Cure/treat Ebola with known drugs
Donation protected
Apply CANDO platform to cure/treat Ebola with known drugs
We are looking to obtain funding for validating computational predictions of known (existing) FDA approved drugs that may be repurposed to work against Ebola using our bioinformatic drug discovery platform. The platform used to make the predictions is called Computational Analysis of Novel Drug Opportunities (CANDO) and is funded by a 2010 NIH Director's Pioneer Award. (I wrote the NIH but haven't gotten a response yet.) However, the CANDO platform is built upon basic science work in protein structural bioinformatics that was funded by grants from the NIH, NSF, and various others. If our attempt were successful (and it has been successful for many other diseases), it would represent a coup for computational/informatic methods quickly discovering a treatment for Ebola where conventional methods are lagging. See this URL for a technical description of what we have done:
http://protinfo.org/cando/results/ebola/readme.html
The CANDO work has been published in places like JAMA, Trends in Pharmacological Sciences, and most recently Drug Discovery Today (see http://compbio.org/publications/therapeutics.html). The error rate is still about 1/10 (as opposed to the 1/1000 rates we get from HTS or random screening or just plain docking) but that enables predictions to be validated by academic labs such as the one being managed by my Ebola collaborator in the Department of Microbiology at the University of Washington who has just published on a new effective mouse model of Ebola.
In terms of CANDO, we've already done validations of over 200 compounds for 11 diseases/indications using Pioneer Award funds but the Ebola work has been held up because of my institution move.
Effective October 1, I've moved to SUNY Buffalo and taken up a position as Professor and Chief of the Division of Bioinformatics. Because of this move, my NIH grant which was funding the Ebola work has been frozen until the transfer is done and then I'd have to get SUNY to issue a subcontract back to UW Microbiology to do the validation which will take time while people are dying. If we could fund this work immediately, it would enable us to do the validation seamlessly and if we got any hits, not only could they be used in patients immediately (since they're all FDA approved drugs) but also point towards a new paradigm of drug discovery that exploits existing structural bioinformatics knowledge, basic science, and work already done by pharmaceutical companies to discover new cures/treatments for underserved and emerging indications.
Specifically, the funds will be used to purchase the drugs, cell culture supplies, and to pay for the labour to do the in vitro testing of these top predictions against the Ebola virus in cell culture. The work will be done by my collaborator Dr. Michael Katze, Professor of Microbiology, the University of Washington and his team at the Rocky Mountain National Labs. This is a collaborative project between my group at SUNY Buffalo, the University of Washington, and others. More info on our groups is available at http://compbio.org, and http://viromics.washington.edu.
Lead PI:
Ram Samudrala, PhD
Professor and Chief, Division of Bioinformatics
Department of Biomedical Informatics
School of Medicine and Biomedical Sciences
State University of New York (SUNY)
Buffalo, NY 14620
V: 1-206-251-8852
F: 1-206-260-8979
W: http://compbio.org
Along with:
Dr. Gaurav Chopra, PhD, UCSF
Dr. Mark Minie, PhD, UW
Kaushik Hatti, SUNY Buffalo
and several others who've contributed (this is a team effort).
We are looking to obtain funding for validating computational predictions of known (existing) FDA approved drugs that may be repurposed to work against Ebola using our bioinformatic drug discovery platform. The platform used to make the predictions is called Computational Analysis of Novel Drug Opportunities (CANDO) and is funded by a 2010 NIH Director's Pioneer Award. (I wrote the NIH but haven't gotten a response yet.) However, the CANDO platform is built upon basic science work in protein structural bioinformatics that was funded by grants from the NIH, NSF, and various others. If our attempt were successful (and it has been successful for many other diseases), it would represent a coup for computational/informatic methods quickly discovering a treatment for Ebola where conventional methods are lagging. See this URL for a technical description of what we have done:
http://protinfo.org/cando/results/ebola/readme.html
The CANDO work has been published in places like JAMA, Trends in Pharmacological Sciences, and most recently Drug Discovery Today (see http://compbio.org/publications/therapeutics.html). The error rate is still about 1/10 (as opposed to the 1/1000 rates we get from HTS or random screening or just plain docking) but that enables predictions to be validated by academic labs such as the one being managed by my Ebola collaborator in the Department of Microbiology at the University of Washington who has just published on a new effective mouse model of Ebola.
In terms of CANDO, we've already done validations of over 200 compounds for 11 diseases/indications using Pioneer Award funds but the Ebola work has been held up because of my institution move.
Effective October 1, I've moved to SUNY Buffalo and taken up a position as Professor and Chief of the Division of Bioinformatics. Because of this move, my NIH grant which was funding the Ebola work has been frozen until the transfer is done and then I'd have to get SUNY to issue a subcontract back to UW Microbiology to do the validation which will take time while people are dying. If we could fund this work immediately, it would enable us to do the validation seamlessly and if we got any hits, not only could they be used in patients immediately (since they're all FDA approved drugs) but also point towards a new paradigm of drug discovery that exploits existing structural bioinformatics knowledge, basic science, and work already done by pharmaceutical companies to discover new cures/treatments for underserved and emerging indications.
Specifically, the funds will be used to purchase the drugs, cell culture supplies, and to pay for the labour to do the in vitro testing of these top predictions against the Ebola virus in cell culture. The work will be done by my collaborator Dr. Michael Katze, Professor of Microbiology, the University of Washington and his team at the Rocky Mountain National Labs. This is a collaborative project between my group at SUNY Buffalo, the University of Washington, and others. More info on our groups is available at http://compbio.org, and http://viromics.washington.edu.
Lead PI:
Ram Samudrala, PhD
Professor and Chief, Division of Bioinformatics
Department of Biomedical Informatics
School of Medicine and Biomedical Sciences
State University of New York (SUNY)
Buffalo, NY 14620
V: 1-206-251-8852
F: 1-206-260-8979
W: http://compbio.org
Along with:
Dr. Gaurav Chopra, PhD, UCSF
Dr. Mark Minie, PhD, UW
Kaushik Hatti, SUNY Buffalo
and several others who've contributed (this is a team effort).
Organizer
Ram Samudrala
Organizer
Buffalo, NY