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 ignored but can have significant influence on drug efficacy. Therefore, increasing attention has been paid on evaluating drug‐binding kinetics early in a drug discovery process. Simulating drug‐binding kinetics at the atomic level is challenging for the long time scale involved. Here, we used the transition‐based reweighting analysis method (TRAM) with the Markov state model to study the dissociation of a ligand from the protein kinase PYK2. TRAM combines biased and unbiased simulations to reduce computational costs. This work used the umbrella sampling technique for the biased simulations. Although using the potential of mean force from umbrella sampling simulations with the transition‐state theory over‐estimated the dissociation rate by three orders of magnitude, TRAM gave a dissociation rate within an order of magnitude of the experimental value. Using the transition‐based reweighing analysis method (TRAM), we showed that the dissociation of an inhibitor from the bound state (4) of the PYK2 protein kinase went through an intermediate state (2) to two pre‐dissociated states (0 and 3) before complete dissociation. We also found a mis‐trapped bound state (1) that bound to PYK2 with a higher energy than the true bound state. The model predicted a dissociation rate within an order of magnitude of experiment.