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Scaffold hopping by fragment replacement.

Mikko J Vainio1, Thierry Kogej, Florian Raubacher

  • 1Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D , Pepparedsleden 1, 43186 Mölndal, Sweden. mikko.vainio@abo.fi

Journal of Chemical Information and Modeling
|July 6, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a novel computational method for scaffold hopping, aiding drug design by finding replacement molecular fragments. The Scaffold Hopping program efficiently identifies bioisosteric replacements using a unique indexing scheme and shape similarity.

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Drug discovery

Background:

  • Scaffold hopping is crucial for lead optimization in drug design.
  • Existing methods for scaffold hopping can be computationally intensive.
  • Identifying bioisosteric replacements requires efficient searching and similarity assessment.

Purpose of the Study:

  • To develop a data-driven method for scaffold hopping via fragment replacement.
  • To create a fast and efficient computational tool for identifying novel scaffolds.
  • To improve the process of finding bioisosteric replacement scaffolds in drug design.

Main Methods:

  • A searchable database of scaffolds was generated by combinatorial bond cutting.
  • 3D scaffold structures were indexed based on broken bond orientation.
  • Scaffolds were ranked using volume overlap and electrostatic similarity.
  • A novel indexing scheme for attachment vector geometry was implemented.
  • A scaffold shape descriptor was defined for improved similarity matching.

Main Results:

  • The Scaffold Hopping program successfully retrieves relevant bioisosteric replacement scaffolds.
  • The novel indexing scheme enables fast searching of the scaffold database.
  • The scaffold shape descriptor enhances the similarity assessment between query and replacement fragments.
  • The method is demonstrated to be suitable for drug design applications.

Conclusions:

  • The developed Scaffold Hopping program provides an efficient computational approach for fragment-based scaffold hopping.
  • The novel indexing and shape descriptor facilitate rapid identification of bioisosteric replacements.
  • This method has the potential to accelerate lead optimization in drug discovery programs.