X-ray structures of five renin inhibitors bound to saccharopepsin: Exploration of active-site specificity

Saccharopepsin is a vacuolar aspartic proteinase involved in activation of a number of hydrolases. The enzyme has great structural homology to mammali an aspartic proteinases including human renin and we have used it as a mode l system to study the binding of renin inhibitors by X-ray crystallography. Five medium-to-high resolution structures of saccharopepsin complexed with transition-state analogue renin inhibitors were determined. The structure of a cyclic peptide inhibitor (PD-129,541) complexed with the proteinase wa s solved to 2.5 Angstrom, resolution. This inhibitor has low affinity for h uman renin yet binds very tightly to the yeast proteinase (K-i = 4 nM). The high affinity of this inhibitor can be attributed to its bulky cyclic moie ty spanning P-2-P-3' and other residues that appear to optimally fit the bi nding sub-sites of the enzyme. Superposition of the saccharopepsin structur e on that of renin showed that a movement of the loop 286-301 relative to r enin facilitates tighter binding of this inhibitor to saccharopepsin. Our 2 .8 Angstrom resolution structure of the complex with CP-108,420 shows that its benzimidazole P-3 replacement retains one of the standard hydrogen bond s that normally involve the inhibitor's main-chain. This suggests a non-pep tide lead in overcoming the problem of susceptible peptide bonds in the des ign of aspartic proteinase inhibitors. CP-72,647 which possesses a basic hi stidine residue at P-2, has a high affinity for renin (K-i = 5 nM) but prov es to be a poor inhibitor for saccharopepsin (K-i = 3.7 muM) This may stem from the fact that the histidine residue would not bind favourably with the predominantly hydrophobic S-2 sub-site of saccharopepsin. (C) 2000 Academi c Press.