Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites

Ying Sheng; Anita Vinjamuri; Michael Russelle S Alvarez; Yixuan Xie; Marisa McGrath; Siyu Chen; Mariana Barboza; Matthew Frieman; Carlito B Lebrilla

doi:10.3389/fmolb.2022.799703

Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites

Front Mol Biosci. 2022 Mar 14:9:799703. doi: 10.3389/fmolb.2022.799703. eCollection 2022.

Authors

Ying Sheng^{1

2}, Anita Vinjamuri¹, Michael Russelle S Alvarez³, Yixuan Xie¹, Marisa McGrath⁴, Siyu Chen¹, Mariana Barboza^{1

5}, Matthew Frieman⁴, Carlito B Lebrilla^{1

2}

Affiliations

¹ Department of Chemistry, University of California, Davis, Davis, CA, United States.
² The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States.
³ University of the Philippines Los Baños, Los Baños, Philippines.
⁴ Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.
⁵ Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.

Abstract

Glycans on the host cell membrane and viral proteins play critical roles in pathogenesis. Highly glycosylated epithelial cells represent the primary boundary separating embedded host tissues from pathogens within the respiratory and intestinal tracts. SARS-CoV-2, the causative agent for the COVID-19 pandemic, reaches into the respiratory tract. We found purified human milk oligosaccharides (HMOs) inhibited the viral binding on cells. Spike (S) protein receptor binding domain (RBD) binding to host cells were partly blocked by co-incubation with exogenous HMOs, most by 2-6-sialyl-lactose (6'SL), supporting the notion that HMOs can function as decoys in defense against SARS-Cov2. To investigate the effect of host cell glycocalyx on viral adherence, we metabolically modified and confirmed with glycomic methods the cell surface glycome to enrich specific N-glycan types including those containing sialic acids, fucose, mannose, and terminal galactose. Additionally, Immunofluorescence studies demonstrated that the S protein preferentially binds to terminal sialic acids with α-(2,6)-linkages. Furthermore, site-specific glycosylation of S protein RBD and its human receptor ACE2 were characterized using LC-MS/MS. We then performed molecular dynamics calculations on the interaction complex to further explore the interactive complex between ACE2 and the S protein. The results showed that hydrogen bonds mediated the interactions between ACE2 glycans and S protein with desialylated glycans forming significantly fewer hydrogen bonds. These results supported a mechanism where the virus binds initially to glycans on host cells preferring α-(2,6)-sialic acids and finds ACE2 and with the proper orientation infects the cell.

Keywords: ACE2 glycosylation; LC/MS; SARS-CoV2; glycocalyx; host-virus interaction; remodeling glycome; spike (S) protein.