Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy

The ability to reliably compute accurate protein−ligand binding affinities is crucial to understanding protein−ligand recognition and to structure-based drug design. A ligand's binding affinity is specified by its absolute binding free energy, ΔGbind, the free energy difference between the bound and unbound states. To compute accurate free energy differences by free energy perturbation (FEP), “alchemical” rather than physical processes are usually simulated by molecular dynamics simulations so as to minimize the perturbation to the system. Here, we report a novel “alchemistic” application of the FEP methodology involving a large perturbation. By mutating a ligand with 11 non-hydrogen atoms into six water molecules in the binding site of a protein, we computed a ΔGbind within 3 kJ/mol of the experimental value. This is the first successful example of the computation of ΔGbind for a protein:ligand pair with full treatment of the solvent degrees of freedom.