Atilgan, S.; Ozdemir, T.: Akkaya, E.U. Org. Lett , ) Bozdemir, O.A.: Cakmak, S.E.: Ekiz, O.: Dana, A. Akkaya, E.U. Angew. Chem. Int. Ed. 2011, 50,

175 PP 56 Understanding Antiandrogen Activity Of Some Benzimidazole And Indole Derivatives By Computational Techniques Abdulkadir Koçak and Hatice Can Chemistry Department, Gebze Technical University, TR Gebze-Kocaeli, Turkey The inhibition of androgen receptors (AR) is an important therapeutic approach to advanced prostate cancer treatment. The treatment with the available commercial antiandrogen drugs causes the drug resistence because of their destination to the hydrophobic androgen binding pocket of androgen receptor (AR). In order dealing with such drug resistence problem, a novel region on AR, named binding function 3 (BF3), was investigated 1 as a target for small molecule antiandrogens. A series of benzimidazole and indole derivatives were explored that effectively inhibited AR transcriptional activity with no noticeable cytotoxicity. 2 In this study, quantitative structure activity relationship (QSAR) analyses were used to identify the ideal physicochemical characteristics of potential benzimidazole and indole derivatives as anti-androgen agents. Thus, QSAR models were obtained using a number of descriptors supplying coverage of the general characteristics of a molecule enclosing electronic properties, polarity, solubility, charge, flexibility and molecular size. Important physicochemical properties that increase androgen inhibition were developed by means of predicting its chemical space as a function of the calculated molecular descriptors. The molecular docking studies of the compounds for AR as the protein target revealed that some compounds showed maximum interactions with the binding site of the protein. The present study highlights the unique binding behaviours of the ligands within the BF3 site of AR. The calculations explains the antiandrogen behaviours of these compounds in the mechanism of inhibition. Resources: 1) Lack, N. A.; Axerio-Cilies, P.; Tavassoli, P.; Han, F. Q.; Chan, K. H.; Feau, C.; LeBlanc, E.; Guns, E. T.; Guy, R. K.; Rennie, P. S.; Cherkasov, J. Med. Chem. 2011, 54, ) Munuganti, R. S.; Leblanc E., Axerio-Cilies P.; Labriere C.; Frewin K.; Singh K.; Hasson M. D.; Lack N. A.; Li H.; Ban F.; Tomlinson Guns E.; Young R.; Rennie P.S.; Cherkasov A.; J. Med. Chem. 2013, 56,

176 PP 57 A QSAR Study Of İnhibitory Activity Of Coumarins And Sulfocoumarins Derivatives Against Tumor-Associated Carbonic Anhydrase İsoforms IX And XII Z. Eda Boyluğ1, Hülya Unan2, Mustafa Tekpınar 2, Erol Eroğlu 3 1 Aksaray University, Faculty of Sciences and Arts, Department of Physics, Aksaray, TURKEY 2 Yüzüncü Yıl University, Faculty of Sciences, Department of Physics, Van, TURKEY 3 Akdeniz University, Faculty of Education, Department of Science Education, Antalya, TURKEY In this study, we present DFT-based QSAR models that demonstrate the correlations between calculated molecular descriptors and the experimental inhibition constant (Ki) data of more than fifty derivatives of coumarin and sulfocoumarin measured against Carbonic anhydrase isoforms IX (CA IX) and XII (CA XII). Many statistically significant linear QSAR models were developed using multi linear regression (MLR) algorithm from the global set (coumarins plus sulfocoumarins) and the subsets. The global model for CA IX, statistically the most significant one which comprises physically interpretable molecular descriptors is a five-parameter linear equation with the statistical values N=59, R2=0.65, Q2=0.54, F=13.13 and R2(ext.)=0.59. The best global model for CA XII has better statistics values N=55, R2=0.78, Q2=0.69, F=22.81 and R2(ext.)=0.69 by comparing to CA IX's one. Statistical quality of models constructed from the subsets have a sharp increase comparing to global ones. For CA IX, the statistics of models for subsets are as follow; the model of coumarins:n=42, R2=0.75, Q2=0.64, F=17.32 and R2(ext.)=0.51, and the model of sulfocoumarins: N=17, R2=0.94, Q2=0.87, F=44.58, R2(ext.)=0.99 For CA XII, the statistics of models for the subsets are as follow; the model of coumarins: N=38, R2=0.83, Q2=0.72, F=27.32 and R2(ext.)=0.83, and the model of sulfocoumarins;n=17, R2=0.95, Q2=0.87, F=53.68 and R2(ext.)=0.94. By visualising some molecular descriptors such as frontier orbitals and electro statics potential maps of compounds which are involved in the some above models let us to interpret some factors that influence the inhibition activity coumarins and sulfocoumarins. 176

177 PP 58 Effect Of Corncockle (Berberis Crataegina) On The MCF-7 Cell Culture Birgütay Şahin a, Ümmahan Karaş a, Fatih Şen a A dumlupınar University SEN Research Group, KÜTAHYA Plant corncockle (Berberis crataegina), anti-bacterial, anti-allergic, anti-mutagenic, anti-oxidant, antiviral, liver protector, derailleur urine, expectorant, relieve chest tightness, fever, appetite, strengthening, constricting blood vessels, anti-vomiting, bile building, relieving constipation and bowel cleansing is a plant used in alternative medicine due to the properties. This study investigated whether there is an effect of corncockle plant extract on cancer cell lines 1. In our study we formed total of three groups one of which is a conrol group. Whit MTT experiment applying various amounts of substances on the MCF-7 breast cells, the outcomes are studied. Then samples are measured with wave length of 570 nm in spectrofotometer. The results of the study indicating the possibility of a small amount of anti-tumoral property of the corncockle plant. Resources: 1) İşgör, Y.G.; İşcan, M.; Öztürk, H.S.; Durak, İ. Turkish Journal of Biochemistry Turk J Biochem, 2008; 33 (3) ;

178 PP 59 Homology Modelling Of Lactate Dehydrogenase From Theileria Annulata Belma Nural a, Ayegül Erdemir b, Özal Mutlu c, Dilek Turgut-Balık b a Eskisehir Osmangazi University, Institute of Science, Department of Biotechnology and Biosafety, Meselik, Eskisehir, Turkey b Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, Esenler, Istanbul, Turkey c Marmara University, Faculty of Arts and Sciences, Department of Biology, Goztepe Campus, Goztepe, Istanbul, Turkey Structure based drug design consists of three major steps; cloning and purification of target molecules; determination of target molecule s structure and synthesis of compounds1. Enzymes are crucial molecules in metabolism2 and suitable targets in drug design studies. Therefore, LDH was chosen as a target molecule to develop a new antitheilerial drug against theileriosis caused by Theileria annulata. The first step of drug design was completed in our previous study. The TaLDH was cloned, expressed and obtained as a pure enzyme. In this study, second step in drug design was achieved by in silico determination of the target molecule TaLDH. A comparative model of TaLDH was predicted by MODELLER v9.12 software and the best model was determined according to the DOPE Score. Energy optimization of the protein was performed by HyperChem version applying AMBER forcefield 99. ERRAT, ProSA and RAMPAGE servers were used in validation. In last step, active site pockets of protein were found by using DoGSiteScorer and GHECOM 1.0: Gridbased HECOMi finder servers. Possible drug binding sites and pockets of protein surface were also defined. As a result, three dimensional structure of the TaLDH was built and an active site loop which is not present in the host enzyme, was modelled. Docking studies suggest that this active site loop may serve as a significant target site for drug binding. Resources: 1) Anderson, A.C., Chem Biol, 2003, 10: ) Turgut-Balik, D., D. Shoemark, K. M. Moreton, R.B. Sessions, and J. J. Holbrook. Biotechn. Let, 2001, 23, Key words: Structure base drug design, Homology modeling, LDH, Theileria annulata 178

179 PP 60 Prepared With Electrodeposition Of Metal (Ni, Pt, Pd) N-Cu Nanoparticles Supported By Multi-Walled Carbon Nanotube Based High Precision Non-Enzymatic Glucose Sensor Gaye Başkaya a, Aysun Şavk, Fatih Şen a* 1. Dumlupınar University, Department of Biochemistry, Kütahya 2. Uşak University, Department of Chemical Engineering, Uşak Nickel-cupper nanostructures (Ni-Cu NSs) electrodeposited on Multiwall carbon nanotube (MWCNT) modified glassy carbon electrode (GCE) was prepared and used for highly sensitive glucose detection. The electrochemical behaviors and electrocatalytic performances of the sensor towards oxidation of glucose were evaluated by cyclic voltammograms,chronoamperometry and amperometric method. Compared to sensors based on monometal Ni or Cu NSs, the sensor based on bimetal Ni-Cu NSs exhibits good electrocatalytic activity towards oxidation of glucose. The results showed that the Ni-Cu NSs/MWCNT/GCE exhibited the best catalytic activity at the potential scan number of 10 and the Ni 2+ /Co 2+ molar ratio of 1:1. Compared to the literature Ni-Co and Cu-Co nanoparticles was found to be approximately 8 times more sensitivity 1-2. This high catalytic activity, good sensitivity and stability of the Ni-Cu NSs/MWCNT/GCE sensor opened up a new kind of hybrid materials in electrochemical detection of glucose. Resources: 1) Wang, L.; Lua, X.; Yea, Y.; Sunb, L.; Songa, Y.; Electrochimica Acta. 2013, 114, ) Wang, L.; Zheng Y.; Lu, X.; Li, Z.; Sun, L.; Son, Y.; Sensors and Actuators B: Chemical. 2013, 195,

180 PP 61 An Amperometric Alcohol Sensor By Using A New Generation Platinum-Rhodium Nanomaterials As A New Working Electrode Handan Pamuk a, Sultan Kuzu, Fatih Sen a 1. Dumlupınar University, Department of Biochemistry, Kütahya 2. Uşak University, Department of Chemical Engineering, Uşak Alcohol sensor in aqueous solution is very widely used in food or brewing, fermentation and cosmetic industries. The alcohol concentration can be directly and easily detected by some instruments, such as semiconductor sensor 1 and biosensor. 2-4 However, many disadvantages, for example, poor stability, low storage temperature, and high cost were found for these two types of sensor. An alcohol sensor with higher quality, more simple structure, and possible low cost is developed in this study. The characteristics of this developed alcohol sensor such as linearity, stability and response time were also explored. The best ratio of reducing agent to ion for deposition nickel on the electrode was also studied. Resources: 1) Liu, Y.; Zhu, W.; Tes, M. S. J. Mater. Sci. Lett. 1995, 14, ) Lazaro, F.; Luque de Castro, M. D.; Valcarcel, M. Microchem. J. 1987,36, ) Albery, W.J.; Bartlett, P. N.; Cass, A. E. G.; Sim, K.W. J. Electroanal. Chem. 1987, 218, 127 4) Tsai, P.P.; Chen, I. C.; Tzeng, M. H. Sensor. Actuator. BChem, 1993, 14, 610,

181 PP 62 Novel Nitroreductase/Morpholine Derivative Prodrug Combinations For Cancer Therapy Ünzile Güven Gülhan a, Tuğba Güngör b, Gülden Yetiş a, Mehmet Ay b, Ayhan Çelik a, Ferah Cömert Önder b, Tuğba Taşkın Tok c, Feray Köçkar d a Gebze Technical University, Faculty Of Science, Department Of Chemistry, Kocaeli, Turkey b Çanakkale Onsekiz Mart University, Faculty Of Sciences And Arts, Department Of Chemistry, Natural Products And Drug Research Laboratory, Çanakkale, Turkey c Gaziantep University, Faculty Of Sciences And Arts, Department Of Chemistry,Gaziantep, Turkey d Balikesir University, Faculty Of Science And Literature, Department Of Molecular Biology And Genetics, Balıkesir, Turkey Enzyme/pro-drug cancer therapy is the most known application of nitroreductases 1 which is based on specific expression of a prodrug-activating enzyme in tumor cells and convertion of less toxic pro-drugs to toxic metabolites, named as active drugs 2. Nitroreductases reduce aromatic nitro groups and convert pro-drugs to hydroxylamine derivatives (active drug) which can bind to DNA and inhibit tumor formation 3. E.coli nitroreductase/cb1954 prodrug (5-aziridinyl-2,4-dinitrobenzamide) is the best known example studied in cancer research (phase I/II trials) for different cancer types 4,5. Since this combination has limitations due to low activity and stability 6, new nitroreductase/prodrug combinations should be investigated. In this study, the interaction of synthesized 4-(2,4-Dinitrofenil)morfolin and 4-(2,4,6- Trinitrofenil)morfolin 7 pro-drugs with two new nitroreductases ((Gk-Ntr-cloned from G. kaustophilus) and (Ssap-NtrB-cloned from S. saprophyticus) were investigated by spectroscopic techniques and HPLC analysis. Proposed compounds were easily reduced by the new nitroreductases with high catalytic efficiencies, indicating a potential to be used in cancer therapy. In the future, characterization of the metabolites, their effects on cancer cell lines will be studied and molecular docking studies will also be performed to better visualize the interactions of proposed nitroreductase/prodrug combinations by using DS software

182 Resources: 1) Knox R.J., et al. Biochem Pharmacol. 1992, 44, ) Helsby N.A. et al., J. Med. Chem. 2004, 47, ) Kobori T., et al., Biol. Chem., 2001, 276, ) Palmer, D.H., et al., Journal of Clinical Oncology, 2004, 22(9), ) Patel, P., et al., Molecular Therapy, 2009, 17(7), ) Emptage CD, et al., Biochemical Pharmacology, (1), ) T. Güngör, M. Ay, 5th EuCheMS Chemistry Congress, 31 Jul.-4 Sep. 2014, İstanbul, PD ) Accelrys Software Inc., Discovery Studio 3.5, San Diego: (P.S. supported by TUBITAK-ARDEB 1001 as 113Z706 project) 182

183 PP 63 Electrospun Collagen Nanofibers As Drug Carriers Onur Aras 1 and Murat Kazanci 2 1 Department of Chemistry, Faculty of Science, Gebze Institute of Technology, Çayırova, Kocaeli, TURKEY. 2 Department of Biophysics, School of Medicine, Bahcesehir University, Sahrayıcedid Mah. Batman Sok. No , Yenisahra, Kadıkoy, Istanbul, Turkey Electrospinning is a versatile system to produce nanoscale fibers. Collagen is the well-known biocompatible and bioactive material. In this research, collagen nanofibers are produced in different solvent systems by using electrospinning method. Electrospun collagen nanofibers are compared with their native structure by means of CD (Circular Dichroism), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), and Differential Scanning Calorimetry (DSC). The results are demonstrated that the solvents and electrospinning process are denatured the collagen and the obtained structure is mainly unfolded. The end product is water susceptible and needs to be crosslinked. Five different crosslinking methods are suggested and their effects on the final structure are demonstrated. 183

184 PP 64 Preparation Of The Pharmaceutical Active 5-Substituted 1H- Tetrazole Group With Platinum Nanoparticles Supported On Vulcan Carbon Esma Erken a, İbrahim Esirden b, Muharrem Kaya a, Fatih Şen a 1. Dumlupınar University, Department of Biochemistry, Kutahya 2. Dumlupinar University, Departman of Chemistry, Kutahya. Tetrazoles are heterocyclic compounds having a five membered ring containing four nitrogen atoms and one carbon atom. These compounds have been captivating increasing attention, due to their wide application, such as they show strong activities in pharmaceutical chemistry as antimicrobial, 1 antibacterial, 2 antifungal, 3 antihypertensive drugs and antiallergic, 4 in AIDS treatments or in cancer. 5, 6 Because of these important applications, recently, various methods have been reported for the synthesis of 5-substituted 1H-tetrazole. Herein we report platinum nanoparticles (Pt NPs) stabilized by Vulcan carbon (VC) as a new heterogeneous catalyst for synthesis of tetrazole derivatives with superior catalytic activity. a b C d e f R -H -NO 2 -Br -Cl -CHO -CH 3 Resources: 1) Dişli, A.; Mercan, S.; Yavuz S. J. Heterocycl. Chem. 2013, 50,

185 2) Narasaiaha, T.; Subba Raoa, D.; Rasheeda, S.; Madhavaa, G.; Srinivasulua, D.; Brahma Naidub, P.; Rajua Naga, C. Pharm. Lett. 2012, 4, ) Ahmad Malik, M.; Al-Thabaiti, S. A.; Malik, M. A. Int. J. Mol. Sci. 2012, 13, ) Ellis, E. P.; West, G. B. Biomedical Press 1980, ) Abell, A. D.; Foulds, G. J. J. Chem. Soc. Perkin Trans. 1997, 1, ) Tamura, Y.; Watanabe, F.; Nakatani, T.; Yasui, K.; Fuji, M.; Komurasaki, T.; Tsuzuki, H.; Maekawa, R.; Yoshioka, T.; Kawada, K.; Sugita, K.; Ohtani, M. J. Med. Chem. 1998, 41,

186 PP 65 Computational Approaches To Develop Doxycycline Imprinted Hydrogels Tugce Inan a, Ozge Kurkcuoglu b, F. Seniha Güner b a Department of Polymer Science & Technology, Istanbul Technical University, Maslak Istanbul, Turkey b Department of Chemical Engineering, Istanbul Technical University, Maslak Istanbul, Turkey Molecular imprinting is a technique which can be used for molecular recognition of the molecules by building template - shaped cavities in polymer structure. This technique is prefered in many application areas such as bioseparation prosesses, biosensors, diagnosis and drug delivery systems for controlled drug release 1. Crosslinker concentration 2 and monomer template interactions 3 are fundamental parameters, which affect molecular recognition and releasing performance of imprinted polymer. This study aims to improve doxycycline imprinted hydrogels, which can be used in many different infection treatments. Before the hydrogel synthesis, computational methods were employed to analyze the interactions between template molecule and functional monomers in prepolymerization step to design higly effective and homogeneous imprinted hydrogels. For this purpose, interaction energies were calculated by using Density Functional Theory (DFT), with B3LYP 6-31+G (d,p) basis set, in order to find out best monomers that have high affinity for the template molecule doxycycline. According to our quantum mechanics calculations, a common hydrogel ingredient acrylic acid seemed as a promising monomer for molecular imprinting of the doxycycline while itaconic acid had the strongest (best) interaction with doxycycline. In order to reveal molecular interactions between template molecule and monomers, such as acrylic acid and itaconic acid, Molecular Dynamic (MD) simulations were also performed for their identical stochiometries in the prepolymerization step MD simulations were run in nanoseconds level with periodic boundary conditions at 298 K and 1 bar being the conditions of the hydrogel synthesis. Conformational changes of molecules, local densities of specified atom-pairs and hydrogen bond interactions were analyzed based on the trajectory, discussed and compared with our DFT calculations. 186

187 Resources: 1) A. Tieppo, C.J. White, A.C. Paine, M.L. Voyles, M.K. McBride, M.E. Byrne, Journal of Controlled Release, 2012, 157, ) H. Hiratani, Y. Fujiwara, Y. Tamiya, Y. Mizutani, C. Alvarez-Lorenzo, Biomaterials, 2005, 26, ) L. Wu, B. Sun, Y. Li, W. Chang, Analyst, 2003, 128,

188 PP 67 Novel Across Adjacent Ring Formed Metallophthalocyanines- Mediated Photodynamic Therapy Inhibits The Proliferation Of Human Lung Adenocarcinoma A549 Cells And Human Keratinocytes Hacat Cells Mehmet Varol A, B, Dilek Elmali C, Bekir Salih D, Ayşegül Varol A, Ayşe Tansu Koparal A a Department of Biology, Faculty of Science, Anadolu University, Yunusemre Campus, 26470, Eskişehir, TURKEY. b Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, Kötekli Campus, 48000, Muğla, TURKEY. c Department of Chemistry, Faculty of Science, Anadolu University, Yunusemre Campus, 26470, Eskişehir, TURKEY. d Department of Chemistry, Faculty of Science, Hacettepe University, Beytepe Campus, 06800, Ankara, TURKEY. Photodynamic therapy (PDT) is clinically approved and non-invasive strategy to treat cancer and hypertrophic scarring, and that takes advantage of the interaction between light and a non-toxic chemotherapeutic agent (photosensitizer) to produce reactive oxygen species (ROS) which are associated with cytodamage by oxidizing and degrading cell components 1-3. Immune responses are also activated by ROS due to the stabilization and activation of both hypoxia-inducible factors and phagocytic effectors 4. In this research, novel metallophthalociyanines; Bis(ethane-1,1-p-phenol-2,2-p-phenoxy)phthalocyaninatotitanium(IV) (TiPc) and 3,9,17,23-bis [4,4'-(1,2-bis(4-(4-(((Z)-pyridine-4- ylmehylene)amino)phenoxy)phenyl)etan-1,2-diyl)diphenoxy] phthalocyaninatozinc (II) (QZnPc) have been synthesized and characterization of the metallophthalocyanines have been performed by using UVvis, IR, 1 H-NMR and MALDI-TOF-mass spectroscopies. The geometric and electronic structures were also investigated by ab initio/dft quantum mechanical calculations using the Gaussian 03 program with HF theory at the B3LYP/3-21G level. The dark and PDT-mediated toxicities of the chosen concentrations of the complexes (0.625, 1.25, 2.5, 5 and 10 µm) were evaluated by using in vitro MTT and LDH assays on A549 and HaCaT cell lines. Additionally, the metallophthalocyanines were positively charged by phosphonolipids (max. 5%) to facilitate their transportation into cells. PDT-mediated toxicities of the complexes were identified at four different fluence rates (25, 100, 150 and 200 mw/cm 2 ) and three different fluences (2.5, 5 and 100 J/cm 2 ) by using Waltmann PDT 1200 L. 188

189 The experiments showed that synthesized metallophthalocyanines have not a significant dark toxicity. However, the complexes showed PDT-mediated cytotoxic and membrane degradative effects on both A549 and HaCaT cell lines by dependent on the concentrations of metallophthalocyanines, and the fluences and fluence rates of the red light. The positively charged complexes showed approximately 50% more cytotoxic activity according to non-charged concentrations and PDT-mediated complexes showed more cytotoxic activity on adenocarcinoma cells than keratinocytes cells. TiPC was found more potent than QZnPc in photodynamic therapy. Consequently, our preliminary findings suggest that these novel across adjacent ring formed metallophthalocyanines would be use in photodynamic treatment of cancer and hypertrophic scarring and should be therefore further investigated by in vitro and in vivo experiments. Resources: 1) Durmuş M. Photosensitizers in Medicine, Environment, and Security (pp ), Springer Netherlands, ) Mfouo-Tynga, I.; Heidi, A. Int. J. Mol. Sci. 2015, 16, ) Wang, Q.; Dong, Y.; Geng, S.; Su, H.; Ge, W.; Zhen, C. Clin. Exp. Dermatol. 2014, 39, ) Rodica-Mariana, I. Photosensitizers in Medicine, Environment, and Security (pp ), Springer Netherlands,

190 PP 68 Fabrication And Characterization Of Nanomaterial As A Methanol Electrochemical Sensor Esma Erken(A), Betül Çelik(B), Hakan Sert(C), Fatih Şen(A) (a)dumlupınar Üniversitesi, Fen-Edebiyat Fakültesi Biyokimya Bölümü, Kütahya (b) Dumlupınar Üniversitesi, Fen-Edebiyat Fakültesi Kimya Bölümü, Kütahya (c) Uşak Üniversitesi, Mühendislik Fakültesi Kimya Mühendisliği Bölümü, Uşak The production and characterization of monodisperse platinum (0) nanomaterials supported on reduced graphene oxide (Pt(0)@RGO) by the double solvent reduction method at room temperature was investigated as potential application of methanol electrochemical sensor. The characterization process of Pt(0)@RGO was carried out by X-ray diffraction (XRD), X-ray photoelectron microscopy (XPS) and transmission electron microscopy (TEM) analyses that prove the fabrication of monodisperse Pt (0) nanoparticles on RGO.1-2 By the use of CV, it was demonstrated that these Pt(0)@RGO nanoparticles in alkaline solution could behave as an potential amperometric sensor for determining the amount of methanol.3 By identifying several parameters, like, short reply time of Pt(0)@RGO (2 s), relatively broad linear range (1 11 mm), low detection limit (0.1 mm), high sensitivity (0.043 ma cm 2 mm 1) and long-term stability (over 90 days), the superior activity of Pt(0)@RGO sensor was discovered.4 Resources: 1) Ozturk, Z.; Sen, F.; S. Sen, and Gokagac, G. J. Mater. Sci. 2012, 47, ) Zhu, R.; Jiang,C.Y.; Liu, B. and Ramakrishna, S. Adv. Mater. 2009, 21, ) Lamy,C.; Belgsir, E. M. and Leger, J. M. J. Appl. Electrochem. 2001, 31, ) Kabbabi, A. Faure, R.; Durand, R.; Beden, B.; Hahn, F.; Leger, J. M. and Lamy, C. J. Electroanal. Chem. 190

191 PP 70 Evaluation Of Potential Nitro Prodrugs Named 26 ı And 26 ıı For Use With Nitroreductase-Mediated Gene-Directed Enzyme Prodrug Therapy Esra Tokay a, Feray Köçkar a, Tuğba Güngör b, Ferah Cömert Önder b, Gülden Yetiş c, Mehmet Ay b, Ayhan Çelik c, Tuğba Taşkin Tok d a Balikesir University, Faculty of Science and Literature, Department of Molecular Biology and Genetics, Balıkesir, Turkey b Çanakkale Onsekiz Mart University, Faculty of Sciences and Arts, Department of Chemistry, Natural Products and Drug Research Laboratory, Çanakkale, Turkey c Gebze Technical University, Faculty of Science, Department of Chemistry, Kocaeli, Turkey d Gaziantep University, Faculty of Sciences and Arts, Department of Chemistry, Gaziantep, Turkey Many of the nitro aromatic agents used in medicine function as prodrugs and must undergo activation before exerting their toxic effects 1. In most cases, this is catalyzed by nitroreductases (NTRs), a class of enzyme absent from higher eukaryotes but expressed by bacteria and several eukaryotic microbes. In this study, two potential prodrugs were evaluated for use in gene-directed enzyme prodrug therapy (GDEPT) using a nitroreductase (Ssap-NtrB) cloned from Staphylococcus saprophyticus strain 2. Firstly, cytotoxic effects of compounds were determining using a quantitative colorometric. MTT assay using Human Hepatoma Cells (Hep3B) and Human Human Umbilical Vein Endothelial cells (HUVEC) for 24h and 48h. Compound 26 ı (1,2-bis(2,4-dinitrophenyl)hydrazine) and compound 26 ıı (1,2- bis(2,4,6-trinitrophenyl)hydrazine) were synthesized with nucleophilic aromatic substitution reaction 3. These compounds exhibited potent cytotoxic efficacy against Hep3B cells but had no effect on HUVEC cells. In addition, the prodrugs and corresponding amine effectors were tested in a cell line panel comprising Hep3B and HUVEC cell lines and were compared with the established NTR substrates CB1954 (5-aziridinyl-2,4-dinitrobenzamide). A cell viability assay, SRB, revealed that cytotoxic effects of 26 ı compound towards Hep3B cells, is significantly enhanced in the presence of Ssap-NtrB suggesting the potential for use of this compound in nitric oxide-based directed prodrug therapy. Furthermore, molecular docking study will be performed to better visualize the interactions of proposed nitroreductase/prodrug combinations and compare with experimental data by using DS 4 software. Keywords: Ssap-NtrB, nitroreductase, nitro compounds, Cell cytoxicity, prodrug, molecular docking. 191

192 Resources: 1) Zhang J, Kale V, Chen M Gene-directed enzyme prodrug therapy. AAPS J. Jan;17, 1, ) Çelik A,Yetiş G An unusually cold active nitroreductase for prodrug activations.. Bioorg Med Chem. 20, 11, ) Paillard E., Alloin F., Cointeaux L., Iojoiu C., Sanchez J., 2011, Electrochimica Acta, 57, Green, Arthur G.; Rowe, Frederick M., Proceeding of the Chemical Society, London, 28, 251. Leemann, H.; Berichte der Deutschen Chemischen Gesellschaft 1908, 41, ) Accelrys Software Inc., Discovery Studio 3.5, San Diego: (P.S. supported by TUBITAK-ARDEB 1001 as 110T754 and 113Z706 projects) 192

193 PP 71 Anticancer Effects Of Nitro-Groups Containing Compounds (3i And 3i ı ) Against Four Different Cell Types Esra Tokay a, Nelin Hacioğlu a, Feray Köçkar a, Tuğba Güngör b, Gülden Yetiş c, Mehmet Ay b, Ayhan Çelik c, Ferah Cömert Önder b, Tuğba Taşkin Tok d A balikesir University, Faculty Of Science And Literature, Department Of Molecular Biology And Genetics, Balıkesir, Turkey B çanakkale Onsekiz Mart University, Faculty Of Sciences And Arts, Department Of Chemistry, Natural Products And Drug Research Laboratory, Çanakkale, Turkey C gebze Technical University, Faculty Of Science, Department Of Chemistry, Kocaeli, Turkey D Gaziantep University, Faculty Of Sciences And Arts, Department Of Chemistry, Gaziantep, Turkey A variety of nitro heterocyclic prodrugs of 3i (N-(2,4,6-trinitrophenyl)naphthalene-2-amine) and 3i ı ( N- (2,4,6-trinitrophenyl)naphthalene-1-amine), covering a wide range of reduction potential were prepared with nucleophilic aromatic substitution reaction 1 and evaluated for cytotoxicity and use in gene-directed enzyme prodrug therapy (GDEPT) using a nitroreductase (Ssap-NtrB) cloned and expressed from Staphylococcus saprophyticus 2. For cytotoxicities of compounds, various concentrations of compounds (150, 75, 38.5, and µm) were treated on Hep3B, PC3, Saos-2 and HT-29 cells for 24 and 48 hour. 2% DMSO was used as vehicle control. Negative growth effect on Hep3B, PC3 and Saos-2 cells were observed. However HUVEC cells weren t affected by these compounds. In addition, the 3i and 3i ı prodrugs and corresponding amine effectors were tested in a cell line panel comprising Hep3B and HUVEC cell lines and were compared with the established NTR substrates CB1954 (5-aziridinyl-2,4- dinitrobenzamide). A cell viability assay, SRB, revealed that cytotoxic effects of 3i towards hepatoma Hep3B cells, is significantly enhanced in the presence of Ssap-NtrB suggesting the potential for use of this compound in nitric oxide-based directed prodrug therapy. Molecular docking will be also performed to better visualize the interactions of proposed nitroreductase/prodrug combinations and compare with experimental data by using DS 3 software. Keywords: Ssap-NtrB, nitroreductase, nitro compounds, Cell cytoxicity, prodrug, molecular docking. 193

194 Resources: 1) Elliot, M.S., F.J. Smith, and A.M. Fraser, Phyrotechnics, 2000, 25,1, ) Çelik A,Yetiş G. 2012, An unusually cold active nitroreductase for prodrug activations.. Bioorg Med Chem. Jun 1;20(11): ) Accelrys Software Inc., Discovery Studio 3.5, San Diego: (P.S. supported by TUBITAK-ARDEB 1001 as 110T754 and 113Z706 projects) 194

195 PP 72 Molecular Docking Studies Of Substituted Coumarin Compounds With Trypsin As A Potential Serin Protease Inhibitors Ferah Cömert Önder a, Mehmet Ay a a Çanakkale Onsekiz Mart University, Faculty of Sciences and Arts, Department of Chemistry, Natural Products and Drug Research Laboratory, Çanakkale, Turkey Proteases, also known as proteolytic enzymes, are enzymes that catalyze the breakdown of proteins by hydrolysis of peptide bonds. Earlier proteases were considered as only protein degrading enzymes, however now the view has dramatically changed. Proteases are extremely important signalling molecules that are involved in numerous vital processes like apoptosis, cell growth and activation, adhesion, invasion, cell migration and metastasis, protein secretion, cellular interactions and signal transduction, phagocytosis and angiogenesis. Thus, show complete anticancer mechanism. Proteases from all six classes have been found to be involved in tumor growth and progression 1, 2. Serine proteases form a group of proteases which have close relationship with cell growth and differentiation. Trypsin, one of the typical well-known digestive serine protease has also been found to be involved in various cancers and promotes proliferation, invasion and metastasis 3, 4. In this study, molecular docking studies were performed to better visualize the interactions of proposed trypsin/coumarin combinations by using Schrodinger 2015 software 5. The coumarin compounds were interacted with trypsin enzyme and the datas were compared with selected standarts 6. Consequently, these compounds may be used as potential trypsin inhibitors. Key words: Serin proteases, serin protease inhibitors, quercetin, trypsin, coumarin, molecular docking Resources: [1] Rakashanda, S.; Amin, S. J. Life Sci, 2013, 5, [2] B.Walker; J.F. Lynas. Cell. Mol. Life Sci. 2001, 58, [3] Rakashanda, S.; Rana, F.; Rafiq, S.; Masood, A.; Amin, S. Biotechnology and Molecular Biology Review, 2012, 7, [4] Hedstrom, L.; Chem. Rev. 2002, 102, [5] Schrodinger Software, Maestro 10.2, [6]Liu, Y.; Zhang, G.; Liao, Y.; Wang, Y. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2015, 151,

196 PP 74 A New Rapid RP-HPLC Method For Determination Of Novel 2-[4-(4-Ethyl Benzamido)Phenyl]-Benzothiazole Gizem Kunal 1, Filiz Arıöz-Özdemir 1, Özlem Bingol-Özakpinar 2, Kayhan Bolelli 3, Esin Aki- Yalcin 3, Ismail Yalcin 3 1 Marmara University, Faculty Of Pharmacy, Department Of Analytical Chemistry, Haydarpasa, Istanbul, Turkey 2 Marmara University, Faculty Of Pharmacy, Department Of Biochemistry, Haydarpasa, Istanbul, Turkey 3 Ankara University, Faculty Of Pharmacy, Department Of Pharmaceutical Chemistry, Tandogan, Ankara, Turkey 2-[4-(4-Ethyl benzamido)phenyl]-benzothiazole was synthesized by Ankara University, Department of Pharmaceutical Chemistry 1. The benzazoles are well known biologically active compounds, as well as anticancer effects 2. This substant (BSN-009) were tested for their cytotoxic activities by Marmara University, Department of Biochemistry and was found to be the most active compound. According to MTT assay, BSN-009 inhibited colon cancer cell lines growth about by 57.53%. Formula. 2-[4-(4-Ethyl benzamido)phenyl]-benzothiazole (BSN-009) In this study, a new, simple, rapid and accurate reverse phase HPLC method developed for the determination of 2-[4-(4-Ethyl benzamido)phenyl]-benzothiazole. An Ace RP C8, 150x4.6 mm, 5µm partical size, with mobile phase consisting of water and ethanol in the ratio of 60:40 v/v was used. The flow rate was 1.0 ml/min and the effluents were monitored at 330 nm. The retention time was 5.2 min. The detector response was linear in the concentration of µg/ml. 196

197 Resources: 1) Bolelli, K., Yalcin, I., Ertan-Bolelli, T., Ozgen, S., KaynakOnurdag, F., Yildiz, I., Aki, E. Med Chem Res. 21 (2011) ) Mahmood-ul-Hassan, Chohan, Z. H., Supuran, C. T. Synthesis And Reactivity In Inorganic And Metal-Organic Chemistry 32 (8) (2002)

198 PP 75 Synthesis Of Novel Azosulfonamide Chalcones And Investigation Of Inhibitory Effects On Some Carbonic Anhydrase Isoenzymes Tayfun Arslan a, Mustafa Orhan b, Lütfi Karagöz c, Murat Şentürk b A giresun University, Vocational High School, Giresun, Turkey B agri Ibrahim Cecen University, Chemistry Department, Agri, Turkey C marmara University, Farmacy Faculty, Istanbul, Turkey Carbonic anhydrases (CAs; EC ), a group of ubiquitously expressed metalloenzymes, are involved in numerous physiological and pathological processes, including gluconeogenesis, lipogenesis, ureagenesis, tumorigenicity and the growth and virulence of various pathogens. In addition to the established role of CA inhibitors (CAIs) as diuretics and antiglaucoma drugs, it has recently emerged that CAIs could have potential as novel anti-obesity, anticancer and anti-infective drugs. 2 Sulfonamide type inhibitors binds to CAs, with coordination to the Zn 2+ ion from the enzyme active site by substituting the fourth, non-protein ligand, a water molecule or hydroxide ion, such as for example acetazolamide (AZA), a clinically used compound since Different researcher groups recently investigated the interactions of sulfonamides and some of their substituted derivatives with all mammalian carbonic anhydrase enzymes, 2-4 demonstrating some low micromolar / submicromolar inhibitors as well as the possibility to design isozyme selective CAIs. 2-4 Novel azosulfonamide chalcones have been synthesized by means of the above ortho-hydroxyazo compound using Claisen- Schmidt condensation, via methyl substituted benzaldehydes. Sulfonamide chalcones derivatives were investigated for the inhibition of different CA isozymes. All these compounds, together with the clinically used sulfonamide acetazolamide, were investigated as inhibitors of the physiologically relevant isozymes. These sulfonamides showed effective inhibition against all these isoforms. Such molecules can be used as leads for discovery of novel effective CA inhibitors against other isoforms with medicinal chemistry applications. This study was financed by Turkish Research Council-TUBITAK (KBAG 115Z078). We are thankfull to TUBITAK for supporting. 198

199 Resources: 18) Supuran, C. T. Nat. Rev. Drug Discov. 2008, 7, ) Alterio, V.; Vitale, R. M.; Monti, S. M.; Pedone, C.; Scozzafava, A.; Cecchi, A.; De Simone, G.; Supuran, C. T. J. Am. Chem. Soc. 2006, 128, ) Ekinci, D.; al-rashida, M.; Abbas, G.; Senturk, M.; Supuran, C. T. J. Enzyme Inhib. Med. Chem. 2012, 27, ) Supuran, C.T. Bioorg. Med. Chem.Lett. 2010, 20,

200 PP 76 Purification Of Carbonic Anhydrase Enzyme From Bovine Liver And Investigation Of Inhibition Effects Of Some Sulfonamide Derivatives Mustafa Orhan a, Habip Çelik a, Esra Şentürk b, Kalim Javed c, Serdar Durdagi d, Deniz Ekinci e, Murat Şentürk a A agri Ibrahim Cecen University, Department Of Chemistry, Agri, Turkey B agri Ibrahim Cecen University, School Of Health Services, Agri, Turkey C hamdard University, Faculty Of Science, Department Of Chemistry, New Delhi, India D bahcesehir University, Medicinal Faculty, Department Of Biophysic, 34349, Istanbul, Turkey E ondokuz Mayıs University, Department Of Agricultural Biotechnology, Samsun, Turkey Carbonic anhydrase (EC , CA) is a family of metalloenzymes that catalyze the conversion of CO 2 to HCO - 3 and H +, being involved in many physiologic processes. 1 CA isoforms are found in a variety of tissues where they participate in several important biological processes such as acid-base balance homeostasy, respiration, carbon dioxide and ion transport, bone resorption, ureagenesis, gluconeogenesis, lipogenesis, electrolyte secretion, and tumorigenesis among others. 1,2 CA isozymes involved in these processes are important therapeutic targets with the potential to be inhibited/activated for the treatment of a range of disorders such as oedema, glaucoma, obesity, cancer, epilepsy and osteoporosis. 1-3 We report here the inhibitory capacities of a series of sulfonamide derivatives (1-12) incorporating substituted pyridazinone moieties were investigated for the inhibition of bovine liver CA enzyme was isolated by means of newly designed chromatography technique. All these compounds, together with the clinically used sulfonamide acetazolamide. Inhibitory capacities of these compounds on bovine liver CA isozyme activity were determined using p-nitrophenilacetate under in vitro conditions. These sulfonamides showed effective inhibition against bovine liver CA. Such molecules can be used as leads for discovery of novel effective CA inhibitors against other isoforms with medicinal chemistry applications. This study was financed by Turkish Research Council-TUBITAK (KBAG 114Z731) for (HC, ES, and MS). We are thankfull to TUBITAK for supporting. 200

201 Resources: 1) Supuran, C. T. Future Med. Chem. 2011, 3, ) Supuran, C. T. Nat. Rev. Drug Discov. 2008, 7, ) Ekinci, D.; al-rashida, M.; Abbas, G., Senturk, M., Supuran, C.T. J. Enzyme Inhib. Med. Chem. 2012, 27,

202 PP 77 Synthesis, Characterization Of New Triazole-Substituted Coumarin Derivatives And Evaluation Their Biological Activity Nurhan Gümrükçüoğlu Vocational School Of Health Sciences, Karadeniz Technical University, TR-61080, Trabzon, Turkey Coumarin nucleus is found in a variety of natural products which exhibit various pharmacological effects. Derivatives of coumarin also form components of important drugs having varied properties. The derivatives of coumarin usually occur as secondary metabolites present in seeds, roots and leaves of many plant species. Their function is far from clear, though suggestions include waste products, plant growth regulators, fungi stats and bacterio stats. There are excellent monographs and review articles 1 describing the structure, synthetic reactions and properties of coumarin. Various 1, 2, 4-triazoles and N-bridged heterocycles derived from then are found to be associated with diverse pharmacological activity. 2 The 1, 2, 4- triazole nucleus has recently been incorporated into a wide variety of therapeutically interesting drugs including Hl/H2 histamine receptor blockers, cholineesterase active agents, CNS stumilants antianxiety agents and sedatives Scheme 1. Synthesized heterocyclic compounds. 202

203 Prompted by the above observations and in continuation of our search for biologically active nitrogen and oxygen containing heterocycles. 4 it was decided to synthesize these heterocyclic coumarins. In this study, it has been synthesized and characterized some new triazole-coumarin derived heterocyclic compounds (1-4). Keywords: Synthesis; 1, 2, 4-Triazole; Coumarin; Complexes; Biological activity Resources: 1) Wawzonek, S., Heterocyclic Compounds, John Wiley & Sons, New York, 1975, 2, ) Bradbury, R. H. ; Rivett, J. E. J. med. Chem. 1991, 34, ) Heindel, N. D. ; Reid, J. R. J. Het. Chem. 1980, 17, ) Rajeswar Rao, V. ; Mohan Rao, G. ; Ravikumar, V. ; Aditya Vardhan, V., Phos. Sulf and Silicon, 1996, 996,

204 PP 78 Evaluation Of Cytotoxic Effects Of Aloe Vera Leaf Extracts And Aloe Emodin On Human Gastric (AGS), Colon (HT-29 And HCT116), Hepatocellular (HEP3B And HEPG2)Tumor Cell Lines Eda Candoken a, Serap ERDEM Kuruca b, Nuriye Akev a A department Of Biochemistry, Faculty Of Pharmacy, Istanbul University, Istanbul, TURKEY. B department Of Physiology, Istanbul Faculty Of Medicine, Istanbul University, Istanbul, TURKEY. Session Title: Applications Related with Original and Generic Drugs It has been well-established that many of the naturally occurring phytochemicals can target multiple pathways involved in cancer cells and are considered as promising candidates for anticancer drug development. Aloe emodin (AE) is an anthraquinone purified from A. vera leaves which has been reported to have antitumor activity. Considerable attention has been given recently to the possibility of utilizing AE as a chemotherapeutic drug for the treatment of various types of cancers. Chemotherapeutic drugs of plant origin are promising strategy for cancer therapy because they might be generally harmless or less toxic than synthetic chemotherapeutic agents on normal cells. At low doses, a variety of injurious stimuli such as heat, radiation, hypoxia and cytotoxic anticancer drugs can induce apoptosis but these same stimuli can result in necrotic cell death, undesirable because it generates inflammation response, at higher doses. Evaluation of cell death type is important as determination of IC50 values, that provide 50% inhibition of cell growth. This study was conducted to evaluate the cytotoxic effects and apoptosis induction potentials of the fresh leaf gel extract, leaf skin aqueous and methanolic extracts as well as shade-dried leaf skin methanolic extracts prepared separately from the leaves of the fresh plant, on several human gasstric and hepatocellular cancer cell lines relative to human normal cell line (Human Umbilical Vein Endothelial HUVEC). Cell viability was assessed by trypan blue exclusion method and cytotoxicity experiments were done using [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] (MTT) assay. A.vera extracts and as positive controls that AE, 5-fluorouracil (5-FU) and Imatinib (IM) were tested at different 204

205 concentrations ( μg/ml; µm; µm; μg/ml respectively). Apoptosis induction was monitored by flow cytometry using the Annexin V-FITC/PI kit. Apoptosis values (apoptosis %) were considered as the total values of gate percentages of early and late apoptosis. AE has selective cytotoxic and apoptotic effects on AGS (19.03 ± 0.25 µm and %) while it showed no effect at the same IC50 concentration on HCT116 (> 150µM and 15.46%), HEPG2 ( ± 5.41 µm and 31.53%), HEP3B ( ± 1.43 µm), HT-29 (ineffective), HUVEC (ineffective) cells respectively. Among the four extracts studied, the gel extract had the highest cytotoxic effect on cancer cells [HCT116 ( ± 6.03 µg/ml and %), HEP3B ( ± µg/ml), HT-29 ( ± 2.67 µg/ml and 0.53 %), AGS ( ± µg/ml), HEBG2 ( ± µg/ml)] while there was no cytotoxic effect on HUVEC normal cells. These results were compared with chemotherapeutic drugs 5-FU and IM. Consequently, A. vera leaf gel and AE as chemotherapeutic drugs of plant origin are promising strategy for cancer therapy that could have an important impact for future drug development research because they are harmless and less toxic than synthetic chemotherapeutic agents on HUVEC normal cells. Key words: Aloe vera, Aloe emodin, human gastric cancer cells AGS, human colon carcinoma cells HT-29, human colon carcinoma cells HCT116, human hepatocellular carcinoma cells HEP3B, human hepatocellular carcinoma cells HEPG2, human umbilical vein endothelial cells HUVEC, cytotoxicity, apoptosis. 205

206 PP 79 Application Of DFT Descriptors For The Discrimination Of Agonist And Antagonist Activity Of Ligands Binding To The NMDA Receptor Zeynep Pınar Haşlak a,b, Berçem Dutağacı, a Gamze Bahadır, a Esra Bozkurt, a Şaron Çatak, a Viktorya Aviyente, a Freija De Vleeschouwer, c Frank De Proft c a Department of Chemistry, Boğaziçi University, Turkey b Department of Chemistry, Piri Reis University, Turkey c Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Belgium N-Methyl-D-Aspartate (NMDA), which is a member of ionotropic glutamate receptors (iglur) becomes active via binding of glycine and glutamate to the subunits of the receptor. Thus, the binding sites of these subunits are important targets for pharmaceutical research. NMDA receptor has two distinctive behaviours which makes it more prominent for medical researches1. The first one is the inactivation of NMDA during its recessing period, and the second one is the "exitotoxic cell death" due to the prolonged stimulation of the receptor. Regulation of receptor activity by introducing partial agonist-antagonist ligands to the glycine and glutamate sites became a promising strategy for the treatment of neuropsychiatric disorders, which are related with dysfunction of NMDA. In this study, quantum chemical calculations are implemented to the ligands for the major subfamily of glutamate receptors, N-methyl-D-aspartate (NMDA). In this manner molecular properties playing a role in ligand binding to NMDA are investigated. Various quantum chemical descriptors are calculated to understand the link between chemical traits of molecules and their activities. These descriptors are further used to discriminate the partial agonism-antagonism nature of the ligands. A number of ligands which bind to the glycine binding site NR1 subunit with different activities2-5 are selected and calculations are carried out using B3LYP with the PCM solvent model in water by utilizing the Gaussian09 program package. The next step of this project will be to connect these molecular descriptors to their activities in order to design a robust QSAR model for the ligands of the NMDA receptor. This will open new opportunities for the drug design in virtual screening and synthesis of novel classes of ligands for glutamate receptors. 206

207 Resources: 1) Leeson, P. D., Iversen, L. L., J. Med. Chem, 1994, 37, 24, ) Yosa, J., Blanco, M., Acevedo, O., Lareo, L.R., European J. Med. Chem., 2009, 44, ) Urwyler, S., Floersheim, P., Roy, B.L., Koller, M., J. Med. Chem., 2009, 52, ) Kreimeyer, A., Laube, B., Sturgess, M., Goeldner, M., Foucoud, B., J. Med. Chem., 1999, 42, ) Nagata, R., Ae, N., Tanno, N., Bioorganic& Med. Chem. Letters, 1995, 5, 14,

208 PP 80 4D-QSAR Investigation And Pharmacophore Identification Of Pyrrolo[2,1-C][1,4]Benzodiazepines Using Ec-Ga Method Ayhan Özalp a, Sevtap Çağlar Yavuz a, Nazmiye Sabancı b, Fatih Çopur c, Zülbiye Kökbudak a, Emin Sarıpınar a a Erciyes University, Science Faculty, Department of Chemistry, Kayseri, Turkey b Siirt University, Science and Arts Faculty, Department of Chemistry, Siirt, Turkey c Abdullah Gül University, Kayseri, Turkey In this study, we present the results of pharmacophore identification and bioactivity prediction for pyrrolo[2,1-c][1,4]benzodiazepine derivatives using the electron conformational genetic algorithm (EC- GA) method as 4D-QSAR analysis [1]. Using the data obtained from quantum chemical calculations at PM3/HF level, electron-conformational matrices of congruity (ECMC) were constructed by EMRE software. The ECMC of the lowest energy conformer of the compound with the highest activity was chosen as template and compared with the ECMCs of the lowest energy conformer of the other compounds within given tolerances to reveal electron conformational submatrix of activity (ECSA, i.e. pharmacophore) by ECSP software. A descriptor pool was generated taking into account the obtained pharmacophore. To predict the theoretical activity and select the best subset of variables affecting bioactivities, nonlinear least square regression method and genetic algorithm were performed. For four types of activity including GI 50, TGI, LC 50 and IC 50 of pyrrolo[2,1-c][1,4] benzodiazepine series, R 2 train, R 2 test and q 2 values are 0.858, 0.810, 0.771; 0.853, 0.848, 0.787; 0.703, 0.787, and 0.776, 0.722, 0.687, respectively. H 3 CO N H H 3 CO N O R 1 [1] E. Sarıpınar, N. Geçen, K. Şahin, E. Yanmaz, Pharmacophore identification and bioactivity prediction for triaminotriazine derivatives by electron conformational-genetic algorithm QSAR method, Eur. J. Med. Chem. 45 (2010)

209 PP 81 Antibacterial And Antifungal Properties Of New Quinone Derivatives Sibel Sahinler Ayla*, Cemil İbis 1 Istanbul University, Engineering Faculty, Department of Chemistry, 34320, Avcilar, Istanbul, TURKEY 1,4-Naphthoquinone pharmacophore are reported to have variety of biological properties such as antifungal, antibacterial and anticancer activity 1-3. Some of the important drugs such as doxorubicin, mitoxantrones, saintopin, contains quinone moiety. The cytotoxic activities of 1,4-naphthoquinones have been widely studied in literature 4. The biologic importance of 1,4-naphthoquinone framework have encouraged chemists to design and synthesize novel derivatives of these kind of compounds. The aim of this study was to synthesize a new series of N- and N,S- substituted compounds derived from 2,3- dichloro-1,4-napthoquinone and to evaluate their antifungal and antibacterial properties. O N N I O N N I O Cl O SR1 R 1 : Aromatic, aliphatic groups etc Resources: 1) Ibis, C.; Tuyun, A. F.; Bahar, H.; Sahinler Ayla, S.; Stasevych, M. V.; Musyanovych, R. Y.; Komarovska-Porokhnyavets, O.; Novikov, V. P. Med. Chem. Res. 2014, 23, ) Kayashima, T.; Mori, M.; Yoshida, H.; Mizushina, Y., Matsubara, K. Cancer Lett. 2009, 278, ) Kanaan, Y.M.; Das, J.R.; Bakare, O.; Enwerem, N.M.; Berhe, S.; Beyene, D.; Williams, V.; Zhou, Y.; Copeland, R.L. Jr. Anticancer Res. 2009, 1, ) R.P., Verma. Anticancer Agents Med. Chem. 2006, 6,

210 PP 82 Kinetic And Docking Study Of Some Malononitrile Derivatives Of Acetylcholinesterase Gamze Koz a, Mustafa Orhan b, Habip Çelik b, Serdar Durdagi c, Deniz Ekinci d, Murat Şentürk b, Necdet Coşgun a a Uludag University, Department of Chemistry, Bursa, Turkey b Agri Ibrahim Cecen University, Department of Chemistry, Agri, Turkey c Bahcesehir University, Medicinal Faculty, Department of Biophysic, 34349, Istanbul, Turkey d Ondokuz Mayıs University, Department of Agricultural Biotechnology, Samsun, Turkey Alzheimer s disease (AD) is a progressive neurodegenerative disorder characterized by intellectual decline and abnormal behaviors and has become one of the main public health problems, especially in the western world due to increasing number of elderly population. 1,2 Although pathogenesis of AD has not been clarified, yet, one of the most accepted theories has been cholinergic hypothesis. Accordingly, a deficiency in levels of the neuromediators called acetylcholine (ACh) and butyrylcholine (BCh) has been observed in the brains of AD patients and inhibition of acetylcholinesterase (AChE) more popularly, along with butyrylcholinesterase (BChE), the key enzymes which hydrolyze ACh and BCh, respectively, has become a major treatment option towards AD. 3 Novel malononitrile derivatives (1-10) were Knoevenagel condensation method synthesized compounds. Therefore, we initiated a study to screen their acetylcholinesterase (AChE, EC ) inhibitory activities, which are the key enzymes taking place in pathogenesis of Alzheimer s disease. Compounds 1-10 showed IC 50 values in the range of nm for AChE. In order to investigate the binding mechanisms of these inhibitors, in silico studies were also applied. Resources: 1) Bachman, D.L.; Wolf, P.A.; Linn, R.T. Neurology 1992, 42, ) Diehl, J.; Kurz, A. Fortschr. Neurol. Psychiatr. 2002, 70, ) Schneider, L.S. Clin. Geriatr. Med. 2001, 17,

211 PP 83 Reengineering Of Trypsin Inhibitor Peptide (SFTI-1) For Cancer Targeting Şeyma Karaoğlu, Muharrem Akcan Dumlupınar University, Faculty of Art and Sciences, Department of Biochemistry, 43100, Kütahya, Turkey Peptides have been preferred as lead molecules in drug design and development studies as they have high target specificity and solubility compared to small and large molecule drugs and hence have low side effects, low toxicity, and limited drug-drug interactions. However, their poor oral bioavailability, poor metabolic stability and high production costs limit their use as drugs. On the other hand, naturally occurring peptides with a cyclic backbone structure and disulfide bonds have attracted the interest in drug design applications. This disulfide-rich cyclic backbone confers them high stability with resistance to thermal, chemical and enzymatic degradations. Peptides such as cyclosporine A and alpha-amanitin from fungus, RTD-1 from monkeys, AS-48 from bacteria, SFTI-1 from sunflower seeds and Kalata B1 from plants are examples of highly stable peptides found in nature. 1 SFTI-1 is a 14 amino acid trypsin inhibitor peptide with a cyclic backbone and a single disulfide bond. 2 In this study, an optimized version of a peptide sequence from a phage display library reported previously to target tumor associated carbonic anhydrase IX (CA IX) was grafted onto SFTI-1 framework to enhance its serum stability. 3 Peptides were synthesized with solid phase peptide synthesis (SPPS) method using Fmoc chemistry. 4 Synthesized peptides were then purified with RP-HPLC and the molecular masses of the peptide fractions were determined with Q-TOF LC/MS. Serum stability assays were carried out by incubating peptides as triplicates in 100% human serum at 37 ⁰C. While the linear peptide degraded completely, the grafted peptide still remained 94% intact in human serum after 120 min. Overall, the study has provided new knowledge of the cyclic peptide backbone to chemical reengineering in drug development applications for cancer targeting. Keywords: Disulfide-rich cyclic peptides, SFTI-1, carbonic anhydrase IX (CA IX), grafting, solid phase peptide synthesis (SPPS), tumor targeting. Resources: 1) Thorstholm L, Craik DJ. Discovery and applications of naturally occurring cyclic peptides. Drug Discovery Today; Technologies, 2012, 9, e13-e

212 2) Korsinczky ML, Schirra HJ, Rosengren KJ, West J, Condie BA, Otvos L, Anderson MA, Craik DJ. Solution structures by 1H NMR of the novel cyclic trypsin inhibitor SFTI-1 from sunflower seeds and an acyclic permutant. J Mol Biol., 2001, 311, ) Rana S, Nissen F, Marr A, Markert A, Altmann A, Mier W, Debus J, Haberkorn U, Askoxylakis V. Optimization of a Novel Peptide Ligand Targeting Human Carbonic Anhydrase IX. PloS ONE, 2012, 7, ) Akcan Muharrem and Craik DJ, Peptide synthesis and applications: Chapter 6: Synthesis of cyclic disulfide-rich peptides, Knud J. Jensen, PernilleTofteng Shelton, Søren L. Pedersen (Eds.), New York, Humana Press-Springer, Pages , July

213 PP 84 Pharmacophore Generation Studies For The Discovery Of Potential Acetylcholinesterase Inhibitors Gözde Yalçın 1, Sanaz Ataei 1, İlkay Yıldız 2 1 Biotechnology Institute, Ankara University, Ankara Turkey 2 Department Of Pharmaceutical Chemistry, Faculty Of Pharmacy, Ankara University, Ankara Turkey Nerves communicate with each other and with muscle cells by using neurotransmitters. These are small molecules that are released from the nerve cells and rapidly diffuse to neighboring cells, stimulating a response once they arrive. Acetylcholine (ACH) is one of these neurotransmitters and the main job of this receptor is to carry the signal from nerve cells to muscle cells. When a motor nerve cell gets the proper signal from the nervous system, it releases acetylcholine into its synapses with muscle cells [1]. There, acetylcholine opens receptors on the muscle cells, triggering the process of contraction. Acetyl cholinesterase (AChE) enzyme terminates the transmission of nerve impulse at the cholinergic synapses by quick hydrolysis of ACH to choline and acetate. AChE is found at mainly neuromuscular junctions and cholinergic brain synapses, where its activity serves to terminate synaptic transmission. It belongs to carboxylesterase family of enzymes [2]. Inhibition of AChE evolves a strategy for the treatment of several diseases as Alzheimer s disease (AD),senile dementia, ataxia, myasthenia gravis and Parkinson s disease [3]. Currently, most of the drugs used for the treatment of AD are AChE inhibitors, including the synthetic compounds tacrine, donepezil, and rivastigmine, which have all been proven to improve the situation of AD patients to some extent. So far, many drugs that have been approved by the Food and Drug Administration (FDA) to treat AD in the US are like tacrine, rivastigmine (E2020), donepezil, and galanthamine, which all have some success in slowing down neurodegeneration in AD patients [4]. In this study, our goal was to generate 3D-common feature hypotheses in Discovery Studio 3.5 [5] by using some of AChE inhibitors such as donepezil, tacrine, rivastigmine, galanthamine, ambenonium, neostigmine, pyridostigmine for developing a novel AChE inhibitors. The dock pose of donepezil, which has obtained from AutoDock Vina v1.5.6 [6], has been chosen as a reference molecule to obtain pharmacophore model. Key words: Acetyl cholinesterase inhibitors, Alzheimer s disease, Pharmacophore Analyses, Molecular Docking 213

214 References 1)Goodsell D., Molecule of the Month, RSCB epub Version, doi: /rcsb_pdb/mom_2004_6, (June 20014). 2) Johnson G., Moore S.W., The carboxylesterase/cholinesterase gene family in invertebrate deuterostomes, Comp Biochem Physiol Part D Genomics Proteomics Jun;7(2): ) Elumalai K, Ali M.A., Elumalai M., Eluri K., Srinivasan S., Acetylcholinesterase enzyme inhibitör activity of some novel pyrazinamide condensed 1,2,3,4-tetrahydropyrimidines, Biotechnology Reports 5 (2015) )Chioua M., Pouplana R., Unzeta M., Samadi A., Synthesis, Biological Evaluation, and Molecular Modeling of Donepezil and N-[(5-(Benzyloxy)-1-methyl-1H-indol-2-yl)methyl]-Nmethylprop- 2-yn-1- amine Hybrids as New Multipotent Cholinesterase/Monoamine Oxidase Inhibitors for the Treatment of Alzheimer s Disease, J. Med. Chem. 2011, 54, ) Ref. Dassault Systèmes BIOVIA, Discovery Studio Modeling Environment, Release 3.5, San Diego: Dassault Systèmes, )Trott O., Olson A.J., AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, ,(2010). 214

215 PP 85 Structural Investigation Of Heterotrimeric G-Protein Alpha (Α) Subunit (Atgpa1) In Arabidopsis Thaliana Ersoy Çolak, Zehra Sayers Sabanci University, Faculty of Engineering and Natural Science, Biological Science and Bioengineering Department, Tuzla, Istanbul, Turkey. The heterotrimeric guanine nucleotide-binding proteins (G-proteins) mediate the transmission of signals from G protein coupled receptors (GPCR) to effector systems such as ion channels, enzymes and intracellular second messengers in several organisms including yeast, mammals and plants. The heterotrimeric complex is comprised of the alpha (Gα), beta (Gβ) and gamma (Gγ) subunits; Gα has GTP binding and hydrolysis activity, and Gβ and Gγ interact with downstream effectors as a dimeric complex. Although the complete structure and activation mechanism for the mammalian complex are known in detail, these are still controversial for plants. Plant heterotrimeric G-proteins have been shown to be involved in multiple physiological processes, such as regulation during development of leaf shape, cell proliferation, lateral root formation, stomatal density as well as control of the post germination process. In order to elucidate the activation mechanism in plants and for a better understanding of the G- protein-mediated molecular pathways, a structural investigation of the Arabidopsis thaliana complex has been undertaken [1,2]. In this study, biochemical and biophysical characterization of the full length wild type (WT) of A.thaliana G alpha subunit (AtGPA1) and structural analyses mainly based on synchrotron radiation data are presented.. AtGPA1 had been cloned and expressed in Pichia pastoris [1]. The recombinant protein is purified by various chromatography techniques and nucleotide (GTP, GDP, GTPγS) binding is determined by absorbance spectroscopy. The level of oligomerization of GPA1 is studied by Dynamic Light Scattering (DLS). The secondary structure elements and its thermal stability are determined by Circular Dichroism Spectropolarimetry (CD). These results show the tendency of GPA1 to remain in solution in trimeric form and also indicate an extended open structure for the protein. Recently Small Angle X-ray Scattering (SAXS) data, batch and in-line, were also collected at the P12 beamline of EMBL on PETRA, DESY, Germany. These data will provide information on levels of oligomerization and help to develop molecular shape models. Combined results will provide insight into the 3D structure of WT GPA1 in solution and will help to elucidate if the structural basis for the proposed activation mechanism, which is based on the crystal structure of a truncated GPA1, is reliable [3] 215

216 Keywords : Heterotrimeric G protein, G protein alpha subunit, Recombinant protein, Small Angle X-ray Scattering *We acknowledge support from Turkish Atomic Agency for SAXS measurements at EMBL Hamburg Outstation, DESY, Germany. [1] B. Kaplan (2009), Structural Investigation of G-Protein Signaling in Plants. PhD Thesis Sabanci University. [2] A. Aktürk (2012), Characterization of A.thaliana G-proein Gamma Subunit (AGG2) and Investigation of DTT Effect on Oligomeric State. Master Thesis Sabanci University. [3] J. C. Jones, J. W. Duffy, M. Machius, B. R. S. Temple, H. G. Dohlman, and A. M. Jones (2011) The crystal structure of a self-activating G protein alpha subunit reveals its distinct mechanism of signal initiation. 216

217 PP 86 Effect Of Protein-Ligand Interactions On Vibrational Dynamics Of Triosephosphate Isomerase Doga Findik, a Zeynep Kurkcuoglu, a Ebru Demet Akten, b and Pemra Doruker a a) Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul b) Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey The effect of ligand binding on global vibrational modes of an enzyme, triosphosphate isomerase (TIM) was investigated using mixed coarse-grained elastic network model (MCG_ENM) 1. For this aim, the average shifts in the lowest mode frequencies of the enzyme were obtained by comparing the ligand bound and removed conformers. First analysis was performed on blind docking poses of five benzothiazoles, three of which are inhibitors of TIM s catalytic activity. Several different binding sites were detected including the tunnel region, catalytic site and others. The inhibitors bound to the tunnel region at the subunit interface could be differentiated based on their impact on global vibrational modes of the enzyme. Later, six independent MD runs (three apo and three complex with inhibitor bt10) were analyzed by performing MCG_ENM on a total of 54,000 MD snapshots of TIM. Through this computationally efficient technique, altered collective modes and positive shifts in eigenvalues were detected in the complex runs due to the constraining effect of inhibitor binding at the tunnel region. Resources: 1) Kurkcuoglu, O., O. T. Turgut, S. Cansu, R. L. Jernigan and P. Doruker, \Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model", Biophysical Journal, Vol. 97, No. 4, pp. 1178{1187,

218 PP 87 Structural Characterization Of Peptide Binding To Class I MHC Proteins Using Protein Energy Networks From Molecular Dynamics Simulations Onur Serçinoğlu, Pemra Özbek Sarıca Department of Bioengineering, Marmara University, Goztepe, Istanbul, Turkey The Class I Major Histocompatibility Complex (MHC) is a heterotrimer consisting of a heavy chain (Human Leukocyte Antigen, HLA), a light chain (β-2-microglobulin, β2m) and a peptide epitope which originates from the proteolytic degradation of self or foreign proteins in the cell. The complex presents the bound peptide to the T-cell receptor in an event determining the initial step in the activation of the adaptive immune response. In humans, HLA chain displays a very high level of polymorphism to account for the enormous number of possible peptide sequences. Understanding the structural details of peptide binding mechanisms and dynamics may help in the prediction of immunogenic epitope sequences. It is known that the polymorphic region of the HLA (α-1 and α-2 domains) directly affects the peptide repertoire of HLA alleles via contacts made with anchor residues of the peptide1. However, long range interactions between peptide and heavy chain residues2 as well as contacts made with β2m3,4 were also shown to play a role in peptide binding. In this work, we studied the effect of β2m on peptide binding dynamics of two HLA-B27 alleles which are differentially associated with the Ankylosing Spondylitis disease. Four peptides, which have differing binding affinities2, were taken into account in duplicate 50 nanoseconds Molecular Dynamics simulations in the absence/presence of β2m and α-3 domains. Using Root Mean Square Fluctuation calculations and a method based on the construction of Protein Energy Networks (PEN) from correlated interaction energy changes between amino acid residues5,6, we demonstrate the existence of allele- and peptide-dependent energy interaction pathways which connect peptide residues to β2m residues. Resources: 1. Batalia MA, Collins EJ. Peptide binding by class I and class II MHC molecules. Biopolymers. 1997;43(4): doi: /(sici) (1997)43:4<281::aid- BIP3>3.0.CO;2-R. 2. Narzi D, Winkler K, Saidowsky J, et al. Molecular determinants of majör histocompatibility complex class I complex stability: shaping antigenic features through short and long range electrostatic interactions. J Biol Chem. 2008;283(34): doi: /jbc.m

219 3. Winkler K, Winter A, Rueckert C, Uchanska-Ziegler B, Alexiev U. Natural MHC class I polymorphism controls the pathway of peptide dissociation from HLA-B27 complexes. Biophys J. 2007;93(8): doi: /biophysj Ostermeir K, Springer S, Zacharias M. Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations. Mol Immunol. 2015;63(2): doi: /j.molimm Bhattacharyya M, Vishveshwara S. Probing the allosteric mechanism in pyrrolysyl-trna synthetase using energy-weighted network formalism. Biochemistry. 2011;50(28): doi: /bi200306u. 6. Ribeiro AAST, Ortiz V. Determination of Signaling Pathways in Proteins through Network Theory: Importance of the Topology. J Chem Theory Comput. 2014;10(4): doi: /ct400977r. 219

220 PP 88 Some Triazine-Benzothiazole Derivatives Induces Cytotoxicity And Apoptosis On A549 Lung Adenocarcinoma Gülşen Akalın Çiftçia, Bahar Demira*, Leyla Yurttaşb, Halide Edip Temela, Begüm Nurpelin Sağlık b a Anadolu University, Faculty of Pharmacy, Department of Biochemistry, 26470, Eskişehir, Turkey b Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey Triazine derivatives and benzothiazoles show antitumor activities. Certain azanucleosides, 6-azauracil and 6-azacytosine), structurally based on 1,2,4-triazine nucleus have displayed an impressive array of biological activities, among which antitumor, antiviral, antimicrobial, anti-inflammatory, antiplatelet, antimalarial, and antifungal properties1. It s known that thiazoles have also different biological activities including anticancer effect2. In this study, we aimed to investigate the cytotoxic and apoptotic properties of series of novel 1,2,4-triazine derivatives bearing benzothiazole moiety against lung adenocarcinoma cell line (A549 cells) which used in our studies. The cytotoxic activities of the tested compounds were determined by cell proliferation analysis using standard (3-(4,5- dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) assay. Apoptosis analyses were performed using BD Pharmingen Annexin V-FITC/PI apoptosis detection kit I, according to the manufacturer s instruction. All measurements were performed on a FACS ARIA I cell sorter flow cytometer3. The IC50 values of the compounds were determined for A549 cells. Benzothiazole including compounds and 6- methylbenzothiazole moieties (LN2), had significant cytotoxic activities and their IC50 values were obtained 10 μg/ml. Second compound (LN3) showed the highest cytotoxic activity with a IC50 value of 5μg/mL, whereas Cisplatin IC50 values were 2.5 μg/ml against A549 cells. Also apoptotic effects of LN2 and LN3 on A549 cells were determined using flow cytometer. Advanced mechanistic studies are still under investigation in our laboratory. Our study results demonstrated that synthesized compounds LN2 and LN3 had considerable anticancer activity against A549 cells compared to Cisplatin. On the other hand LN3, namely 2-[(5,6-diphenyl-1,2,4-triazin-3- yl)thio]-n-(6-methylbenzothiazol-3-yl)- acetamide, has the most anticancer compound against the A549 cell line. References: 1) Yurttas et.al., Bioorg Med Chem Nov 15;22(22): ) Shi et al. Molecules 2012, 17, ; 3) Yurttaş et al. Arch Pharm (Weinheim). 2013, 346(5),

221 PP 89 The Transfer Of Aminoacids to the Plant through Irrigation Water and the Use Of Plants in the Depression Disturbance Gümüş Funda Gökçea, Haydar Göksua Kaynasli Vocational College, Düzce University, Düzce 81900, Turkey Amino acids which include carboxylic acid within their structure show a water-soluble characteristic because of their structural properties although they are organic molecules. That the water solubility of amino acids which are important components for human body is quite good plays an important role in these organic molecules having a wide usage area in the field of agriculture. Amino acids are used in pollination, fructification and organization of nitrogen metabolism in plants during their stress periods.1 In this study, as amino acids, cysteine, tyrosin, histidine, arginine was used. The aminoacids, anionic and cationic plant nutrient elements are to be procured to transfer from the earth to the plant or from the plant to the earth. While amino acids provide the metabolic track in the plant and the earth to be in balance by activating/inhibiting enzymes, with the purpose of meeting the body need, nutrients rich in protein are produced at the same time.for example, tyrosine received from irrigation water of cucumbers and bean, it is an aminoacid required by the human body. The tyrosine, through the method in the study from any desired plant it can be met. Particularly tyrosine is converted to noradrenaline in the human body. Noradrenaline is a neurotransmitter which needed in depressive disturbance (Scheme 1).2,3 Scheme 1 221

222 Resources: 1) a)hudaky, P., Beke, T., Perczel, A., Journal of Molecular Structure (Theochem), 2002, 583, b) Dinakar, C., Djilianov, D., Bartels, D., Plant Science, 2012, 182, ) Uguz, S., Yurdagul, E., Klinik Psikiyatri, 2002, ) Brunello, N., Mendlewicz, S., Kasper, S. ve ark., Eur Neuropsychopharmacol, 2000, 12(5),

223 PP 90 Determination Of Antigenic Epitopes Of Her2 Protein By Using Bioinformatic Tools To Develop A DNA Vaccine Immunotheraphy Model Against Her2 Positive Breast Cancer Muge Anil a, Esra Atalay Sahar b, Huseyin Can b, Mert Doskaya c, Sultan Gulce Iz a* A Ege University, Faculty Of Engineering, Department Of Bioengineering, Bornova/Izmir, 35100, Turkey B Ege University, Faculty Of Science, Department Of Biology, Molecular Biology Division, Bornova/Izmir, 35100, Turkey C Ege University, Faculty Of Medicine, Department Of Parasitology, Bornova/Izmir, 35100, Turkey Her2 (human epidermal growth factor receptor 2) is a surface receptor exists approximately %25 of all breast cancers also its expression increases in a wide range of epithelial-based tumours. Her2 has an extracellular domain (ECD), which is the target of B cell antibodies and monoclonal antibody therapies like Trastzumab and Pertuzumab. The aim of this study is to determine the MHC-I and B cell epitopes of Her2 ECD for development of a DNA vaccine model which can be classified as an immunotherapy strategy that uses patient s self immune system to control Her2 over-expressing breast cancers. For this purpose, Her2 ECD was thoroughly analysed to determine immunogenic epitopes. MHC-I epitopes were determined by using IEDB (Immunoepitope Database and Analysis Resource), B cell epitopes were determined by using SVMTriP (Support Vector Machine, Tri-peptide similarity and Propensity scores). The antigenic epitopes that will be used in the DNA vaccine construct were determined both in human and murine immune systems for the reason of the fact that the DNA vaccine model will be evaluated in mouse model for pre-clinical studies and may be used in human clinical trials if the epitopes are promising enough to stimulate strong immune responses to eradicate the tumour. For analysing peptides binding to MHC class I molecules in human immune system, HLA- A*02:06, HLA- A*31:01, HLA-B*35:01, HLA-B *54:01 alleles 2 whose have 14 amino acid length and percentile ranks equal to or lower than 1 were used as setting parameters. For analysing peptides binding to MHC class I molecules in murine immune system, all mouse alleles were used at the same settings as humans. As a result, 7 different highly antigenic epitopes having 80 or higher percent similarity in sequence in both immune systems were selected for using in the multiepitope DNA vaccine construct which therapeutic and prophylactic effects will be evaluated in Her2 over expressing breast cancer murine models. 223

224 Resources: 1) Dissanayake, D., Murakami, K., Tran, M.D., Elford, A.R., Millar, D.G., Ohashi, P.S., PLoS ONE, 2014, 9(3): e doi: /journal.pone ) Tsuda, B., Kametani, Y., Goto, Y., Saito, Y., Suzuki, Y., Habu, S., Inoko., H., Tokuda, Y.; Vaccines & Vaccination. 2012, 3(7): doi: /

225 PP 91 Molecular Dynamics Simulation Of Water Transport Through Charged Carbon Nanotubes İn An Electric Field Seifollah Jalilia,b and Mojdeh Akhavanb adepartment of Chemistry, K. N. Toosi University of Technology, P.O. Box , Tehran, Iran bcomputational Physical Sciences Research Laboratory, School of Nanoscience, Institute for Research in Fundamental Sciences (IPM), P.O. Box , Tehran, Iran In this research we have investigated a water transport systemusing molecular dynamics simulations. (10,0) zigzag and (6,6) armchair carbon nanotubes with a length of ~14 Å have been used as a channel for water flow. The effects of partial atomic charges, calculated using quantum mechanical methods, together with electric fields with various strengths have been taken into the account. Figure 1 shows a schematic diagram of simulated systems. Figure 1. The Simulation box for water transport through carbon nanotubes. Table 1 shows that with the increase in electric field strength, the capacity of nanotubes for water molecules and the water dipole orientation in the nanotube is strongly modified. The flow rate of water in nanotube also depends on electric field strength. The inclusion of partial charges for carbon nanotube reduces the capacity for water molecules, but the frequency of water dipole reorientation in charged nanotubes is much higher in the presence of electric fields. 225