The design of combinatorial libraries using properties and 3D pharmacophore fingerprints.

Molecular diversity and similarity methods relevant to drug-receptor interactions are key for the design of combinatorial libraries for lead discovery and optimization. BCUT chemistry-space values for ligands have been used for many diversity-related applications and incorporate receptor-relevant properties such as hydrogen bonding and polarizability. Three-dimensional (3D) multiple-point pharmacophore descriptors (fingerprints) quantify diversity (or similarity) in terms of combinations of three or four functional groups associated with non-covalent ligand-receptor binding. BCUTs and pharmacophore fingerprints have been effectively utilized to design diversity libraries, and also show promise for focused library design.