Investigating drug–target residence time in kinases through enhanced sampling simulations

D Gobbo, V Piretti, RMC Di Martino… - Journal of Chemical …, 2019 - ACS Publications
It is widely accepted that drug–target association and dissociation rates directly affect drug
efficacy and safety. To rationally optimize drug binding kinetics, one must know the atomic …

A supervised molecular dynamics approach to unbiased ligand–protein unbinding

G Deganutti, S Moro, CA Reynolds - Journal of Chemical …, 2020 - ACS Publications
The recent paradigm shift toward the use of the kinetics parameters in place of
thermodynamic constants is leading the computational chemistry community to develop …

Combined free-energy calculation and machine learning methods for understanding ligand unbinding kinetics

M Badaoui, PJ Buigues, D Berta… - Journal of chemical …, 2022 - ACS Publications
The determination of drug residence times, which define the time an inhibitor is in complex
with its target, is a fundamental part of the drug discovery process. Synthesis and …

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 …

Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics

Y Miao, A Bhattarai, J Wang - Journal of chemical theory and …, 2020 - ACS Publications
Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

Molecular dynamics simulations and kinetic measurements to estimate and predict protein–ligand residence times

L Mollica, I Theret, M Antoine… - Journal of medicinal …, 2016 - ACS Publications
Ligand–target residence time is emerging as a key drug discovery parameter because it can
reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding …

Simulation of ligand dissociation kinetics from the protein kinase PYK2

J Spiriti, F Noé, CF Wong - Journal of computational chemistry, 2022 - Wiley Online Library
Early‐stage drug discovery projects often focus on equilibrium binding affinity to the target
alongside selectivity and other pharmaceutical properties. The kinetics of drug binding are …

Ligand Gaussian accelerated molecular dynamics 2 (LiGaMD2): Improved calculations of ligand binding thermodynamics and kinetics with closed protein pocket

J Wang, Y Miao - Journal of chemical theory and computation, 2023 - ACS Publications
Ligand binding thermodynamics and kinetics are critical parameters for drug design.
However, it has proven challenging to efficiently predict ligand binding thermodynamics and …

Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters

J Chen, W Wang, H Sun, W He - Mini Reviews in Medicinal …, 2024 - ingentaconnect.com
Rational predictions on binding kinetics parameters of drugs to targets play significant roles
in future drug designs. Full conformational samplings of targets are requisite for accurate …

The prediction of protein–ligand unbinding for modern drug discovery

Q Zhang, N Zhao, X Meng, F Yu, X Yao… - Expert Opinion on Drug …, 2022 - Taylor & Francis
Introduction Drug–target thermodynamic and kinetic information have perennially important
roles in drug design. The prediction of protein–ligand unbinding, which can provide …