Design of D-amino acids SARS-CoV-2 Main protease inhibitors using the cationic peptide from rattlesnake venom as a scaffold

  1. Raphael J. Eberle
  2. Ian Gering
  3. Markus Tusche
  4. Philipp N. Ostermann
  5. Lisa Müller
  6. Ortwin Adams
  7. Heiner Schaal
  8. Danilo S. Olivier
  9. Marcos S. Amaral
  10. Raghuvir K. Arni
  11. Dieter Willbold
  12. Mônika A. Coronado

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Abstract

The C30 Endopeptidase (3C-like protease; 3CL pro ) is essential for the life cycle of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) since it plays a pivotal role in viral replication and transcription and is hence a promising drug target. Molecules isolated from animals, insects, plants or microorganisms can serve as a scaffold for the design of novel biopharmaceutical products. Crotamine, a small cationic peptide from the venom of the rattlesnake Crotalus durissus terrificus has been the focus of many studies since it exhibits activities such as analgesic, in vitro antibacterial and hemolytic activities. The crotamine derivative L-peptides (L-CDP) that inhibit the 3CL protease in the low µM range were examined since they are susceptible to proteolytic degradation; we explored the utility of their D-enantiomers form. Comparative uptake inhibition analysis showed D-CDP as a promising prototype for a D-peptide-based drug. We also found that the D-peptides can impair SARS-CoV-2 replication in vivo , probably targeting the viral protease 3CL pro .

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    SciScore for 10.1101/2021.11.10.468025: (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

    Experimental Models: Cell Lines
    SentencesResources
    Vero cells (ATCC-CCL-81, obtained from LGC Standards) were seeded into the wells of a 96-well plate in Dulbecco’s Modified Eagle Medium - DMEM (Gibco, Carlsbad, California) with 2% fetal calf serum (PAN Biotech, Germany) and 1% penicillin/streptomycin (Gibco, Carlsbad, California) at a density of 5×103 cells well-1.
    Vero
    suggested: None
    MTT assay of D-CDP1 and D-CDP7 on Vero CCL-81 cells.
    Vero CCL-81
    suggested: None
    Software and Algorithms
    SentencesResources
    The IC50 value was calculated by plotting the initial velocity against various concentrations of the combined molecules using a dose-response curve in GraphPad Prism5 software (Tecan, Männedorf, Switzerland), and data are presented as mean ± SD. 4.6 Determination of inhibition mode: The inhibition mode was determined using different final concentrations of the inhibitors and substrate.
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    All statistical analyses were performed with GraphPad Prism software version 8 (San Diego, CA, USA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    4GV5), the D-CDP1 was generated using the tleap in Amber.
    Amber
    suggested: (AMBER, RRID:SCR_016151)
    The top four structures were downloaded and viewed by PyMOL.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    4.17 Molecular Dynamics Analysis and Interaction Energy Calculation: MD results were analyzed using CPPTRAJ [53] tools for the AmberTools19 package [54].
    AmberTools19
    suggested: None

    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.

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  2. Version published to 10.1101/2021.11.10.468025v1 on bioRxiv