Molecular dynamics simulations and novel drug discovery

X Liu, D Shi, S Zhou, H Liu, H Liu… - Expert opinion on drug …, 2018 - Taylor & Francis
Introduction: Molecular dynamics (MD) simulations can provide not only plentiful dynamical
structural information on biomacromolecules but also a wealth of energetic information …

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods

S Kassem, M Ahmed, S El-Sheikh… - Journal of Molecular …, 2015 - Elsevier
Entropy of binding constitutes a major, and in many cases a detrimental, component of the
binding affinity in biomolecular interactions. While the enthalpic part of the binding free …

Dynamics of human protein kinase Aurora A linked to drug selectivity

W Pitsawong, V Buosi, R Otten, RV Agafonov, A Zorba… - Elife, 2018 - elifesciences.org
Protein kinases are major drug targets, but the development of highly-selective inhibitors
has been challenging due to the similarity of their active sites. The observation of distinct …

Human PD-1 binds differently to its human ligands: a comprehensive modeling study

C Viricel, M Ahmed, K Barakat - Journal of Molecular Graphics and …, 2015 - Elsevier
Abstract Programmed death-1 (PD-1) is a potent inhibitory receptor of T cells which binds to
two different ligands, namely PD-L1 and PD-L2, and upon binding, it inhibits T cell …

A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug …

A Anwar-Mohamed, KH Barakat, R Bhat, SY Noskov… - Toxicology letters, 2014 - Elsevier
Acquired cardiac long QT syndrome (LQTS) is a frequent drug-induced toxic event that is
often caused through blocking of the human ether-á-go-go-related (hERG) K+ ion channel …

Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade

M Ahmed, H Jalily Hasani, A Ganesan… - Drug Design …, 2017 - Taylor & Francis
Abnormalities in the human Nav1. 5 (hNav1. 5) voltage-gated sodium ion channel (VGSC)
are associated with a wide range of cardiac problems and diseases in humans. Current …

A refined model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes

KH Barakat, A Anwar-Mohamed… - Journal of chemical …, 2015 - ACS Publications
Many direct-acting antiviral agents (DAAs) that selectively block hepatitis C virus (HCV)
replication are currently under development. Among these agents is Daclatasvir, a first-in …

A 'deep dive'into the SARS-Cov-2 polymerase assembly: identifying novel allosteric sites and analyzing the hydrogen bond networks and correlated dynamics

K Barakat, M Ahmed, Y Tabana… - Journal of Biomolecular …, 2022 - Taylor & Francis
Replication of the SARS-CoV-2 genome is a fundamental step in the virus life cycle and
inhibiting the SARS-CoV2 replicase machinery has been proven recently as a promising …

Molecular dynamics simulation and prediction of druggable binding sites

T Feng, K Barakat - Computational drug discovery and design, 2018 - Springer
Binding site identification and druggability evaluation are two essential steps in structure-
based drug design. A druggable binding site tends to have high binding affinity to drug-like …

Combining machine learning, molecular dynamics, and free energy analysis for (5HT)-2A receptor modulator classification

X Yu, Y Eid, M Jama, D Pham, M Ahmed… - Journal of Molecular …, 2024 - Elsevier
Abstract The 5-Hydroxytryptamine (5HT)-2A receptor, a key target in psychoactive drug
development, presents significant challenges in the design of selective compounds. Here …