Mutational landscape and in silico structure models of SARS-CoV-2 spike receptor binding domain reveal key molecular determinants for virus-host interaction

  1. Shijulal Nelson-Sathi
  2. P. K. Umasankar
  3. E. Sreekumar
  4. R. Radhakrishnan Nair
  5. Iype Joseph
  6. Sai Ravi Chandra Nori
  7. Jamiema Sara Philip
  8. Roshny Prasad
  9. K. V. Navyasree
  10. Shikha Ramesh
  11. Heera Pillai
  12. Sanu Ghosh
  13. T. R. Santosh Kumar
  14. M. Radhakrishna Pillai

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Abstract

Background

SARS-CoV-2, the causative agent of COVID-19 pandemic is a RNA virus prone to mutations. Formation of a stable binding interface between the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike (S) protein and Angiotensin-Converting Enzyme 2 (ACE2) of host is pivotal for viral entry. RBD has been shown to mutate frequently during pandemic. Although, a few mutations in RBD exhibit enhanced transmission rates leading to rise of new variants of concern, most RBD mutations show sustained ACE2 binding and virus infectivity. Yet, how all these mutations make the binding interface constantly favourable for virus remain enigmatic. This study aims to delineate molecular rearrangements in the binding interface of SARS-CoV-2 RBD mutants.

Results

Here, we have generated a mutational and structural landscape of SARS-CoV-2 RBD in first six months of the pandemic. We analyzed 31,403 SARS-CoV-2 genomes randomly across the globe, and identified 444 non-synonymous mutations in RBD that cause 49 distinct amino acid substitutions in contact and non-contact amino acid residues. Molecular phylogenetic analysis suggested independent emergence of RBD mutants. Structural mapping of these mutations on the SARS-CoV-2 Wuhan reference strain RBD and structural comparison with RBDs from bat-CoV, SARS-CoV, and pangolin-CoV, all bound to human or mouse ACE2, revealed several changes in the interfacial interactions in all three binding clusters. Interestingly, interactions mediated via N487 residue in cluster-I and Y449, G496, T500, G502 residues in cluster-III remained largely unchanged in all RBD mutants. Further analysis showed that these interactions are evolutionarily conserved in sarbecoviruses which use ACE2 for entry. Importantly, despite extensive changes in the interface, RBD-ACE2 stability and binding affinities were maintained in all the analyzed mutants. Taken together, these findings reveal how SARS-CoV-2 uses its RBD residues to constantly remodel the binding interface.

Conclusion

Our study broadly signifies understanding virus-host binding interfaces and their alterations during pandemic. Our findings propose a possible interface remodelling mechanism used by SARS-CoV-2 to escape deleterious mutations. Future investigations will focus on functional validation of in-silico findings and on investigating interface remodelling mechanisms across sarbecoviruses. Thus, in long run, this study may provide novel clues to therapeutically target RBD-ACE2 interface for pan-sarbecovirus infections.

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  1. Version published to 10.1186/s12860-021-00403-4
  2. Version published to 10.1101/2020.05.02.071811v3 on bioRxiv
  3. Version published to 10.1101/2020.05.02.071811v2 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.05.02.071811: (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
    Further, 31,403 spike protein sequences along with Wuhan reference spike protein (YP_009724390.1) were aligned using Mafft (maxiterate 1,000 and global pair-ginsi) (Katoh et al. 2002).
    Mafft
    suggested: (MAFFT, RRID:SCR_011811)
    The alignments were visualized in Jalview (Waterhouse AM et al., 2009) and the amino acid substitutions in each position were extracted using custom python script.
    Jalview
    suggested: (Jalview, RRID:SCR_006459)
    Sequences were aligned using Mafft (maxiterate 1,000 and global pair-ginsi), and phylogeny was reconstructed using IQ-Tree (Nguyen et al., 2015).
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)
    The best evolutionary model (GTR+F+I+G4) was picked using the ModelFinder program (Kalyaanamoorthy et al., 2017).
    ModelFinder
    suggested: None
    The crystal structure of the SARS-CoV-2 RBD-hACE2 receptor complex was downloaded from Protein Data Bank (PDB ID:6LZG) and the mutagenesis analysis was performed using Pymol (DeLano WL et al., 2002).
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    The YASARA server (Krieger et al., 2002) was used for the energy minimization of analysed structures.
    YASARA
    suggested: (YASARA, RRID:SCR_017591)

    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 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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  5. Version published to 10.1101/2020.05.02.071811v1 on bioRxiv