Steered molecular dynamics simulation in rational drug design

PC Do, EH Lee, L Le - Journal of Chemical Information and …, 2018 - ACS Publications
Conventional de novo drug design is time consuming, laborious, and resource intensive. In
recent years, emerging in silico approaches have been proven to be critical to accelerate the …

Revealing the mechanistic pathway of cholinergic inhibition of Alzheimer's disease by donepezil: a metadynamics simulation study

S Ghosh, K Jana, B Ganguly - Physical Chemistry Chemical Physics, 2019 - pubs.rsc.org
Donepezil, an acetylcholinesterase inhibitor, is an approved drug for the symptomatic
treatment of Alzheimer's disease (AD). The mechanistic pathway for the inhibition …

Molecular modeling studies on the multistep reactivation process of organophosphate-inhibited acetylcholinesterase and butyrylcholinesterase

J Jończyk, J Kukułowicz, K Łątka, B Malawska… - Biomolecules, 2021 - mdpi.com
Poisoning with organophosphorus compounds used as pesticides or misused as chemical
weapons remains a serious threat to human health and life. Their toxic effects result from …

The protonation state of Glu202 in acetylcholinesterase

J Wang, S Lai, Y Kong, W Yao… - … Structure, Function, and …, 2022 - Wiley Online Library
Acetylcholinesterase (AChE) is the crucial enzyme in the central nervous system. It is the
target of various organophosphorus nerve agents and pesticides, and the inhibition of AChE …

Discovery of RTA ricin subunit inhibitors: A computational study using PM7 quantum chemical method and steered molecular dynamics

EJF Chaves, LE Gomes da Cruz… - Journal of …, 2022 - Taylor & Francis
Ricin is a potent toxin derived from the castor bean plant and comprises two subunits, RTA
and RTB. Because of its cytotoxicity, ricin has alarmed world authorities for its potential use …

Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies

S Ghosh, NB Chandar, K Jana, B Ganguly - Journal of Computer-Aided …, 2017 - Springer
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a
detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators …

[PDF][PDF] Effective docking program for designing reactivator for treating organophosphorus inhibited AChE

S Ghosh, NB Chandar, R Lo, B Ganguly - JSM Chem, 2016 - academia.edu
Docking tools are computer-aided simulation process by which appropriate ligand
molecules (drugs) are screened for receptor molecules such as protein/enzyme. Molecular …

Assessment of DNA-binding affinity of cholinesterase reactivators and electrophoretic determination of their effect on topoisomerase I and II activity

J Janockova, E Zilecka, J Kasparkova, V Brabec… - Molecular …, 2016 - pubs.rsc.org
In this paper, we describe the biochemical properties and biological activity of a series of
cholinesterase reactivators (symmetrical bisquaternary xylene-linked compounds, K106 …

Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies

S Ghosh, K Jana, B Ganguly - Journal of Computer-Aided Molecular …, 2018 - Springer
The neutral oxime reactivator RS194B with a seven-membered ring has shown better
efficacy towards the tabun-inhibited AChE than that of RS69N with a six-membered ring and …

Exploration of assisting behavior of molecular-MO2 (M= Ti, Zr) reagents towards the detoxication of tabun: A DFT study

T Ash, T Debnath, S Sarkar, P Gurey, AK Das - Chemical Physics Letters, 2019 - Elsevier
In this study, the gas phase MO 2 (M= Ti, Zr) assisted detoxication of tabun (nerve agent) is
explored by employing DFT, where the energetics of assisted pathways are compared with …