A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication

Hesong Han; Albert Vallejo Gracia; Joachim J Røise; Lydia Boike; Kristoffer Leon; Ursula Schulze-Gahmen; Michael R Stentzel; Teena Bajaj; Dake Chen; I-Che Li; Maomao He; Kamyar Behrouzi; Zahra Khodabakhshi; Daniel K Nomura; Mohammad R K Mofrad; G Renuka Kumar; Melanie Ott; Niren Murthy

doi:10.1039/d3ra00426k

A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication

RSC Adv. 2023 Apr 4;13(16):10636-10641. doi: 10.1039/d3ra00426k. eCollection 2023 Apr 3.

Authors

Hesong Han¹, Albert Vallejo Gracia², Joachim J Røise^{1

3}, Lydia Boike^{3

4

5}, Kristoffer Leon^{2

6}, Ursula Schulze-Gahmen², Michael R Stentzel¹, Teena Bajaj⁷, Dake Chen¹, I-Che Li¹, Maomao He¹, Kamyar Behrouzi^{8

9}, Zahra Khodabakhshi^{8

9}, Daniel K Nomura^{3

4

5

10

11}, Mohammad R K Mofrad^{8

9}, G Renuka Kumar², Melanie Ott^{2

6

12}, Niren Murthy^{1

4}

Affiliations

¹ Department of Bioengineering, University of California at Berkeley Berkeley CA USA nmurthy@berkeley.edu.
² Gladstone Institute of Virology, Gladstone Institutes San Francisco CA USA melanie.ott@gladstone.ucsf.edu.
³ Department of Chemistry, University of California Berkeley CA USA.
⁴ Innovative Genomics Institute Berkeley CA USA.
⁵ Novartis-Berkeley Center for Proteomics and Chemistry Technologies Berkeley CA USA.
⁶ Department of Medicine, University of California San Francisco CA USA.
⁷ Graduate Program of Comparativ Biochemistry, University of California at Berkeley Berkeley CA USA.
⁸ Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley CA USA.
⁹ Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory Berkeley USA.
¹⁰ Department of Molecular and Cell Biology, University of California Berkeley CA USA.
¹¹ Department of Nutritional Sciences and Toxicology, University of California Berkeley CA USA.
¹² Chan Zuckerberg Biohub San Francisco CA USA.

Abstract

Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has limited their development. In this report, we performed an 8000 molecule electrophile screen against PLpro and identified an α-chloro amide fragment, termed compound 1, which inhibited SARS-CoV-2 replication in cells, and also had low non-specific reactivity with thiols. Compound 1 covalently reacts with the active site cysteine of PLpro, and had an IC50 of 18 μM for PLpro inhibition. Compound 1 also had low non-specific reactivity with thiols and reacted with glutathione 1-2 orders of magnitude slower than other commonly used electrophilic warheads. Finally, compound 1 had low toxicity in cells and mice and has a molecular weight of only 247 daltons and consequently has great potential for further optimization. Collectively, these results demonstrate that compound 1 is a promising lead fragment for future PLpro drug discovery campaigns.