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Pharmacophore
 
 
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A pharmacophore was first defined by Paul Ehrlich
Paul Ehrlich

Paul Ehrlich was a German scientist in the fields of hematology, immunology, and chemotherapy, and Nobel Prize in Physiology or Medicine. He is noted for his research in autoimmunity, calling it "horror autotoxicus"....
 in 1909 as "a molecular framework that carries (phoros) the essential features responsible for a drug’s (=pharmacon's) biological activity
Biological activity

Pharmacological or biological activity is an expression describing the beneficial or adverse effects of a drug on organism. When the drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other constituents....
" (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
Receptor (biochemistry)

In biochemistry, a receptor is a protein molecule, embedded in either the plasma membrane or cytoplasm of a cell, to which a mobile signaling molecule may attach....
 site and is responsible for that molecule's biological activity" (Gund.






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A pharmacophore was first defined by Paul Ehrlich
Paul Ehrlich

Paul Ehrlich was a German scientist in the fields of hematology, immunology, and chemotherapy, and Nobel Prize in Physiology or Medicine. He is noted for his research in autoimmunity, calling it "horror autotoxicus"....
 in 1909 as "a molecular framework that carries (phoros) the essential features responsible for a drug’s (=pharmacon's) biological activity
Biological activity

Pharmacological or biological activity is an expression describing the beneficial or adverse effects of a drug on organism. When the drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other constituents....
" (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
Receptor (biochemistry)

In biochemistry, a receptor is a protein molecule, embedded in either the plasma membrane or cytoplasm of a cell, to which a mobile signaling molecule may attach....
 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".

In modern computational chemistry
Computational chemistry

Computational chemistry is a branch of chemistry that uses computers to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids....
, pharmacophores are used to define the essential features of one or more molecules with the same biological activity
Biological activity

Pharmacological or biological activity is an expression describing the beneficial or adverse effects of a drug on organism. When the drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other constituents....
. A database of diverse chemical compound
Chemical compound

A chemical compound is a Chemical substance consisting of two or more different chemical element Chemical bond together in a fixed mass ratio that can be split into simpler substances....
s 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
Hydrogen bond

A hydrogen bond is the attractive force between one electronegative atom and a hydrogen covalently bonded to another electronegative atom. It results from a dipole-dipole force with a hydrogen atom bonded to nitrogen, oxygen or fluorine ....
 acceptor, a hydrogen bond
Hydrogen bond

A hydrogen bond is the attractive force between one electronegative atom and a hydrogen covalently bonded to another electronegative atom. It results from a dipole-dipole force with a hydrogen atom bonded to nitrogen, oxygen or fluorine ....
 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
    Cheminformatics

    Cheminformatics is the use of computer and Information science techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery....
  • Molecule mining
    Molecule mining

    This page describes Data mining for molecules. Since molecules may be represented by molecular graphs this is strongly related to graph mining and structured data mining....
  • Pharmaceutical company
    Pharmaceutical company

    The pharmaceutical industry develops, produces, and markets drugs licensed for use as medications. Pharmaceutical companies can deal in Generic drug and/or brand medications....
  • QSAR
  • Chromophore
    Chromophore

    A chromophore is part of a molecule responsible for its color.When a molecule absorbs certain wavelengths of visible spectrum and transmits or reflects others, the molecule has a color....
     (colour)


Pharmacophore Modelling Software

  • by Accelrys
    Accelrys

    Accelrys is a software company headquartered in the United States, with representation in Europe and Japan. It provides software for chemical research, especially in the areas of drug discovery and materials science....
  • LigandScout
    LigandScout

    LigandScout is a software tool that allows to model 3D pharmacophore models from structural data of macromolecule/ligand complexes. It incorporates a complete definition of three-dimensional chemical features that describe the interaction of a bound small organic molecule and the surrounding binding site of the macromolecule....
     () by Inte:ligand
    Inte:Ligand

    Inte:Ligand is a software company headquartered in Vienna, Austria. It provides software and services for chemical research, especially in the areas of drug discovery....
  • by
  • by the Chemical Computing Group
    Chemical Computing Group

    Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking , pharmacophore and molecular dynamics....