Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L
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Abstract
X-ray crystal structures of SARS-CoV-2 M pro with dual inhibitors provide a new direction for the designing of COVID-19 antivirals.
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SciScore for 10.1101/2020.07.27.223727: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The velocities were randomized and MD simulation for 12 ps was performed in the NPT ensemble and a Berendsen barostat55 with solute heavy atoms equally restrained at 10 K and another one at 300 K. 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 The cells were then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary … SciScore for 10.1101/2020.07.27.223727: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The velocities were randomized and MD simulation for 12 ps was performed in the NPT ensemble and a Berendsen barostat55 with solute heavy atoms equally restrained at 10 K and another one at 300 K. 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 The cells were then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary antibody (ThermoFisher Scientific). SARS-CoV-2 NPsuggested: (Sino Biological Cat# 40588-R0004, RRID:AB_2857931)GTX635679suggested: Noneanti-mousesuggested: NoneExperimental Models: Cell Lines Sentences Resources Human rhabdomyosarcoma (RD), MDCK, Vero, Huh-7, and HCT-8 cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) medium; Caco-2 and MRC-5 cell lines were maintained in Eagle's Minimum Essential Medium (EMEM) medium. MDCKsuggested: CLS Cat# 602280/p823_MDCK_(NBL-2), RRID:CVCL_0422Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059Huh-7suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336HCT-8suggested: KCLB Cat# 10244, RRID:CVCL_2478Caco-2suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025MRC-5suggested: CLS Cat# 300395/NA, RRID:CVCL_0440Vero E6 cells in 96-well plates (Corning) were infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI of 0.05 in DMEM supplemented with 1% FBS. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources The total number of cells, as indicated by the nuclei staining, and the fraction of the infected cells, as indicated by the NP staining, were quantified with the cellular analysis module of the Gen5 software (BioTek) Gen5suggested: (Gen5, RRID:SCR_017317)Rigid and restrained refinements were performed using REFMAC and model building was performed with COOT. REFMACsuggested: (Refmac, RRID:SCR_014225)COOTsuggested: (Coot, RRID:SCR_014222)Protein structure figures were made using PyMOL (Schrödinger, LLC). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
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.
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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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SciScore for 10.1101/2020.07.27.223727: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The velocities were randomized and MD simulation for 12 ps was performed in the NPT ensemble and a Berendsen barostat55 with solute heavy atoms equally restrained at 10 K and another one at 300 K. 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 The cells were then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary … SciScore for 10.1101/2020.07.27.223727: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The velocities were randomized and MD simulation for 12 ps was performed in the NPT ensemble and a Berendsen barostat55 with solute heavy atoms equally restrained at 10 K and another one at 300 K. 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 The cells were then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary antibody (ThermoFisher Scientific). SARS-CoV-2 NPsuggested: NoneGTX635679suggested: (GeneTex Cat# GTX635679, RRID:AB_2888553)anti-mousesuggested: NoneExperimental Models: Cell Lines Sentences Resources Cell lines and viruses: Human rhabdomyosarcoma (RD), MDCK, Vero, Huh-7, and HCT-8 cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) medium; Caco-2 and MRC-5 cell lines were maintained in Eagle’s Minimum Essential Medium (EMEM) medium. MDCKsuggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Huh-7suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)HCT-8suggested: ICLC Cat# HTL99005, RRID:CVCL_2478)Caco-2suggested: NoneMRC-5suggested: ICLC Cat# HL95001, RRID:CVCL_0440)Plaque assay: Vero E6 cells in 6-well plates (Corning) were infected with SARS-CoV-2 (USA-WA1/2020 isolate) at approximately 40 PFU per well. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources The total number of cells, as indicated by the nuclei staining, and the fraction of the infected cells, as indicated by the NP staining, were quantified with the cellular analysis module of the Gen5 software (BioTek). Gen5suggested: (Gen5, RRID:SCR_017317)Rigid and restrained refinements were performed using REFMAC and model building was performed with COOT. REFMACsuggested: (Refmac, RRID:SCR_014225)COOTsuggested: (Coot, RRID:SCR_014222)Protein structure figures were made using PyMOL (Schrödinger, LLC). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
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.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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SciScore for 10.1101/2020.07.27.223727: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The velocities were randomized and MD simulation for 12 ps was performed in the NPT ensemble and a Berendsen barostat55 with solute heavy atoms equally restrained at 10 K and another one at 300 K. 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 The cells were then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary … SciScore for 10.1101/2020.07.27.223727: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The velocities were randomized and MD simulation for 12 ps was performed in the NPT ensemble and a Berendsen barostat55 with solute heavy atoms equally restrained at 10 K and another one at 300 K. 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 The cells were then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary antibody (ThermoFisher Scientific). SARS-CoV-2 NPsuggested: (Sino Biological Cat# 40588-R0004, RRID:AB_2857931)GTX635679suggested: Noneanti-mousesuggested: NoneExperimental Models: Cell Lines Sentences Resources Human rhabdomyosarcoma (RD), MDCK, Vero, Huh-7, and HCT-8 cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) medium; Caco-2 and MRC-5 cell lines were maintained in Eagle's Minimum Essential Medium (EMEM) medium. MDCKsuggested: CLS Cat# 602280/p823_MDCK_(NBL-2), RRID:CVCL_0422Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059Huh-7suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336HCT-8suggested: KCLB Cat# 10244, RRID:CVCL_2478Caco-2suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025MRC-5suggested: CLS Cat# 300395/NA, RRID:CVCL_0440Vero E6 cells in 6-well plates (Corning) were infected with SARS-CoV-2 (USAWA1/2020 isolate) at approximately 40 PFU per well. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources The total number of cells, as indicated by the nuclei staining, and the fraction of the infected cells, as indicated by the NP staining, were quantified with the cellular analysis module of the Gen5 software (BioTek) Gen5suggested: (Gen5, RRID:SCR_017317)Rigid and restrained refinements were performed using REFMAC and model building was performed with COOT. REFMACsuggested: (Refmac, RRID:SCR_014225)COOTsuggested: (Coot, RRID:SCR_014222)Protein structure figures were made using PyMOL (Schrödinger, LLC). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
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.
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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
-
SciScore for 10.1101/2020.07.27.223727: (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 then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary antibody (ThermoFisher Scientific). SARS-CoV-2 NPsuggested: (Sino Biological Cat# 40588-R0004, AB_2857931)<div style="margin-bottom:8px"> <div><b>GTX635679</b></div> <div>suggested: None</div> </div> <div style="margin-bottom:8px">
SciScore for 10.1101/2020.07.27.223727: (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 then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton-100, blocked with DMEM containing 10% FBS, and stained with a rabbit monoclonal antibody against SARS-CoV-2 NP (GeneTex, GTX635679) and an Alexa Fluor 488-conjugated goat anti-mouse secondary antibody (ThermoFisher Scientific). SARS-CoV-2 NPsuggested: (Sino Biological Cat# 40588-R0004, AB_2857931)<div style="margin-bottom:8px"> <div><b>GTX635679</b></div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div><b>anti-mouse</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Human rhabdomyosarcoma (RD), MDCK, Vero, Huh-7, and HCT-8 cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) medium; Caco-2 and MRC-5 cell lines were maintained in Eagle's Minimum Essential Medium (EMEM) medium.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>MDCK</b></div> <div>suggested: CLS Cat# 602280/p823_MDCK_(NBL-2), <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0422">CVCL_0422</a></div> </div> <div style="margin-bottom:8px"> <div><b>Vero</b></div> <div>suggested: CLS Cat# 605372/p622_VERO, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0059">CVCL_0059</a></div> </div> <div style="margin-bottom:8px"> <div><b>Huh-7</b></div> <div>suggested: CLS Cat# 300156/p7178_HuH7, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0336">CVCL_0336</a></div> </div> <div style="margin-bottom:8px"> <div><b>HCT-8</b></div> <div>suggested: KCLB Cat# 10244, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_2478">CVCL_2478</a></div> </div> <div style="margin-bottom:8px"> <div><b>Caco-2</b></div> <div>suggested: CLS Cat# 300137/p1665_CaCo-2, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0025">CVCL_0025</a></div> </div> <div style="margin-bottom:8px"> <div><b>MRC-5</b></div> <div>suggested: CLS Cat# 300395/NA, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0440">CVCL_0440</a></div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Vero E6 cells in 6-well plates (Corning) were infected with SARS-CoV-2 (USAWA1/2020 isolate) at approximately 40 PFU per well.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Vero E6</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The total number of cells, as indicated by the nuclei staining, and the fraction of the infected cells, as indicated by the NP staining, were quantified with the cellular analysis module of the Gen5 software (BioTek)</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Gen5</b></div> <div>suggested: (Gen5, <a href="https://scicrunch.org/resources/Any/search?q=SCR_017317">SCR_017317</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Rigid and restrained refinements were performed using REFMAC and model building was performed with COOT.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>REFMAC</b></div> <div>suggested: (Refmac, <a href="https://scicrunch.org/resources/Any/search?q=SCR_014225">SCR_014225</a>)</div> </div> <div style="margin-bottom:8px"> <div><b>COOT</b></div> <div>suggested: (Coot, <a href="https://scicrunch.org/resources/Any/search?q=SCR_014222">SCR_014222</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Protein structure figures were made using PyMOL (Schrödinger, LLC)</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>PyMOL</b></div> <div>suggested: (PyMOL, <a href="https://scicrunch.org/resources/Any/search?q=SCR_000305">SCR_000305</a>)</div> </div> </td></tr></table>
Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
-