Predicting Molecular Interactions in silico: I. A Guide to Pharmacophore Identification and its Applications to Drug Design

Author(s): Oranit Dror, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson.

Journal Name: Current Medicinal Chemistry

Volume 11 , Issue 1 , 2004


A major goal in contemporary drug design is to develop new ligands with high affinity of binding toward a given protein receptor. Pharmacophore, which is the three-dimensional arrangement of essential features that enable a molecule to exert a particular biological effect, is a very useful model for achieving this goal. If the three-dimensional structure of the receptor is known, pharmacophore is a complementary tool to standard techniques, such as docking. However, frequently the structure of the receptor protein is unknown and only a set of ligands together with their measured binding affinities towards the receptor is available. In such a case, a pharmacophore-based strategy is one of the few applicable tools. Here we present a broad, yet concise guide to pharmacophore identification and review a sample of applications for drug design. In particular, we present the framework of the algorithms, classify their modules and point out their advantages and challenges.

Keywords: pharmacophore mapping, pharmacophore modeling, receptor-based pharmacophore, pharmacophore fingerprints, virtual screening, pharmacophore searching, docking, de-novo design, lead generation, computer-aided drug design

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Article Details

Year: 2004
Page: [71 - 90]
Pages: 20
DOI: 10.2174/0929867043456287

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PDF: 37