Along the allostery stream: Recent advances in computational methods for allosteric drug discovery

D Ni, Z Chai, Y Wang, M Li, Z Yu, Y Liu… - Wiley …, 2022 - Wiley Online Library
Allostery is a universal, biological phenomenon in which orthosteric sites are fine‐tuned by
topologically distal allosteric sites triggered by perturbations, such as ligand binding, residue …

Drugs for allosteric sites on receptors

CJ Wenthur, PR Gentry, TP Mathews… - Annual review of …, 2014 - annualreviews.org
The presence of druggable, topographically distinct allosteric sites on a wide range of
receptor families has offered new paradigms for small molecules to modulate receptor …

Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

L Chang, A Mondal, B Singh… - Wiley …, 2024 - Wiley Online Library
Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

[HTML][HTML] AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis

JG Greener, MJE Sternberg - BMC bioinformatics, 2015 - Springer
Background Despite being hugely important in biological processes, allostery is poorly
understood and no universal mechanism has been discovered. Allosteric drugs are a largely …

Unraveling structural mechanisms of allosteric drug action

R Nussinov, CJ Tsai - Trends in pharmacological sciences, 2014 - cell.com
Orthosteric drugs block the active site to obstruct function; allosteric drugs modify the
population of the active state, to modulate function. Available data lead us to propose that …

Are deep learning structural models sufficiently accurate for virtual screening? application of docking algorithms to AlphaFold2 predicted structures

AM Díaz-Rovira, H Martín, T Beuming… - Journal of Chemical …, 2023 - ACS Publications
Machine learning-based protein structure prediction algorithms, such as RosettaFold and
AlphaFold2, have greatly impacted the structural biology field, arousing a fair amount of …

A biophysical framework for double-drugging kinases

C Kim, H Ludewig, A Hadzipasic… - Proceedings of the …, 2023 - National Acad Sciences
Selective orthosteric inhibition of kinases has been challenging due to the conserved active
site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of …

Emerging computational methods for the rational discovery of allosteric drugs

JR Wagner, CT Lee, JD Durrant, RD Malmstrom… - Chemical …, 2016 - ACS Publications
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

[HTML][HTML] Integrated computational approaches and tools for allosteric drug discovery

O Sheik Amamuddy, W Veldman, C Manyumwa… - International journal of …, 2020 - mdpi.com
Understanding molecular mechanisms underlying the complexity of allosteric regulation in
proteins has attracted considerable attention in drug discovery due to the benefits and …

Exploring and exploiting allostery: Models, evolution, and drug targeting

A Peracchi, A Mozzarelli - Biochimica et Biophysica Acta (BBA)-Proteins …, 2011 - Elsevier
The concept of allostery was elaborated almost 50years ago by Monod and coworkers to
provide a framework for interpreting experimental studies on the regulation of protein …