Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations

T Bastys, V Gapsys, NT Doncheva… - Journal of Chemical …, 2018 - ACS Publications
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 …

Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free …

J Chen - RSC advances, 2016 - pubs.rsc.org
Drug resistance of mutations in HIV-1 protease (PR) badly reduce the efficiency of the
current inhibitors in clinical treatments of AIDS. In this work, molecular dynamics (MD) …

Molecular dynamics simulations of HIV-1 protease suggest different mechanisms contributing to drug resistance

F Wartha, AHC Horn, H Meiselbach… - Journal of Chemical …, 2005 - ACS Publications
A major problem in the antiretroviral treatment of HIV-infections with protease-inhibitors is
the emergence of resistance, resulting from the occurrence of distinct mutations within the …

Interdependence of inhibitor recognition in HIV-1 protease

JL Paulsen, F Leidner, DA Ragland… - Journal of chemical …, 2017 - ACS Publications
Molecular recognition is a highly interdependent process. Subsite couplings within the
active site of proteases are most often revealed through conditional amino acid preferences …

Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV

Y Cai, CA Schiffer - Journal of chemical theory and computation, 2010 - ACS Publications
Darunavir (DRV) is a high affinity (4.5× 10− 12 M, Δ G=− 15.2 kcal/mol) HIV-1 protease
inhibitor. Two drug-resistant protease variants FLAP+ (L10I, G48V, I54V, V82A) and ACT …

Evaluating the potency of HIV‐1 protease drugs to combat resistance

T Hou, WA McLaughlin, W Wang - Proteins: Structure, Function …, 2008 - Wiley Online Library
HIV‐1 protease has been an important drug target for the antiretroviral treatment of HIV
infection. The efficacy of protease drugs is impaired by the rapid emergence of resistant …

Drug resistance mutations alter dynamics of inhibitor-bound HIV-1 protease

Y Cai, W Myint, JL Paulsen, CA Schiffer… - Journal of chemical …, 2014 - ACS Publications
Under the selective pressure of therapy, HIV-1 protease mutants resistant to inhibitors
evolve to confer drug resistance. Such mutations can impact both the dynamics and …

Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations

H Meiselbach, AHC Horn, T Harrer, H Sticht - Journal of Molecular …, 2007 - Springer
Drug resistance is a very important factor contributing to the failure of current HIV therapies.
The ability to understand the resistance mechanism of HIV-protease mutants may be useful …

Computational studies of a mechanism for binding and drug resistance in the wild type and four mutations of HIV-1 protease with a GRL-0519 inhibitor

G Hu, A Ma, X Dou, L Zhao, J Wang - International journal of molecular …, 2016 - mdpi.com
Drug resistance of mutations in HIV-1 protease (PR) is the most severe challenge to the long-
term efficacy of HIV-1 PR inhibitor in highly active antiretroviral therapy. To elucidate the …

Full quantum mechanical study of binding of HIV‐1 protease drugs

DW Zhang, JZH Zhang - International journal of quantum …, 2005 - Wiley Online Library
Fully quantum mechanical studies of detailed binding interactions between HIV‐1 protease
and six FDA (Food and Drug Administration)‐approved drugs (saquinavir, indinavir …