A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of …

DB Kokh, B Doser, S Richter, F Ormersbach… - The Journal of …, 2020 - pubs.aip.org
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …

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 …

Kinetics of ligand–protein dissociation from all-atom simulations: Are we there yet?

JML Ribeiro, ST Tsai, D Pramanik, Y Wang… - Biochemistry, 2018 - ACS Publications
Large parallel gains in the development of both computational resources and sampling
methods have now made it possible to simulate dissociation events in ligand–protein …

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 …

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 …

Can one trust kinetic and thermodynamic observables from biased metadynamics simulations?: Detailed quantitative benchmarks on millimolar drug fragment …

D Pramanik, Z Smith, A Kells… - The Journal of Physical …, 2019 - ACS Publications
Understanding ligand dissociation mechanisms at an atomic resolution is a highly desired
but difficult to achieve objective in experiments as well as in computer simulations. Structural …

Data-driven classification of ligand unbinding pathways

D Ray, M Parrinello - … of the National Academy of Sciences, 2024 - National Acad Sciences
Studying the pathways of ligand–receptor binding is essential to understand the mechanism
of target recognition by small molecules. The binding free energy and kinetics of protein …

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 …

[HTML][HTML] Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations

A Nunes-Alves, DB Kokh, RC Wade - Current Research in Structural …, 2021 - Elsevier
The protein-ligand residence time, τ, influences molecular function in biological networks
and has been recognized as an important determinant of drug efficacy. To predict τ …