Kinetics of Ligand–Protein Dissociation from All-Atom Simulations: Are We There Yet?

• Published in: Biochemistry (Easton) 2019-01, Vol.58 (3), p.156-165
• Main Authors: Ribeiro, João Marcelo Lamim, Tsai, Sun-Ting, Pramanik, Debabrata, Wang, Yihang, Tiwary, Pratyush
• Format: Article
• Language: English
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/acs.biochem.8b00977

Large parallel gains in the development of both computational resources and 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, and in force-field development, where it can provide a catalog of transient molecular structures with 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 enhanced sampling methods based on molecular dynamics (MD) simulations used to investigate the kinetics and mechanisms of ligand–protein dissociation processes. Due to the time scales 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 and shortcomings in extracting mechanistic insight into ligand–protein dissociation. We conclude with a critical and provocative appraisal attempting to answer the title of this Perspective.