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A hybrid approach for addressing ring flexibility in 3D database searching

¹Bayer AG, PH-R Structural Research, Wuppertal, Germany.

Journal of Computer-Aided Molecular Design

|January 1, 1997

Summary

This study introduces a hybrid 3D database searching method to improve drug discovery by handling flexible rings. The new approach enhances hit rates and accuracy in identifying potential drug compounds.

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Area of Science:

Computational Chemistry
Cheminformatics
Drug Discovery

Background:

Flexible ring structures pose challenges in 3D database searching.
Existing methods may yield unrealistic hit geometries.
Accurate conformational representation is crucial for effective virtual screening.

Purpose of the Study:

To develop and evaluate a hybrid approach for flexible 3D database searching.
To improve the accuracy and efficiency of virtual screening processes.
To address limitations of previous 3D searching techniques.

Main Methods:

A hybrid approach combining explicit storage of multiple ring conformations (generated by CORINA) with torsional fitting (in UNITY).
Utilized a database of ~130,000 entries and five pharmacophore queries for comparison.

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Investigated the impact of varying the number of ring conformations per molecule.

Main Results:

The hybrid approach yielded 10-20% more hits on average compared to the original UNITY method.
Eliminated unrealistic hit geometries observed with the previous approach.
Identified an optimal number of 10 ring conformations per molecule for improved performance.

Conclusions:

The hybrid method offers a more robust and accurate solution for flexible 3D database searching.
This approach enhances hit identification and reduces false positives in drug discovery.
Optimizing the number of conformations is key to maximizing the effectiveness of 3D searching tools.