Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential

Meyer, Bjoern, Chiaravalli, Jeanne, Gellenoncourt, Stacy, Brownridge, Philip, Bryne, Dominic P, Daly, Leonard A ORCID: 0000-0001-9712-9676, Grauslys, Arturas ORCID: 0000-0002-6736-6854, Walter, Marius, Agou, Fabrice, Chakrabarti, Lisa A
et al (show 9 more authors) (2021) Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. NATURE COMMUNICATIONS, 12 (1). 5553-.

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SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.

Item Type: Article
Uncontrolled Keywords: Cell Line, Animals, Humans, Myosin-Light-Chain Kinase, src-Family Kinases, Dipeptides, Viral Proteins, RNA, Small Interfering, Protease Inhibitors, Antiviral Agents, Proteomics, Virus Replication, Mutation, Virus Internalization, Proteolysis, COVID-19, SARS-CoV-2, Viral Proteases, COVID-19 Drug Treatment
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User: Symplectic Admin
Date Deposited: 30 Sep 2021 15:56
Last Modified: 11 Feb 2023 02:57
DOI: 10.1038/s41467-021-25796-w
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