World Community Grid is helping “FightAIDS@Home” by completing computational calculations related to molecular structures of potential anti-HIV drugs..  Image courtesy of World Community Grid

Starting on World AIDS Day on 1 December, the World Community Grid will sponsor a month-long challenge via its FightAIDS@home project, with the goal of increasing the number of computers and computer cycles available to researchers conducting HIV/AIDS research.

Like all molecules, HIV—the virus that causes AIDS—is dependent upon its three-dimensional shape to attack the human immune system, in much the same way that a key must fit into a lock in order to gain entry. If the lock can be blocked—with a drug, for example—then the key cannot fit, and the virus is prevented from maturing. Such blockers, known as “protease inhibitors,” are one way of avoiding the onset of AIDS.

Researchers have been able to determine by trial-and-error the shapes of a “lock” and a “key” separately, but not always for the two together. If scientists knew how a drug molecule fits inside the active site of its target, chemists could see how they could design even better blockers, more potent than existing ones.

At the laboratory of Arthur Olson in the molecular biology department at The Scripps Research Institute in La Jolla, California, computational methods are used  to identify new candidates for drugs with the right shape and chemical characteristics to block HIV. Known as “Structure-Based Drug Design,” this approach requires vast computational resources. (To make things more challenging, HIV is constantly evolving new variants, some of which are resistant to existing drugs. Consequently, scientists must continually search for new and better drugs to aim at a rapidly moving target.)

A tangible, three-dimensional physical model of HIV protease, a target for AIDS therapy. Scientists at Scripps utilize these types of models to help design new drug candidates that may be robust against viral resistance. The model was created by using software that processes atomic coordinates (generated by computer modeling, x-ray crystallography, or nuclear magnetic resonance) or volumetric images, such as from electron microscopy. This information is then used to build a geometric model that can be fed into a three-dimensional fabricating printer that “prints” solid objects out of thousands of layers of a special fine plaster powder. Image courtesy of BioMedical Graphics and the laboratory of Arthur Olson

A different direction

To address these challenges, the FightAIDS@Home project runs a software program called AutoDock developed in Olson’s laboratory. AutoDock is a suite of tools that predicts how small molecules, such as drug candidates, might bind or “dock” to a receptor of known 3D structure.

With help from the World Community Grid—a philanthropic public computing grid organization started by computer giant IBM in November 2004—hundreds of thousands of volunteers have so far donated over 84,000 years of unused computer time to researchers worldwide.

Grid computing joins together many individual computers, creating a large system with massive computational power that far surpasses the power of several supercomputers. Because the work is split into small pieces that can be processed simultaneously, research time is reduced from years to months or even days.

According to UNAIDS - the Joint United Nations Program on HIV/AIDS, there are now 33.2 million people living with HIV, including 2.5 million children. Around half of those infected with HIV do so before they are 25, and are killed by AIDS before they are 35.

To find out more about World Community Grid in general or FightAIDS@Home in particular, click here.

If you already belong to World Community Grid, all you need to do to participate is click on this web address and then click on the “join now” button that appears.

—Dan Drollette, iSGTW