Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

Abstract

A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, beginning with single poses from docking, then including multiple poses, additional protein conformational changes, and using an improved charge model. Computed absolute binding free energies had an RMS error of 1.9 kcal/mol relative to previously determined experimental values. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys in a set of putative binders identified by docking. In these prospective tests, the RMS error in predicted binding free energies relative to those subsequently determined experimentally was only 0.6 kcal/mol. X-ray crystal structures of the new ligands bound in the cavity corresponded closely to predictions from the free energy calculations, but sometimes differed from those predicted by docking. Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved.

Separated topologies—A method for relative binding free energy calculations using orientational restraints

“…These orientational restraints are commonly applied in absolute binding free energy calculations. 22,23,12,24 In essence, two absolute binding calculations are performed at once, in different directions, and overlapping in the middle. The path (representing transformation G site in Figure 1) is shown in Figure 2.…”

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

“…The ligands are shown in Figure 1. The avidinbiotin and lysozyme-benzene systems have been the subject of several previous theoretical studies [21,33,34,35,36,37,38,39,40,41,42,43,44,45],…”

Protein–Ligand Binding Free Energies from Exhaustive Docking

“…18 They were able to improve agreement with experiment by performing separate local minimizations of the complex for each ligand prior to simulations with a rigid protein. 18 However, these local minimizations were still not sufficient to obtain good agreement with experimental values. The impact of the use of a rigid or partially rigid protein is greater in the context of molecular dynamics sampling because a ligand can get trapped in a particular orientation if concerted motion with the protein is required to pass from one orientation to another.…”