Heparinase I-specific disaccharide unit of heparin is a key structure but insufficient for exerting anti-prion activity in prion-infected cells

• We studied heparin structures that affect prion formation in prion-infected cells.
• Heparinase I-sensitive structures are needed for anti-prion activity of heparin.
• A heparinase I substrate disaccharide unit binds the N-terminal domain of PrP.
• Synthetic compounds made of disaccharide unit or multimers show no anti-prion activity.
• The disaccharide unit is important but insufficient to exert anti-prion activity.

Glycosaminoglycans reportedly play important roles in prion formation, but because of their structural complexity, the chemical structures affecting prion formation have not been fully evaluated. Here, we compared two types of low molecular weight heparins and found that heparinase I-sensitive structures influenced anti-prion activity in prion-infected cells. Surface plasmon resonance analyses showed significant binding of a representative heparinase I substrate disaccharide unit, GlcNS6S-IdoA2S, to recombinant prion protein (PrP) fragments, such as full-length PrP23–231 and N-terminal domain PrP23–89, but not to PrP89–230. This binding was competitively inhibited by heparin or pentosan polysulfate, but not by Cu2+. These PrP binding profiles of the disaccharide unit are consistent with those previously reported for heparin. However, synthetic compounds comprising disaccharide unit alone or its multimers exhibited no anti-prion activity in prion-infected cells. Consequently, the findings suggest that the heparin disaccharide unit that binds to the N-terminal region of PrP is a key structure, but it is insufficient for exerting anti-prion activity.