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Updated: Oct 27, 2025

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
Published on: September 26, 2025
SARS-CoV-2 Mpro inhibition by a zinc ion: structural features and hints for drug design
Deborah Grifagni1, Vito Calderone2, Stefano Giuntini1
1Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. francesca.cantini@unifi.it marco.fragai@unifi.it lucia.banci@unifi.it.
Abstract:
Structural data on the SARS-CoV-2 main protease in complex with a zinc-containing organic inhibitor are already present in the literature and gave hints on the presence of a zinc binding site involving the catalytically relevant cysteine and histidine residues. In this paper, the structural basis of ionic zinc binding to the SARS-CoV-2 main protease has been elucidated by X-ray crystallography. The zinc binding affinity and its ability to inhibit the SARS-CoV-2 main protease have been investigated. These findings provide solid ground for the design of potent and selective metal-conjugated inhibitors of the SARS-CoV-2 main protease.

