Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production

  1. Natalia Fintelman-Rodrigues
  2. Carolina Q. Sacramento
  3. Carlyle Ribeiro Lima
  4. Franklin Souza da Silva
  5. André C. Ferreira
  6. Mayara Mattos
  7. Caroline S. de Freitas
  8. Vinicius Cardoso Soares
  9. Suelen da Silva Gomes Dias
  10. Jairo R. Temerozo
  11. Milene D. Miranda
  12. Aline R. Matos
  13. Fernando A. Bozza
  14. Nicolas Carels
  15. Carlos Roberto Alves
  16. Marilda M. Siqueira
  17. Patrícia T. Bozza
  18. Thiago Moreno L. Souza

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is already responsible for far more deaths than previous pathogenic coronaviruses (CoVs) from 2002 and 2012. The identification of clinically approved drugs to be repurposed to combat 2019 CoV disease (COVID-19) would allow the rapid implementation of potentially life-saving procedures. The major protease (Mpro) of SARS-CoV-2 is considered a promising target, based on previous results from related CoVs with lopinavir (LPV), an HIV protease inhibitor.

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  1. Version published to 10.1128/aac.00825-20
  2. ScreenIT

    SciScore for 10.1101/2020.04.04.020925: (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
    SentencesResources
    The purity of human monocytes was above 95%, as determined by flow cytometric analysis (FACScan; Becton Dickinson) using anti-CD3 (BD Biosciences) and anti-CD16 (Southern Biotech) monoclonal antibodies.
    anti-CD3
    suggested: None
    anti-CD16
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV-2 was prepared in Vero E6 cells from an isolate contained on a nasopharyngeal swab obtained from a confirmed case in Rio de Janeiro, Brazil.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Yield-reduction assay: Cells were infected with a multiplicity of infection (MOI) of 0.01. Vero or A549 cells were infected at densities of 5 × 105 cells/well.
    A549
    suggested: None
    Virus titration: Monolayers of Vero cells (2 × 104 cell/well) in 96-well plates were infected with a log-based dilution of supernatants containing SARS-CoV-2 for 1h at 37°C.
    Vero
    suggested: RRID:CVCL_ZW93)
    Software and Algorithms
    SentencesResources
    ELISA assays were purchased from R&D Bioscience.
    R&D Bioscience
    suggested: (UMD Bioprocess Scale-Up Facility, RRID:SCR_012703)
    Molecular docking: ATV (PubChem CID: 148192) and LPV (PubChem CID: 92727) were used as inhibitors of the SARS-CoV-2 Mpro.
    PubChem
    suggested: (PubChem, RRID:SCR_004284)
    Molecular docking experiments were performed with DOCK 6.946 for identifying the binding site of the Mpro.
    DOCK
    suggested: (DOCK, RRID:SCR_000128)
    Molecular dynamics: Since the tertiary structure (3D) of the SARS-CoV-2 Mpro is a homodimer, we focused the molecular dynamics only one chain, henceforward chain A. Molecular dynamics calculations were performed using NAMD 2.949 and Charmm27* force field50 at pH 7, i.e., with deprotonated Glu and Asp, protonated Arg and Lys, and neutral His with a protonated Nε atom.
    NAMD
    suggested: (NAMD, RRID:SCR_014894)
    The dose-response curves used to calculate EC50 and CC50 values were generated by variable slope plot from Prism GraphPad software 8.0.
    Prism GraphPad
    suggested: None

    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: 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: Please consider improving the rainbow (“jet”) colormap(s) used on page 22. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    About SciScore

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  3. Version published to 10.1101/2020.04.04.020925v2 on bioRxiv
  4. Version published to 10.1101/2020.04.04.020925v1 on bioRxiv