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Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.

Ning-Ning Wei¹, Adel Hamza

¹University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536, United States.

Journal of Chemical Information and Modeling

|December 17, 2013

Summary

This summary is machine-generated.

We developed a shape-based virtual screening method, SABRE (shape-approach-based routines enhanced), that efficiently identifies active drug compounds. This approach significantly improves early retrieval rates from large databases, aiding drug discovery and chemogenomics.

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Area of Science:

Computational Chemistry
Drug Discovery
Bioinformatics

Background:

Virtual screening is crucial for identifying potential drug candidates.
Existing methods often struggle with diverse chemical structures and binding site complementarity.
A need exists for efficient and accurate shape-based screening tools.

Purpose of the Study:

To present an efficient ligand/structure shape-based virtual screening approach.
To combine ligand shape similarity (SABRE) with receptor binding site 3D shape.
To improve the early retrieval rate of active compounds from large databases.

Main Methods:

Developed a consensus molecular-shape pattern recognition algorithm.
Utilized 4D fingerprints from conformer states and SABRE-computed active ligand 3D shapes.
Validated the SABRE algorithm using the Database of Useful Decoys (DUD) and WOMBAT datasets.

Main Results:

SABRE outperformed other virtual screening methods in early retrieval rates.
Achieved high enrichment factors: EF(0.1%) = 69.0% and EF(1%) = 98.7%.
Demonstrated superior performance on a database of ~95,000 structures.

Conclusions:

The SABRE approach is highly effective for identifying compounds similar to known actives.
This method can predict activity against new targets, supporting chemogenomics.
The SABRE program is available for academic use.