Understanding the dynamic substrate binding mechanism of human heparanase

Ahmed FH1,3, Marsavelski A1,2, Mohamed AE1, Jamieson E1, Correy G1 and Jackson CJ1

  1. The Australian National University, Research School of Chemistry, Sullivan’s Creek Road, Acton, ACT 2601, Australia.
  2. Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
  3. Current address: CSIRO, Land and Water, Clunies Ross Street, Acton, ACT 2601, Australia.

Heparanase (HPSE) hydrolyzes heparan sulfate (HS) in the extracellular matrix. It mediates the release of regulatory molecules bound to HS, and hence is essential for processes that control cell growth, coagulation and inflammation. Inhibition of the increased HPSE activity observed in a variety of pathological conditions such as tumour metastasis, angiogenesis and auto-immune diseases attenuates disease progression, making HPSE a promising drug target. Although crystal structures of HSPE are now available, the dynamic nature of its interaction with its flexible polysaccharide substrate HS is not fully understood. We have explored the ligand binding mechanism of HPSE by analysing its conformational landscape with molecular dynamics (MD)-simulations and multi-conformer models generated by crystallographic ensemble refinement. We found that HS binding is a complex process, whereby the molecule is stabilized at the active site for catalysis, but the outer regions of the enzyme:substrate complex are dominated by ionic interactions and exhibit substantial conformational flexibility. This dynamic binding mechanism allows HSPE to retain high affinity while minimizing the entropic costs associated with binding highly flexible molecules. These findings have direct implications on efforts in identifying and optimising inhibitors for this promising drug target.