Towards the prediction of protein-ligand binding affinities: A new class of methods for free energy calculations

his thesis consists of three essays on the validation and development of a new method for free energy calculations. It uses the method to compute conformational free energies with the CHARMm empirical force field and the generalized Born solvation model. The first study computes pKa shifts for a series of small difunctional compounds, and for the active-site aspartyl dyad in HIV-1 protease. The calculations agree rather well with experiment for the small molecules. The calculations for HIV-1 protease agree reasonably well with experiment, despite the complexity of the system. The second study uses the same computer model to study the energetics of solvent-exposed salt-bridges. Satisfactory agreement is obtained in comparison with the measured binding affinities of ion-pairs in solution and with the salt-bridge energetics deduced from studies of salt-bridges in helical peptides. The calculations suggest that stabilizing charge-charge interactions in helical peptides are not associated with well-defined salt bridge conformations, in agreement with relevant crystallographic studies. The method is also used to make a testable prediction that arginine and phosphotyrosine residues in an...