Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease
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Abstract
A new coronavirus SARS-CoV-2, also called novel coronavirus 2019 (2019-nCoV), started to circulate among humans around December 2019, and it is now widespread as a global pandemic. The disease caused by SARS-CoV-2 virus is called COVID-19, which is highly contagious and has an overall mortality rate of 6.35% as of May 26, 2020. There is no vaccine or antiviral available for SARS-CoV-2. In this study, we report our discovery of inhibitors targeting the SARS-CoV-2 main protease (M pro). Using the FRET-based enzymatic assay, several inhibitors including boceprevir, GC-376, and calpain inhibitors II, and XII were identified to have potent activity with single-digit to submicromolar IC 50 values in the enzymatic assay. The mechanism of action of the hits was further characterized using enzyme kinetic studies, thermal shift binding assays, and native mass spectrometry. Significantly, four compounds (boceprevir, GC-376, calpain inhibitors II and XII) inhibit SARS-CoV-2 viral replication in cell culture with EC 50 values ranging from 0.49 to 3.37 µM. Notably, boceprevir, calpain inhibitors II and XII represent novel chemotypes that are distinct from known substrate-based peptidomimetic M pro inhibitors. A complex crystal structure of SARS-CoV-2 M pro with GC-376, determined at 2.15 Å resolution with three protomers per asymmetric unit, revealed two unique binding configurations, shedding light on the molecular interactions and protein conformational flexibility underlying substrate and inhibitor binding by M pro. Overall, the compounds identified herein provide promising starting points for the further development of SARS-CoV-2 therapeutics.
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The COVID-19 pandemic has emphasized the impact of zoonotic diseases on human health and highlighted veterinary drugs as a potential source of viable antivirals.
“The recent COVID-19 pandemic has emphasized the impact of zoonotic diseases on human health but has also highlighted veterinary drugs as a potential source of viable antivirals (15).”
From DrugCentral 2023 extends human clinical data and integrates veterinary drugs (2023) · cites this paper as [15]
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- Authors
- Ma, C., Sacco, M. D., Hurst, B., Townsend, J. A., Hu, Y., Szeto, T., Zhang, X., Tarbet, B., Marty, M. T., Chen, Y., & Wang, J.
- Affiliations
- University of Arizona (US)
- University of South Florida (US)
- Utah State University (US)
- Corresponding author
- Chen, Yu
- Wang, Jun
- ORCID
- Venue
- Cell Research
- Published
- 2020-06-15
- Volume
- 30
- Issue
- 8
- Pages
- 678-692
- ISSN
- 1001-0602 (ISSN-L)
- 1748-7838
- PMC
- PMC7263507
- OpenAlex
- W3034228022
- Cited by
- 880
- References
- 53
- Citations by year
- 2026: 37 · 2025: 68 · 2024: 111 · 2023: 147 · 2022: 175 · 2021: 250 · 2020: 90 · 2019: 1
- FWCI
- 22.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cell Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (AI147325, N01-AI-30048)
- ADHS | Arizona Biomedical Research Commission (ADHS18-198859)
- DOE | Advanced Research Projects Agency - Energy (DE-AC02-06CH11357)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, COVID-19 pandemic, main protease, boceprevir, calpain inhibitors, viral replication inhibition, antiviral drug discovery, enzyme kinetics, native mass spectrometry, crystal structure, protein flexibility, substrate binding, peptidomimetic inhibitors
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