COSMOsim3D: 3D-similarity and alignment based on COSMO polarization charge densities.

COSMO σ-surfaces resulting from quantum chemical calculations of molecules in a simulated conductor, and their histograms, the so-called σ-profiles, are widely proven to provide a very suitable and almost complete basis for the description of molecular interactions in condensed systems. The COSMOsim method therefore introduced a global measure of molecular similarity on the basis of similarity of σ-profiles, but it had the disadvantage of neglecting the 3D distribution of molecular polarities, which is crucially determining all ligand-receptor binding. This disadvantage is now overcome by COSMOsim3D, which is a logical and physically sound extension of the COSMOsim method, which uses local σ-profiles on a spatial grid. This new method is used to measure intermolecular similarities on the basis of the 3D representation of the surface polarization charge densities σ of the target and the probe molecule. The probe molecule is translated and rotated in space in order to maximize the sum of local σ-profile similarities between target and probe. This sum, the COSMOsim3D similarity, is a powerful descriptor of ligand similarity and allows for a good discrimination between bioisosters and random pairs. Validation experiments using about 600 pharmacological activity classes in the MDDR database are given. Furthermore, COSMOsim3D represents a unique and very robust method for a field-based ligand-ligand alignment.