Biological and Medicinal Chemistry

Mutations in Spike Protein of SARS-CoV-2 Modulate Receptor Binding, Membrane Fusion and Immunogenicity: An Insight into Viral Tropism and Pathogenesis of COVID-19


SARS-CoV-2 uses RBD of Spike (S) protein to attach with human cell via ACE2 receptor, followed by protease priming at S1/S2 site resulted in host cell entry and pathogenesis. In this context, we focused our aim in studying natural mutations harboring in Spike protein of SARS-CoV-2. We have analyzed 420 COVID-19 cases. G476S and V483G mutation are observed which lies in the RBD region where as the prevalent D614G mutation is observed in the vicinity of S1/S2 site. Interestingly MD simulation supports strong favorable interaction of ACE2 with RBD region containing V483A mutation as compared to G476S and reference wild Wuhan S protein. Radius of gyration analysis also showed high degree of compactness in V483A. The landscape plot and Gibbs free energy also support our findings. Overall, our study indicates that V483G in the RBD region can enhance its binding with the human ACE2 receptor. Interestingly D614G mutation in vicinity of S1/S2 region introduced a new cleavage site specific for a serine protease elastase that is anticipated to broaden the virus host cell tropism. Hence, both V483A and D614G mutations led to enhanced and broaden the virus host cell entry and transmission of the disease. Further epitope mapping analysis revealed G476S and D614G mutations as antigenic determinants and thus these mutations are important while designing a therapeutics vaccine or chimeric antibody. This finding will help in further understanding the role of such arising mutations in modulating immunogenicity, viral tropism and pathogenesis of the disease, which in lieu will help in designing vaccine more precisely to mitigate pandemic COVID-19.


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Supplementary material

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Suppl File 3 Mutation S analysis