Open Source COVID-19 Vaccine
Humanity’s urgent need for a vaccine, or set of vaccines, for SARS-CoV-2 needs no elaboration. Quite simply, this is one of the more pressing scientific/humanitarian needs of the century.
There is an enormous amount of ongoing work in the public, private, and nonprofit sectors. The bulk of it, however, is along business-as-usual lines, with heavy competition among companies, even nations. (See “Search for Coronavirus Vaccine Becomes a Global Competition,” NY Times, March 19, 2020).
In open source software, not only are the incoming and outgoing results widely usable, but the very process of development itself, the actual daily work, is open, collaborative, global. The magic of this collaboration created, for example, Linux, which dominates the supercomputer market, and the LAMP stack, which birthed the World Wide Web. Can we learn from these principles, and apply them to the process of vaccine R&D?
If we were really serious about developing a vaccine, we would not work through single labs, or even consortia. Rather, we would have the entire world look at the problem at once.
Read full project and contribute a hypothesis below.
Open Source COVID-19 Drugs: In Silico Drug Repurposing
This crowdsourcing for open source COVID-19 drug repurposing research project can be broken down into the following steps:
- Crowdsource to build a systems biology model for the virus, and for drug target identification
- Search literature, and characterize each of the proteins of SARS-CoV-2 (COVID_19), as well as their homologues.
- Place all of these proteins in their functional context; namely, specific to the host target and its self-assembly.
- Identify the most essential proteins as the specific targets of interest for therapeutic development (e.g., Spike Trimer, TMPRSS2, etc.).
- Build InSilco 3D structures, based on homology modeling.
- Undertake molecular docking for each target.
- Examine at the interacting surface of the spike trimmer protein and search for potential inhibitors.
- Virus target on host receptor (ACE2) modeling.
- Identify all of the host receptor (ACE2) polymorphisms in the various populations profiled in the global each population human genome databases. Try to correlate these with the potential affinity variation with spike protein.
- Search (in silico) for inhibitors that can block this interaction.
- Host factors that can protect from the virus
- Various host miRNA and other variabilities that can target the virus RNA and block processing and/or degrade the viral RNA.
- Determine what targets can reduce a cytokine storm.
Project conceptualized by and mentored by Professor Samir K. Brahmachari.
OSP Idea Factory: C-19 Drug Discovery Hypotheses
This is a Massive Online Open Research (MOOR) initiative for COVID-19, a global collaborative research effort of the open source pharma community that seeks to tap into the minds of scientists and researchers across the world to virtually screen molecules to fight the virus. Through collective intelligence and open source approaches, we can support the rapid discovery of molecules and COVID-19 targets. Phase 1 of this project involves docking various molecules in the targets of COVID-19. We welcome all to contribute their hypotheses using the form below.
Join/ Contribute to this Project
Please use this form below to suggest a molecule, target, or specific pair of molecule and biological target for docking (e.g. Metformin and Protease PDB id 6LU7), based upon which mapping of the interactions and theoretical validations can be carried out. These suggestions will be displayed on our hypotheses page and we will then conduct molecular docking in our lab to be displayed on our results page.
If you have multiple molecules or targets to suggest, please get in touch with email@example.com.
Crowdsourced Face Masks
In collaboration with its community and professional networks, the Open Source Pharma Foundation (OSPF) is exploring the production and distribution of face masks to fight the spread of COVID-19. Through crowdsourcing thoughts, open source designs, and ideas from the public, we aim to help the effort to create low-cost and effective masks on a large-scale. Please share your ideas here!