Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design

Oranit Dror, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson

Research output: Contribution to journalReview articlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)71-90
Number of pages20
JournalCurrent Medicinal Chemistry
Volume11
Issue number1
DOIs
StatePublished - 2004

Keywords

  • Computer-aided drug design
  • De-Novo design
  • Docking
  • Lead generation
  • Pharmacophore fingerprints
  • Pharmacophore mapping
  • Pharmacophore modeling
  • Pharmacophore searching
  • Receptor-based pharmacophore
  • Virtual screening

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