[HTML][HTML] Enhanced-sampling simulations for the estimation of ligand binding kinetics: current status and perspective
The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …
parameter of fundamental importance in drug design. Here we review recent major …
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 …
roles in drug design. The prediction of protein–ligand unbinding, which can provide …
Predicting biomolecular binding kinetics: A review
Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
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 …
efficacy and safety. To rationally optimize drug binding kinetics, one must know the atomic …
Toward high-throughput predictive modeling of protein binding/unbinding kinetics
SH Chiu, L Xie - Journal of chemical information and modeling, 2016 - ACS Publications
One of the unaddressed challenges in drug discovery is that drug potency determined in
vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in …
vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in …
Combined free-energy calculation and machine learning methods for understanding ligand unbinding kinetics
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 …
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 …
between milliseconds and several hours is a prime challenge for biased molecular …
A supervised molecular dynamics approach to unbiased ligand–protein unbinding
The recent paradigm shift toward the use of the kinetics parameters in place of
thermodynamic constants is leading the computational chemistry community to develop …
thermodynamic constants is leading the computational chemistry community to develop …
Predicting ligand binding affinity using on-and off-rates for the SAMPL6 SAMPLing challenge
Interest in ligand binding kinetics has been growing rapidly, as it is being discovered in more
and more systems that ligand residence time is the crucial factor governing drug efficacy …
and more systems that ligand residence time is the crucial factor governing drug efficacy …
Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and
toxicity of a drug candidate. Binding affinity for the biological target has been usually …
toxicity of a drug candidate. Binding affinity for the biological target has been usually …