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Updated: Dec 10, 2025

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
Published on: September 26, 2025
A protein interaction map identifies existing drugs targeting SARS-CoV-2
Claudia Cava1, Gloria Bertoli2, Isabella Castiglioni3
1Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F. Cervi 93, 20090 Segrate-Milan, Milan, Italy. claudia.cava@ibfm.cnr.it.
This study used bioinformatics to identify potential COVID-19 treatments by analyzing gene expression and drug interactions. Several existing drugs show promise as antiviral therapies against SARS-CoV-2.
Area of Science:
- Bioinformatics
- Genomics
- Drug Discovery
Background:
- Severe acute respiratory syndrome coronavirus (SARS-CoV-2) causes COVID-19.
- Angiotensin converting enzyme 2 (ACE2) is the primary cell receptor for SARS-CoV-2 entry.
- No specific antiviral treatments or vaccines are currently available.
Purpose of the Study:
- To identify potential therapeutic agents for COVID-19 using in silico drug screening.
- To explore drug repurposing strategies for treating SARS-CoV-2 infections.
Main Methods:
- Differential gene expression analysis in COVID-19 patients correlated with ACE2.
- Network analysis integrating gene-gene and drug-gene interactions.
- Molecular docking analysis of central network drugs.
Main Results:
- Identified 825 differentially expressed genes linked to ACE2.
- Constructed a protein-protein interaction network of 474 genes and 1130 interactions.
- Identified several drugs with potential antiviral activity through network and docking analyses.
Conclusions:
- Bioinformatics analysis can rapidly identify potential COVID-19 therapies.
- Repurposed drugs show promise as standalone or combination treatments for COVID-19.
- Further investigation of identified drugs is warranted for clinical application.
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