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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 active molecule(s) are called active ingredients of a drug.

It is alternatively described as an ensemble of interactive functional groups with a defined geometry. Basically, one tries to talk the protein language by finding the structural and chemical complementaries (also known as the pharmacophore hypothesis) to target receptors.

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 and where these features are a similar distance apart from each other. There are several reasons to find compounds with similar biological activity to known compounds: new compounds may have beneficial effects at different doses, they may be taken up more readily by different tissues, they may have fewer deleterious effects, they may have a different biological halflife, and they may be produced more efficiently. In addition, new compounds may not covered by existing patents.

Typical pharmacophore features are for where a molecule is hydrophobic, aromatic, a hydrogen bond acceptor, a hydrogen bond donor, a cation, or an anion.

• Molecular modelling
• Cheminformatics
• Molecule mining
• Pharmaceutical company
• QSAR
• Chromophore (colour)

• 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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