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

X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity
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 mammalian aspartic proteinases including human renin and we have used it as a model 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 was solved to 2.5 Å resolution. This inhibitor has low affinity for human renin yet binds very tightly to the yeast proteinase (Ki=4 nM). The high affinity of this inhibitor can be attributed to its bulky cyclic moiety spanning P2-P3? and other residues that appear to optimally fit the binding sub-sites of the enzyme. Superposition of the saccharopepsin structure on that of renin showed that a movement of the loop 286–301 relative to renin facilitates tighter binding of this inhibitor to saccharopepsin. Our 2.8 Å resolution structure of the complex with CP-108,420 shows that its benzimidazole P3 replacement retains one of the standard hydrogen bonds that normally involve the inhibitor’s main-chain. This suggests a non-peptide lead in overcoming the problem of susceptible peptide bonds in the design of aspartic proteinase inhibitors. CP-72,647 which possesses a basic histidine residue at P2, has a high affinity for renin (Ki=5 nM) but proves to be a poor inhibitor for saccharopepsin (Ki=3.7 ?M). This may stem from the fact that the histidine residue would not bind favourably with the predominantly hydrophobic S2 sub-site of saccharopepsin.
renin inhibitors, aspartic proteinases, saccharopepsin
0022-2836
745-760
Cronin, N.B.
1149a769-495d-4db7-89cb-d326422b24aa
Badasso, M.O.
59a5d949-d29d-4be7-ab09-930dcf76d889
Tickle, I.J.
7d0714ba-37d0-4b7d-8680-8a4b89ea0a37
Dreyer, T.
c109e4f3-fff1-4c3f-86ac-d84a7a500541
Hoover, D.J.
a74c4570-053e-4ca9-ad2d-42c669345b62
Rosati, R.L.
86552044-8773-4ad5-82c5-e75d627948ad
Humblet, C.C.
c29bf69e-cc54-4680-9c7d-8f89874f39b1
Lunney, E.A.
db0eaa29-1028-4163-a360-353e95a0ffb9
Cooper, J.B.
d9f0f6a8-1260-48fc-aa5c-3dbc650e3ec0
Cronin, N.B.
1149a769-495d-4db7-89cb-d326422b24aa
Badasso, M.O.
59a5d949-d29d-4be7-ab09-930dcf76d889
Tickle, I.J.
7d0714ba-37d0-4b7d-8680-8a4b89ea0a37
Dreyer, T.
c109e4f3-fff1-4c3f-86ac-d84a7a500541
Hoover, D.J.
a74c4570-053e-4ca9-ad2d-42c669345b62
Rosati, R.L.
86552044-8773-4ad5-82c5-e75d627948ad
Humblet, C.C.
c29bf69e-cc54-4680-9c7d-8f89874f39b1
Lunney, E.A.
db0eaa29-1028-4163-a360-353e95a0ffb9
Cooper, J.B.
d9f0f6a8-1260-48fc-aa5c-3dbc650e3ec0

Cronin, N.B., Badasso, M.O., Tickle, I.J., Dreyer, T., Hoover, D.J., Rosati, R.L., Humblet, C.C., Lunney, E.A. and Cooper, J.B. (2000) X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity. Journal of Molecular Biology, 303 (5), 745-760. (doi:10.1006/jmbi.2000.4181).

Record type: Article

Abstract

Saccharopepsin is a vacuolar aspartic proteinase involved in activation of a number of hydrolases. The enzyme has great structural homology to mammalian aspartic proteinases including human renin and we have used it as a model 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 was solved to 2.5 Å resolution. This inhibitor has low affinity for human renin yet binds very tightly to the yeast proteinase (Ki=4 nM). The high affinity of this inhibitor can be attributed to its bulky cyclic moiety spanning P2-P3? and other residues that appear to optimally fit the binding sub-sites of the enzyme. Superposition of the saccharopepsin structure on that of renin showed that a movement of the loop 286–301 relative to renin facilitates tighter binding of this inhibitor to saccharopepsin. Our 2.8 Å resolution structure of the complex with CP-108,420 shows that its benzimidazole P3 replacement retains one of the standard hydrogen bonds that normally involve the inhibitor’s main-chain. This suggests a non-peptide lead in overcoming the problem of susceptible peptide bonds in the design of aspartic proteinase inhibitors. CP-72,647 which possesses a basic histidine residue at P2, has a high affinity for renin (Ki=5 nM) but proves to be a poor inhibitor for saccharopepsin (Ki=3.7 ?M). This may stem from the fact that the histidine residue would not bind favourably with the predominantly hydrophobic S2 sub-site of saccharopepsin.

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More information

Published date: 10 November 2000
Keywords: renin inhibitors, aspartic proteinases, saccharopepsin

Identifiers

Local EPrints ID: 56414
URI: https://eprints.soton.ac.uk/id/eprint/56414
ISSN: 0022-2836
PURE UUID: 6c575706-b68e-412e-baba-1c2577611b99

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Date deposited: 22 Aug 2008
Last modified: 17 Jul 2017 14:30

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