Alchemical absolute
binding free energy calculations are of increasing
interest in drug discovery. These calculations require restraints
between the receptor and ligand to restrict their relative positions
and, optionally, orientations. Boresch restraints are commonly used,
but they must be carefully selected in order to sufficiently restrain
the ligand and to avoid inherent instabilities. Applying multiple
distance restraints between anchor points in the receptor and ligand
provides an alternative framework without inherent instabilities which
may provide convergence benefits by more strongly restricting the
relative movements of the receptor and ligand. However, there is no
simple method to calculate the free energy of releasing these restraints
due to the coupling of the internal and external degrees of freedom
of the receptor and ligand. Here, a method to rigorously calculate
free energies of binding with multiple distance restraints by imposing
intramolecular restraints on the anchor points is proposed. Absolute
binding free energies for the human macrophage migration inhibitory
factor/MIF180, system obtained using a variety of Boresch restraints
and rigorous and nonrigorous implementations of multiple distance
restraints are compared. It is shown that several multiple distance
restraint schemes produce estimates in good agreement with Boresch
restraints. In contrast, calculations without orientational restraints
produce erroneously favorable free energies of binding by up to approximately
4 kcal mol–1. These approaches offer new options
for the deployment of alchemical absolute binding free energy calculations.