Conservation and Enhanced Binding of SARS-CoV-2 Omicron Spike Protein to Coreceptor Neuropilin-1 Predicted by Docking Analysis

The Omicron variant of SARS-CoV-2 bears peptide sequence alterations that correlate with a higher infectivity than was observed in the original SARS-CoV-2 isolated from Wuhan, China. We analyzed the CendR motif of spike protein and performed in silico molecular docking with neuropilin-1 (Nrp1), a receptor-ligand interaction known to support infection by the original variant. Our analysis predicts conserved and slightly increased energetic favorability of binding for Omicron CendR:Nrp1. We propose that the viral spike:Nrp1 coreceptor pathway may contribute to the infectivity of the Omicron variant of SARS-CoV-2.

Automated summary

The Omicron variant of SARS-CoV-2 exhibits altered peptide sequences in the spike protein, which may contribute to its higher infectivity compared to the original variant. Through analysis and in silico simulations, we predict that these alterations may affect the binding between the spike protein and the receptor Nrp1, potentially explaining the increased infectivity of the Omicron variant.