Molecule-pharmacophore superpositioning and pattern matching in computational drug design

Three-dimensional (3D) pharmacophore modeling is a technique for describing the interaction of a small molecule ligand with a macromolecular target. Since chemical features in a pharmacophore model are well known and highly transparent for medicinal chemists, these models are intuitively understandable and have been increasingly successful in computational drug discovery in the past few years. The performance and applicability of pharmacophore modeling depends on two main factors: the definition and placement of pharmacophoric features and the alignment techniques used to overlay 3D pharmacophore models and small molecules. An overview of key technologies and latest developments in the area of 3D pharmacophores is given and provides insight into different approaches as implemented by the 3D pharmacophore modeling packages like Catalyst, MOE, Phase and LigandScout.