VE607 stabilizes SARS-CoV-2 Spike in the “RBD-up” conformation and inhibits viral entry

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1. Version published to 10.1016/j.isci.2022.104528

   Jul 1, 2022
2. 

   ScreenIT

   Feb 8, 2022

   SciScore for 10.1101/2022.02.03.479007: (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	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   AlexaFluor-647-conjugated goat anti-human IgG (H+L) Ab (Invitrogen) and AlexaFluor-conjugated donkey anti-goat IgG (H+L) Ab (Invitrogen) was used as secondary antibodies.	anti-human IgG suggested: None AlexaFluor-conjugated donkey anti-goat IgG suggested: None
   An anti-mouse SARS-CoV-2 nucleocapsid protein (Clone 1C7, Bioss Antibodies)	anti-mouse SARS-CoV-2 nucleocapsid protein suggested: None
   Following extensive washing (3×) with PBS, an anti-mouse IgG HRP secondary antibody solution was …

   SciScore for 10.1101/2022.02.03.479007: (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	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   AlexaFluor-647-conjugated goat anti-human IgG (H+L) Ab (Invitrogen) and AlexaFluor-conjugated donkey anti-goat IgG (H+L) Ab (Invitrogen) was used as secondary antibodies.	anti-human IgG suggested: None AlexaFluor-conjugated donkey anti-goat IgG suggested: None
   An anti-mouse SARS-CoV-2 nucleocapsid protein (Clone 1C7, Bioss Antibodies)	anti-mouse SARS-CoV-2 nucleocapsid protein suggested: None
   Following extensive washing (3×) with PBS, an anti-mouse IgG HRP secondary antibody solution was formulated in PBS + 1% non-fat milk.	anti-mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The 293T-ACE2 cell line was previously reported (Prevost et al., 2020)	293T-ACE2 suggested: None
   Briefly, 293T cells were transfected by the calcium phosphate method with the lentiviral vector pNL4.3 R-E-Luc (NIH AIDS Reagent Program) and a plasmid encoding for SARS-CoV-2 Spike at a ratio of 5:4.	293T suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
   All virus-compounds supernatant was removed from wells without disrupting the Vero E6 monolayer.	Vero E6 suggested: RRID:CVCL_XD71)
   Cell viability test: To measure the cytotoxicity of VE607 and its stereoisomers on 293T-ACE2 or Vero-E6 cells, a cell viability assay using CellTiter-Glo® One Solution Assay (Promega) was performed.	Vero-E6 suggested: None
   Recombinant DNA
   Sentences	Resources
   The codon-optimized RBD sequence (encoding residues 319-541) fused to a C-terminal hexahistidine tag was cloned into the pcDNA3.1(+) expression vector and was reported elsewhere (Beaudoin-Bussieres et al., 2020).	pcDNA3.1(+) suggested: RRID:Addgene_129020)
   Plasmid encoding the Delta (B.1.617.2) and Omicron (B.1.1.529) Spikes were generated by overlapping PCR using a codon-optimized wild-type SARS-CoV-2 Spike gene (GeneArt, ThermoFisher) that was synthesized (Biobasic) and cloned in pCAGGS as a template (Chatterjee et al., 2021; Gong et al., 2021b; Tauzin et al., 2022).	pCAGGS suggested: RRID:Addgene_127347)
   The vesicular stomatitis virus G (VSV-G)-encoding plasmid (pSVCMV-IN-VSV-G) was previously described (Emi et al., 1991).	VSV-G)-encoding suggested: None pSVCMV-IN-VSV-G suggested: None
   Briefly, 293T cells were transfected by the calcium phosphate method with the lentiviral vector pNL4.3 R-E-Luc (NIH AIDS Reagent Program) and a plasmid encoding for SARS-CoV-2 Spike at a ratio of 5:4.	pNL4.3 suggested: None
   Cell surface staining and flow cytometry analysis: Using the standard calcium phosphate method, 10 μg of Spike expressor and 2.5 μg of a green fluorescent protein (GFP) expressor (pIRES-GFP) were transfected into 2 × 106 293T cells.	pIRES-GFP suggested: RRID:Addgene_78264)
   Software and Algorithms
   Sentences	Resources
   VE607 compound was structurally preprocessed using LigPrep (Schrödinger, 2020) to generate multiple states for stereoisomers, tautomers, ring conformations, and protonation states at a selected pH range.	LigPrep suggested: (Ligprep, RRID:SCR_016746)
   Samples were acquired on a LSRII cytometer (BD Biosciences, Mississauga, ON, Canada) and data analysis was performed using FlowJo vX.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Densitometry data were acquired with a Typhoon Trio Variable Mode Imager (Amersham Biosciences) in storage phosphor acquisition mode and analyzed using ImageQuant 5.2 (Molecular Dynamics).	ImageQuant suggested: (ImageQuant, RRID:SCR_014246)
   Quantification and statistical analysis: Statistics were analyzed using GraphPad Prism version 8.0.2 (GraphPad, San Diego, CA, (USA).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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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: No clinical trial numbers were referenced.

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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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.02.03.479007 on bioRxiv

   Feb 4, 2022