Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing



Meyer, Bjoern ORCID: 0000-0002-7903-5710, Chiaravalli, Jeanne, Gellenoncourt, Stacy, Brownridge, Philip, Bryne, Dominic ORCID: 0000-0001-9712-9676, Daly, Leonard ORCID: 0000-0001-6280-239X, Walter, Marius, Agou, Fabrice, Chakrabarti, Lisa ORCID: 0000-0002-4400-771X, Craik, Charles ORCID: 0000-0002-3239-8178
et al (show 7 more authors) (2020) Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing.

[img] Text
SARS-Cov-2-Protease-Biorxiv.pdf - Submitted Version

Download (2MB) | Preview

Abstract

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, and responsible for over 100 million infections, and over 2 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, and inhibitors targeting proteases have already shown success at inhibiting SARS-CoV-2 in cell culture models. 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 antigenic proteins S and N, which are the main targets for vaccine and antibody testing efforts. We discovered 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, validating a subset with in vitro assays. We showed 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, showed 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 disease.

Item Type: Article
Depositing User: Symplectic Admin
Date Deposited: 09 Nov 2020 08:19
Last Modified: 08 Apr 2021 12:10
DOI: 10.1101/2020.09.16.297945
URI: https://livrepository.liverpool.ac.uk/id/eprint/3106341