Crystal structure of SARS-CoV-2 papain-like protease
Open accessAbstract
The pandemic of coronavirus disease 2019 (COVID-19) is changing the world like never before. This crisis is unlikely contained in the absence of effective therapeutics or vaccine. The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. Given the PLpro proteases of SARS-CoV-2 and SARS-CoV share significant homology, inhibitor developed for SARS-CoV PLpro is a promising starting point of therapeutic development. In this study, we sought to provide structural frameworks for PLpro inhibitor design. We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111S, which shares many structural features of SARS-CoV PLpro. This crystal form has unique packing, high solvent content and reasonable resolution 2.5 Å, hence provides a good possibility for fragment-based screening using crystallographic approach. We characterized the protease activity of PLpro in cleaving synthetic peptide harboring nsp2/nsp3 juncture. We demonstrate that a potent SARS-CoV PLpro inhibitor GRL0617 is highly effective in inhibiting protease activity of SARS-CoV-2 with the IC50 of 2.2 ± 0.3 μmol/L. We then determined the structure of SARS-CoV-2 PLpro complexed by GRL0617 to 2.6 Å, showing the inhibitor accommodates the S3–S4 pockets of the substrate binding cleft. The binding of GRL0617 induces closure of the BL2 loop and narrows the substrate binding cleft, whereas the binding of a tetrapeptide substrate enlarges the cleft. Hence, our results suggest a mechanism of GRL0617 inhibition, that GRL0617 not only occupies the substrate pockets, but also seals the entrance to the substrate binding cleft hence prevents the binding of the LXGG motif of the substrate.
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DIS is a potent SARS-CoV-2 main protease Mpro and PLpro inhibitor, also targets other SARS-CoV-2 proteins such as nsp13 and nsp14, and is an inhibitor of pyroptosis via inhibition of gasdermin D.
“Recently, DIS was confirmed to be potent SARS-CoV-2 main proteases Mpro and PLpro inhibitor, but also targets other SARS-CoV-2 proteins such as nsp13 and nsp14 and is even an inhibitor of pyroptosis via inhibition of gasdermin D.93,94,95,96”
From Off-label and repurposed use of disulfiram beyond alcohol dependence: A systematic review of clinical and preclinical evidence (2026) · cites this paper as [95]
In Results and discussion (page not supplied), the authors report that disulfiram was ineffective against SARS-CoV-2 PLpro in their assay, contrary to the claim that it is a potent inhibitor. They report potent PLpro inhibition for GRL0617 instead. The cited passages do not establish the claim's other proposed targets or its effect on pyroptosis. (LLM, conf=0.90)
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- Authors
- Gao, X., Qin, B., Chen, P., Zhu, K., Hou, P., Wojdyla, J. A., Wang, M., & Cui, S.
- Affiliations
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Paul Scherrer Institute (CH)
- Corresponding author
- Cui, Sheng
- Venue
- Acta Pharmaceutica Sinica B
- Publisher
- Elsevier BV
- Published
- 2021-01
- Volume
- 11
- Issue
- 1
- Pages
- 237-245
- ISSN
- 2211-3835 (ISSN-L)
- PMC
- PMC7467110
- OpenAlex
- W3082311967
- Cited by
- 336
- References
- 57
- Citations by year
- 2026: 25 · 2025: 34 · 2024: 41 · 2023: 52 · 2022: 93 · 2021: 81 · 2020: 10
- FWCI
- 7.81
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Acta Pharmaceutica Sinica B (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DORA PSI (Paul Scherrer Institute) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by-nc-nd)
- Funders
- Science and Technology Major Project of Guangxi (2018ZX10101001)
- Chinese Academy of Medical Sciences
- National Key Research and Development Program of China (2016YFD0500300)
- Beijing Municipal Natural Science Foundation (7174288, 7182117)
- National Natural Science Foundation of China (81772207, 81572005, 81802057, 81971985, 11775308)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Protease and Inhibitor Mechanisms
- Keywords
- SARS-CoV-2, papain-like protease, protease inhibitors, crystal structure, substrate-binding cleft, fragment-based drug discovery, COVID-19 treatment
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