Heparan Sulfate Oligosaccharides Modulate SARS-CoV-2 Spike-Host Recognition

Heparan sulfate (HS) is a key host-factor mediator of SARS-CoV-2 attachment and an attractive target for antiviral intervention, yet the synthesis of structurally defined HS oligosaccharides remains challenging. Here, we show that a defined HS hexasaccharide, heparin-dp6, efficiently inhibits RBD-ACE2 binding and exhibits superior antiviral activity compared with longer HS mimetics. Electronic-structure analyses suggest that the strong recognition capacity of HS arises from sulfate and carboxylate groups, which create highly negative electrostatic surfaces and serve as dominant hydrogen-bond acceptors, governing charge distribution and electronic properties along the glycan backbone to modulate binding specificity and affinity. Stepwise virtual screening of a comprehensive HS database further identified several high-affinity oligosaccharides, with top candidates displaying favorable RBD-binding properties. These findings indicate that HS activity is determined not only by chain length and sulfation pattern, but also by the spatial arrangement of charged functional groups, providing mechanistic insight into HS-RBD recognition and guiding the rational design of HS-based decoy inhibitors against SARS-CoV-2 entry. Graphical A systematic heparan sulfate oligosaccharide database reveals distinct structural features governing recognition of the SARS-CoV-2 receptor-binding domain. Molecular simulations uncover sequence-dependent binding patterns and highlight a hexasaccharide with particularly favorable RBD binding. Experimental studies further demonstrate that heparin oligosaccharides inhibit spike-ACE2 recognition and viral entry, supporting their potential as SARS-CoV-2 entry inhibitors.