MOLECULAR RECOGNITION OF CYCLIC UREA HIV-1 PROTEASE INHIBITORS

As long as the threat of human immunodeficiency virus (HIV) protease d rug resistance still exists, there will be a need for more potent anti retroviral agents. We have therefore determined the crystal structures of HIV-1 protease in complex with six cyclic urea inhibitors: XK216, XK263, DMP323, DMP450, XV638, and SD146, in an attempt to identify 1) the key interactions responsible for their high potency and 2) new int eractions that might improve their therapeutic benefit. The structures reveal that the preorganized, C-2 symmetric scaffolds of the inhibito rs are anchored in the active site of the protease by six hydrogen bon ds and that their P1 and P2 substituents participate in extensive van der Waals interactions and hydrogen bonds. Because all of our inhibito rs possess benzyl groups at P1 and P1', their relative binding affinit ies are modulated by the extent of their P2 interactions, e.g. XK216, the least potent inhibitor (K-i (inhibition constant) = 4.70 nM), poss esses the smallest P2 and the lowest number of P2-S2 interactions; whe reas SD146, the most potent inhibitor (K-i = 0.02 nM), contains a benz imidazolylbenzamide at P2 and participates in fourteen hydrogen bonds and similar to 200 van der Waals interactions. This analysis identifie s the strongest interactions between the protease and the inhibitors, suggests ways to improve potency by building into the S2 subsite, and reveals how conformational changes and unique features of the viral pr otease increase the binding affinity of HIV protease inhibitors.