Entrectinib—A SARS-CoV-2 Inhibitor in Human Lung Tissue (HLT) Cells

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1. Version published to 10.3390/ijms222413592

   Dec 18, 2021
2. 

   ScreenIT

   Sep 9, 2021

   SciScore for 10.1101/2021.09.07.459123: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   On Day 3, cells were incubated with 20ul of 6x concentrations in HBSS of either the small molecules/peptides or an anti ACE2 antibody (AG-20A-0037PF-C500, Adipogen) for three hours.	anti ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Top hits were analyzed using VMD 1.9.3 software [30]. 4.4. Plasmids & Cell lines: The Lenti X 293T cell line (632180) was purchased from Takara Bio.	X 293T suggested: None
   Pseudovirus production: On Day 1, Lenti X 293T cells were seeded at a density of 60,000 cells/cm2 per T175 flask in 34ml DMEM supplemented with 10% FBS and 1mM Sodium Pyruvate.	Lenti X …

   SciScore for 10.1101/2021.09.07.459123: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   On Day 3, cells were incubated with 20ul of 6x concentrations in HBSS of either the small molecules/peptides or an anti ACE2 antibody (AG-20A-0037PF-C500, Adipogen) for three hours.	anti ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Top hits were analyzed using VMD 1.9.3 software [30]. 4.4. Plasmids & Cell lines: The Lenti X 293T cell line (632180) was purchased from Takara Bio.	X 293T suggested: None
   Pseudovirus production: On Day 1, Lenti X 293T cells were seeded at a density of 60,000 cells/cm2 per T175 flask in 34ml DMEM supplemented with 10% FBS and 1mM Sodium Pyruvate.	Lenti X 293T suggested: None
   Pseudovirus assay: On Day 1, 293T cells were seeded at 30,000 per well in white solid bottom 96 well plates that were either Poly L Lysine or Collagen coated in completed media (DMEM + 10% FBS + 1mM Sodium Pyruvate) at 37°C and 5% CO2.	293T suggested: None
   Recombinant DNA
   Sentences	Resources
   pLenti CMV Puro Luc (17477), pMDLg.pRRE (12251), pRSV.	pMDLg.pRRE suggested: None
   REV (12253), pMD2.G (12259) were purchased from Addgene.	pMD2 . G suggested: None
   The Spike ORF was subcloned into pcDNA3.1(+) vector via Gibson Assembly (NEB).	pcDNA3.1 ( + ) suggested: None
   Δ Spike: 20μg pLenti Luc, 20μg pMDLg.pRRE, 9.5μg pRSV.	pRSV suggested: RRID:Addgene_106453)
   Firefly Luciferase, encoded by pLenti Luc was used as the assay reporter. VSV.G, encoded by pMD2.	pMD2 suggested: None
   Software and Algorithms
   Sentences	Resources
   For this purpose, DrugBank [	DrugBank suggested: (DrugBank, RRID:SCR_002700)
   22] and PubChem [23] databases were used, merging both of them in a single database in SDF format.	PubChem suggested: (PubChem, RRID:SCR_004284)
   Then, different conformations for each compound were found using LigPrep software [27].	LigPrep suggested: (Ligprep, RRID:SCR_016746)
   4.3 Molecular Docking: For the molecular docking, AutoDock Vina 1.1.2 software [25,26] was used.	AutoDock suggested: (AutoDock, RRID:SCR_012746)
   Data was analysed on GraphPad Prism software.	GraphPad Prism 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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 10.1101/2021.09.07.459123v1 on bioRxiv

   Sep 7, 2021