Lane W Votapka, Anupam Anand Ojha, Naoya Asada, and Rommie E Amaro (2024).
The journal of physical chemistry letters, 10.1021/acs.jpclett.4c02332.   (PubMed)

Accurately describing protein-ligand binding and unbinding kinetics remains challenging. Computational calculations are difficult and costly, while experimental measurements often lack molecular detail and can be unobtainable. Here, we extend our multiscale milestoning method, Simulation-Enabled Estimation of Kinetics Rates (SEEKR), with metadynamics molecular dynamics simulations to yield accurate small molecule drug residence times. Using the pharmaceutically relevant threonine-tyrosine kinase (TTK) and eight long-residence-time (tens of seconds to hours) inhibitors, we demonstrate accurate prediction of absolute and rank-ordered ligand residence times and free energies of binding.


This work describes an example of using Metadynamics in kinetic calculations.

The following methods are also used: