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 …

Tau and neuroinflammation in Alzheimer's disease: Interplay mechanisms and clinical translation

Y Chen, Y Yu - Journal of neuroinflammation, 2023 - Springer
Alzheimer's Disease (AD) contributes to most cases of dementia. Its prominent
neuropathological features are the extracellular neuritic plaques and intercellular …

Modeling the expansion of virtual screening libraries

J Lyu, JJ Irwin, BK Shoichet - Nature chemical biology, 2023 - nature.com
Recently,'tangible'virtual libraries have made billions of molecules readily available.
Prioritizing these molecules for synthesis and testing demands computational approaches …

Common activation mechanism of class A GPCRs

Q Zhou, D Yang, M Wu, Y Guo, W Guo, L Zhong, X Cai… - Elife, 2019 - elifesciences.org
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human
physiology. Understanding receptor activation mechanism is critical for discovering novel …

GPCR activation mechanisms across classes and macro/microscales

AS Hauser, AJ Kooistra, C Munk… - Nature structural & …, 2021 - nature.com
Two-thirds of human hormones and one-third of clinical drugs activate~ 350 G-protein-
coupled receptors (GPCR) belonging to four classes: A, B1, C and F. Whereas a model of …

Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design

S Lu, X He, Z Yang, Z Chai, S Zhou, J Wang… - Nature …, 2021 - nature.com
G protein-coupled receptors (GPCRs) are the most common proteins targeted by approved
drugs. A complete mechanistic elucidation of large-scale conformational transitions …

ProLIF: a library to encode molecular interactions as fingerprints

C Bouysset, S Fiorucci - Journal of cheminformatics, 2021 - Springer
Interaction fingerprints are vector representations that summarize the three-dimensional
nature of interactions in molecular complexes, typically formed between a protein and a …

Mechanisms of signalling and biased agonism in G protein-coupled receptors

D Wootten, A Christopoulos, M Marti-Solano… - … reviews Molecular cell …, 2018 - nature.com
G protein-coupled receptors (GPCRs) are the largest group of cell surface receptors in
humans that signal in response to diverse inputs and regulate a plethora of cellular …

Impact of GPCR structures on drug discovery

M Congreve, C de Graaf, NA Swain, CG Tate - Cell, 2020 - cell.com
Structures of 70 unique G protein-coupled receptors (GPCRs) have been determined, with
over 370 structures in total bound to different ligands and the receptors in various …

How accurately can one predict drug binding modes using AlphaFold models?

M Karelina, JJ Noh, RO Dror - Elife, 2023 - elifesciences.org
Computational prediction of protein structure has been pursued intensely for decades,
motivated largely by the goal of using structural models for drug discovery. Recently …