An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

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1. Version published to 10.1038/s41392-021-00568-6

   Apr 24, 2021
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.11.986836: (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
   The cells were further incubated with a rabbit polyclonal antibody against a SARS-CoV nucleocapsid protein (Cambridgebio, USA) as primary antibody at a dilution of 1:200 for 2 h, followed by incubation with the secondary Alexa 488-labeled goat anti-rabbit antibody (Beyotime, China) at a dilution of 1:500.	SARS-CoV nucleocapsid protein suggested: (Creative Diagnostics Cat# DMAB8869, RRID:AB_2392503) anti-rabbit suggested: None
   The blot was probed with the antibody against the viral nucleocapsid protein (Cambridgebio, USA) and the horseradish peroxidase-conjugated Goat Anti-Rabbit IgG (Abcam, USA) as the …

   SciScore for 10.1101/2020.03.11.986836: (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
   The cells were further incubated with a rabbit polyclonal antibody against a SARS-CoV nucleocapsid protein (Cambridgebio, USA) as primary antibody at a dilution of 1:200 for 2 h, followed by incubation with the secondary Alexa 488-labeled goat anti-rabbit antibody (Beyotime, China) at a dilution of 1:500.	SARS-CoV nucleocapsid protein suggested: (Creative Diagnostics Cat# DMAB8869, RRID:AB_2392503) anti-rabbit suggested: None
   The blot was probed with the antibody against the viral nucleocapsid protein (Cambridgebio, USA) and the horseradish peroxidase-conjugated Goat Anti-Rabbit IgG (Abcam, USA) as the primary and the secondary antibodies, respectively.	Anti-Rabbit IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Indirect immunofluorescence assay: Vero E6 cells were treated with CVL218 at 5 µM, 15 µM and 25 µM, respectively, following the same procedure of “full-time” treatment.	Vero E6 suggested: RRID:CVCL_XD71)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Pharmacokinetics and toxicity study: Sprague-Dawley rats were purchased from Shanghai Laboratory Animal Center, China.	Sprague-Dawley suggested: RRID:RGD_70508)
   Software and Algorithms
   Sentences	Resources
   The virus target-drug interaction network was constructed from the integrated data from DrugBank (version 5.1.0) [17], ChEMBL (release 26) [54], TTD (last update 11 Nov, 2019) [55], IUPHAR BPS (release 13, Nov, 2019) [56], BindindDB [57] and GHDDI (https://ghddi-ailab.github.io/Targeting2019-nCoV/CoV_Experiment_Data/), with a cut-off threshold of IC50/EC50/Ki/Kd <10 µM.	DrugBank suggested: (DrugBank, RRID:SCR_002700) ChEMBL suggested: (ChEMBL, RRID:SCR_014042)
   The human protein-protein interaction network and the virus protein-human protein interaction network were constructed from the integrated data from BioGRID (release 3.5.181) [58], HuRI [59], Instruct [60], MINT (2012 update) [61], PINA (V2.0) [62], SignaLink (V2.0) [63] and innatedb [64].	BioGRID suggested: (BioGrid Australia, RRID:SCR_006334) MINT suggested: (MINT, RRID:SCR_001523) SignaLink suggested: (SignaLink, RRID:SCR_003569)
   Noted that we collected additional protein sequences of SARS-CoV-2 from UniProt [66] and added them into the corresponding networks for the final prediction.	UniProt suggested: (UniProtKB, RRID:SCR_004426)
   The training corpus we used was curated automatically from nearly 20 million PubMed (http://www.pubmed.gov) abstracts by a distant supervision technique [75].	PubMed suggested: (PubMed, RRID:SCR_004846)
   We used the connectivity map (CMap) [5], which contains the cellular gene expression profiles under the perturbation of 2428 well annotated reference compounds, to measure the associations of gene expression patterns between SARS-CoV infected patients and the reference compound-perturbed cells.	CMap suggested: (CMAP, RRID:SCR_009034)
   The dose-response curves were plotted according to viral RNA copies and the drug concentrations using GraphPad Prism (GraphPad Software, USA). 4.9.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   The plasma concentration-time data were analyzed using a non-compartmental method (Phoenix, version 1.3, USA) to derive the pharmacokinetic parameters. 4.14.	Phoenix suggested: (Phoenix, RRID:SCR_003163)
   The figures were prepared using GraphPad Prism (GraphPad Software, USA).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   The statistical significance was calculated by SPSS (ver.12), and two values were considered significantly different if the p-value is < 0.05. 4.17.	SPSS suggested: (SPSS, RRID:SCR_002865)
   The AutoGrid program was used to generate a grid map with 60×60×60 points spaced equally at 0.375 Å for evaluating the binding energies between the protein and the ligands.	AutoGrid suggested: (Autogrid, RRID:SCR_015982)

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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
   NCT04257656	Terminated	A Trial of Remdesivir in Adults With Severe COVID-19

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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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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 10.1101/2020.03.11.986836v1 on bioRxiv

   Mar 12, 2020