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Supercomputers to focus brains on AIDS dilemma

erck's drug discovery group, and her colleagues at Merck and the Instituto Ricerche di Biologia Moleculaire in Rome published in the August 3, 2004 Proceedings of the National Academy of Sciences reports on how the molecular dynamics simulations of the McCammon group dovetailed with Merck research, helping the company's scientists make sense of puzzling data of their own: seemingly similar inhibitors were binding to different parts of the enzyme's active site region. "With the help of our simulations, the Merck scientists were able to understand this and then go on to prove experimentally the effectiveness of compounds in binding to different parts of the HIV integrase enzyme," said McCammon.

Because of the great promise these compounds are showing for treating HIV/AIDS, the Merck scientists are proceeding with development of a series of drug candidates that rely on the remarkable flexibility revealed by the McCammon group's simulations in the integrase binding site. The first of these compounds is expected to go into clinical trials this year, with UCSD as one of the trial sites.

The Merck scientists have chosen a drug development strategy in which they are developing "single wing" compounds, whose wings, or cyclic moieties, can bind to either the west or the east in the integrase enzyme. "These compounds are especially interesting because they'll be less likely to lead to drug-resistant strains of HIV-1," said McCammon. This is because the inhibitor can flip to the east if an integrase mutation arises in the west, or to the west if a mutation arises in the east. And because emerging HIV-1 mutations have significantly reduced the usefulness of many previously effective drugs, maintaining the ability to bind even when mutations occur is an important advantage.

"These results, combining our computer simulations at SDSC and Merck experimental research, are giving real hope that the remarkable story of molecular dynamics simulations in helping d
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Source:SDSC


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