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Computer simulation hints at new HIV drug target

ermal motion of their atoms. Drug-binding sites that may be closed most of the time can be transiently exposed by an imperceptible atomic shudder. "This 'foot in the door' mechanism of drug binding and action is a relatively new way of thinking about things, arising from the greater appreciation of proteins as dynamic molecular machines," McCammon explained.

The drug cocktails now used in the treatment of HIV infection are referred to under the umbrella term, highly active antiretroviral therapy, or HAART therapy. Current HAART regimens generally include three antiretroviral drugs, usually two nucleoside analogs and either a protease inhibitor or a non-nucleoside reverse-transcriptase inhibitor. This drug regimen has, in some cases, been effective in controlling the progression of disease and prolonging survival. It has succeeded where other therapies have failed because HAART therapy makes it difficult for even a fast-mutating virus like HIV to develop resistance to all of the drugs at once.

But the specter of drug resistance is a real threat to each individual's therapy and to the long-term success of HAART for newly infected people. By one estimate, about 50 percent of patients receiving antiretroviral therapy in the United States harbor HIV viruses that are resistant to at least one of the available drugs. In fact, people with an infection typically have a diverse array of HIV mutants, some of which are resistant to antiviral drugs. Drug-resistant strains of HIV are being found more often in recently infected people, indicating that transmission of resistant strains is occurring at an increased frequency.

As a graduate student in McCammon's lab, Perryman initially set out to put the HIV protease enzyme in motion in a computer simulation, to catalog its many possible configurations. "HIV can wiggle and jiggle and move around into different shapes," he said. "We wanted to generate a bunch of conformations as possible targets for drug desig
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Source:Howard Hughes Medical Institute


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