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Roff wrote:We were delighted to find several compounds that were highly effective protease inhibitors. Once our labs reopen, we will test the antiviral activity of these compounds in cell culture.
Hello again from Galveston! Below is a status update that will be posted on our web site update board. However, I thought I would get it out via the forums as well.
Thanks again for all your help!
- Stan coffee
April 13, 2009
We are back on track with our DiscoveringDengueDrugs-Together project, and life is returning to some semblance of normalcy in Galveston and at UTMB. We thank World Community Grid members for their support and patience during the past 6 months following Hurricane Ike.
The Autodock phase (Phase 1) of our dengue project is now complete! We have screened (i.e., computationally tested) more than 3 million potential drug candidates against each of 10 different proteases from dengue, West Nile, and hepatitis C viruses. Inhibiting these target proteases prevents virus replication. We continue to analyze the 30 million Phase 1 results. We are using biochemical, cell-based, and small animal assays to characterize some of the inhibitors identified during our recently completed Phase 1 calculations.
The CHARMM phase (Phase 2) of our project is being optimized at Texas Advanced Computer Center (TACC; http://www.tacc.utexas.edu) in Austin, Texas and ported by IBM to the grid for testing. This phase will perform extensive molecular dynamics calculations to accurately calculate binding free energies for the best potential drug candidates predicted in Phase 1. These calculations will significantly reduce the number of false positive predictions produced in Phase 1, thereby increasing our success rate for identifying experimentally active compounds from ~10% to >80%. Launch of Phase 2 is anticipated for early summer, 2009.
As we prepare to launch Phase 2 of our project to discover drugs for dengue, West Nile, and hepatitis C infections, we will also begin Autodock calculations in support of a collaborative drug discovery effort against leishmaniasis disease. This work is done in partnership with researchers from Universidad de Antioquia, Colombia (http://www.pecet-colombia.org). Leishmania affects ~12 million people throughout the tropics, subtropics, and southern Europe, with ~2 million new cases each year. The disease is spread by the bite of sand flies infected the Leishmania parasite. Although a handful of antimicrobials exist to treat some forms of leishmaniasis, concerns about their modes of delivery, effectiveness, resistance, and cost spur our drug discovery efforts into novel anti-Leishmania drugs. For this project, scientists in Colombia identified a set of enzymes critical for survival of the Leishmania parasite. Atomic structures exist for each of these enzymes, this allowing us to computationally examine our drug candidate library for compounds that prevent the Leishmania enzymes from functioning.
As reported earlier, this project is now running better than ever before. We have moved our main computational tasks (those required to prepare workunits for World Community Grid and analyze results returned from the grid) to the supercomputers housed at TACC. This establishes a nice synergy between one of the world?s most powerful supercomputers and the world?s largest computer grid. Our storage capabilities have increased in size and robustness with redundant storage occurring at TACC and locally on our 12 TByte IBM DS3200 disk system.
As stated before, we greatly appreciate the computer time that has been unselfishly provided by the members of the World Community Grid!
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