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Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro

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Matrix-based Molecular Descriptors for Prospective Virtual Compound Screening.

Francesca Grisoni^1,2, Daniel Reker², Petra Schneider^2,3

¹University of Milano-Bicocca, Dept. of Earth and Environmental Sciences, P.za della Scienza 1, 20126, Milano, Italy.

Molecular Informatics

|September 22, 2016

Summary

This summary is machine-generated.

We developed novel matrix-based (MB) descriptors for molecular similarity searching in drug discovery. These MB descriptors proved effective in virtual screening, identifying a new cyclooxygenase-2 inhibitor.

Keywords:

cheminformatics cyclooxygenase drug discovery molecular similarity natural product

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Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

Molecular descriptors are crucial for ligand-based similarity searching.
Existing descriptors may not fully capture complex molecular structural information.

Purpose of the Study:

To introduce and evaluate topological matrix-based (MB) descriptors for virtual screening.
To compare MB descriptors with topological pharmacophore descriptors.
To assess the impact of data preprocessing and similarity metrics on virtual screening performance.

Main Methods:

Development of topological matrix-based (MB) descriptors.
Retrospective virtual screening evaluation comparing MB and topological pharmacophore descriptors.
Prospective virtual screening of a commercial compound library.

Main Results:

MB descriptors demonstrated competitive and complementary performance to existing descriptors.
Data preprocessing and similarity metrics significantly influenced virtual screening outcomes.
A novel natural-product-derived cyclooxygenase-2 inhibitor was identified through prospective screening.

Conclusions:

Matrix-based descriptors are a valuable tool for molecular similarity-based virtual screening.
MB descriptors offer a complementary approach to existing methods, aiding hit discovery and scaffold hopping.
The identified cyclooxygenase-2 inhibitor presents a unique interaction profile with the target protein.