Baseline model for predicting protein–ligand unbinding kinetics through machine learning

N Amangeldiuly, D Karlov… - Journal of Chemical …, 2020 - ACS Publications
Derivation of structure–kinetics relationships can help rational design and development of
new small-molecule drug candidates with desired residence times. Efforts are now being …

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 …

Prediction of the drug–target binding kinetics for flexible proteins by comparative binding energy analysis

A Nunes-Alves, F Ormersbach… - Journal of Chemical …, 2021 - ACS Publications
There is growing consensus that the optimization of the kinetic parameters for drug–protein
binding leads to improved drug efficacy. Therefore, computational methods have been …

Computational modeling approaches to quantitative structure–binding kinetics relationships in drug discovery

PG De Benedetti, F Fanelli - Drug Discovery Today, 2018 - Elsevier
Highlights•The interplay of kinetic rates and binding affinity is essential in drug
design/discovery.•Examples of linear correlations between kinetic rates and binding affinity …

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 …

15 Years of molecular simulation of drug-binding kinetics

CF Wong - Expert Opinion on Drug Discovery, 2023 - Taylor & Francis
Introduction Drug-binding kinetics has been increasingly recognized as an important factor
to be considered in drug discovery. Long residence time could prolong the action of some …

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 …

[HTML][HTML] Understanding ligand-receptor non-covalent binding kinetics using molecular modeling

Z Tang, CC Roberts, AC Chia-en - Frontiers in bioscience …, 2017 - ncbi.nlm.nih.gov
Kinetic properties may serve as critical differentiators and predictors of drug efficacy and
safety, in addition to the traditionally focused binding affinity. However the quantitative …

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 …

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 …