The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules
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SciScore for 10.1101/2020.05.16.091520: (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 not detected. Table 2: Resources
Antibodies Sentences Resources LysoTracker Deep Red (L12492), goat-anti-mouse AlexaFluor-647 (A-21242, RRID:AB_2535811), HCS Cell Mask Green (H32714) goat-anti-mouse AlexaFluor-647detected: (Thermo Fisher Scientific Cat# A-21242, RRID:AB_2535811)LC3B primary rabbit antibody (3868S, RRID:AB_2137707) was purchased from Cell Signaling Technologies. Cell Staining Buffer (420201) was purchased from BioLegend. LC3Bdetected: (Cell Signaling Technology Cat# 3868, RRID:AB_2137707)Plates were then … SciScore for 10.1101/2020.05.16.091520: (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 not detected. Table 2: Resources
Antibodies Sentences Resources LysoTracker Deep Red (L12492), goat-anti-mouse AlexaFluor-647 (A-21242, RRID:AB_2535811), HCS Cell Mask Green (H32714) goat-anti-mouse AlexaFluor-647detected: (Thermo Fisher Scientific Cat# A-21242, RRID:AB_2535811)LC3B primary rabbit antibody (3868S, RRID:AB_2137707) was purchased from Cell Signaling Technologies. Cell Staining Buffer (420201) was purchased from BioLegend. LC3Bdetected: (Cell Signaling Technology Cat# 3868, RRID:AB_2137707)Plates were then incubated with rabbit-anti-LC3B (Cell Signaling Technologies, Danvers, MA) antibodies in Cell Staining Buffer for 2 h at room temperature. rabbit-anti-LC3B ( Cell Signaling Technologies , Danvers , MA )suggested: NonePlates were washed three times with PBS and secondary antibody goat-anti-mouse AlexaFluor-647 (Invitrogen) were added in Cell Staining Buffer for 1 h. AlexaFluor-647 (Invitrogen)suggested: NoneExperimental Models: Cell Lines Sentences Resources The following items were purchased from ATCC: EMEM (30-2003), Vero-E6 (CRL-1586, RRID:CVCL_0574), HeLa (CCL-2, RRID:CVCL_0030) ATCC: EMEM ( 30-2003 ) , Vero-E6 ( CRL-1586detected: (IZSLER Cat# BS CL 87, RRID:CVCL_0574)HeLadetected: (BCRC Cat# 60005, RRID:CVCL_0030), HEK293T (CRL-3216, RRID:CVCL_0063). HEK293Tdetected: (CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)Cell Culture: Vero-E6 cells previously selected for high ACE2 expression (82) were cultured in MEM/10% HI FBS supplemented with 0.5 μg/mL amphotericin B and passaged twice per week at 1:5 dilutions using trypsin. Vero-E6suggested: None, HeLa CCL-2, HEK293T and Huh-7.5 (grown in DMEM, 10% FBS, and 1% Penicillin/Streptomycin) were cultured in T175 flasks and passaged at 95% confluency. HeLasuggested: NoneHEK293Tsuggested: NoneHuh-7.5suggested: RRID:CVCL_7927)The plates were transported into the BSL-3 facility were a 25 μL aliquot of virus inoculated cells (4000 Vero E6 cells/well) was added to each well in columns 3-24. Vero E6suggested: NoneExperimental Models: Organisms/Strains Sentences Resources TrypLE (12604013), PBS -/- (w/o Ca2+ or Mg2+) ( PBS -/-suggested: NoneVero-E6 (grown in EMEM, 10% FBS, and 1% Penicillin/Streptomycin) Vero-E6suggested: NoneSoftware and Algorithms Sentences Resources Image montages were prepared using Fiji (ImageJ, NIH). Fijisuggested: (Fiji, RRID:SCR_002285)ImageJsuggested: (ImageJ, RRID:SCR_003070)High-content image analysis data was downloaded as a Microsoft Excel spreadsheet. Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)EC50 values were obtained using non-linear regression in Graphpad Prism 7.04. Graphpad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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:However, there are limitations to the CPE assay including its dependence on the host response and the fact that it is an indirect measurement of SARS-CoV-2 infection and replication. The phenotypic outcome can also vary depending on culture conditions and viral multiplicity of infection (MOI), number of virions that are added per cell during infection (58). The potencies of drug protection against virally-induced cell death can be lower than in other assays that directly measure viral load. Nevertheless, this study confirms that SARS-CoV-2 infection in Vero-E6 cells results in cell death similar to other reports, and that CPE can be suppressed by blocking autophagy with small molecule inhibitors to the same extent as positive control remdesivir (59, 60). Recently, a drug-repurposing screen of FDA-approved compounds, using a similar CPE assay with SARS-CoV-2 in Vero-E6 cells, found clomipramine (IC50 5.93 μM; CC50 >30 μM) and mefloquine (IC50 7.11 μM; CC50 >18.5 μM) to be active with low toxicity (61). The same study found HCQ to be more active than CQ with an IC50 of 9.21 μM and 42.03 μM, respectively. Mefloquine was also found to be active in another SARS-CoV-2 CPE screen using Caco-2 cells with an IC50 of 14.1 μM (62). In our study, the SI was calculated using the ratio of the EC50, the half-maximal effective concentration, and the CC50, the half-maximal cytotoxic concentration. Between the CPE and the autophagy assays there was good correspondence in the cytotoxicity measu...
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.
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