Structure of SARS-CoV-2 2′- O -methyltransferase heterodimer with RNA Cap analog and sulfates bound reveals new strategies for structure-based inhibitor design

  1. Monica Rosas-Lemus
  2. George Minasov
  3. Ludmilla Shuvalova
  4. Nicole Inniss
  5. Olga Kiryukhina
  6. Joseph Brunzelle
  7. Karla J. F. Satchell

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Abstract

There are currently no antiviral therapies specific against SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an X-ray crystallographic study of the nsp16/nsp10 2′- O -methyltransferase complex that methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. Heterodimer structures are determined with the methyl donor S -adenosylmethionine (SAM), the reaction product S -adenosylhomocysteine (SAH) or the SAH analog sinefungin (SFG). Furthermore, structures of nsp16/nsp10 with the methylated Cap-0 analog (m 7 GpppA) and SAM or SAH bound were obtained. Comparative analysis revealed flexible loops in open and closed conformations at the m 7 GpppA binding pocket. Bound sulfates in several structures suggested the location of the phosphates in the ribonucleotide binding groove. Additional nucleotide binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for development of antiviral inhibitors.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.03.234716: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Structure solution and refinement: The first structure of nsp16/nsp10 from SARS-CoV-2 in complex with SAM with the small unit cell was determined by Molecular Replacement with Phaser (48) from the CCP4 Suite (49) using the crystal structure of the nsp16/nsp10 heterodimer from SARS-CoV as a search model (PDB ID 3R24, (14)).
    SAM
    suggested: (SAM, RRID:SCR_010951)
    The initial solutions went through several rounds of refinement in REFMAC v.
    REFMAC
    suggested: (Refmac, RRID:SCR_014225)
    5.8.0258 (50) and manual model corrections using Coot (51).
    Coot
    suggested: (Coot, RRID:SCR_014222)
    MolProbity (54) (http://molprobity.biochem.duke.edu/) was used for monitoring the quality of the model during refinement and for the final validation of the structure.
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)
    Structural alignment: The PDB coordinates of SARS-CoV nsp16 and nsp10 were analyzed on the FATCAT (29) and PDBFlex servers (55) to perform structural and sequence alignment.
    FATCAT
    suggested: (FATCAT, RRID:SCR_014631)
    Structural alignments and structure figures were downloaded from the servers and modeled in Pymol open source V 2.1 (56).
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)

    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 did not find any issues relating to the usage of bar graphs.

    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

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  2. Version published to 10.1101/2020.08.03.234716 on bioRxiv