Equilibrium and Non-equilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations

17 October 2024, Version 3
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Free energy calculations for protein-ligand complexes have become widespread in recent years owing to several conceptual, methodological and technological advances. Central among these is the use of ensemble methods which permits accurate, precise and reproducible predictions and are necessary for uncertainty quantification. Absolute binding free energies (ABFEs) are challenging to predict using alchemical methods and their routine application in drug discovery has remained out of reach until now. Here, we apply ensemble alchemical ABFE methods to a large dataset comprising 219 ligand-protein complexes and obtain statistically robust results with high accuracy (< 1 kcal/mol). We compare equilibrium and non-equilibrium methods for ABFE predictions at large scale and provide a systematic critical assessment of each method. The equilibrium method is more accurate, precise, faster, computationally more cost-effective and requires a much simpler protocol, making it preferable for large scale and blind applications. We find that the calculated free energy distributions are non-normal and discuss the consequences. We recommend a definitive protocol to perform ABFE calculations optimally. Using this protocol, it is possible to perform thousands of ABFE calculations within a few hours on modern exascale machines.

Keywords

Absolute Binding Affinity
Alchemical methods
Thermodynamic Integration
Large scale Dataset
Non-equilibrium methods
Molecular Dynamics
Protein-Ligand Binding
Stochasticity
Aleatoric Uncertainty Quantification
Alchemical ABFE protocol
Drug Discovery
Ensemble Simulations

Supplementary materials

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Supporting Information
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Additional analyses including tables and figures referred to in the main text.
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