A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: a systematic MM-PBSA and thermodynamic integration study.

The emergence of HIV-1 drug-resistant mutations is the major problem against AIDS treatment. We employed molecular dynamics (MD) calculations and free energy (MM-PBSA and thermodynamic integration) analyses on wild-type (WT) and mutated HIV-1 protease (HIV-1 PR) complexes with darunavir, amprenavir, indinavir, and saquinavir to clarify the mechanism of resistance due to the I50V flap mutation. Conformational analysis showed that the protease flaps are increasingly flexible in the I50V complexes. In the WT, stabilization of the HIV-1 PR structure is achieved via interflap and water-mediated hydrogen-bonding interactions between the flaps. Furthermore, hydrogen bonds between drugs and binding cavity residues (Asp29/29'/30/30') are crucial for effective inhibition. All these interactions were significantly diminished (or absent) in the mutated forms, thus denoting their importance toward binding. Thermodynamic integration calculations reproduced the experimental data to within ≈1 kcal mol⁻¹ and showed that the I50V mutation results in weaker binding free energies for all analyzed complexes with respect to the WT. It was observed that the loss in binding energy upon mutation was mostly enthalpically driven in all complexes, with the greatest effect coming from the reduction of van der Waals interactions. Our results motivated us to test two novel compounds that have been synthesized to maximize interactions with HIV-1 PR. MM-PBSA and TI calculations showed that compound 3c (Ghosh et al. Bioorg. Med. Chem. Lett. 2012, 22, 2308) is a promising protease inhibitor, which presents very effective binding to the WT PR (ΔG(MM-PBSA) = -17.2 kcal mol⁻¹, ΔG(exp) = -16.1 kcal mol⁻¹). Upon I50V mutation, the complex binding free energy was weakened by a ΔΔG(TI) of 1.8 kcal mol⁻¹, comparable to the marketed inhibitors. This predicts that I50V may confer low resistance to 3c. This computational comparative study contributes toward elucidation of the I50V drug-resistance mechanism in HIV-1 PR.