Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein–ligand complexes

For routine pKa calculations of protein–ligand complexes in drug design, the PEOE method to compute partial charges was modified. The new method is applicable to a large scope of proteins and ligands. The adapted charges were parameterized using experimental free energies of solvation of amino acids and small organic ligands. For a data set of 80 small organic molecules, a correlation coefficient of r2 = 0.78 between calculated and experimental solvation free energies was obtained. Continuum electrostatics pKa calculations based on the Poisson–Boltzmann equation were carried out on a validation set of nine proteins for which 132 experimental pKa values are known. In total, an overall RMSD of 0.88 log units between calculated and experimentally determined data is achieved. In particular, the predictions of significantly shifted pKa values are satisfactory, and reasonable estimates of protonation states in the active sites of lysozyme and xylanase could be obtained. Application of the charge‐assignment and pKa‐calculation procedure to protein–ligand complexes provides clear structural interpretations of experimentally observed changes of protonation states of functional groups upon complex formation. This information is essential for the interpretation of thermodynamic data of protein–ligand complex formation and provides the basis for the reliable factorization of the free energy of binding in enthalpic and entropic contributions. The modified charge‐assignment procedure forms the basis for future automated pKa calculations of protein–ligand complexes. Proteins 2006; © 2006 Wiley‐Liss, Inc.