The role of water and steric constraints in the kinetics of cavity-ligand unbinding

TL;DR

This study uses advanced molecular dynamics simulations to investigate how water and steric factors influence the unbinding kinetics of a ligand from a protein cavity, revealing multiple unbinding pathways and the impact of constraints on residence time.

Contribution

It introduces a metadynamics-based approach to directly assess unbinding kinetics and elucidates the effects of steric constraints and solvent behavior on ligand dissociation pathways.

Findings

Unbinding time is approximately 4000 seconds under axial constraints.

Removing steric constraints accelerates unbinding by 20 times.

Dewetting transition shifts from sharp to continuous when constraints are removed.

Abstract

A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but extremely difficult task due to the long timescales involved. This gets further complicated by the presence of biophysical factors such as steric and solvation effects. In this work, we perform molecular dynamics (MD) simulations of the unbinding of a popular prototypical hydrophobic cavity-ligand system using a metadynamics based approach that allows direct assessment of kinetic pathways and parameters. When constrained to move in an axial manner, we find the unbinding time to be on the order of 4000 sec. In accordance with previous studies, we find that the ligand must pass through a region of sharp dewetting transition manifested by sudden and high fluctuations in solvent density in the cavity. When we remove the steric constraints on ligand, the unbinding happens predominantly by an alternate pathway, where the unbinding becomes 20 times faster, and the sharp dewetting transition instead becomes continuous. We validate the unbinding timescales from metadynamics through a Poisson analysis, and by comparison through detailed balance to binding timescale estimates from unbiased MD. This work demonstrates that enhanced sampling can be used to perform explicit solvent molecular dynamics studies at timescales previously unattainable, obtaining direct and reliable pictures of the underlying physio-chemical factors including free energies and rate constants.