De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

  1. Longxing Cao
  2. Inna Goreshnik
  3. Brian Coventry
  4. James Brett Case
  5. Lauren Miller
  6. Lisa Kozodoy
  7. Rita E. Chen
  8. Lauren Carter
  9. Alexandra C. Walls
  10. Young-Jun Park
  11. Eva-Maria Strauch
  12. Lance Stewart
  13. Michael S. Diamond
  14. David Veesler
  15. David Baker

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is decorated with spikes, and viral entry into cells is initiated when these spikes bind to the host angiotensin-converting enzyme 2 (ACE2) receptor. Many monoclonal antibody therapies in development target the spike proteins. Cao et al. designed small, stable proteins that bind tightly to the spike and block it from binding to ACE2. The best designs bind with very high affinity and prevent SARS-CoV-2 infection of mammalian Vero E6 cells. Cryo–electron microscopy shows that the structures of the two most potent inhibitors are nearly identical to the computational models. Unlike antibodies, the miniproteins do not require expression in mammalian cells, and their small size and high stability may allow formulation for direct delivery to the nasal or respiratory system.

Science , this issue p. 426

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  1. ScreenIT

    SciScore for 10.1101/2020.08.03.234914: (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
    Plates were washed and sequentially incubated with 1 μg/mL of CR3022 (5) anti-S antibody and HRP-conjugated goat anti-human IgG in PBS supplemented to contain 0.1% saponin and 0.1% BSA.
    anti-S
    suggested: None
    anti-human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Virus stocks were produced in Vero CCL81 cells (ATCC) and titrated by focus-forming assay on Vero E6 cells.
    Vero CCL81
    suggested: None
    RBD binder-virus complexes were added to Vero E6 cell monolayers in 96-well plates and incubated for 1 h at 37°C.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    All libraries were amplified using Kapa HiFi Polymerase (Kapa Biosystems) with a qPCR machine (BioRAD CFX96).
    BioRAD
    suggested: None
    Data was processed using Prism software (GraphPad Prism 8.0).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Movie frame alignment, estimation of the microscope contrast-transfer function parameters, particle picking, and extraction were carried out using Warp.
    Warp
    suggested: (Warp, RRID:SCR_018071)
    Local resolution estimation, filtering, and sharpening were carried out using CryoSPARC.
    CryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)

    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 pages 26 and 28. 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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  2. Version published to 10.1126/science.abd9909
  3. Version published to 10.1101/2020.08.03.234914v1 on bioRxiv