Download MendeleyEstimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations.
Wolf, S., Amaral, M., Lowinski, M., Vallee, F., Musil, D., Guldenhaupt, J., Dreyer, M.K., Bomke, J., Frech, M., Schlitter, J., Gerwert, K.(2019) J Chem Inf Model 59: 5135-5147
- PubMed: 31697501
- DOI: https://doi.org/10.1021/acs.jcim.9b00592
- Primary Citation of Related Structures:
5LRL - PubMed Abstract:
We here report on nonequilibrium targeted molecular dynamics simulations as a tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray crystallography on two small molecule compound libraries bound to the N-terminal domain of the chaperone Hsp90, we show that the mean nonequilibrium work computed in an ensemble of trajectories of enforced ligand unbinding is a promising predictor for ligand unbinding rates. We furthermore investigate the molecular basis determining unbinding rates within the compound libraries. We propose ligand conformational changes and protein-ligand nonbonded interactions to impact on unbinding rates. Ligands may remain longer at the protein if they exhibit strong electrostatic and/or van der Waals interactions with the target. In the case of ligands with a rigid chemical scaffold that exhibit longer residence times, transient electrostatic interactions with the protein appear to facilitate unbinding. Our results imply that understanding the unbinding pathway and the protein-ligand interactions along this path is crucial for the prediction of small molecule ligands with defined unbinding kinetics.
Organizational Affiliation:
Department of Biophysics , Ruhr-University Bochum , 44780 Bochum , Germany.
