Decomposing the Energetic Impact of Drug Resistant Mutations in HIV-1 Protease on Binding DRV

Abstract

Darunavir (DRV) is a high affinity (4.5 × 10⁻¹² M, ΔG = −15.2 kcal/mol) HIV-1 protease inhibitor. Two drug-resistant protease variants FLAP+ (L10I, G48V, I54V, V82A) and ACT (V82T, I84V) decrease the binding affinity with DRV by 1.0 and 1.6 kcal/mol, respectively. In this study, the absolute and relative binding free energies of DRV with wild-type protease, FLAP+, and ACT were calculated with MM-PB/GBSA and thermodynamic integration methods, respectively. Free energy decomposition elucidated that the mutations conferred resistance by distorting the active site of HIV-1 protease so that the residues that lost binding free energy were not limited to the sites of mutation. Specifically the bis-tetrahydrofuranylurethane moiety of DRV maintained interactions with the FLAP+ and ACT variants, whereas the 4-amino phenyl group lost more binding free energy with the protease in the FLAP+ and ACT complexes than in the wild-type protease, which could account for the majority of the loss in binding free energy. This suggested that replacement of the 4-amino phenyl group might generate new inhibitors less susceptible to the drug resistant mutations.