Perryman's first results, which were published in the April 1, 2004, issue of Protein Science, showed that the mechanism of drug resistance seemed to involve the motion of the flaps. More specifically, the double-mutant virus displayed larger flap motions, especially at the tips. These larger movements seem to make it more difficult for the current drugs to function, since they must force the flaps to close and remain closed in order to prevent the enzyme from working. It probably takes more energy for the drugs to close the more mobile flaps of the mutant.
Perryman and his colleagues also observed that the flaps opened in a seesaw motion on each side, pinching the "cheek and "ear" together. That observation suggested to them that a small molecule might be able to wedge between the ear and cheek, blocking the flap opening.
"Some drugs act by binding to the active site of a target molecule, such as the site that an enzyme normally uses to catalyze reactions," McCammon said. "But increasingly, scientists are finding that other binding sites can be important. For HIV/AIDS, an important class of drugs called non-nucleotide inhibitors for reverse transcriptase typically bind at such alternate sites."
Once Perryman had a hypothesis to test in a second round of simulations -- the proposed mechanics of the protease enzyme's nanomachinery--he used artificial restraints in the comp
Source:Howard Hughes Medical Institute