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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
Summary
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.
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.
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