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Construction of an integrated database for hERG blocking small molecules.

Tomohiro Sato1, Hitomi Yuki1, Keiji Ogura1

  • 1Center for Life Science Technologies, RIKEN, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan.

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|July 7, 2018
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Summary

Researchers created the largest database of hERG inhibitors by integrating multiple sources. This comprehensive resource aids in developing safer drug candidates and identifying hazardous compounds by assessing hERG channel inhibition risk.

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Area of Science:

  • Pharmacology
  • Medicinal Chemistry
  • Computational Chemistry

Background:

  • hERG potassium channel inhibition is linked to prolonged QT intervals, posing risks for drug development and safety.
  • Machine learning models have shown success in predicting hERG inhibition, but are often limited by single-database usage.
  • Data integration challenges due to format and ontology differences hinder the creation of comprehensive hERG inhibitor datasets.

Purpose of the Study:

  • To curate and integrate hERG-related data from multiple public databases (ChEMBL, PubChem, GOSTAR, hERGCentral).
  • To establish the largest integrated database of small molecule hERG inhibitors.
  • To enhance the structural diversity and chemical space coverage of hERG inhibitor data.

Main Methods:

  • Data curation from ChEMBL, PubChem, GOSTAR, and hERGCentral.
  • Integration of disparate hERG inhibitor datasets.
  • Structural diversity assessment using Murcko frameworks.

Main Results:

  • The largest integrated database of hERG inhibition by small molecules was created.
  • The integrated database contains over twice the chemical scaffolds compared to individual databases.
  • The database covers 18.2% of the Murcko framework-based chemical space found in ChEMBL.
  • Demonstrated significant enhancement in structural diversity and coverage of hERG inhibitor chemical space.

Conclusions:

  • The integrated database offers the most comprehensive information on hERG inhibitors to date.
  • This resource will significantly aid in the design of safer therapeutic compounds.
  • Facilitates risk assessment for drug development and identification of potentially hazardous marketed drugs.