Ligand dissociation mechanisms from all-atom simulations: Are we there yet?

TL;DR

This paper reviews recent advances in all-atom molecular dynamics simulations for studying ligand-protein dissociation, highlighting new methods, their successes, limitations, and implications for drug design and force-field refinement.

Contribution

It provides a comprehensive overview of current MD methods for ligand dissociation, including innovative sampling techniques and critical analysis of their effectiveness.

Findings

Recent methods enable detailed mechanistic insights into ligand dissociation.

Sampling techniques have improved timescale access, revealing transient states.

Challenges remain in accurately predicting kinetics and refining force-fields.

Abstract

Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress, together with the inherent spatiotemporal resolution associated with molecular simulations, has left their use for investigating dissociation processes brimming with potential, both in rational drug design, where it can be an invaluable tool for determining the mechanistic driving forces behind dissociation rate constants, as well as in force-field development, where it can provide a catalog of transient molecular structures on which to refine force-fields. Although much progress has been made in making force-fields more accurate, reducing their error for transient structures along a transition path could yet prove to be a critical development helping to make kinetic predictions much more accurate. In what follows we will provide a state-of-the-art compilation of the molecular dynamics (MD) methods used to investigate the kinetics and mechanisms of ligand-protein dissociation processes. Due to the timescales of such processes being slower than what is accessible using straightforward MD simulations, several ingenious schemes are being devised at a rapid rate to overcome this obstacle. Here we provide an up-to-date compendium of such methods and their achievements/shortcomings in extracting mechanistic insight into ligand-protein dissociation. We conclude with a critical and provocative appraisal attempting to answer the title of this review.