Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease

  1. Vasundara Srinivasan
  2. Hévila Brognaro
  3. Prince R. Prabhu
  4. Edmarcia Elisa de Souza
  5. Sebastian Günther
  6. Patrick Y. A. Reinke
  7. Thomas J. Lane
  8. Helen Ginn
  9. Huijong Han
  10. Wiebke Ewert
  11. Janina Sprenger
  12. Faisal H. M. Koua
  13. Sven Falke
  14. Nadine Werner
  15. Hina Andaleeb
  16. Najeeb Ullah
  17. Bruno Alves Franca
  18. Mengying Wang
  19. Angélica Luana C. Barra
  20. Markus Perbandt
  21. Martin Schwinzer
  22. Christina Schmidt
  23. Lea Brings
  24. Kristina Lorenzen
  25. Robin Schubert
  26. Rafael Rahal Guaragna Machado
  27. Erika Donizette Candido
  28. Danielle Bruna Leal Oliveira
  29. Edison Luiz Durigon
  30. Stephan Niebling
  31. Angelica Struve Garcia
  32. Oleksandr Yefanov
  33. Julia Lieske
  34. Luca Gelisio
  35. Martin Domaracky
  36. Philipp Middendorf
  37. Michael Groessler
  38. Fabian Trost
  39. Marina Galchenkova
  40. Aida Rahmani Mashhour
  41. Sofiane Saouane
  42. Johanna Hakanpää
  43. Markus Wolf
  44. Maria Garcia Alai
  45. Dusan Turk
  46. Arwen R. Pearson
  47. Henry N. Chapman
  48. Winfried Hinrichs
  49. Carsten Wrenger
  50. Alke Meents
  51. Christian Betzel

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Abstract

SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.

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  1. Version published to 10.1038/s42003-022-03737-7
  2. ScreenIT

    SciScore for 10.1101/2021.11.17.468943: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    1.5 Cytotoxicity assays: Vero cell lines (ATCC® CCL-81™) were cultivated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS).
    Vero
    suggested: None
    Recombinant DNA
    SentencesResources
    1.1 Cloning, protein overexpression and purification of SARS-CoV-2 PLpro: A fragment of SARS-CoV-2 ORF pp1a/ab encoding the PLpro domain and corresponding to amino acids 746-1060 of non-structural protein 3 (YP_009742610.1) was cloned into pETM11(EMBL), which encodes N-terminal hexa-his tag followed by a tobacco etch virus (TEV) protease cleavage site.
    pETM11
    suggested: RRID:Addgene_108943)
    Software and Algorithms
    SentencesResources
    Final rounds of manual refinement with either Refmac48 or Phenix49 together with manual model building applying COOT resulted in the final refined structures.
    COOT
    suggested: (Coot, RRID:SCR_014222)
    Microsoft Excel and GraphPad Prism (version 8.3.1) were used for analyzing the results and preparation of corresponding figures.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    Cell culture supernatant was harvest 42 h post-infection and viral RNA was purified using MagMAX™
    MagMAX™
    suggested: None
    EC50-values were calculated by fitting the data using GraphPad Prism version 8.00 (GraphPad Software, La Jolla California USA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 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).

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.11.17.468943v1 on bioRxiv