PHCO 701 Short title Molecular Pharmacology Long title Introduction to Molecular Pharmacology

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1 PHCO 701 Short title Molecular Pharmacology Long title Introduction to Molecular Pharmacology Effective term Fall Course units/hours 3 credit hours M/W/F 9:00am-9:50am in 4007 Genetic Medicine Bldg. Grading basis (GRAD H,P,L, F) Course Component (lecture or lab) lecture Course Description This is a graduate-level first year course outlining the basics of molecular pharmacology, including molecular biology, bioinformatics, drug/receptor interactions, receptor and ion channels, regulation of second messengers, drug metabolism and system pharmacology. Permission of the instructor required for registration. Three credit hours a week. Course objectives (learning outcomes): The objectives of this course are to provide graduate students in biomedical research programs familiarity with the molecular principles of pharmacology involved in the design and action of drugs. Students will increase critical thinking skills in the context of the specific topics listed in the syllabus, which includes molecular biology underlying drug development, key drugable pathways and the interactions between drugs and human body. By the end of this course students should be familiar with molecular principles of drug development including knowledge of gene expression pathways related to drugs, key drugable targets and the interaction between drugs and their receptors. Students should have working knowledge sufficient to apply those principles to new research topics and to propose appropriate strategies to solve relevant research questions. Course Assignments Reading assignments may be posted by the individual instructors and will be a combination of review articles, research papers of seminal importance to the field, and recent research articles of significant impact. There may be written assignments, including quizzes/homework and short essay-style exams designed to test both the assimilation of the readings and the application of principles to new scientific scenarios posted by individual instructors. Assessments Achievement of course objectives and individual student grades will be determined from one take home project and two in-class exams at the end of each of three modules. By the end of the course, the students should have a good understand the principles of drug development and able to use the tools and knowledge introduced in the course in a new scientific questions related to drug actions. The students should also demonstrate a working vocabulary in the field and have a working knowledge of the pharmacologic principles.

2 Syllabus DRAFT PHCO 701 Introduction to Molecular Pharmacology Fall Semester 2014 Course Director: Zefeng Wang Monday/Wednesdays/Fridays 9:00-9:50 AM, 4007 Genetic Medicine Bldg. Topic Lecture hours Block Leader I. Genes to Protein/Molecular Biology 13 Zefeng Wang II. Drugable molecular pathways 10 Lee Grave III. Principles of Drug/Receptor Interactions 10 Terry Kenakin IV System pharmacology 7 Tim Elston I. Genes to Protein/Molecular Biology W Aug. 20 Intro. to Course / Molecular Biology and Bioinformatics I : Genes and Genomes (Zefeng Wang) Cover the basics of gene expression and its regulation, introduce the common databases for DNA/RNA/protein sequence, and how to mine the data F Aug 22 Molecular Biology and Bioinformatics II: Gene Expression and new sequencing technology (Zefeng Wang) Continue on data mining, database of regulatory elements, and introduction on the new techniques for genomic biology. High throughput sequencing, CHIP-seq, RNA-seq ect. M Aug 25 Basic statistics or algorithms in bioinformatics (Shawn Gomez) Cover the statistic aspect of genomics, hypothesis testing, multiple comparison. May use microarray and next generation sequencing data as examples. W Aug 27 Gene expression analysis (Shawn Gomez) Cover the statistic aspect of genomics, hypothesis testing, multiple comparison. May use microarray and next generation sequencing data as examples. May cover related topic like gene ontology analysis? F Aug 29 Protein expression, Purification and Structure Determination (Michael Miley) Also need to cover the basics concept and technology of protein translation

3 (e.g. codon optimization) M Sept. 1 Labor Day - NO CLASS W Sept 3 Bioinformatics III: Proteins structure database /PDB search and visualization/ Structural Bioinformatics (Michael Miley) F Sept. 5 Gene Manipulation techniques /Macromolecular Therapeutics (Zefeng Wang) Cover the basic method to manipulate gene expression, like gene cloning, over expression, antisense technology. M Sept. 8 W Sept 10 Non-coding RNA (Mauro Calabrese) Transcriptional Regulation as a Therapeutic Target (Zefeng Wang) Including the common database for transcriptions, TALE, ZNF W Sep 10 F Sept. 12 Student Project assigned. Post-transcription of gene regulation (Zefeng Wang) Regulation of splicing, non-coding RNA function, RFAM database M Sept. 15 Genetic screen (RNAi screen and phenotype analysis) (Gary Johnson) W Sept. 17 Student Project Presentation (group 1 and 2) F Sept. 19 Student Project presentation (group 3 and 4) II. Drugable molecular pathways (Receptors/ Ion Channels and Regulation of Second Messengers) M Sept. 22 Overview of signal transduction (Lee Grave) Kinase database W Sept. 24 F Sept. 26 M Sept. 29 W Oct. 1 F Oct. 3 Chemical genetics and (Bryan Roth) Neuroreceptor and Neuropharmacology (Bryan Roth) Receptor Tyrosine Kinases (Lee Graves) Activation of PKA by camp, regulation of camp by cyclase and PDEs. (L. Graves) Cell cycle regulation (Michael Emanuele)

4 M Oct. 6 W Oct. 8 F Oct. 10 M Oct.13 Ion Channels (T. Kash) Activation and inactivation of Ras-family GTP binding proteins (C. Der) GPCRs (Henrik Dohlman) Activation and inactivation of G proteins (includes RGS proteins); Introduction to effectors and second messengers (H. Dohlman) W Oct.15 F Oct 17 M Oct. 20 Calcium: its regulation and its targets (Ken McCarthy) FALL BREAK (NO CLASS) EXAM II (In-class: 8:00AM 9:50AM) III. Principles of Drug/Receptor Interactions and Drug Metabolism W Oct. 22 F Oct 24 M Oct 27 W Oct 29 Drug receptor interactions (T. Kenakin) Drug receptor interactions-introductions (T. Kenakin) Drug receptor interactions (T. Kenakin) Drug receptor interactions (T. Kenakin) Will include use of common software and web tools F Oct 31 M Nov. 3 W Nov. 5 F Nov. 7 M Nov. 10 W Nov. 12 Drug Metabolism I (J. Sondek), including common web-tools and database Drug Metabolism II (J. Sondek) Pharmacokinetics I (K. Hahn) Pharmacokinetics II (K. Hahn) Pharmacokinetics III (K. Hahn) EXAM III (In-class: 8:00AM 9:50AM) IV System pharmacology F Nov 14 Tim Elston) Introduction of system biology and implication on drug development (Bryan Roth/

5 M Nov. 17 Modeling of Cell Signals/system biology/ polypharmacology (Tim Elston/ T. Kenakin /Shawn Gomez/ Denis Tsygankov) W Nov. 19 Modeling of Cell Signals/system biology/ polypharmacology (Tim Elston/ T. Kenakin /Shawn Gomez/ Denis Tsygankov F Nov. 21 M Nov 24 M Nov 24 W Nov 26 F Nov 28 Data aquisition by imaging analyses I (Denis Tsygankov) Novel microscopic technologies and common software Data aquisition by imaging analyses II (Denis Tsygankov) Applications with live cell analysis and reporter Student project assigned Thanksgiving BREAK (NO CLASS) Thanksgiving BREAK (NO CLASS) M Dec 1 Student Project Presentation (group 1 and 2) W Dec. 3 Student Project Presentation (group 3 and 4)

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