Collaboration of 1.5 Million computers in 80 countries has discovered two new compounds that prove the existence of new binding sites on HIV protease

A team of researchers at the renowned Scripps Research Institute has discovered two new compounds that prove the existence of new binding sites on HIV protease. Associate Professor C. David Stout, senior author of the study, explained “These results open the door to a whole new approach to drug design against HIV protease,” which is an enzyme used by HIV to create new, infectious viral particles.



Two members of the FightAIDS@Home team, Research Associate Alex L. Perryman, Ph.D., and Professor Arthur J. Olson, were part of this innovative research and are now working to extend it. This experimental breakthrough will serve as the basis for new drug development to combat the increasing number of drug-resistant HIV strains and to improve the potency of current drug therapies. The results form the groundwork for a new class of more powerful treatments to fight HIV/AIDS. The findings appear as the March cover story in the journal Chemical Biology and Drug Design.

Utilizing computing power from 1.5 million devices networked through IBM’s World Community Grid, the new sites on the HIV protease are being used as docking targets for virtual screening experiments, in order to guide the development of these chemical compounds into a new class of potent HIV inhibitors. Using the massive computational resources of the World Community Grid, the FightAIDS@Home team has already docked over 500,000 compounds against these newly characterized binding sites.

By aggregating the unused cycle time of 1.5 million personal computers donated by volunteers in over 80 countries, World Community Grid is now the world’s largest public humanitarian grid, equivalent in power to a Top 15 supercomputer, and crunched more than 107,000 years of computational time in just 5 years for the Scripps Research Institute project, providing more than 104 million calculations.

“IBM’s World Community Grid and its volunteers help us run millions of computations to evaluate the potential interactions between compounds and mutant viral proteins,” said Dr. Arthur J. Olson, Anderson Research Chair Professor, Department of Molecular Biology at The Scripps Research Institute. “Through this effort we were able to significantly speed up our investigation. Without the computational power of World Community Grid, it would have taken us many more years to get to this important step in our research.”

Once the HIV virus enters a human cell, it uses a small set of proteins called enzymes to force the cell to produce many new copies of itself, which then go on to infect other cells. Most HIV drugs work by blocking the operation of one or more of these enzymes. In the current work, the Scripps researchers are looking for new compounds that will stabilize the inhibited conformation, or shape, of the HIV protease enzyme, and thus help stop the virus from replicating. Because HIV mutates so frequently, some drugs that inhibit the enzyme from replicating are no longer working, or are not working as effectively. By running calculations on the World Community Grid FightAIDS@Home project, the team at Scripps is trying to develop new drugs that bind to more parts of the mutant enzyme, thereby shutting it down more effectively.