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 …
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 …
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 …
Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics
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 …
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 …
reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding …
Simulation of ligand dissociation kinetics from the protein kinase PYK2
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 …
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
Ligand binding thermodynamics and kinetics are critical parameters for drug design.
However, it has proven challenging to efficiently predict ligand binding thermodynamics and …
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 …
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 …
roles in drug design. The prediction of protein–ligand unbinding, which can provide …