Predicting absolute binding free energies in a model binding site

COMP 343

David L. Mobley, dmobley@maxwell.compbio.ucsf.edu1, Alan P. Graves, agraves@blur.compbio.ucsf.edu2, John D. Chodera, jchodera@ugcs.caltech.edu3, Andrea McReynolds4, Brian K Shoichet, shoichet@cgl.ucsf.edu1, and Ken A. Dill, dill@maxwell.compbio.ucsf.edu4. (1) Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Box 2240, San Francisco, CA 95616, (2) Graduate Group in Biophysics, University of California San Francisco, 1700 4th Street, Byers Hall Rm 501, San Francisco, CA 94143, (3) Graduate Group in Biophysics, University of California, San Francisco, UCSF Mission Bay, Box 2240, 600 16th Street, San Francisco, CA 94143-2280, (4) Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143
A central challenge in structure-based ligand design is the accurate prediction of binding free energies. We discuss work appling alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, we encountered several challenges, such as multiple ligand binding modes and frustrated protein degrees of freedom. In retrospective tests, our methods were able to compute absolute binding free energies within 1.9 kcal/mol of previously determined experimental values on average. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys from a set of putative binders identified by docking. In these prospective tests, the 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 the predictions of 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.
 

Poster Session
6:00 PM-8:00 PM, Tuesday, August 21, 2007 BCEC -- Ballroom Foyer, Poster

Sci-Mix
8:00 PM-10:00 PM, Monday, August 20, 2007 BCEC -- Exhibit Hall - B2, Sci-Mix

Division of Computers in Chemistry

The 234th ACS National Meeting, Boston, MA, August 19-23, 2007