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Using Spherical Harmonic Surface Property Representations for Ligand-Based Virtual Screening.

Violeta I Pérez-Nueno1, Vishwesh Venkatraman2, Lazaros Mavridis2

  • 1Equipe Orpailleur, INRIA Nancy - Grand Est, LORIA, 54506 Vandoeuvre-lès-Nancy, France. violeta.pereznueno@loria.fr, clark@chemie.uni-erlangen.de.

Molecular Informatics
|July 29, 2016
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Summary
This summary is machine-generated.

This study introduces a novel shape and surface property approach for drug discovery, improving ligand-based virtual screening (VS) performance over traditional shape-only methods. Retaining 3D conformations is crucial for flexible ligands.

Keywords:
Spherical harmonics, Consensus properties, Genetic algorithm, Virtual screening, Difficult targets, P38, FXA, PPAR-γ

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Area of Science:

  • Computational chemistry and cheminformatics
  • Drug discovery and development

Background:

  • Ligand-based virtual screening (VS) is a key technique in drug discovery.
  • Challenges remain in selecting initial query compounds and their conformations for VS.

Purpose of the Study:

  • To propose and evaluate a novel shape plus surface property approach for VS.
  • To investigate consensus queries based on spherical harmonic (SH) functions.

Main Methods:

  • Utilized multiple local spherical harmonic (SH) functions for shape and surface property analysis.
  • Developed and compared shape-based and shape plus property-based consensus SH queries.
  • Evaluated performance against 40 pharmaceutically relevant targets in the DUD database.

Main Results:

  • Combined SH-based properties significantly improved VS performance compared to shape-only queries.
  • Shape-based consensus queries demonstrated good performance.
  • Explicit 3D shape-property conformations are essential for highly flexible ligands.

Conclusions:

  • The proposed shape plus surface property method enhances VS efficacy.
  • Consensus SH queries offer a robust strategy for ligand screening.
  • Preserving 3D conformational information is vital for optimizing VS of flexible molecules.