2/3D Pharmacophore Definitions and Their Application

The concept of a pharmacophore has been very useful in the field of drug design, to explain the structure–activity of a series of ligands, and to search for new or alternative chemotypes. We start by placing pharmacophores in their biological context, to discuss the best situations for their use. The next section deals with the fundamentals of pharmacophore elucidation, dealing with feature definition and the role of protonation and tautomer states. Methods for aligning the feature model and for scoring the alignment are then presented. The final sections deal with the use of pharmacophores and the issues that can arise in their application.