Around this same time, the McCammon group began new molecular dynamics studies of HIV-1 integrase using SDSC's supercomputers. As the power of computers and the sophistication of the scientists' simulation methods have advanced hand in hand, the researchers have been able to discern ever more detailed insights into the microscopic dance of molecular dynamics, where events take place in nanoseconds at length scales far shorter than the wavelength of light. By putting the molecules into motion in their simulations, the researchers discovered that there is a great deal of unexpected flexibility in this binding region, indicating that instead of only one there might be multiple ways that inhibitors could bind to the integrase enzyme.
The most recently reported of these simulations is in an article by Julie Schames, Richard Henchman, Jay Siegel, Christoph Sotriffer, Haihong Ni, and McCammon in the Journal of Medicinal Chemistry of April 8, 2004. These simulations revealed that a "trench" opens intermittently in the area of the integrase catalytic site, suggesting that it should be possible to develop inhibitors that bind with their cyclic moieties to the "east" of the active center as well as to the "west." Based on these simulations, the researchers were also able to predict that the strongest binding inhibitors should be possible with moieties on both sides, what the scientists have called "butterfly" compounds with "wings" extending to both the east and west.
"This pointed the way to new classes of drugs," said McCammon. "And it's very exciting that scientists at Merck have now verified all of this experimentally."
A paper by Daria Hazuda, a leader of M