Open Source Drug Discovery
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CSIR-Open Source Drug Discovery (OSDD) is a translational platform for drug discovery for neglected tropical diseases [1] [2] [3]. This CSIR-led program has a global community with over 7300 participants from 130 countries comprising of researchers, academia, students, industries, educational institutions and so on [4] [5]. Anyone who is committed to the discovery of drugs for neglected diseases in an open source mode can participate in the program. OSDD functions by bringing together experts from diverse backgrounds to focus on discovering and developing affordable drugs for tropical infections like Tuberculosis, Malaria and Leishmaniasis, which draw limited attention of research, based pharmaceutical enterprises.
History
CSIR-OSDD was launched in September 2008 and is based on the three cardinal principles of “Collaborate, Discover and Share”. This project was conceived by Prof Samir K Brahmachari, the Founder Director of CSIR-Institute of Genomics and Integrative Biology as a 11th Five year plan project of CSIR. This was approved by the Government of India with an overall outlay of Rs 45.96 crores (about $12 million).
The project motto is “Affordable healthcare for all” and makes use of open source philosophy, crowd –sourcing concepts and a collaborative research model, capitalizing on web based tools to fuel innovation and discover novel therapies. All the data and resources generated by the community are openly shared through a web based portal called Sysborg 2.0 specifically designed for this purpose. The community had adopted a unique healthcare model that blends together the policies of patenting and innovative open source research and aims make novel drugs available as generic drugs, without Intellectual Property encumbrances to ensure affordability and accessibility.
Funding
The core funding of OSDD is from the Government of India. For the period of September 2008 to March 2012, Government of India had earmarked Rs 45.96 crores (about $12 million) for the project. The funds are used for funding the scientific projects, setting up infrastructure, and supporting ongoing activities of the project. . Up to 2012, OSDD was a project under ‘National Laboratories Scheme’ of CSIR. For the 12th five year plan during 2013-2017, the plan-ning commission has approved the continuation of OSDD as a part of Scheme for Open Innovation of CSIR.
Achievements
The OSDD platform has successfully demonstrated the following:
An Alternate Innovation Model
OSDD offers an innovation model wherein the collaborative approach reduces levels of risk associated with early stage of drug discovery. It advocates public funding of clinical trials to share the risk in the clinical development. In return OSDD ensures that these molecules are available on non-exclusive basis to patients offering a sustainable innovation model for diseases without market.
Making Open Source Drug Discovery Work
Though, there have been few initiatives in open source, none has progressed the way in which OSDD has progressed. OSDD has demonstrated that Open Innovation can work in the field of pharmaceuticals, and a workable model for drug discovery. OSDD has been established as a CSIR led team India consortium with global partnerships
Development of Science 2.0 Portal
OSDD brought Science 2.0 to drug discovery. Its scientific portal has a semantic search facility with an RDF data store. It seamlessly integrates social networking with various steps of implementing scientific projects in drug discovery. This portal thus connects complementary expertise in order to facilitate projects demanding varied skill sets and infrastructure. This portal was developed in collaboration with the IT giant Infosys and has been published as a chapter in the book Collaborative Computational Technologies for Biomedical research, published by Wiley, US .
Dovetailing Process Driven Activities to Innovation Activities
OSDD has demonstrated that the highly process driven activities in drug discovery can be integrated into an immensely creative innovation driven crowd sourced early stage discovery process. This is best exemplified by SysBorg a collaborative portal developed free of cost by Infosys in collaboration with OSDD Scientists.
Open Peer-review
Contrary to the conventional peer-review processes of grants which are anonymous and confidential, OSDD follows an open peer-review process to bring transparency and foster collaborations. Any project that needs support for infrastructure or funds is posted online on Sysborg portal. This allows the community to review the project right from its inception and give feedback. This has the potential to improvise study design and approach and is expected to reduce failures. It also gives an opportunity to identify collaborators and resources from the community. The comments of the reviews are open for anyone to see and comment and the project(s) are funded after open peer-review. It is for the first time that such an open peer-review process has been established for funding research projects.
Crowd Sourced Model as a New Paradigm in Science
OSDD demonstrated that large complex scientific problems which need enormous manpower and effort can be managed by utilising large distributed community for purposeful activity maintaining the quality, in effect a crowd sourced model. The OSDD community has published Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis. PLoS One. 2012;7(7):e39808.
Development of Resources for the Scientific Community
OSDD has developed and provided the following online community resources to facilitate drug discovery projects
- IPW- The largest manually curated interactome of M tb that can be searched for interacting partners
- TBrowse - Largest integrative genomic resource on Mtb H37Rv
- CRDD - Comprehensive Resource for Drug Discovery
- OSDDChem - Database of molecules with possible anti-TB properties
- MetaPred - Predict Cytochrome P450 isoform responsible for drug metabolism
- KetoDrug - Binding affinity prediction of ketoxazole derivatives against FAAH
- KiDoQ - Docking energy score based prediction of antibacterials
- GiDoQ - Prediction of GLMU inhibitors using Autodock and QSAR
- ccPDB - Compilation and creation of datasets from PDB
Open Access Repositories
Biological research often require access to physical biological materials to carry out research activities. OSDD has set up open access repositories to facilitate such access possibly for the first time in a drug discovery endeavour. These are:
a.A Biological Repository of Strains, Clones etc. b.A Chemical Repository of Small Molecules c.Open Access Screening Facility
Large Scale Screening of Compounds in Open Mode
OSDD has screened more than 20,000 Chemical Compounds against Mtb out of which about 40 compounds have been identified for further development. This is probably one of the largest screening of molecules against TB ever done in India by a public research institutions.
Engagement of Private Partners
OSDD demonstrated that private partners can be actively engaged in open source approach and that intellectual property issues will not hamper such collaborations of open source projects and private sector. OSDD is currently lead optimising two molecules with two different private partners, who are renowned contract research organisations (CROs). It also engaged IT industry giants like HP, Infosys, etc.
Attracting Wetlab Scientist to Open Source
OSDD has shattered the myth that wet lab scientists will not participate in open source collaboration. OSDD has integrated the in silico or computer based approaches with the actual laboratory experiments with researchers sharing data in the open portal and receiving feedback from the open, collaborative community. OSDD has enthused a large number of wet lab scientists who were traditionally thought of wary of open collaboration to work in the open source mode.
Student Community as a Resource
Data intensive scientific discovery can be made possible using the above crowd sourced model involving students and young researchers who are willing to voluntarily solve problems. Its crowd sourcing approach has successfully curated most extensive annotation on Mtb which served as the primer for generating the largest ever metabolome and protein-protein functional network of Mtb enabling identification of potential drug targets. As per published estimates, this innovative approach packed nearly 300 man-years into 4 months .
Training of Young Researchers
Based on the crowd sourcing model, OSDD has created a large trained pool of researchers by reaching out to educational institutions outside major cities. Its Junior Scientists Forum which organises OSDD clubs in colleges attracts students to scientific research in general and drug discovery. Above all, it increases awareness of need for new drugs for diseases like TB among students and scientists. A Women Scientists Forum has been set up to tap into the competencies of qualified women trained in scientific activities but are homebound due to family circumstances.