Challenges for Targeting SARS-CoV-2 Proteases as a Therapeutic Strategy for COVID-19

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1. Version published to 10.1021/acsinfecdis.0c00815

   Feb 11, 2021
2. 

   ScreenIT

   Nov 24, 2020

   SciScore for 10.1101/2020.11.21.392753: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	Contamination: Cell lines: VeroE6 and A549 cells were obtained from American Type Culture Collection (ATCC) and tested at regular intervals for mycoplasma contamination.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After three times washing with PBS, bound primary antibody was detected with a secondary antibody (anti-mouse IgG), conjugated to horseradish peroxidase.	anti-mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   This Heidelberg strain was passaged in VeroE6 cells, aliquoted and …

   SciScore for 10.1101/2020.11.21.392753: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	Contamination: Cell lines: VeroE6 and A549 cells were obtained from American Type Culture Collection (ATCC) and tested at regular intervals for mycoplasma contamination.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After three times washing with PBS, bound primary antibody was detected with a secondary antibody (anti-mouse IgG), conjugated to horseradish peroxidase.	anti-mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   This Heidelberg strain was passaged in VeroE6 cells, aliquoted and stored at −80° C.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Cell lines: VeroE6 and A549 cells were obtained from American Type Culture Collection (ATCC) and tested at regular intervals for mycoplasma contamination.	A549 suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
   Lentivirus stocks were produced by transfection of HEK293T cells with a pWPI plasmid encoding for TMPRSS2 and the pCMV-Gag-Pol and pMD2-VSV-G packaging plasmids (kind gifts from D. Trono, Geneva).	HEK293T suggested: None
   For all other assays, A549+ACE2 cells were cultured in Roswell Park Memorial Institute (	A549+ACE2 suggested: None
   Software and Algorithms
   Sentences	Resources
   PLpro expression and purification: For cloning of PLpro with an N-terminal 6xHis-SUMO1 tag, synthetic fragments of the Nsp3 coding sequence derived from the original Wuhan strain were purchased from BioCat.	BioCat suggested: (BioCAT, RRID:SCR_001440)
   All data were analyzed using GraphPad Prism (v8.4)	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Densitometric analysis of protein bands on gels was performed using ImageJ (v1.52p)	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   The LC-MS systems used was either a Thermo Fisher Finnigan Surveyor Plus equipped with an Agilent Zorbax 300SB-C18 column (3.5 μm, 3.0 × 150 mm) coupled to a Finnigan LTQ mass spectrometer or an Agilent 1100 Series HPLC equipped with a Luna 4251-E0 C18 column (3 μm, 4.6 x 150 mm) coupled to a PE SCIEX API 150EX mass spectrometer (wavelengths monitored = 220, 254 and 646 nm).	Thermo Fisher Finnigan Surveyor Plus suggested: None

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   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).

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04535167	Recruiting	First-In-Human Study To Evaluate Safety, Tolerability, And P…

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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.

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3. 

   Version published to 10.1101/2020.11.21.392753 on bioRxiv

   Nov 23, 2020