INNATE ANTIINFLAMMATORY RESPONSES
2. Rationale and aim of the project
The aim of this project is to find selective inhibitors against human neutrophil elastase and cathepsin G, starting from the scaffold of the naturally occurring sunflower trypsin inhibitor 1. The primary focus is to determine the structure-function relationship and the structural principles that govern specificity for this type of inhibitors.
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Authors: Merz Tobias, Roschizki-Voser Heidi1, Gompert Frank2, Mittl Peer R.E.1 und Grütter*, Markus, G.
Affiliation: 1: Department of Biochemistry, University of Zürich, Winterthurer Str.
190, 8057 Zürich, Switzerland.
2: Polyphor Ltd., Allschwil, Switzerland.
*: to whom correspondence should be addressed.
Tel. +41-44-635 5580, Fax. +41-44-635 6834, e-mail: [email protected]
Running title: Cathepsin G inhibitor derived from SFTI-1
Keywords: Cathepsin G, SFTI-1, elastase, inhibitor design, conformation
Abstract
The 14 amino acid long naturally occurring sunflower trypsin inhibitor (SFTI-1) scaffold is a popular, small and bi-cyclic peptide that has thoroughly been investigated with respect to its inhibitory potency and selectivity for trypsin, cathepsin G and human matriptase as well as its susceptibility for modifications. In this work, SFTI-1 was redesigned into a potent cathepsin G inhibitor (Ki = 11 nM, POL4634) and a neutrophil elastase inhibitor (Ki = 35 nM, POL4957). They were crystallized in complex with cathepsin G, porcine pancreatic elastase and human neutrophil elastase. The structural analysis in combination with inhibitory data suggests that imposed conformational restraints of the peptidase have more impact on the inhibitory activity of the non-covalently binding peptidomimetic inhibitors than measurable inhibitor-peptidase-interaction parameters.
Introduction
Naturally occurring peptidase inhibitors are conformationally restricted and show remarkable stability towards heat, proteases and denaturing agents [Makhatadze, 1993], [Colgrave, 2004].
These beneficial properties can often be attributed to disulfide cross-linking or backbone cyclization, which compensate the lack of a hydrophobic core. The pancreatic trypsin inhibitors from the Kunitz- and Kazal-types, the soybean Bowman-Birk inhibitors and the cyclotides [Makhatadze, 1993], [Qi, 2005], [Avrutina, 2005], [Craik, 1999] are molecules that show these properties. Disulfide bridges and hydrogen bonds rigidify the fold and restrict the canonical peptidase-binding loop into an extended conformation forming an anti-parallel β-sheet in the proper conformation to facilitate hydrogen bond formation within the enzyme binding site [Laskowski, 2000], [Apostoluk, 1998], [Tyndall, 2005].
The bi-cyclic trypsin inhibitor from sunflower seeds (SFTI-1) consists of 14 amino acids and folds into a short anti-parallel β-hairpin structure. SFTI-1 is cross-linked by a single disulfide bridge and its binding loop shows high sequence and structural similarity to Bowman-Birk inhibitors [Luckett, 1999]. The stability and small size of SFTI-1 as well as the availability of structural data makes it an interesting molecular template for drug design applications. SFTI-1 exhibits a strong inhibitory activity against trypsin Ki = 0.3 – 1x10-10 M [Luckett, 1999], [Daly, 2006], [Garcia Boy, 2009] and cathepsin G (Ki < 1.5x10-10 M) [Luckett, 1999] but only very weak affinity against elastase (Ki ~ 1x10-4 M) [Luckett, 1999].
Several studies show, that SFTI-1 is well suited as a template for the design of β-hairpin peptidomimetics, maintaining strong inhibitory activity against trypsin, cathepsin G or matriptase [Descours, 2002],[Legowska, 2009], [Li, 2007]. The serine peptidases cathepsin G, human leucocyte elastase and proteinase 3 are secreted by neutrophils at sites of
inflammation. They play a critical role in the activation of cytokines and growth factors and stimulate various cellular receptors (reviewed in [Wiedow, 2005]).
The focus of our study was the structural analysis of a redesigned SFTI-1 inhibitor in complex with cathepsin G, human neutrophil elastase and porcine pancreatic elastase. Kinetic experiments showed strong inhibitory potency against cathepsin G and neutrophil elastase while trypsin could not be inhibited with the modified inhibitors. The redesign of SFTI-1 included four changes: (i) Ile7 was changed to Asp7, because cathepsin G, in contrast to trypsin, revealed a patch of positive charge density around the S2` binding site. (ii) The β-turn forming tripeptide Pro13-Asp14-Gly1 in the non-prime site of SFTI-1 was replaced by the shorter DPro13-LPro1 dipeptide with the aim to improve the stability and to lock the inhibitor in a favorable conformation. (iii) Arg2 in P4 was replaced by Phe2 to satisfy the requirements of the hydrophobic S4 pocket of cathepsin G. (iv) Lys5 in P1, the selectivity discriminating residue for trypsin-like peptidases [Daly, 2006], [Descours, 2002], was substituted with the non-standard aliphatic amino acid norleucine (Figure 1). Norleucine lacks the terminal ε-amino group and disables the formation of a selectivity determining salt bridge at the bottom of the S1 pocket. The cyclic and non-covalent cathepsin G inhibitor POL4634 finally consisted of 13 amino acids including the two non-natural amino acids norleucine and D-proline at positions 5 and 13, respectively.
We determined the crystal structures of the SFTI-1 derivative POL4634 in complex with cathepsin G and porcine pancreatic elastase and of the SFTI-1 derivative POL4957 in complex with human neutrophil elastase and analyzed the respective binding interfaces. These complex structures not only revealed the necessary structural features of the inhibitors that are required for binding, but also the necessary structural predisposition of the binding site. The conformation of the inhibitor hereby plays an essential role leading to decreased affinity when
the binding site of the enzyme imposes a conformational strain. Moreover, we were able to solve the structure of POL4634 bound to PPE in three different states (i) in its cyclic form, (ii) in its cyclic form before nucleophilic attack and (iii) in a cleaved state that represents a stable acyl-enzyme intermediate state.