Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations

2019 ◽  
Vol 37 (10) ◽  
pp. 2608-2626 ◽  
Author(s):  
Vasavi C.S. ◽  
Ramasamy Tamizhselvi ◽  
Punnagai Munusami
Keyword(s):  
Molecular Dynamics ◽  
Drug Resistance ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Resistance Mechanism ◽  
Free Energy Calculations ◽  
Cooperative Effects ◽  
Dynamics Simulations ◽  
Hiv 1

Revealing the binding and drug resistance mechanism of amprenavir, indinavir, ritonavir, and nelfinavir complexed with HIV-1 protease due to double mutations G48T/L89M by molecular dynamics simulations and free energy analyses

2020 ◽  
Vol 22 (8) ◽  
pp. 4464-4480
Author(s):  
Rui-Ge Wang ◽  
Hong-Xing Zhang ◽  
Qing-Chuan Zheng
Keyword(s):  
Molecular Dynamics ◽  
Drug Resistance ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Resistance Mechanism ◽  
Md Simulations ◽  
Resistance Mechanisms ◽  
Dynamics Simulations ◽  
Hiv 1

MD simulations, MM-PBSA, and SIE analyses were used to investigate the drug resistance mechanisms of two mutations G48T and L89M in HIV-1 protease toward four inhibitors.

Molecular Simulations to Rationalize Humanized Ab2/3H6 Activity

2011 ◽  
Vol 64 (7) ◽  
pp. 900 ◽  
Author(s):  
Anita de Ruiter ◽  
Alexander Mader ◽  
Renate Kunert ◽  
Chris Oostenbrink
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Heavy Chain ◽  
Free Energy Calculations ◽  
Binding Affinities ◽  
Dynamics Simulations ◽  
Idiotypic Antibody ◽  
Mouse Antibody ◽  
Hiv 1

The murine anti-idiotypic antibody 3H6 (Ab2/3H6) is directed against the human 2F5 antibody, which is capable of neutralizing HIV-1. Recently, four humanized Ab2/3H6 models have been developed in order to reduce the risk of human anti-mouse antibody (HAMA) responses in case of administration to humans. In this study, molecular dynamics simulations were performed on these models as well as on the murine Ab2/3H6 in solution and bound to 2F5, in order to rationalize the differences in binding affinities of the models towards 2F5. Analysis of these simulations suggested that the orientation and dynamics of the residues TYR54 and TYR103 of the heavy chain of Ab2/3H6 play an important role in these differences. Subsequently, the contribution of these residues to the binding affinity was quantified by applying free energy calculations.

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

RSC Advances ◽  
2016 ◽  
Vol 6 (63) ◽  
pp. 58573-58585 ◽  
Author(s):  
Jianzhong Chen
Keyword(s):  
Molecular Dynamics ◽  
Drug Resistance ◽  
Free Energy ◽  
Binding Free Energy ◽  
Resistance Mechanisms ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Probe Drug ◽  
Dynamics Simulations ◽  
Hiv 1

Molecular dynamics simulation and binding free energy calculations were used to probe drug resistance of HIV-1 protease mutations toward inhibitors.

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