Molecular model of human heparanase with proposed binding mode of a heparan sulfate oligosaccharide and catalytic amino acids

Abstract

Heparan sulfate is abundantly present in the extracellular matrix. As other glycosaminoglycans, it is synthesized in the Golgi apparatus and then exposed on the cell surface. The glucuronidase activity of human heparanase plays a major role in the structural remodeling of the extracellular matrix, which underlies cell migration, hence tumor invasion. Heparanase is therefore a major target for anti-cancer treatment. Several inhibitors of its enzymatic activity have been synthesized. However, their design is limited by the absence of experimental structure of the protein. Homology modeling is proposed based on the structure of the endoxylanase from Penicillium simplicissimum co-crystallized with a series of xylan oligosaccharide. The new heparanase model is consistent with the few experimental data suited for the validation of such work. Furthermore, the presence of natural substrates in the template structure allowed us to propose a binding model for a hydrolyzed heparin sulfate pentasaccharide. Several lysine residues have been identified to play a key role in binding to the anionic polysaccharide substrate. In addition, two phenylalanine residues are also potentially important for the interaction with the substrate. The enzymatic mechanism investigated in the light of this new model allows for the proposal of several amino acids that can influence the protonation state of the nucleophile and the proton donor.

Aspirin Inhibits Cancer Metastasis and Angiogenesis via Targeting Heparanase

“…The oxygen in carboxyl group interacted with Glu225, Ser228, and Lys231, whereas acetyl group formed hydrogen bonds with Gln157 and Lys159. The hydrogen bonds formed between the carboxyl group and Glu225 and Lys231 were also reported in Sapay's work (40). We further investigated the binding modes of biotin-aspirin and heparanase (Fig.…”

Mechanisms of heparanase inhibition by the heparan sulfate mimetic PG545 and three structural analogues

“…This diversity is unusual considering, firstly, their similarity and, secondly, that heparanase is thought to exist as a heterodimer with one active site, thus precluding interaction between active sites. A structure of heparanase has not been published although information about the three‐dimensional arrangement of important parts of the protein has been gleaned from comparative modelling of the sequence based upon the structures of related proteins [27,6,28]. The enzymatic domain of heparanase comprises an (α/β) 8 TIM‐barrel with two catalytic glutamate residues located at the surface, close to the rotational axis of this motif.…”

Deciphering Mode of Action of Heparanase Using Structurally Defined Oligosaccharides

“…Another site is responsible for the gapped cleavage mode and recognizes the substrate with GlcNS6S at the nonreducing end. However, only one active site has been identified based on the homology model (23). Alternatively, the trisaccharide domain from the nonreducing end serves as a modulator to direct heparanase to display the consecutive or gapped cleavage mode.…”