Pharmacophore

A pharmacophore was first defined by Paul Ehrlich in 1909 as "a molecular framework that carries (phoros) the essential features responsible for a drug’s (=pharmacon's) biological activity" (Ehrlich. Dtsch. Chem. Ges. 1909, 42: p.17). In 1977, this definition was updated by Peter Gund to "a set of structural features in a molecule that is recognized at a receptor site and is responsible for that molecule's biological activity" (Gund. Prog. Mol. Subcell. Biol. 1977, 5: pp 117–143). The IUPAC definition of a pharmacophore is "an ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target and to trigger (or block) its biological response".^[1]

In modern computational chemistry, pharmacophores are used to define the essential features of one or more molecules with the same biological activity. A database of diverse chemical compounds can then be searched for more molecules which share the same features located a similar distance apart from each other.

Typical pharmacophore features are for where a molecule is hydrophobic, aromatic, a hydrogen bond acceptor, a hydrogen bond donor, a cation, or an anion. The features need to match different chemical groups with similar properties, in order to identify novel ligands. Ligands receptor interactions are typically “polar positive”, “polar negative” or “hydrophobic”. A well-defined pharmacophore model includes both hydrophobic volumes and hydrogen bond vectors.

See also

• Cheminformatics
• Molecule mining
• Pharmaceutical company
• QSAR
• in silico

Pharmacophore Modelling Software

• Discovery Studio by Accelrys
• LigandScout (external link) by Inte:ligand
• Phase by Schroedinger
• MOE by the Chemical Computing Group
• ICM-Chemist by MolSoft

References

• Osman F. Güner (2000) Pharmacophore Perception, Development, and use in Drug Design ISBN 0-9636817-6-1 Table of contents and preface

• Thierry Langer and Rémy D. Hoffmann (2006) Pharmacophores and Pharmacophore Searches ISBN 3-527-31250-1 Table of contents and preface

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