title: Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps.
abstract: The ability to predict the mechanisms and the associated rate constants of protein-ligand unbinding is of great practical importance in drug design. In this work we demonstrate how a recently introduced metadynamics-based approach allows exploration of the unbinding pathways, estimation of the rates, and determination of the rate-limiting steps in the paradigmatic case of the trypsin-benzamidine system. Protein, ligand, and solvent are described with full atomic resolution. Using metadynamics, multiple unbinding trajectories that start with the ligand in the crystallographic binding pose and end with the ligand in the fully solvated state are generated. The unbinding rate k off is computed from the mean residence time of the ligand. Using our previously computed binding affinity we also obtain the binding rate k on. Both rates are in agreement with reported experimental values. We uncover the complex pathways of unbinding trajectories and describe the critical rate-limiting steps with unprecedented detail. Our findings illuminate the role played by the coupling between subtle protein backbone fluctuations and the solvation by water molecules that enter the binding pocket and assist in the breaking of the shielded hydrogen bonds. We expect our approach to be useful in calculating rates for general protein-ligand systems and a valid support for drug design.
authors.affiliation: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8006 Zurich, Switzerland; Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland;
authors.forename: Pratyush
authors.initials: P
authors.lastname: Tiwary
authors.affiliation: Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland; Department of Pharmacy, University of Naples Federico II, I-80131 Naples, Italy; and.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Limongelli
authors.affiliation: Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland; Institute of Process Engineering, Eidgenössische Technische Hochschule Zürich, 8006 Zurich, Switzerland.
authors.forename: Matteo
authors.initials: M
authors.lastname: Salvalaglio
authors.affiliation: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8006 Zurich, Switzerland; Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland; parrinello@phys.chem.ethz.ch.
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
mesh_terms: D007700:Kinetics; D008024:Ligands; D011506:Proteins / Q000378:metabolism*
chemical_list: D008024:Ligands; D011506:Proteins
keywords: drug design; enhanced sampling; kinetics; protein–ligand unbinding