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Related Experiment Videos

Report and Application of a Tool Compound Data Set.

Kyle V Butler1, Ian A MacDonald2,3, Nathaniel A Hathaway2,3

  • 1Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.

Journal of Chemical Information and Modeling
|October 17, 2017
PubMed
Summary

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Researchers identified 407 high-quality small molecule tool compounds for 278 protein targets. These compounds aid in understanding biological processes and led to the discovery of new modulators for the CBX5 gene repression pathway.

Area of Science:

  • Life Science Research
  • Chemical Biology
  • Bioinformatics

Background:

  • Small molecule tool compounds are crucial for interrogating biological processes due to their potency, cell activity, and selectivity.
  • Effective utilization of these compounds requires accurate characterization and researcher awareness.
  • The ChEMBL database serves as a valuable resource for identifying and cataloging bioactive small molecules.

Purpose of the Study:

  • To systematically identify and curate high-quality small molecule tool compounds from the ChEMBL database.
  • To develop computational tools for data visualization and automated pharmacological hypothesis generation.
  • To discover novel chemical modulators for the Chromobox Protein Homologue 5 (CBX5) mediated gene repression pathway.

Main Methods:

Related Experiment Videos

  • Mining the ChEMBL bioactivity database to identify best-in-class tool compounds.
  • Developing informatics functions and a web application for data visualization and analysis.
  • Utilizing predictive modeling to identify potential inhibitors of CBX5-mediated gene repression.
  • Validating predicted inhibitors using cell-based assays to assess modulation of heterochromatin formation.

    • Main Results:

    • Identification of 407 best-in-class tool compounds for 278 protein targets, presented in an annotated dataset.
    • Development of a web application enabling data visualization and automated hypothesis generation.
    • Prediction and subsequent validation of novel chemical modulators targeting the CBX5 pathway.
    • Discovery of new compounds that modulate CBX5-mediated heterochromatin formation.

    Conclusions:

    • The curated dataset and developed tools enhance the utility of small molecule tool compounds in life science research.
    • This work provides valuable resources for researchers investigating biological pathways and seeking novel therapeutic agents.
    • The study successfully identified new chemical modulators for the CBX5 pathway, addressing a current gap in available inhibitors.