Consistent Prediction of Mutation Effect on Drug Binding in HIV‑1 Protease Using Alchemical Calculations

• Published in: Journal of chemical theory and computation 2018-07, Vol.14 (7), p.3397-3408
• Main Authors: Bastys, Tomas, Gapsys, Vytautas, Doncheva, Nadezhda T, Kaiser, Rolf, de Groot, Bert L, Kalinina, Olga V
• Format: Article
• Language: English
• Subjects: Algorithms; Catalysis; Computer simulation; Drug Resistance, Multiple, Viral; Free energy; HIV Infections - drug therapy; HIV Infections - virology; HIV Protease - genetics; HIV Protease - metabolism; HIV Protease Inhibitors - pharmacology; HIV-1 - drug effects; HIV-1 - enzymology; HIV-1 - genetics; Humans; Mathematical analysis; Models, Biological; Molecular Docking Simulation; Molecular dynamics; Mutation; Point Mutation; Predictions; Protease; Protein Binding; Proteins; Protonation; Rams; Thermodynamics
• ISSN: 1549-9618; 1549-9626
• DOI: 10.1021/acs.jctc.7b01109

Despite a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy ΔG, as well as in mechanistic terms. In this study, we analyze ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial drug binding regions of the protease.