The binding energetics of first- and second-generation HIV-1 protease inhibitors: Implications for drug design

KNI-764 is a powerful HIV-1 protease inhibitor with a reported low suscepti bility to the effects of protease mutations commonly associated with drug r esistance. In this paper the binding thermodynamics of KNI-764 to the wild- type and drug-resistant mutant V82F/IS4V are presented and the results comp ared to those obtained with existing clinical inhibitors. KNI-764 binds to the wild-type HIV-1 protease with very high affinity (3.1 x 10(10) M-1 or 3 2 pM) in a process strongly favored by both enthalpic and efitropic contrib utions to the Gibbs energy of binding (DeltaG = -RTlnK(a)), When compared t o existing clinical inhibitors, the binding affinity of KNI-764 is about 10 0 fold higher than that of indinavir, saquinavir, and nelfinavir, but compa rable to that of ritonavir, Unlike the existing clinical inhibitors, which bind to the protease with unfavorable or only slightly favorable enthalpy c hanges, the binding of KNI-764 is strongly exothermic (-7,6 kcal/mol). The resistant mutation V82F/I84V lowers the binding affinity of KNI-764 26-fold , which can be accounted almost entirely by a less favorable binding enthal py to the mutant. Since KNI-764 binds to the wild type with extremely high affinity, even after a 26-fold decrease, it still binds to the resistant mu tant with an affinity comparable to that of other inhibitors against the wi ld type. These results indicate that the effectiveness of this inhibitor ag ainst the resistant mutant is related to two factors: extremely high affini ty against the wild type achieved by combining favorable enthalpic and entr opic interactions, and a mild effect of the protease mutation due to the pr esence of flexible structural elements at critical locations in the inhibit or molecule. The conclusions derived from the HIV-1 protease provide import ant thermodynamic guidelines that can be implemented in general drug design strategies. (C) 2001 Academic Press.