Prediction of\nThreonine-Tyrosine Kinase Receptor–Ligand\nUnbinding Kinetics with Multiscale Milestoning and Metadynamics

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