From Docking and Molecular Dynamics to Experimental Discovery: Exploring the Hydrophobic Landscapes of Heparanase to Design Potent Inhibitors

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.