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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
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Scaffold explorer: an interactive tool for organizing and mining structure-activity data spanning multiple

Dimitris K Agrafiotis1, John J M Wiener

  • 1Johnson & Johnson Pharmaceutical Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, USA. dagrafio@its.jnj.com

Journal of Medicinal Chemistry
|June 8, 2010
PubMed
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Scaffold Explorer is an interactive tool enabling medicinal chemists to explore chemical data by organizing scaffolds into hierarchical trees. This visual analytics tool aids in navigating chemical space and understanding structure-activity relationships (SAR).

Area of Science:

  • Medicinal Chemistry
  • Cheminformatics
  • Drug Discovery

Background:

  • Exploring chemical space and understanding structure-activity relationships (SAR) are crucial in drug discovery.
  • Existing methods for scaffold analysis often rely on automated extraction, limiting medicinal chemists' intuitive input.
  • Navigating complex datasets to identify promising chemotypes remains a challenge.

Purpose of the Study:

  • To introduce Scaffold Explorer, an interactive tool for medicinal chemists.
  • To enable the definition and exploration of chemical scaffold hierarchies within project data.
  • To facilitate the visualization and analysis of structure-activity relationships (SAR) across diverse chemotypes.

Main Methods:

  • Development of Scaffold Explorer, an interactive software tool.

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  • Users construct hierarchical trees where nodes represent chemical scaffolds.
  • The defined scaffold trees are mapped onto compound collections for data exploration.

    • Main Results:

    • Scaffold Explorer provides visual analytics for a bird's-eye view of chemical space.
    • The tool allows mapping of physicochemical properties and biological activities onto scaffold nodes.
    • It serves as an aggregator for compound properties, distinguishing promising from problematic chemotypes.

    Conclusions:

    • Scaffold Explorer enhances medicinal chemists' ability to explore project data through interactive scaffold hierarchies.
    • The tool's interactivity and accommodation of user intuition, including arbitrary substructures, differentiate it from automated approaches.
    • It offers a powerful method for navigating chemical space and optimizing drug discovery efforts.