Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant

A Lauria, M Ippolito, AM Almerico - Journal of Molecular Modeling, 2007 - Springer
The emergence of drug-resistant mutants of HIV-1 is a tragic effect associated with
conventional long-treatment therapies against acquired immunodeficiency syndrome. These …

HIV‐1 protease molecular dynamics of a wild‐type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs

AL Perryman, JH Lin, JA McCammon - Protein Science, 2004 - Wiley Online Library
The protease from type 1 human immunodeficiency virus (HIV‐1) is a critical drug target
against which many therapeutically useful inhibitors have been developed; however, the set …

Studies on adaptability of binding residues flap region of TMC-114 resistance HIV-1 protease mutants

R Purohit, V Rajendran… - Journal of Biomolecular …, 2011 - Taylor & Francis
Drug resistant mutations have severely restricted the success of HIV therapy. These
mutations frequently involve the aspartic protease encoded by the virus. Knowledge of the …

A molecular dynamics study comparing a wild‐type with a multiple drug resistant HIV protease: Differences in flap and aspartate 25 cavity dimensions

SA Seibold, RI Cukier - Proteins: Structure, Function, and …, 2007 - Wiley Online Library
HIV proteases can develop resistance to therapeutic drugs by mutating specific residues, but
still maintain activity with their natural substrates. To gain insight into why mutations confer …

Molecular dynamics and ligand docking of a hinge region variant of South African HIV-1 subtype C protease

J Zondagh, V Balakrishnan, I Achilonu, HW Dirr… - Journal of Molecular …, 2018 - Elsevier
HIV-1 protease is an important antiretroviral drug target due to its key role in viral maturation.
Computational models have been successfully used in the past to understand the dynamics …

Effects of the V82A and I54V mutations on the dynamics and ligand binding properties of HIV-1 protease

P Dirauf, H Meiselbach, H Sticht - Journal of molecular modeling, 2010 - Springer
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 …

Restrained molecular dynamics simulations of HIV‐1 protease: the first step in validating a new target for drug design

AL Perryman, JH Lin… - … : Original Research on …, 2006 - Wiley Online Library
To test the anticorrelated relationship that was recently displayed in conventional molecular
dynamics (MD) simulations, several different restrained MD simulations on a wild type and …

Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations

A Badaya, YU Sasidhar - Scientific reports, 2020 - nature.com
HIV-1 protease is an essential enzyme in the life cycle of the HIV-1 virus. The conformational
dynamics of the flap region of the protease is critical for the ligand binding mechanism, as …

Cantilever-centric mechanism of cooperative non-active site mutations in HIV protease: Implications for flap dynamics

D Sherry, R Worth, ZS Ismail, Y Sayed - Journal of Molecular Graphics and …, 2021 - Elsevier
The HIV-1 protease is an important drug target in antiretroviral therapy due to the crucial role
it plays in viral maturation. A greater understanding of the dynamics of the protease as a …

A coarse grained model for the dynamics of flap opening in HIV-1 protease

V Tozzini, JA McCammon - Chemical Physics Letters, 2005 - Elsevier
A coarse grained model for proteins is developed and applied to HIV-1 protease. Molecular
dynamics simulations on the μsec timescale and the use of a flexible force field allow study …