Molecular dynamics simulations have already proved their value in steering drug design, McCammon said. "They helped in the discovery of the current HIV protease inhibitors, which bind to the active site of the enzyme. They were also key to the development of potential inhibitors of the third enzyme associated with HIV, the integrase enzyme.
"Other simulations by our group discovered an unknown binding site on the integrase enzyme, " McCammon explained. "Merck's new anti-integrase inhibitors include molecules that are designed to hit that site, in addition to a site that was known earlier from x-ray crystallography studies." These new inhibitors are moving into phase III human trials, he said.
For his first round of simulations, Perryman chose a rare double-mutant protease enzyme with two mutations in the 99 amino acids that make up each half of the enzyme. One of those mutations, V82F, is common, and it can emerge early during failure of therapy with most protease inhibitors. The other mutation, I84V, is frequently found after prolonged ineffective therapy with protease inhibitors and likely confers high-level resistance to most drugs in that class. The researchers wanted to compare the differences in the shapes of the non-mutated or wild-type enzyme, against which the drugs still worked well, and the drug-resistant double-mutant strain.
Perryman used a computer simulation program called AMBER that performs several different types of calculations. The x-ray crystal structure of the molecule is used as the input, and the various motions and shapes sampled are governed by Newtonian physics, the electric forces among atoms, the complementarity or clash of the different shapes that the enzyme takes, and penalties or bonuses for creating or relieving geometric strain.
The scientists depict the protease enzyme in a brightly colored cartoon, with features that resemble a fat cat face. From the front or the back, the identical ha
Source:Howard Hughes Medical Institute