Ligand design for neutrophil serine proteases

Serine proteinases of the polymorphonuclear neutrophils (PMN), including proteinase 3 (PR3), human neutrophil elastase (HNE) are involved in proteolytic events associated with inflammation and play a role in several diseases such as emphysema, cystic fibrosis, rheumatoid arthritis or vasculitis. Because of their sequence similarity they have been thought for a long time to have similar localization, ligand specificity and function. However  studies indicate that they might have different and yet complementary physiologic roles. Specifically, PR3 has intracellular specific protein substrates resulting in the involvement of PR3 in regulation of intracellular functions such as proliferation or apoptosis.  Moreover, in contrast to HNE, PR3 is the preferred target antigen in Wegener's granulomatosis, a particular type of vasculitis. These activities were not observed for HNE. Using a computational biology approach, we have mapped the substrate binding sites of both enzymes and proposed a sequence motif specific for human PR3 (Hajjar et al, J Med Chem, 2006). This led us to design a peptide, which was indeed shown, by enzymatic assays, to be specific for human PR3 vs. HNE. The same computational approach was used to show that peptidic substrates efficiently and specifically cleaved by human PR3 have a poor interaction pattern with mouse and rat PR3s (Hajjar et al., Febs Lett., 2007).