Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

Abstract

Accurate prediction of standard binding free energies describing protein–ligand association remains a daunting computational endeavor. This challenge is rooted to a large extent in the considerable changes in conformational, translational, and rotational entropies underlying the binding process that atomistic simulations cannot easily sample. In spite of significant methodological advances, reflected in a continuously improving agreement with experiment, a characterization of alternate strategies aimed at measuring binding affinities, notably their respective advantages and drawbacks, is somewhat lacking. Here, two distinct avenues to determine the standard binding free energy are compared in the case of a short, proline-rich peptide associating to the Src homology domain 3 of tyrosine kinase Abl. These avenues, one relying upon alchemical transformations and the other on potentials of mean force (PMFs), invoke a series of geometrical restraints acting on collective variables designed to alleviate sampling limitations inherent to classical molecular dynamics simulations. The experimental binding free energy of Δ G bind = −7.99 kcal/mol is well reproduced by the two strategies developed herein, with Δ G bind = −7.7 for the alchemical route and Δ G bind = −7.8 kcal/mol for the alternate PMF-based route. In detailing the underpinnings of these numerical strategies devised for the accurate determination of standard binding free energies, many practical elements of the proposed rigorous, conceptual framework are clarified, thereby paving way to tackle virtually any recognition and association phenomenon.