Cathepsin substrates

Cleavage occur s at the scissile bond. Residues in the substrate towards the N-terminus are numbered PI, P2, P3, etc, whereas residues towards the C-terminus are numbered PI, P2, P3 etc. Cleavage occurs between PI and P1. For a peptidase with limited specificity, only the residue in PI or PI is important for specificity. A peptidase with an extended substrate binding site will have a preference for residues in other positions. For example cathepsin L prefers substrates with phenylalanine in P2 and arginine in PI. However, this is a preference only, and cathepsin L cleaves substrates after other amino acids. Caspase-3 has a preference for Asp in both P4 and PI, but it is unusual for substrate specificity to extend much further from the scissile bond. The peptidase with the most extended substrate specificity may be mitochondrial intermediate peptidase that removes an octopeptide targeting signal from the N-terminus of cytoplasmically synthesized proteins that are destined for import into the mitochondrial lumen. 

Li J, Petrassi HM, Tumanut C et al (2009) Substrate optimization for monitoring cathepsin C activity in live cells. Bioorg Med Chem 17 1064-1070... 

Screening of over 66,000 compounds from the MLSMR by scientists at the PCMD for inhibitors of Cathepsin B resulted in the identification and characterization of an alternate substrate, SID 16952359 [29]. This study also describes issues relating to the nucleophilicity of dithiothreitol (DTT) and cysteine, reductants frequently used in HTS protocols, and the potential for reactivity with electrophilic sites of probe molecules. 

Figure 7. Two examples of irreversible inactivators that are not suicide substrates a) TPCK, a classic" affinity label of the serine protease chymotrypsin, b) ZFK-CH2-mesitoate, a quiescent" affinity label of the cysteine protease cathepsin B, and c) the kinetic scheme for both forms of affinity label-inactivation.

It is generally believed that proteases enhance cancer spread primarily by catalyzing degradation of the extracellular matrix. Since multiple substrates are encountered in this matrix, a number of different proteases are likely to be required to complete the metastatic process. Multiple proteases may also be required to activate different inactive precursor forms. Thus, in vitro, plasmin (D7), cathepsin B (D7), and a trypsin-like protease (K12) can all activate pro-uPA, while plasmin, which results from the action of uPA on plasminogen, can activate certain metalloproteases (M4). As mentioned earlier, completion of the metastatic process may require a cascade of different proteases operating, as shown in Fig. 2. 

Fig. 5.3 Substrate conversion reaction for cathepsin B. Substrate Z-FR-AMC is converted by cathepsin B into two products, Z-FR and AMC, that are employed as reporter molecules at their corresponding m/z traces.

We have demonstrated the feasibility of miniaturized MS assays by converting the cathepsin B assay described in Section 5.2.2 to a chip format, using the same substrate and products for the MS-based readout [27]. The assay set-up is identical to the format described in Fig. 5.1. The advantages of chips as micro reactors over fused silica capillaries are in their compactness, strength, greater degrees of freedom in design and material, and the presence of hair-pin curves to increase the diffusion rate. 

Fig. 5.9 Design of the chip-based enzyme ESI-MS assay. MS instrument Ion-trap mass spectrometer (LCQ Deca, Thermo Electron). I Sample components/inhibitors injected by flow injection or eluting from capillary HPLC column. E Infusion pump delivering the enzyme cathepsin B. S infusion pump delivering the substrate Z-FR-AMC. Micro-chip design Vrije Universiteit Amsterdam. Micro-chip production Micronit Microfluidics BV (Enschede, The Netherlands).

The sensitivity of the microfluidic system was determined by measuring calibration curves of four cathepsin B inhibitors. The inhibitors caused negative peaks in the product mass chromatograms by inhibiting cathepsin B and thus the substrate turnover. The measured order of afEnities of the four inhibitors is in agreement with the affinities determined in microtiter plate assays and the macro-scale system. 

This lysosomal enzyme [EC 3.4.22.1], also known as cathepsin Bl, is a member of the peptidase family Cl. The catalyzed reaction is the hydrolysis of peptide binds with a broad specificity. The enzyme prefers the ArgArg—Xaa bond in small peptide substrates (thus distinguishing this enzyme from cathepsin L). The enzyme also exhibits a peptidyl-dipeptidase activity, releasing C-terminal dipeptides from larger polypeptides. 

This peptidase family Cl enzyme [EC 3.4.22.15] is an lysosomal endopeptidase with specificity akin to papain. Cathepsin L displays a higher activity toward protein substrates than does cathepsin B. 

Figure 6. An example of inter-family target hopping between human and viral aspartyl proteases. The aspartyl protease active site is located at a homodimer interface in HIV and within a single domain in Cathepsin D, so sequence and structure alignments between these proteins cannot be constructed. By using an approach independent of sequence or structure homology to directly align the sites, SiteSorter finds that the HIV protease and Cathepsin D substrate sites are highly similar (identical chemical groups within 1 A are colored dark blue). It has been verified experimentally that Cathepsin D is susceptible to inhibition by HIV-protease inhibitors. ...

The prerequisite is the knowledge of the interactions taking place in the enzyme-substrate complex. This was known for the model enzymes. However, for cathepsin B, the most important enzyme in the lysosomal compartment from the drug release point of view, only limited information was available [26], It was known that the amino acid residues in positions P2 and P3 should be... 

Fig. 14. Initial interval of cleavage of HPMA copolymer based polymeric substrates by lysosomal cysteine proteinase cathepsin B (isolated from bovine spleen). Only the cleavage of the bond between the distal amino acid residue and p-nitroaniline was monitored. Conditions of cleavage [Cathepsin B] = 1.9 x 10 7 M [NAp] = 1.2 x 1(T3 M [EDTA] = 1 x 10 3 M [Cys] = 2.5 x 10 2 M 0.1 M phosphate buffer pH = 6.0 40 °C. Data from [249]...

The cysteinyl proteases include papain calpains I and II cathepsins , H, and L proline endopeptidase and interleukin-converting enzyme (ICE) and its homologs. The most well-studied cysteinyl protease is likely papain, and the first x-ray crystallographic structures of papain [193] and a peptide chloromethylketone inhibitor-papain complex [194] provided the first high resolution molecular maps of the active site. Pioneering studies in the discovery of papain substrate peptide-based inhibitors having P, electrophilic moieties such as aldehydes [195], ketones (e.g., fluoromethylketone, which has been determined [196] to exhibit selectivity for cysteinyl proteases versus serinyl proteases), semicarbazones, and nitriles are noteworthy since 13C-NMR spectro-... 

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