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Updated: Dec 12, 2025

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
Published on: September 26, 2025
Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study
Soumita Mukherjee1, Subrata Dasgupta1, Tapasendra Adhikary2
1Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India.
This study investigated SARS-CoV-2 main protease as a drug target for COVID-19. Molecular docking and simulations of Hydroxychloroquine and novel ligands revealed a key water-mediated catalytic triad for inhibitor design.
Area of Science:
- Biochemistry
- Drug Discovery
- Virology
Background:
- Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes COVID-19, a global pandemic.
- The SARS-CoV-2 3C-like protease is crucial for viral replication and a significant drug target.
Purpose of the Study:
- To explore the potential of Hydroxychloroquine (HCQ) and novel ligands against SARS-CoV-2 main protease.
- To elucidate the structural interactions within the protease active site for inhibitor development.
Main Methods:
- Molecular docking simulations were performed.
- Molecular dynamics (MD) simulations were utilized.
- Ligand molecules (HCQ, Mod-I, Mod-II) were modeled and analyzed.
Main Results:
- The study identified structural organization of active site residues in SARS-CoV-2 main protease.
- A conserved water-mediated catalytic triad was revealed.
- This triad facilitates the recognition of Mod-I and Mod-II ligands.
Conclusions:
- The findings provide structural insights into the SARS-CoV-2 main protease active site.
- The identified water-mediated catalytic triad is a promising target for novel inhibitor design.
- This research aids in developing effective therapeutic strategies against COVID-19.
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