Investigating cryptic binding sites by molecular dynamics simulations

A Kuzmanic, GR Bowman… - Accounts of chemical …, 2020 - ACS Publications
Conspectus This Account highlights recent advances and discusses major challenges in
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …

Rational design of allosteric modulators: Challenges and successes

A Chatzigoulas, Z Cournia - Wiley Interdisciplinary Reviews …, 2021 - Wiley Online Library
Recent advances in structural biology and computational techniques have revealed
allosteric mechanisms for an abundance of targets leading to the establishment of rational …

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 …

Structure based virtual screening: Fast and slow

A Varela‐Rial, M Majewski… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
For many decades virtual screening methods have provided a convenient and cost effective
in silico solution in the early stages of drug discovery. In particular, molecular docking uses …

Manifold learning in atomistic simulations: a conceptual review

J Rydzewski, M Chen, O Valsson - Machine Learning: Science …, 2023 - iopscience.iop.org
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …

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 …

Aminergic gpcr–ligand interactions: A chemical and structural map of receptor mutation data

M Vass, S Podlewska, IJP De Esch… - Journal of medicinal …, 2018 - ACS Publications
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in
various diseases and represents a major drug discovery target class. Structure …

[HTML][HTML] The impact of the secondary binding pocket on the pharmacology of class A GPCRs

A Egyed, DJ Kiss, GM Keserű - Frontiers in Pharmacology, 2022 - frontiersin.org
G-protein coupled receptors (GPCRs) are considered important therapeutic targets due to
their pathophysiological significance and pharmacological relevance. Class A receptors …

Cryptic pocket formation underlies allosteric modulator selectivity at muscarinic GPCRs

SA Hollingsworth, B Kelly, C Valant… - Nature …, 2019 - nature.com
Allosteric modulators are highly desirable as drugs, particularly for G-protein-coupled
receptor (GPCR) targets, because allosteric drugs can achieve selectivity between closely …

Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells

JM Mattheisen, C Limberakis, RB Ruggeri… - Journal of the …, 2023 - ACS Publications
G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are
important drug targets. Despite the availability of high-resolution structures, the discovery of …