Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

  1. Abhisek Dwivedy
  2. Richard Mariadasse
  3. Mohammed Ahmad
  4. Sayan Chakraborty
  5. Deepsikha Kar
  6. Satish Tiwari
  7. Sankar Bhattacharyya
  8. Sudipta Sonar
  9. Shailendra Mani
  10. Prafullakumar Tailor
  11. Tanmay Majumdar
  12. Jeyaraman Jeyakanthan
  13. Bichitra Kumar Biswal

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Abstract

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

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  1. Version published to 10.1371/journal.pcbi.1009384
  2. ScreenIT

    SciScore for 10.1101/2021.02.03.429510: (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: Organisms/Strains
    SentencesResources
    The ligated product was transformed into chemically competent Escherichia coli strain DH5α and grown on LB agar medium containing 50 µg/ml kanamycin for selection at 310 K.
    DH5α
    suggested: None
    Software and Algorithms
    SentencesResources
    For sequence analysis, all the coronavirus RdRp sequences were retrieved from the NCBI database and subjected to multiple sequence alignment using the Clustal Omega [65] and Multalin [66] servers.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    Functional analyses were performed using the MPI Bioinformatics Toolkit [17], the DALI server [68] and the DSIMB server [18,69].
    DALI
    suggested: (Dali Server, RRID:SCR_013433)
    All visualization were performed in Pymol [71].
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    PSIPRED [73], CDD [74]
    PSIPRED
    suggested: (PSIPRED, RRID:SCR_010246)
    , MyHits [75], and PhosphoPredict [76].
    MyHits
    suggested: (MyHits, RRID:SCR_006757)
    In silico ligand preparation, active site pocket prediction and molecular docking: The coordinate files for all the inhibitors were retrieved from the PubChem Database and/or from Protein Data Bank.
    PubChem
    suggested: (PubChem, RRID:SCR_004284)
    The accuracy of the sites were verified using the Phyre [78] and CASTp servers [79] and the results were compared.
    Phyre
    suggested: (Phyre, RRID:SCR_010270)
    All DFT calculations were carried out using Jaguar, version 9.1 [87,88]
    Jaguar
    suggested: (Jaguar, RRID:SCR_014895)
    The graphs were plotted using GraphPad Prism 7.0.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 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.

    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 checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.02.03.429510v1 on bioRxiv