A “Deep Dive” into the SARS-Cov-2 Polymerase Assembly: Identifying Novel Allosteric Sites and Analyzing the Hydrogen Bond Networks and Correlated Dynamics

  1. Khaled Barakat
  2. Marawan Ahmed
  3. Yasser Tabana
  4. Minwoo Ha

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Abstract

Replication of the SARS-CoV-2 genome is a fundamental step in the virus life cycle and inhibiting the SARS-CoV2 replicase machinery has been proven recently as a promising approach in combating the virus. Despite this recent success, there are still several aspects related to the structure, function and dynamics of the CoV-2 polymerase that still need to be addressed. This includes understanding the dynamicity of the various polymerase subdomains, analyzing the hydrogen bond networks at the active site and at the template entry in the presence of water, studying the binding modes of the nucleotides at the active site, highlighting positions for acceptable nucleotides’ substitutions that can be tolerated at different positions within the nascent RNA strand, identifying possible allosteric sites within the polymerase structure and studying their correlated dynamics relative to the catalytic site. Here, we combined various cutting-edge modelling tools with the recently resolved SARS-CoV-2 cryo-EM polymerase structures to fill this gap in knowledge. Our findings provide a detailed analysis of the hydrogen bond networks at various parts of the polymerase structure and suggest possible nucleotides’ substitutions that can be tolerated by the polymerase complex. We also report here three “druggable” allosteric sites within the nsp12 RdRp that can be targeted by small molecule inhibitors. Our correlated motion analysis shows that the dynamics within one of the newly identified sites are linked to the active site, indicating that targeting this site can significantly impact the catalytic activity of the SARS-CoV-2 polymerase.

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    SciScore for 10.1101/2020.06.02.130849: (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

    Software and Algorithms
    SentencesResources
    For selecting the best templates to incorporate the missing residues, sequence alignments were performed in BLASTP suite using BLOSUM62 algorithm.
    BLASTP
    suggested: (BLASTP, RRID:SCR_001010)
    Several homology models were built using I-TASSER, Modeller Suite and SWISS-MODEL.
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    Clustering Analysis Protocol: To analyze the conformational dynamics of the bound nucleotides and to extract their dominant mode(s) of binding within the active site, we carried out RMSD conformational clustering on the whole MD trajectories.
    Clustering Analysis Protocol
    suggested: None
    To do that, we used accelerated MD simulations (AMDS) module as implemented in AMBER, which applied a boosting potential with a positive value (ΔV(r)) when the potential energy falls below a certain energy threshold39.
    AMBER
    suggested: (AMBER, RRID:SCR_016151)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.06.02.130849 on bioRxiv