Unbinding Kinetics of Muscarinic M3 Receptor Antagonists Explained by Metadynamics Simulations

• Published in: Journal of chemical information and modeling 2023-05, Vol.63 (9), p.2842-2856
• Main Authors: Galvani, Francesca, Pala, Daniele, Cuzzolin, Alberto, Scalvini, Laura, Lodola, Alessio, Mor, Marco, Rizzi, Andrea
• Format: Article
• Language: English
• Subjects: Binding sites; Design parameters; Kinetics; Ligands; Molecular Dynamics Simulation; Pharmaceutical Modeling; Physics; Receptor, Muscarinic M3; Receptors; Simulation
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.3c00042

The residence time (RT), the time for which a drug remains bound to its biological target, is a critical parameter for drug design. The prediction of this key kinetic property has been proven to be challenging and computationally demanding in the framework of atomistic simulations. In the present work, we setup and applied two distinct metadynamics protocols to estimate the RTs of muscarinic M3 receptor antagonists. In the first method, derived from the conformational flooding approach, the kinetics of unbinding is retrieved from a physics-based parameter known as the acceleration factor α (i.e., the running average over time of the potential deposited in the bound state). Such an approach is expected to recover the absolute RT value for a compound of interest. In the second method, known as the t META‑D approach, a qualitative estimation of the RT is given by the time of simulation required to drive the ligand from the binding site to the solvent bulk. This approach has been developed to reproduce the change of experimental RTs for compounds targeting the same target. Our analysis shows that both computational protocols are able to rank compounds in agreement with their experimental RTs. Quantitative structure–kinetics relationship (SKR) models can be identified and employed to predict the impact of a chemical modification on the experimental RT once a calibration study has been performed.