A series of 17 new analogues of trypsin inhibitor SFTI-1 were designed and synthesized to obtain matriptase-2 inhibitors. A number of the modified bicyclic peptides displayed much higher affinity towards matriptase-2 than towards the highly homologous matriptase-1. Replacement of Lys5 by Arg in the wild-type SFTI-1 led to an 11-fold increase in the matriptase-2 inhibitory activity. Replacement of Arg2 by its enantiomer (D-arginine) slightly lowered the inhibition of matriptase-2, but almost completely abolished the affinity towards matriptase-1, thus yielding the most selective matriptase-2 inhibitor. This is the first report describing inhibitors of the recently discovered matriptase-2 based on the SFTI-1 structure. The results showed that SFTI-1 is a promising scaffold for the design of potent and selective inhibitors of this enzyme.

HtrA2(Omi), belonging to the high-temperature requirement A (HtrA) family of stress proteins, is involved in the maintenance of mitochondrial homeostasis and in the stimulation of apoptosis, as well as in cancer and neurodegenerative disorders. The protein comprises a serine protease domain and a postsynaptic density of 95 kDa, disk large, and zonula occludens 1 (PDZ) regulatory domain and functions both as a protease and a chaperone. Based on the crystal structure of the HtrA2 inactive trimer, it has been proposed that PDZ domains restrict substrate access to the protease domain and that during protease activation there is a significant conformational change at the PDZ–protease interface, which removes the inhibitory effect of PDZ from the active site. The crystal structure of the HtrA2 active form is not available yet. HtrA2 activity markedly increases with temperature. To understand the molecular basis of this increase in activity, we monitored the temperature-induced structural changes using a set of single-Trp HtrA2 mutants with Trps located at the PDZ–protease interface. The accessibility of each Trp to aqueous medium was assessed by fluorescence quenching, and these results, in combination with mean fluorescence lifetimes and wavelength emission maxima, indicate that upon an increase in temperature the HtrA2 structure relaxes, the PDZ–protease interface becomes more exposed to the solvent, and significant conformational changes involving both domains occur at and above 30 °C. This conclusion correlates well with temperature-dependent changes of HtrA2 proteolytic activity and the effect of amino acid substitutions (V226K and R432L) located at the domain interface, on HtrA2 activity. Our results experimentally support the model of HtrA2 activation and provide an insight into the mechanism of temperature-induced changes in HtrA2 structure.Electronic supplementary materialThe online version of this article (doi:10.1007/s12192-012-0355-1) contains supplementary material, which is available to authorized users.

This study examines peptide splicing catalyzed by serine proteinases. A series of two-peptide-chain analogs of trypsin inhibitor SFTI-1 were designed and synthesized via the solid-phase method. All consisted of two peptide chains (also called N-and C-terminal fragments) joined together by one disulfide bridge. The analogs were incubated with bovine b-trypsin or bovine a-chymotrypsin. Analysis of MS data analysis showed that, after enzyme-catalyzed degradation of the single peptide bond between the Lys and Ser residues located at the C-terminus of the C-terminal peptide chain, a new peptide bond was formed. This bond brought together the separated peptide chains, and, as a result, monocyclic SFTI-1 was recovered. This proteolytic route of peptide rearrangement appears to be similar to peptide splicing catalyzed by proteasomes. However, the proteasome is much more complex than 'classical' serine proteinases.

Serine-proteinase-catalyzed peptide splicing was demonstrated in analogues of the trypsin inhibitor SFTI-1: both single peptides and two-peptide chains (C- and N-terminal peptide chains linked by a disulfide bridge). In the second series, peptide splicing with catalytic amount of proteinase was observed only when formation of acyl-enzyme intermediate was preceded by hydrolysis of the substrate Lys-Ser peptide bond. Here we demonstrate that with an equimolar amount of the proteinase, splicing occurs in all the two-peptide-chain analogues. This conclusion was supported by high resolution crystal structures of selected analogues in complex with trypsin. We showed that the process followed a direct transpeptidation mechanism. Thus, the acyl-enzyme intermediate was formed and was immediately used for a new peptide bond formation; products associated with the hydrolysis of the acyl-enzyme were not observed. The peptide splicing was sequence- not structure-specific.

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