Comprehending the structure, dynamics, and mechanism of action of drug-resistant HIV protease

A Dakshinamoorthy, A Asmita, S Senapati - ACS omega, 2023 - ACS Publications
Since the emergence of the Human Immunodeficiency Virus (HIV) in the 1980s, strategies to
combat HIV-AIDS are continuously evolving. Among the many tested targets to tackle this …

Fragment‐based screen against HIV protease

AL Perryman, Q Zhang, HH Soutter… - Chemical biology & …, 2010 - Wiley Online Library
We have employed a fragment‐based screen against wild‐type (NL4‐3) HIV protease (PR)
using the Active Sight fragment library and X‐ray crystallography. The experiments reveal …

Electrostatics plays a crucial role in HIV-1 protease substrate binding, drugs fail to take advantage

M Ahsan, C Pindi, S Senapati - Biochemistry, 2020 - ACS Publications
HIV-1 protease (HIVPR) is an important drug target for combating AIDS. This enzyme is an
aspartyl protease that is functionally active in its dimeric form. Nuclear magnetic resonance …

Dynamic flaps in HIV‐1 protease adopt unique ordering at different stages in the catalytic cycle

S Karthik, S Senapati - Proteins: Structure, Function, and …, 2011 - Wiley Online Library
The flexibility of HIV‐1 protease flaps is known to be essential for the enzymatic activity.
Here we attempt to capture a multitude of conformations of the free and substrate‐bound HIV …

Role of water in the enzymatic catalysis: study of ATP+ AMP→ 2ADP conversion by adenylate kinase

BV Adkar, B Jana, B Bagchi - The Journal of Physical Chemistry A, 2011 - ACS Publications
The catalytic conversion ATP+ AMP→ 2ADP by the enzyme adenylate kinase (ADK)
involves the binding of one ATP molecule to the LID domain and one AMP molecule to the …

Switches of hydrogen bonds during ligand–protein association processes determine binding kinetics

YM Huang, M Kang, CA Chang - Journal of Molecular …, 2014 - Wiley Online Library
Revealing the processes of ligand–protein associations deepens our understanding of
molecular recognition and binding kinetics. Hydrogen bonds (H‐bonds) play a crucial role in …

Dynamics of “flap” structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy

VY Torbeev, H Raghuraman, K Mandal… - Journal of the …, 2009 - ACS Publications
The unliganded form of nitroxide spin-labeled HIV-1 protease and three different complexes
with inhibitors were studied by pulse-EPR spectroscopy to determine “interflap” distance …

Identifying the Molecular Mechanics and Binding Dynamics Characteristics of Potent Inhibitors to HIV‐1 Protease

D Li, MS Liu, B Ji, KC Hwang… - Chemical Biology & Drug …, 2012 - Wiley Online Library
Human immunodeficiency virus type 1 protease (HIV‐1 PR) is one of the primary inhibition
targets for chemotherapy of AIDS because of its critical role in the replication cycle of the …

[HTML][HTML] Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design

SL Rath, S Senapati - PloS one, 2013 - journals.plos.org
Cyclin-dependent kinases (CDKs) belong to the CMGC subfamily of protein kinases and
play crucial roles in eukaryotic cell division cycle. At least seven different CDKs have been …

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 …