Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations

• Published in: Journal of chemical theory and computation Vol. 20; no. 10; pp. 4350 - 4362
• Main Authors: Champion, Candide, Hünenberger, Philippe H., Riniker, Sereina
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 28.05.2024
• Subjects: Biomolecular Systems; Energy methods; Factor Xa Inhibitors - chemistry; Free energy; Glycogen Synthase Kinase 3 beta - antagonists & inhibitors; Glycogen Synthase Kinase 3 beta - chemistry; Glycogens; Humans; Isomerism; Kinases; Molecular dynamics; Molecular Dynamics Simulation; Molecular properties; Protonation; Protons; Thermodynamics
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.4c00370

The majority of drug-like molecules contain at least one ionizable group, and many common drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a mixture of protonation and/or tautomeric states at physiological pH. Intrinsically, standard classical molecular dynamics (MD) simulations cannot describe such equilibria between states, which negatively impacts the prediction of key molecular properties in silico. Following the formalism described by de Oliveira and co-workers (J. Chem. Theory Comput. 2019, 15, 424–435) to consider the influence of all states on the binding process based on alchemical free-energy calculations, we demonstrate in this work that the multistate method replica-exchange enveloping distribution sampling (RE-EDS) is well suited to describe molecules with multiple protonation and/or tautomeric states in a single simulation. We apply our methodology to a series of eight inhibitors of factor Xa with two protonation states and a series of eight inhibitors of glycogen synthase kinase 3β (GSK3β) with two tautomeric states. In particular, we show that given a sufficient phase-space overlap between the states, RE-EDS is computationally more efficient than standard pairwise free-energy methods.