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

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

*Corresponding author for this work

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. All right reserved -

Original languageEnglish
Pages (from-to)551-584
Number of pages34
JournalFrontiers in Medicinal Chemistry
Volume3
Issue number1
StatePublished - Jan 2006

Funding

FundersFunder number
National Cancer InstituteZ01BC010442

    Keywords

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

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