Comparative analysis of the substrate preferences of two post-proline cleaving endopeptidases, prolyl oligopeptidase and fibroblast activation protein α

Isolation and characterization of natural inhibitors of post-proline specific peptidases from the leaves of Cotinus coggygria Scop

ETHNOPHARMACOLOGICAL RELEVANCE

Cotinus coggygria has a number of applications in traditional medicine most of which are connected with its anti-inflammatory and anti-oxidant properties. Since inflammation and oxidative stress are recognized as triggering factors for cancer, anti-cancer activity has also been documented and the possible mechanisms of this activity are under investigation. Important components of C. coggygria extracts are shown to be hydrolysable gallotannins of which pentagalloyl-O-glucose has been studied in details. This compound inhibits various enzymes including prolyl oligopeptidase which is involved in tumorigenesis and tumour growth. According to our pilot studies, oligo-O-galloylglucoses with more than five galloyl residues are also presented in the herb of Bulgarian origin, but their activities have not been examined.

AIM OF THE STUDY

To establish an extraction method by which it is possible to concentrate high molecular hydrolysable gallotannins from dried leaves of Cotinus coggygria and to determine their inhibitory properties towards prolyl oligopeptidase and fibroblast activation protein α.

MATERIALS AND METHODS

Dried leaves of C. coggygria were extracted using different solvents in single-phase or biphasic systems under various extraction conditions. Main compounds of the extracts were identified by using high performance liquid chromatography and liquid chromatography - high resolution mass spectrometry. The extracts' inhibitory properties towards prolyl oligopeptidase and fibroblast activation protein α were studied on recombinant human enzymes by enzyme kinetic analyses using a fluorogenic substrate.

RESULTS

Ethyl acetate/water (pH 3.0) extraction of dried plant leaves proved to be the most efficient method for isolation of high molecular hydrolysable gallotannins which can be further concentrated by precipitation of dicyclohexylammonium salts in ethyl acetate. The main components of those extracts were oligo-O-galloyl glucoses with more than five gallic acid residues. They were shown to inhibit both enzymes studied but were about 30 times more effective inhibitors of prolyl oligopeptidase.

CONCLUSIONS

C. coggygria from Bulgarian origin is shown to possess a substantial quantity of oligo-O-galloyl glucoses with more than five gallic acid residues which has not been described thus far in the same herb from other sources. An extraction method useable for concentrating those compounds is established. They are found to inhibit prolyl oligopeptidase with a very good selectivity to fibroblast activation protein α. The previously described antitumor activity of this plant may be at least in part due to the inhibition of the above enzymes which has been shown to participate in the genesis and development of various types of tumors.

Advanced Fibroblast Activation Protein-Ligand Developments: FAP Imaging Agents: A Review of the Structural Requirements

Fibroblast activation protein-α (FAP) has attracted increasing attention as a selective marker of cancer-associated fibroblasts (CAFs) and more broadly, of activated fibroblasts in tissues undergoing remodeling of their ECM due to chronic inflammation, fibrosis, or wound healing. Since FAP is critical to the initiation of metastatic growth, its expression will serve as a molecular marker to detect tumors at an earlier stage of development compared to currently available methods. The design of high affinity small molecule FAP inhibitor will allow for noninvasive imaging of activated fibroblast in cancer patients. Small molecule inhibitors of FAP are being developed for targeted radiotherapy of tumors.

Post-Proline Cleaving Enzymes (PPCEs): Classification, Structure, Molecular Properties, and Applications

Proteases or peptidases are hydrolases that catalyze the breakdown of polypeptide chains into smaller peptide subunits. Proteases exist in all life forms, including archaea, bacteria, protozoa, insects, animals, and plants due to their vital functions in cellular processing and regulation. There are several classes of proteases in the MEROPS database based on their catalytic mechanisms. This review focuses on post-proline cleaving enzymes (PPCEs) from different peptidase families, as well as prolyl endoprotease/oligopeptidase (PEP/POP) from the serine peptidase family. To date, most PPCEs studied are of microbial and animal origins. Recently, there have been reports of plant PPCEs. The most common PEP/POP are members of the S9 family that comprise two conserved domains. The substrate-limiting β-propeller domain prevents unwanted digestion, while the α/β hydrolase catalyzes the reaction at the carboxyl-terminal of proline residues. PPCEs display preferences towards the Pro-X bonds for hydrolysis. This level of selectivity is substantial and has benefited the brewing industry, therapeutics for celiac disease by targeting proline-rich substrates, drug targets for human diseases, and proteomics analysis. Protein engineering via mutagenesis has been performed to improve heat resistance, pepsin-resistant capability, specificity, and protein turnover of PPCEs for pharmacological applications. This review aims to synthesize recent structure-function studies of PPCEs from different families of peptidases to provide insights into the molecular mechanism of prolyl cleaving activity. Despite the non-exhaustive list of PPCEs, this is the first comprehensive review to cover the biochemical properties, biological functions, and biotechnological applications of PPCEs from the diverse taxa.

Structure-activity relationship and biochemical evaluation of novel fibroblast activation protein and prolyl endopeptidase inhibitors with α-ketoamide warheads

Peptidomimetic inhibitors of fibroblast activation protein (FAP) are regarded as promising tools for tumor targeting in vivo. Even though several peptidomimetic compounds with nanomolar potency have been described, broad chemical space for further modification remained unexplored. Therefore, we set to analyze the structure-activity relationship (SAR) of pseudopeptide compound series with α-ketoamide warheads in order to explore the contributions of the P1' and P2' moieties to the inhibitory potency. A series of novel inhibitors bearing varied P1' and/or P2' moieties was synthesized by combining a Passerini reaction-Amine Deprotection-Acyl Migration (PADAM) approach with peptide coupling and subsequent oxidation. The resulting compounds inhibited FAP and the related prolyl endopeptidase (PREP) with potencies in the nanomolar to sub-nanomolar range. The most potent FAP inhibitor IOCB22-AP446 (6d, IC₅₀ = 89 pM) had about 36-fold higher inhibition potency than the most potent inhibitor published to date. The compounds were selective over FAP's closest homolog DPP-IV, were stable in human and mouse plasma and in mouse microsomes, and displayed minimal cytotoxicity in tissue cultures.

Molecular recognition of fibroblast activation protein for diagnostic and therapeutic applications

Fibroblast activation protein (FAP) is a non-classical serine protease expressed predominantly in conditions accompanied by tissue remodeling, particularly cancer. Due to its plasma membrane localization, FAP represents a promising molecular target for tumor imaging and treatment. The unique enzymatic activity of FAP facilitates development of diagnostic and therapeutic tools based on molecular recognition of FAP by substrates and small-molecule inhibitors, in addition to conventional antibody-based strategies. In this review, we provide background on the pathophysiological role of FAP and discuss its potential for diagnostic and therapeutic applications. Furthermore, we present a detailed analysis of the structural patterns crucial for substrate and inhibitor recognition by the FAP active site and determinants of selectivity over the related proteases dipeptidyl peptidase IV and prolyl endopeptidase. We also review published data on targeting of the tumor microenvironment with FAP antibodies, FAP-targeted prodrugs, activity-based probes and small-molecule inhibitors. We describe use of a recently developed, selective FAP inhibitor with low-nanomolar potency in inhibitor-based targeting strategies including synthetic antibody mimetics based on hydrophilic polymers and inhibitor conjugates for PET imaging. In conclusion, recent advances in understanding of the molecular structure and function of FAP have significantly contributed to the development of several tools with potential for translation into clinical practice.

Human FGF-21 Is a Substrate of Fibroblast Activation Protein

FGF-21 is a key regulator of metabolism and potential drug candidate for the treatment of type II diabetes and other metabolic disorders. However, the half-life of active, circulating, human FGF-21 has recently been shown to be limited in mice and monkeys by a proteolytic cleavage between P171 and S172. Here, we show that fibroblast activation protein is the enzyme responsible for this proteolysis by demonstrating that purified FAP cleaves human FGF-21 at this site in vitro, and that an FAP-specific inhibitor, ARI-3099, blocks the activity in mouse, monkey and human plasma and prolongs the half-life of circulating human FGF-21 in mice. Mouse FGF-21, however, lacks the FAP cleavage site and is not cleaved by FAP. These findings indicate FAP may function in the regulation of metabolism and that FAP inhibitors may prove useful in the treatment of diabetes and metabolic disorders in humans, but pre-clinical proof of concept studies in rodents will be problematic.

Fibroblast activation protein-α, a stromal cell surface protease, shapes key features of cancer associated fibroblasts through proteome and degradome alterations

Cancer associated fibroblasts (CAFs) constitute an abundant stromal component of most solid tumors. Fibroblast activation protein (FAP) α is a cell surface protease that is expressed by CAFs. We corroborate this expression profile by immunohistochemical analysis of colorectal cancer specimens. To better understand the tumor-contextual role of FAPα, we investigate how FAPα shapes functional and proteomic features of CAFs using loss- and gain-of function cellular model systems. FAPα activity has a strong impact on the secreted CAF proteome ("secretome"), including reduced levels of anti-angiogenic factors, elevated levels of transforming growth factor (TGF) β, and an impact on matrix processing enzymes. Functionally, FAPα mildly induces sprout formation by human umbilical vein endothelial cells. Moreover, loss of FAPα leads to a more epithelial cellular phenotype and this effect was rescued by exogenous application of TGFβ. In collagen contraction assays, FAPα induced a more contractile cellular phenotype. To characterize the proteolytic profile of FAPα, we investigated its specificity with proteome-derived peptide libraries and corroborated its preference for cleavage carboxy-terminal to proline residues. By "terminal amine labeling of substrates" (TAILS) we explored FAPα-dependent cleavage events. Although FAPα acts predominantly as an amino-dipeptidase, putative FAPα cleavage sites in collagens are present throughout the entire protein length. In contrast, putative FAPα cleavage sites in non-collagenous proteins cluster at the amino-terminus. The degradomic study highlights cell-contextual proteolysis by FAPα with distinct positional profiles. Generally, our findings link FAPα to key aspects of CAF biology and attribute an important role in tumor-stroma interaction to FAPα.

Sample collection in clinical proteomics--proteolytic activity profile of serum and plasma

PURPOSE

Proteolytic enzymes are promising diagnostic targets since they play key roles in diverse physiological processes and have been implicated in numerous human diseases. Human blood is a relatively noninvasive source for disease-specific protease biomarker detection and subsequent translation into diagnostic tests. However, the choice of serum or plasma, and more specifically, which anticoagulant to choose in plasma preparation, is important to address in the sample preparation phase of biomarker discovery.

EXPERIMENTAL DESIGN

We have previously utilized a combinatorial library of internally quenched fluorogenic probes to successfully map the global proteolytic profiles of various biological fluids. In this study, we utilized the platform to ascertain the impact of three commonly used anticoagulants (EDTA, heparin, and citrate) on the proteolytic activity profile of plasma and serum collected from a healthy Caucasian male.

RESULTS

Serum and plasma citrate were observed to be most proteolytically active, followed by plasma heparin and then plasma EDTA. Detailed analysis of the amino acid distribution of motifs cleaved and not cleaved by the samples offered significant insights in to active proteolytic components within them.

CONCLUSION AND CLINICAL RELEVANCE

Broad quantitative comparison of proteolytic profiles of these samples revealed several novel insights related to the differential substrate recognition of proteases present in these biological fluids.

Extended structure-activity relationship and pharmacokinetic investigation of (4-quinolinoyl)glycyl-2-cyanopyrrolidine inhibitors of fibroblast activation protein (FAP)

Fibroblast activation protein (FAP) is a serine protease related to dipeptidyl peptidase IV (DPPIV). It has been convincingly linked to multiple disease states involving remodeling of the extracellular matrix. FAP inhibition is investigated as a therapeutic option for several of these diseases, with most attention so far devoted to oncology applications. We previously discovered the N-4-quinolinoyl-Gly-(2S)-cyanoPro scaffold as a possible entry to highly potent and selective FAP inhibitors. In the present study, we explore in detail the structure-activity relationship around this core scaffold. We report extensively optimized compounds that display low nanomolar inhibitory potency and high selectivity against the related dipeptidyl peptidases (DPPs) DPPIV, DPP9, DPPII, and prolyl oligopeptidase (PREP). The log D values, plasma stabilities, and microsomal stabilities of selected compounds were found to be highly satisfactory. Pharmacokinetic evaluation in mice of selected inhibitors demonstrated high oral bioavailability, plasma half-life, and the potential to selectively and completely inhibit FAP in vivo.

Quantitation of fibroblast activation protein (FAP)-specific protease activity in mouse, baboon and human fluids and organs

The protease fibroblast activation protein (FAP) is a specific marker of activated mesenchymal cells in tumour stroma and fibrotic liver. A specific, reliable FAP enzyme assay has been lacking. FAP's unique and restricted cleavage of the post proline bond was exploited to generate a new specific substrate to quantify FAP enzyme activity. This sensitive assay detected no FAP activity in any tissue or fluid of FAP gene knockout mice, thus confirming assay specificity. Circulating FAP activity was ∼20- and 1.3-fold less in baboon than in mouse and human plasma, respectively. Serum and plasma contained comparable FAP activity. In mice, the highest levels of FAP activity were in uterus, pancreas, submaxillary gland and skin, whereas the lowest levels were in brain, prostate, leukocytes and testis. Baboon organs high in FAP activity included skin, epididymis, bladder, colon, adipose tissue, nerve and tongue. FAP activity was greatly elevated in tumours and associated lymph nodes and in fungal-infected skin of unhealthy baboons. FAP activity was 14- to 18-fold greater in cirrhotic than in non-diseased human liver, and circulating FAP activity was almost doubled in alcoholic cirrhosis. Parallel DPP4 measurements concorded with the literature, except for the novel finding of high DPP4 activity in bile. The new FAP enzyme assay is the first to be thoroughly characterised and shows that FAP activity is measurable in most organs and at high levels in some. This new assay is a robust tool for specific quantitation of FAP enzyme activity in both preclinical and clinical samples, particularly liver fibrosis.

•

A novel synthetic fluorogenic substrate is proven to be FAP-specific.

•

Mice have higher levels of circulating FAP activity compared to baboons or humans.

•

No FAP activity was detected in urine or bile but bile contained high DPP4 activity.

•

FAP activity is greatest in pancreas, uterus, salivary gland, skin and lymph node.

•

FAP activity and protein is elevated in both serum and liver in human liver disease.