TY - JOUR
T1 - Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations
AU - Bastys, Tomas
AU - Gapsys, Vytautas
AU - Doncheva, Nadezhda T.
AU - Kaiser, Rolf
AU - De Groot, Bert L.
AU - Kalinina, Olga V.
PY - 2018/7/10
Y1 - 2018/7/10
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85047996801&partnerID=8YFLogxK
U2 - 10.1021/acs.jctc.7b01109
DO - 10.1021/acs.jctc.7b01109
M3 - Journal article
C2 - 29847122
AN - SCOPUS:85047996801
SN - 1549-9618
VL - 14
SP - 3397
EP - 3408
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
IS - 7
ER -
