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 …

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 …

Kinetics of ligand binding through advanced computational approaches: a review

A Dickson, P Tiwary, H Vashisth - Current topics in medicinal …, 2017 - ingentaconnect.com
Ligand residence times and binding rates have been found to be useful quantities to
consider during drug design. The underlying structural and dynamic determinants of these …

Thermodynamics and kinetics of drug-target binding by molecular simulation

S Decherchi, A Cavalli - Chemical Reviews, 2020 - ACS Publications
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness

P Conflitti, S Raniolo, V Limongelli - Journal of chemical theory …, 2023 - ACS Publications
Computational techniques applied to drug discovery have gained considerable popularity
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …

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 …

Predicting biomolecular binding kinetics: A review

J Wang, HN Do, K Koirala, Y Miao - Journal of Chemical Theory …, 2023 - ACS Publications
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 …

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 …

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 …

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 …