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3D virtual screening of large combinatorial spaces.

Ingo Muegge1, Qiang Zhang1

  • 1Boehringer Ingelheim Pharmaceuticals, Department of Medicinal Chemistry, 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA.

Methods (San Diego, Calif.)
|July 5, 2014
PubMed
Summary

PharmShape and PharmShapeCC software enable rapid 3D in silico screening of vast chemical libraries. This approach successfully identified novel compounds, including a CXCR5 antagonist and new chemotypes for various targets.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • cheminformatics

Background:

  • Virtual screening is crucial for identifying novel drug candidates.
  • Existing methods struggle with the scale of combinatorial chemistry libraries.
  • Efficient screening of large chemical spaces is a significant challenge.

Purpose of the Study:

  • To introduce PharmShape and PharmShapeCC, novel software for 3D in silico screening.
  • To demonstrate the capability of screening millions to trillions of compounds.
  • To validate the software's performance in identifying novel bioactive molecules.

Main Methods:

  • Utilizing a multi-conformational pharmacophore and shape-based approach.
  • Implementing customizable pharmacophore features and composite inclusion spheres.
Keywords:
Combinatorial libraryPharmacophoreScoringShape

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  • Employing library core intermediate clustering and consensus orientation determination for orthogonal enumeration.

    • Main Results:

    • PharmShape screens millions of compounds; PharmShapeCC screens trillions from combinatorial libraries.
    • Successfully identified a novel CXCR5 antagonist.
    • Discovered novel chemotypes for CCR1, LTA4 hydrolase, and MMP-13 targets through synthesis and evaluation.

    Conclusions:

    • PharmShape and PharmShapeCC offer a powerful platform for large-scale virtual screening.
    • The software effectively identifies novel compounds and chemotypes from diverse chemical libraries.
    • This method accelerates the drug discovery process by enabling efficient exploration of chemical space.