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Diversifying chemical libraries with generative topographic mapping.

Arkadii Lin1,2, Bernd Beck3, Dragos Horvath1

  • 1Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, 4, Blaise Pascal Str., 67081, Strasbourg, France.

Journal of Computer-Aided Molecular Design
|August 14, 2019
PubMed
Summary
This summary is machine-generated.

Generative topographic mapping diversified Boehringer Ingelheim's (BI) compound collection by identifying novel drug-like structures from a large chemical database. This approach enhances drug discovery pipelines by exploring new chemical space.

Keywords:
Big dataChemical library diversity enrichmentGenerative topographic mapping

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Drug discovery

Background:

  • Boehringer Ingelheim (BI) sought to diversify its internal compound collection.
  • Existing compound libraries may have limited chemical diversity for drug discovery.

Purpose of the Study:

  • To explore the diversification of the Boehringer Ingelheim (BI) compound collection.
  • To identify novel chemical structures and substructures for drug discovery.

Main Methods:

  • Generative topographic mapping (GTM) was employed to create a 2D chemical space map.
  • The BI compound library was compared against the Aldrich-Market Select (AMS) database (>8M compounds).
  • A novel 'AutoZoom' tool was developed to analyze chemotypes and extract maximum common substructures from populated map regions.

Main Results:

  • A 2D map representing relevant chemical space was successfully trained.
  • Over 401,000 new structures were retrieved from the AMS database.
  • The retrieved structures were evaluated for drug-likeness and potential biological activity.

Conclusions:

  • Generative topographic mapping is a viable strategy for diversifying corporate compound collections.
  • The AutoZoom tool facilitates the identification of novel substructures within large chemical databases.
  • This methodology aids in expanding the chemical space accessible for drug discovery programs.