Pathogen-sugar interactions revealed by universal saturation transfer analysis

Abstract

Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily-modified pathogen proteins can be confounded by overlapping sugar signals and/or compound with known experimental constraints. ‘Universal saturation transfer analysis’ (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin lineage SARS-CoV-2 spike trimer binds sialoside sugars in an ‘end-on’ manner. uSTA-guided modelling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar-binding in SARS CoV 2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins in deeper human lung as potentially relevant to virulence and/or zoonosis.

The SARS-CoV-2 spike N-terminal domain engages 9-O-acetylated α2-8-linked sialic acids

“…Finally, the NTD of HCoV-HKU1 was characterized, which recognizes 9-O-acetyl sialic acid [21]. Consistently, the 1 H STD-NMR spectrum of the [23] .…”

“…S1 spike interaction with sialic acids has been further shown by four independent studies, however, the contribution of S1-NTD towards sialoside recognition and dual-receptor functionality has not been verified [8,53,65,66]. [23] have identified a clear "end-on" interaction of S1-NTD with α2-3-or α2-6-linked sialic acids, describing a cryptic sialic acid binding domain. A cryo-EM-derived map of the S1-NTD has proposed H69, Y145 and S247 as the sialic acidinteracting amino acids [23].…”

“…The lectin function for 501Y.V2-1 VoC is a clear convergent evolutionary path of adaptation to 9-O-acetylated sialoside recognition by the NTD, similarly to β-CoV HKU1 and OC43 [7,20,22,23,[49][50][51][52][53]. However, ablation in later Beta/501Y.V2 variants induced by the L242-244deletion [35,36] and in other VoC (Alpha, Delta and Omicron) raises the question of why this increased binding capacity towards sialic acids is lost.…”

“…Recently, the NTD of SARS-CoV-2 has been shown to contain a sialic acid binding site [22,23], and low-affinity binding has been demonstrated by using Saturation Transfer Difference (STD)-NMR methods. Importantly, the NTD is also an important antigenic site [24,25], indicating its importance in the viral life cycle with an apparent function.…”

Glycosylated gold nanoparticles in point of care diagnostics: from aggregation to lateral flow

“…227,230 Similarly, alterations to the polymer itself i.e., to a more sterically bulky polymer can be used to stabilise AuNPs 237 and favour binding but avoid aggregation. 238 Baker et al, reported that SARS-COV-2 (the causative agent of COVID-19) spike protein has affinity towards certain sialic acids, 239 (confirmed with microarrays 240 and STD NMR 241 ) discovered using glycosylated nanoparticles against spike protein immobilised on a biolayer interferometry sensor. N-Acetyl neuraminic acid functionalised poly(hydroxyethyl acrylamide) were immobilised onto AuNPs and were used to detect a SARS-COV-2 spike protein bearing pseudovirus in what was the first report of a complete lateral flow glyco-assay device (using a BSA-glycoconjugate test-line).…”