Azapeptide activity-based probes for the SARS-CoV-2 main protease enable visualization of inhibition in infected cells

Roeland Vanhoutte; Marta Barniol-Xicota; Winston Chiu; Laura Vangeel; Dirk Jochmans; Steven De Jonghe; Hadeer Zidane; Haim M Barr; Nir London; Johan Neyts; Steven H L Verhelst

doi:10.1039/d2sc04147b

Azapeptide activity-based probes for the SARS-CoV-2 main protease enable visualization of inhibition in infected cells

Chem Sci. 2023 Jan 6;14(7):1666-1672. doi: 10.1039/d2sc04147b. eCollection 2023 Feb 15.

Authors

Affiliations

¹ Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven Herestraat 49 box 802 3000 Leuven Belgium steven.verhelst@kuleuven.be.
² Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven Herestraat 49, Box 1043 3000 Leuven Belgium.
³ Maurice and Vivienne Wohl Institute for Drug Discovery, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science Rehovot 7610001 Israel.
⁴ Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot 7610001 Israel.
⁵ AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS Otto-Hahn-Str. 6b 44227 Dortmund Germany.

Abstract

The COVID-19 pandemic has revealed the vulnerability of the modern, global society. With expected waves of future infections by SARS-CoV-2, treatment options for infected individuals will be crucial in order to decrease mortality and hospitalizations. The SARS-CoV-2 main protease is a validated drug target, for which the first inhibitor has been approved for use in patients. To facilitate future work on this drug target, we designed a solid-phase synthesis route towards azapeptide activity-based probes that are capped with a cysteine-reactive electrophile for covalent modification of the active site of M^pro. This design led to the most potent ABP for M^pro and one of the most potent inhibitors reported thus far. We demonstrate that this ABP can be used to visualize M^pro activity and target engagement by drugs in infected cells.