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 …

Targeting structural flexibility in HIV-1 protease inhibitor binding

V Hornak, C Simmerling - Drug discovery today, 2007 - Elsevier
HIV-1 protease remains an important anti-AIDS drug target. Although it has been known that
ligand binding induces large conformational changes in the protease, the dynamic aspects …

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 …

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 …

How mutations can resist drug binding yet keep HIV-1 protease functional

R Appadurai, S Senapati - Biochemistry, 2017 - ACS Publications
Human immunodeficiency virus-1 (HIV-1) protease is an important drug target for acquired
immune deficiency syndrome therapy. Nearly 10 small molecule drugs have been approved …

Computational characterization of structural role of the non-active site mutation M36I of human immunodeficiency virus type 1 protease

H Ode, S Matsuyama, M Hata, S Neya… - Journal of molecular …, 2007 - Elsevier
A prominent characteristic of human immunodeficiency virus type 1 (HIV-1) is its high
genetic variability, which generates diversity of the virus and often causes a serious problem …

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

S Piana, P Carloni, M Parrinello - Journal of molecular biology, 2002 - Elsevier
The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the
common view of the reaction mechanism of this enzyme. Here, we address this issue by …

Binding to the open conformation of HIV‐1 protease

KW Lexa, HA Carlson - Proteins: Structure, Function, and …, 2011 - Wiley Online Library
A recent crystal structure of HIV‐1 protease (HIVp) was the first to experimentally observe a
ligand targeting an open‐flap conformation. Researchers studying a symmetric pyrrolidine …

Reaction path and free energy calculations of the transition between alternate conformations of HIV‐1 protease

SW Rick, JW Erickson, SK Burt - Proteins: Structure, Function …, 1998 - Wiley Online Library
Two different structures of ligand‐free HIV protease have been determined by X‐ray
crystallography. These structures differ in the position of two 12 residue, β‐hairpin regions …