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Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
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PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach.

Xiaofeng Liu1, Sisheng Ouyang, Biao Yu

  • 1Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Nucleic Acids Research
|May 1, 2010
PubMed
Summary

PharmMapper is a web server for identifying drug targets using pharmacophore mapping. It efficiently screens small molecules against a large database of potential targets, aiding drug discovery.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • In silico drug target identification is crucial in early drug discovery.
  • Pharmacophore mapping offers an alternative to molecular docking for identifying drug-target interactions.
  • The PharmMapper server utilizes a pharmacophore approach to predict drug targets.

Purpose of the Study:

  • To introduce PharmMapper, a freely accessible web server for drug target identification.
  • To provide a tool for identifying potential targets for small molecules using pharmacophore mapping.
  • To leverage a comprehensive pharmacophore database for efficient target screening.

Main Methods:

  • PharmMapper employs a pharmacophore mapping approach.
  • It utilizes a large, in-house pharmacophore database (PharmTargetDB) derived from multiple sources.
  • The server uses a triangle hashing mapping method for efficient screening.

Main Results:

  • PharmMapper identifies potential drug targets for given small molecules.
  • It screens against over 7000 receptor-based pharmacophore models covering more than 1500 drug targets.
  • The server provides top-fitted hits, target annotations, and aligned poses within an average of 1 hour.
  • A retrospective test with tamoxifen successfully identified proper targets.

Conclusions:

  • PharmMapper is an efficient and high-throughput web server for drug target identification.
  • The tool aids in discovering potential drug targets for small molecules.
  • It offers a valuable resource for the drug discovery pipeline.