Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Ligand binding free energy and kinetics calculation in 2020

V Limongelli - Wiley Interdisciplinary Reviews: Computational …, 2020 - Wiley Online Library
Ligand/protein binding (LPB) is a major topic in medicine, chemistry and biology. Since the
advent of computers, many scientists have put efforts in developing theoretical models that …

Estimation of drug-target residence times by τ-random acceleration molecular dynamics simulations

DB Kokh, M Amaral, J Bomke, U Grädler… - Journal of chemical …, 2018 - ACS Publications
Drug-target residence time (τ), one of the main determinants of drug efficacy, remains highly
challenging to predict computationally and, therefore, is usually not considered in the early …

New approaches for computing ligand–receptor binding kinetics

NJ Bruce, GK Ganotra, DB Kokh, SK Sadiq… - Current opinion in …, 2018 - Elsevier
Highlights•Many new approaches to computing biomolecular binding kinetics developed
recently.•Enhanced sampling simulation methods permit long-time binding kinetics to be …

Predicting protein–ligand binding and unbinding kinetics with biased MD simulations and coarse-graining of dynamics: Current state and challenges

S Wolf - Journal of Chemical Information and Modeling, 2023 - ACS Publications
The prediction of drug–target binding and unbinding kinetics that occur on time scales
between milliseconds and several hours is a prime challenge for biased molecular …

Applying structure-based drug design approaches to allosteric modulators of GPCRs

M Congreve, C Oswald, FH Marshall - Trends in pharmacological sciences, 2017 - cell.com
Structural insights have been revealed from X-ray co-complexes of a range of G protein-
coupled receptors (GPCRs) and their allosteric ligands. The understanding of how small …

Mechanistic understanding from molecular dynamics in pharmaceutical research 2: lipid membrane in drug design

T Róg, M Girych, A Bunker - Pharmaceuticals, 2021 - mdpi.com
We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …

Structure-based optimization strategies for G protein-coupled receptor (GPCR) allosteric modulators: a case study from analyses of new metabotropic glutamate …

JA Christopher, Z Orgován, M Congreve… - Journal of medicinal …, 2018 - ACS Publications
Two interesting new X-ray structures of negative allosteric modulator (NAM) ligands for the
mGlu5 receptor, M-MPEP (3) and fenobam (4), are reported. The new structures show how …

Binding kinetics survey of the drugged kinome

V Georgi, F Schiele, BT Berger, A Steffen… - Journal of the …, 2018 - ACS Publications
Target residence time is emerging as an important optimization parameter in drug discovery,
yet target and off-target engagement dynamics have not been clearly linked to the clinical …

How do molecular dynamics data complement static structural data of GPCRs

M Torrens-Fontanals, TM Stepniewski… - International Journal of …, 2020 - mdpi.com
G protein-coupled receptors (GPCRs) are implicated in nearly every physiological process
in the human body and therefore represent an important drug targeting class. Advances in X …