Prediction and validation of host cleavage targets of SARS-CoV-2 3C-like protease
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Abstract
How SARS-CoV-2 causes the observed range of clinical manifestations and disease severity remains poorly understood. SARS-CoV-2 encodes for two proteases (3CLPro and PLPro), vital for viral production, but also promiscuous with respect to host protein targets, likely contributing to the range of disease. Pharmacological inhibition of the 3C-like3 protease has revealed remarkable reduction in hospitalization and death in phase 2/3 clinical studies. However, the mechanisms responsible for the pathology mediated by those proteases are still unclear. In this study, we develop a bioinformatic algorithm, leveraging experimental data from SARS-CoV, to predict host cleavage targets of the SARS-CoV-2 3C-like protease, or 3CLPro. We capture targets of the 3CL protease described previously for SARS-CoV, and we identify hundreds of new putative targets. We experimentally validate a number of these predicted targets, including the giant sarcomeric protein Obscurin, and show that expression of 3CL protease alone recapitulates the sarcomeric disorganization seen by SARS-CoV-2 infection of hiPSC-derived cardiomyocytes. Our data provide a resource to identify putative host cleavage targets of 3CL protease that contribute to mechanisms and heterogeneity of disease in COVID-19 and future coronavirus outbreaks.
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SciScore for 10.1101/2022.01.17.476677: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding Images assignments were blinded during quantification. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Lysate preparation and Western blotting: For western blotting of 293T cell lysates, traditional RIPA buffer was used to lyse cells. 293Tsuggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing …SciScore for 10.1101/2022.01.17.476677: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding Images assignments were blinded during quantification. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Lysate preparation and Western blotting: For western blotting of 293T cell lysates, traditional RIPA buffer was used to lyse cells. 293Tsuggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our computational algorithm overcomes these limitations and provides a comprehensive atlas of the putative SARS-CoV-2 3CLpro degradome. The SARS-CoV-2 3CLpro is the target of ongoing therapeutic efforts to treat COVID-19. Recent interim analysis of the phase 2/3 EPIC-HR (Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients)22, which tested the combination therapy of PF-07321332, a 3CLpro inhibitor, with ritonavir, a CYP3A4 inhibitor that prevents the metabolism of protease inhibitors, reported a nearly 90% reduction in hospitalization or death compared to placebo in non-hospitalized high-risk adults with COVID-19 (P<0.0001). Our data suggest that these remarkable benefits of 3CLpro inhibition may accrue from effects beyond suppression of viral replication. For example, infected cells that do not sustain replication may nevertheless experience significant cellular damage from 3CLpro activity on the host proteome, and PF-07321332 and other 3CLpro inhibitors would be predicted to prevent this cellular damage. Similarly, expression of 3CLpro is one of the earliest events in the viral life cycle, and may thus cause early cellular damage, potentially suppressing cellular defenses against the ensuing viral replication. Lingering effects of 3CLpro may also contribute to persistent symptoms, as observed with the long-COVID syndrome. In sum, the remarkable benefits of 3CLpro inhibition in COVID-19 patients underscores the need to further understand the impact of 3CLpro ...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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