HPSE Inhibitors(Wayne State University)

Heparanase (HPSE), a glycoside hydrolase that cleaves heparan sulfate chains, plays a crucial role in cancer progression by remodeling the extracellular matrix and facilitating tumor metastasis. This study employed a computational design approach to develop novel HPSE inhibitors using aminoglycoside paromomycin and neomycin analogs. These analogs feature a defined N-sulfation sequence combined with either charged or hydrophobic groups. Initial docking screenings indicated that hydrophobic-capped ligands exhibit binding energies comparable to the free hydroxyl ligands, despite displaying lower overall binding efficiencies. Molecular dynamics simulations revealed that these hydrophobic-capped ligands adopt a folded conformation, with the saccharide moiety anchored in the enzyme's active site and the hydrophobic aromatic groups stabilizing the interaction. This conformation exposes the hydrophobic groups to the solvent, potentially enhancing inhibitory potency by increasing ligand retention within the active site. Further analysis revealed that the hydrophobic capped ligands exhibited a higher ligand binding stability as shown by a lower RMSD during the MD simulation. Experimental validation corroborated the computational findings, demonstrating that the introduction of hydrophobic aromatic groups led to a >100-fold increase in inhibitory potency, with IC₅₀ values in the low nanomolar range. These results suggest that simultaneously targeting the charged and hydrophobic pockets of HPSE could yield more potent inhibitors, offering a promising strategy for future cancer therapeutics.

Heparanase (HPSE) remodeling of the extracellular matrix makes it a crucial therapeutic target. The development of effective glycan-based HPSE inhibitors has been limited by bleeding and thromboembolic disorders. In this report, we present a structure-based design approach that rapidly generates a library of potent and selective HS mimetics, synthesized in 8 to 9 steps from readily available aminoglycoside tobramycin. Computational analyses indicate that hydrophobic molecular markers modulate HPSE activity. Consequently, we identified naphthalene-based N-sulfated tobramycin derivatives to enhance both stability and potency. These findings suggest that, in addition to the influence of charged groups, hydrophobic moieties substantially contribute to interactions with the heparin-binding domain of HPSE. The lead ligands demonstrated high selectivity (>300-fold) for HPSE compared to other heparin-binding proteins (platelet factor 4 and antithrombin III), and diminished proliferation in some cancer cell lines. These results could provide a foundation for the development of oligosaccharide-based HPSE inhibitors for cancer therapy.