Comparison of COSMO Water Models in Quantum Quasi-Docking

Abstract

Two solvent models, COSMO (old parametrization) and COSMO2 (new parametrization) are compared for a set of protein–ligand complexes in quantum quasi-docking, which is two-stage docking: positioning of a ligand in a target protein and calculation of binding enthalpy of the protein–ligand system using the PM7 quantum-chemical semiempirical method. In quantum quasi-docking, a wide spectrum of unique low-energy minima of the protein–ligand system is first found while employing the classical force field. Then energies of all these minima are recalculated within one of the continual models using the modern PM7 method with allowance for the solvent, and the global energy minimum is determined among the recalculated energies. The solution of the quantum quasi-docking problem is the position of the ligand in the protein corresponding to the global minimum of the protein–ligand system energy calculated by the quantum-chemical method with allowance for the solvent. Effectiveness of quantum quasi-docking is defined by the value (below 2 Å) of the root-mean-square deviation of ligand atoms from one another in two positions, namely, the position of the ligand in the protein corresponding to the calculated global energy minimum and the experimentally found crystallized position of the ligand with the protein. Comparison is performed for ten protein–ligand test complexes with well-defined structures taken from the Protein Data Bank, for which the ligand–protein binding enthalpy is measured and the positioning of the ligand in the protein is successful in quasi-docking within both solvent models used. In both methods, PM7 + COSMO and PM7 + COSMO2, a high correlation coefficient of the experimental and calculated ligand–protein binding enthalpy is obtained for both calculation techniques. Allowance for moveability of protein atoms in calculations of binding enthalpy leads to an increase in its negative values and to a slight decrease in the correlation coefficient of the experimental and calculated values. The role of hydrogen bonds between protein and ligand atoms is revealed: their contribution to binding enthalpy ranges from 14 to 24% for different complexes. The results indicate the way of implementing quantum docking so that the global minimum of the protein–ligand system energy calculated by the quantum-chemical technique is immediately obtained using the global optimization procedure.