Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index.

TitleHydrophobic similarity between molecules: a MST-based hydrophobic similarity index.
Publication TypeJournal Article
Year of Publication2002
AuthorsMuñoz, J, Barril X, Hernández B, Orozco Modesto, and F Luque Javier
JournalJ Comput Chem
Date Published2002 Apr 15
KeywordsAlgorithms, Animals, Chemical, Computational Biology, DNA, Energy Transfer, Guanidines, Histamine H2 Antagonists, Hydrogen Bonding, Intestines, Models, Molecular Conformation, Molecular Structure, Rats, Solvents, Structure-Activity Relationship, Thermodynamics, Water

A similarity index based on the hydrophilic/hydrophobic properties of molecules is presented. Such an index is defined based on the fractional partition of the free energy of solvation developed within the framework of the self-consistent reaction field MST model, which divides the free energy of solvation or the free energy of transfer into contributions assigned to the surface elements defining the solute/solvent interface. These surface contributions can be integrated to derive atomic or group contributions. The suitability of the index to compute the molecular similarity based on hydrophobic/hydrophilic properties is examined by considering their application in a variety of test systems, including structure-activity relationships, absorption properties, and molecular recognition. The similarity index is expected to be a very powerful tool in molecular similarity studies for compounds of chemical, biochemical, and pharmaceutical interest.