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Supercomputers to focus brains on AIDS dilemma

More than two decades after it burst onto the scene, HIV/AIDS has claimed more than twenty million lives and continues to devastate societies around the world, particularly in Africa and other developing countries. In the late 1980s and early 1990s, after years of effort AIDS researchers succeeded in developing a class of drugs that proved to be highly effective against AIDS. By blocking the activity of the viral enzyme HIV protease, these protease inhibitors brought greatly extended life-spans to patients who previously faced early deaths. Structural biology and molecular dynamics computer simulations played an important role in these discoveries.

However, in recent years, mutant strains of HIV have shown increasing resistance to many of these formerly effective drugs, raising the specter of reduced life-spans and wider spread of HIV.

"Fortunately, in this ongoing battle, computational and structural biology may once again be on the verge of contributing a new class of drugs for the treatment of HIV/AIDS," said J. Andrew McCammon, a Howard Hughes Medical Institute investigator and UCSD professor of Pharmacology who holds the Joseph Mayer Chair of Theoretical Chemistry at UCSD. "This time, we're targeting HIV integrase, the only HIV enzyme for which no effective drugs have previously been discovered." The other two HIV enzymes are reverse transcriptase, the target for AZT and other drugs, and protease, the target for the protease inhibitors that had proven so effective until the recent emergence of drug-resistant mutants.

The new drug possibilities flow out of a long series of molecular dynamics simulations by McCammon's group. These simulations have focused on the catalytic domain of HIV-1 integrase, and relied on the large-scale computational resources of the San Diego Supercomputer Center (SDSC) at UC San Diego. In 1999, related results from traditional x-ray crystallography studies of the structure of a complex between the HIV-1 integrase
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Source:SDSC


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