CASE STUDY THE MEDICINAL CHEMISTRY LABORATORY AT THE UNIVERSIDAD COMPLUTENSE DE MADRID ADOPTS DOTMATICS ONE-CLICK ELN TO ENHANCE CHEMISTRY RESEARCH
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1 CASE STUDY THE MEDICINAL CHEMISTRY LABORATORY AT THE UNIVERSIDAD COMPLUTENSE DE MADRID ADOPTS DOTMATICS ONE-CLICK ELN TO ENHANCE CHEMISTRY RESEARCH
2 The starting point Chemistry research is 1% inspiration and 99% perspiration, who said that? Is it time to capture inspired ideas as well as hard work in an electronic format so not to repeat experiments or reworked ideas that didn t go according to plan? Those were the thoughts that concerned Prof Dr Maria Luz Lopez-Rodriguez and Prof Dr Silvia Ortega-Gutierrez, two experienced researchers based at the Medicinal Chemistry Laboratory (MedChemLab), Universidad Complutense de Madrid. The group s research is focused on the synthesis, development and preliminary biological testing of new drug candidates and the validation of novel targets. MedChemLab scientists complement the design of new chemical entities (NCEs) with computational techniques in order to estimate and optimise the pharmacological properties of the new compounds before going to the laboratory. Decisions regarding what compound should be synthesised are made based on: - previously known information from references - predictions of pharmacological properties - ease of synthesis - availability of materials - previous experience from the scientists In this context, it is important for scientists to be able to record, search and analyse: (a) all known information from references and from their previous experience, (b) in-silico results, (c) experimental designs, and (d) actual outputs from the experiment including spectra and images. In addition, Information Technology (IT) resources including personnel and infrastructure are limited within many academic organisations. As such, implementing an informatics platform to take care of the data management needs of a laboratory must have minimal impact on the IT department. All these factors were considered during the decision making process when selecting an ELN to capture and report MedChemLab s activities. Fortunately, ELN technologies have matured over the past few years and there are now flexible, low-cost, easy to use, cloud-hosted systems available which fulfil academic needs perfectly. The MedChemLab implemented the Dotmatics One-Click ChemELN in order to address these requirements.
3 We wanted to streamline our experimental data gathering process, increase accessibility to current and historical data, and standardise the quality of data stored so we evaluated different options in the market. We talked to Dotmatics and explored the different options that they could provide. We established that the One- Click ELN was perfect for our needs and cost effective too, said Prof Ortega- Gutierrez. The Dotmatics Platform is flexible and offers scientists various options: from a simple, preconfigured, out-of-the- box ELN to a more flexible and feature-rich comprehensive informatics solution. The selection of the final solution will always depend on budget and final requirements. The out-of-the-box solution is called One-Click and can be deployed in a University within a matter of minutes. It is a standardised and simplified version of the more comprehensive Dotmatics Platform. The configuration covers typical chemistry and biology workflows. One-Click is available in the cloud, where users can easily store, retrieve and share their data in a secure way, without any IT burdens. The system comes with a set of self-training videos that can be accessed by users at their convenience, thus ensuring the proficient and easy adoption by all users. Dotmatics solutions are powered by Amazon Web Services (AWS). AWS provides end-to-end security and privacy to its customers through its secure infrastructure. The One-Click ELN replaced our paper notebooks and simplified the need to cut and paste printed spectral and other information into the old style notebooks. It has increased our research efficiency and supports our need for an effective way of handing over data from one generation of students to the next, said Prof Ortega- Gutierrez. It is extremely simple to use and data can be found and reported very easily. We were able to roll out the system to the whole team within just a few hours.
4 Figure 1: The MedChemLab team data input process Storing data: no longer an art and crafts job The workflow at the MedChemLab is clear and it includes the design of New Chemical Entities (NCE), experimental design, synthesis, and testing. NCEs are designed based on scientists previous experience or bibliographic research in addition to some predicted properties (such as ADME(T) properties) that are calculated to minimise the risk of synthesising non-drug-like compounds. Most of our data is captured on the One-Click. We did an initial test that was very valuable and clarified our questions in regards to the adoption of the system by the team members. We started simply by capturing our initial reactions, stoichiometry and related experimental information. Now we are adding references and additional documents to ensure that no data is ever lost, said Prof Ortega-Gutierrez. We aim to develop good practices within the team in order to preserve the maximum amount of data to ensure that experiments are not duplicated unnecessarily, that new members of the team can understand the context of a project quickly, and that no potential drug candidates are missing. Figure 2: Reaction input on the One-Click ELN
5 Retrieving data: never repeat an experiment unnecessarily It is difficult to quantify the value of implementing an ELN until one of the following happens: you try to find an experiment that was done a few years back you synthesise a compound without realising that was done already you need to find all the reactions made with a particular reagent you try to update a new member of your team with all of the information you try to duplicate an experiment and you only need to change a few variables but realise that you must re-write the whole reaction by hand you are writing a manuscript for publication and cannot easily find the experimental data It is in these moments that a scientist wishes that he/she had an ELN solution where experiments could easily be searched, cloned and shared, saving countless hours and money. An ELN will minimise the risk of missing valuable information in the mist of large routine research data. The One-Click ELN has a preconfigured search form that enables users to easily access past information, aggregate it, and create reports. This form looks and feels similar to the one used in the data input however, it enables users to retrieve all of the information related to a compound, project or a result type with only a few clicks. Figure 3: The MedChemLab team can retrieve and report all information stored in the system easily The value of the information captured about a compound, a reaction or an experiment is now maximised because it is searchable, accessible, reusable, and
6 shareable. One of the great advantages is that it ensures that experiments are not repeated unnecessarily, simply because they have gone missing amongst a large amount of paper notebook pages. Now, I am able to access experimental information live from wherever I am. This makes the writing of papers much more straightforward. In addition, if new members join the team they can simply browse through past experiments and get up to speed with a particular project very quickly, said Prof Lopez-Rodriguez. Sharing, Security, IP protection and the ability to review notebooks when time permits Today, university laboratories work very closely with industry partners and other universities. Sharing information, sometimes in real-time, is essential to the smooth running of collaborative projects. In addition, the information must be secured so it cannot be misappropriated or misused by third parties. Fortunately, cloud systems are now well-established, secure environments for collaboration. There are many systems that do that for different purposes such as Dropbox, icloud, Salesforce, etc. The One-Click ELN is the ideal virtual space for sharing and collaborating around a particular project. Using the ELN, administrators are able to inforce who can access the project and who cannot. Finer levels of security granularity are available on more advanced Dotmatics systems. Furthermore, a laboratory notebook is an important tool that goes well beyond research management and can have important implications for issues ranging from intellectual property management to the prevention of fraud. We decided that all researchers from our group should access, store and search their own notebooks and, in addition, they should be able to see the work of other members of the team. In that way, they can learn from each other much quicker and avoid the repetition of mistakes. Supervisors can see and review all ELNs allowing us a global view of the project. Having to supervise multiple researchers implied that I had to look at several notebooks at the same time which, at times, could be quite time consuming. In addition, busy travelling schedules could delay the review of paper notebooks for a while. Because the system is in the cloud and it is easily accessible, I can now review and countersign experiments wherever I am, which means that students and researchers don t need to wait long periods of time to close an experiment and publish the subsequent results, said Prof Lopez- Rodriguez.
7 Conclusions In short, ELNs are increasingly becoming a key tool on a scientist s tool belt. They safeguard laboratories experimental information, design, annotation and help to optimise resources, including equipment down time, consumables and scientists time. They play a key role in collaborative projects and guarantee real-time data access at all times. In the MedChemLab, the One-Click ELN helps to record new reactions, develop new chemical entities, and enhance collaboration amongst team members and external partners. Live access to research data helps us to eliminate redundancy whilst optimising resources, concluded Prof Lopez-Rodriguez. The implementation of new good practices will ensure that we explore new ideas in a consistent and focused manner without spending any time on avenues that were already explored previously. Biographies Prof María Luz López Rodríguez María Luz López Rodríguez studied Chemistry and obtained her PhD from Universidad Complutense de Madrid (UCM). After a postdoctoral stay in the Sloan Kettering Institute and Florida University (USA) with a Fulbright Grant, she joined the Department of Organic Chemistry at UCM where she started her independent career as the leader of the Medicinal Chemistry Laboratory. In 2004 she was promoted to Full Professor of Organic Chemistry in this University, position that currently holds. Her research is focused on the Medicinal Chemistry and Chemical Biology fields, including the design and development of small molecules in challenging therapeutic targets related to cancer and central nervous system as well as the development of chemical platforms for the identification of new therapeutic targets. She has published 129 original research articles in prestigious journals (Science, Nature Neuroscience, J. Neurosci., Clin. Cancer Res., Mol. Pharmacol., J. Med. Chem., J. Am. Chem. Soc., Angew. Chem. Int. Ed., J. Biol. Chem, J. Allergy Clin. Immunol...) and she is an inventor of 13 patents in current exploitation by the pharmaceutical industry. In addition to this research profile, during her academic trajectory she has supervised 23 PhD students and trained numerous postdoctoral researchers. She is also Associate Editor of different journals in the Medicinal
8 Chemistry field and has received the Medal of the Royal Academy of Medicine (2011) and the Award in Excellence Research (Spanish Royal Society of Chemistry, 2014). Prof Silvia Ortega Gutiérrez Silvia Ortega-Gutiérrez obtained her PhD degree in Complutense University, in Madrid, working under the supervision of Prof María Luz López-Rodríguez in the field of Medicinal Chemistry. After that, she joined Prof Ben Cravatt s lab at The Scripps Research Institute (California, USA) to work in the field of Chemical Biology and Proteomics with a Fulbright Fellowship. Between 2008 and 2012 she was Ramón y Cajal Scholar in the Organic Chemistry Department at Complutense University where she was promoted to Associate Professor in 2013, position that she currently holds. Her areas of interest are medicinal chemistry and chemical biology and, in particular, the fields of the endogenous cannabinoid and lysophosphatidic acid systems, the validation of new targets in cancer and the development of chemical probes for the study of G protein-coupled receptors. Her work has been published in prestigious journals including Science, Nature Neuroscience, Angewandte Chemie and the Journal of Medicinal Chemistry, and also in patents that have been transferred to the pharmaceutical industry. In 2011 she received the Runner-up Prize for a Young Medicinal Chemist in Academia by the European Federation of Medicinal Chemistry and in 2012 the Young Researcher Award by the Spanish Royal Chemical Society.
9 ABOUT DOTMATICS: At the forefront of innovation, Dotmatics is a leading global scientific informatics software and services provider, delivering solutions tailored to the modern, highly collaborative and mobile pharmaceutical, biotechnology and chemical industries as well as academia. Dotmatics enterprise solutions are flexible, scalable and configurable, providing effective scientific information management across entire organizations, from discovery research to development and early manufacturing. Dotmatics has significant expertise in scientific informatics, including database management for chemistry and biologics, electronic laboratory notebooks, chemical and biological registration, screening data management, SAR analysis, reporting, and visualization. Dotmatics solutions are available for local or cloud deployment and they are supported on Microsoft Windows, Mac OS X and Linux. A privately owned company, Dotmatics was founded in 2005 and their headquarters is based south of Cambridge in the UK. Dotmatics Limited The Old Monastery, Windhill Bishops Stortford, CM23 2ND United Kingdom Tel: +44(0) marketing@dotmatics.com Dotmatics Inc Sorrento Valley Road San Diego, CA USA Tel: Dotmatics Inc. 800 West Cummings Park Woburn, MA USA Tel:
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