Fluorogenic Protease Research Articles

Latent Blue and Red Fluorophores Based on the Trimethyl Lock

Latent Blue and Red Fluorophores Based on the Trimethyl Lock

Fluorescein-based amino acids for solid phase synthesis of fluorogenic protease substrates

An efficient synthesis of new type fluorescent amino acids is described. The Fmoc-protected dyes can be prepared in a four-step procedure with ∼30% overall yield from aminofluoresceins and other inexpensive commercially available precursors. The dyes are much more photostable compared to fluorescein and exhibit constant pH-independent fluorescence that is advantageous in biological applications. The Fmoc-protected fluorescent amino acids are ready for use in solid phase peptide synthesis. As a proof of concept, a fluorogenic papain substrate was synthesized and employed for on-bead detection of the protease activity. By using a novel technique for quantitative analysis of bead fluorescence, a ∼2.7-fold increase in mean bead brightness was measured and was attributed to substrate cleavage by papain. The new type fluorescent amino acids seem to be a promising tool for the synthesis of fluorescent peptide ligands and fluorogenic protease substrates.

High Throughput Substrate Specificity Profiling of Serine and Cysteine Proteases Using Solution-phase Fluorogenic Peptide Microarrays

Proteases regulate numerous biological processes with a degree of specificity often dictated by the amino acid sequence of the substrate cleavage site. To map protease/substrate interactions, a 722-member library of fluorogenic protease substrates of the general format Ac-Ala-X-X-(Arg/Lys)-coumarin was synthesized (X=all natural amino acids except cysteine) and microarrayed with fluorescent calibration standards in glycerol nanodroplets on glass slides. Specificities of 13 serine proteases (activated protein C, plasma kallikrein, factor VIIa, factor IXabeta, factor XIa and factor alpha XIIa, activated complement C1s, C1r, and D, tryptase, trypsin, subtilisin Carlsberg, and cathepsin G) and 11 papain-like cysteine proteases (cathepsin B, H, K, L, S, and V, rhodesain, papain, chymopapain, ficin, and stem bromelain) were obtained from 103,968 separate microarray fluorogenic reactions (722 substrates x 24 different proteases x 6 replicates). This is the first comprehensive study to report the substrate specificity of rhodesain, a papain-like cysteine protease expressed by Trypanasoma brucei rhodesiense, a parasitic protozoa responsible for causing sleeping sickness. Rhodesain displayed a strong P2 preference for Leu, Val, Phe, and Tyr in both the P1=Lys and Arg libraries. Solution-phase microarrays facilitate protease/substrate specificity profiling in a rapid manner with minimal peptide library or enzyme usage.

Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays

A novel microarray-based proteolytic profiling assay enabled the rapid determination of protease substrate specificities with minimal sample and enzyme usage. A 722-member library of fluorogenic protease substrates of the general format Ac-Ala-X-X-(Arg/Lys)-coumarin was synthesized and microarrayed, along with fluorescent calibration standards, in glycerol nanodroplets on microscope slides. The arrays were then activated by deposition of an aerosolized enzyme solution, followed by incubation and fluorometric scanning. The specificities of human blood serine proteases (human thrombin, factor Xa, plasmin, and urokinase plasminogen activator) were examined. The arrays provided complete maps of protease specificity for all of the substrates tested and allowed for detection of cooperative interactions between substrate subsites. The arrays were further utilized to explore the conservation of thrombin specificity across species by comparing the proteolytic fingerprints of human, bovine, and salmon thrombin. These enzymes share nearly identical specificity profiles despite approximately 390 million years of divergent evolution. Fluorogenic substrate microarrays provide a rapid way to determine protease substrate specificity information that can be used for the design of selective inhibitors and substrates, the study of evolutionary divergence, and potentially, for diagnostic applications.

Proteolytically Degradable Hydrogels with a Fluorogenic Substrate for Studies of Cellular Proteolytic Activity and Migration

We have developed proteolytically degradable hydrogels with covalently immobilized fluorogenic protease substrates to visualize extracellular proteolytic activity and cell migration in three dimensions. Dye quenched-bovine serum albumin (DQ-BSA), a quenched, proteolytically activated fluorogenic substrate, was conjugated to poly(ethylene glycol) (PEG)-monoacrylate, and the product (DQ-BSA-PEG) was then covalently incorporated into proteolytically degradable and cell adhesive PEG hydrogels via photopolymerization. The DQ-BSA-PEG substrate in solution and incorporated into hydrogels exhibited significantly enhanced fluorescence after exposure to enzymes. Fibroblasts seeded within this hydrogel spread in three dimensions and extended lamellipodia. Cell migration and proteolytic activity were visualized using confocal microscopy. Proteolytic activity was concentrated near cell surfaces and remained present in the tracks where cell migration had occurred.

Norepinephrine induces apoptosis in neonatal rat cardiomyocytes through a reactive oxygen species-TNF alpha-caspase signaling pathway.

Norepinephrine (NE)-induced apoptosis in cardiomyocytes is an important cause of heart failure. Previous studies revealed that reactive oxygen species (ROS) are involved in apoptosis. Tumor necrosis factor-alpha (TNF), a well-known mediator that stimulates apoptosis, is not only produced by macrophages but also by cardiomyocytes. Until now, the role of TNF and its relationship to ROS in NE-induced apoptosis of cardiomyocytes have never been investigated. Neonatal rat cardiomyocytes were treated with various concentrations of NE. Apoptosis of cardiomyocytes was determined using the TUNEL assay. The level of secreted TNF was measured by ELISA and TNF mRNA expression was determined by semiquantitative reverse transcriptional polymerase chain reaction. Caspase activity was measured by a fluorogenic protease assay kit. Anti-TNF antibodies, caspase inhibitors and antioxidants (N-acetyl-L-cysteine or vitamin C) were added to determine if they could inhibit the apoptotic effect of NE. NE induced apoptosis of cardiomyocytes in a dose- and time-dependent manner. NE up-regulated TNF mRNA expression and increased TNF secretion and caspase-2,-3,-6, and -9 activities. A neutralizing anti-TNF antibody and caspase-2 and -3 inhibitors significantly attenuated NE-induced apoptosis. Antioxidants completely abrogated NE-induced TNF secretion, caspase activation, and apoptotic death. NE induced apoptosis in neonatal rat cardiomyocytes through a ROS-TNF-caspase signaling pathway.

Norepinephrine induces apoptosis in neonatal rat cardiomyocytes through a reactive oxygen species?TNF$alpha;?caspase signaling pathway

Objective: Norepinephrine (NE)-induced apoptosis in cardiomyocytes is an important cause of heart failure. Previous studies revealed that reactive oxygen species (ROS) are involved in apoptosis. Tumor necrosis factor-α (TNF), a well-known mediator that stimulates apoptosis, is not only produced by macrophages but also by cardiomyocytes. Until now, the role of TNF and its relationship to ROS in NE-induced apoptosis of cardiomyocytes have never been investigated. Methods: Neonatal rat cardiomyocytes were treated with various concentrations of NE. Apoptosis of cardiomyocytes was determined using the TUNEL assay. The level of secreted TNF was measured by ELISA and TNF mRNA expression was determined by semiquantitative reverse transcriptional polymerase chain reaction. Caspase activity was measured by a fluorogenic protease assay kit. Anti-TNF antibodies, caspase inhibitors and antioxidants (N-acetyl-l-cysteine or vitamin C) were added to determine if they could inhibit the apoptotic effect of NE. Results: NE induced apoptosis of cardiomyocytes in a dose- and time-dependent manner. NE up-regulated TNF mRNA expression and increased TNF secretion and caspase-2,-3,-6, and -9 activities. A neutralizing anti-TNF antibody and caspase-2 and -3 inhibitors significantly attenuated NE-induced apoptosis. Antioxidants completely abrogated NE-induced TNF secretion, caspase activation, and apoptotic death. Conclusion: NE induced apoptosis in neonatal rat cardiomyocytes through a ROS–TNF–caspase signaling pathway.

Facile synthesis of 7-amino-4-carbamoylmethylcoumarin (ACC)-containing solid supports and Their corresponding fluorogenic protease substrates

The bifunctional fluorophore, 7-amino-4-carbamoylmethylcoumarin (ACC) without any protection groups, was regioselectively attached to different solid supports functionalized with a primary amino group. The resulting resins were used to synthesize fluorogenic protease substrates with high yield and purity.

Expedient solid-phase synthesis of fluorogenic protease substrates using the 7-amino-4-carbamoylmethylcoumarin (ACC) fluorophore.

A highly efficient solid-phase synthesis method for the preparation of fluorogenic protease substrates based upon the bifunctional leaving group 7-amino-4-carbamoylmethylcoumarin (ACC) is reported. Methods for the large-scale preparation of the novel fluorogenic leaving-group ACC are provided (Scheme 1). Detailed procedures are also provided for loading a diverse set of amino acids to support-bound ACC in good yields and with minimal racemization. Finally, procedures are included for the preparative synthesis of optimized ACC substrates for HIV-1 protease and plasmin.

A general and direct method for the solid phase synthesis of intramolecular quenched fluorogenic protease substrates using a bifunctional coumarin derivative

A general method for the solid phase preparation offluorogenic peptide substrates or intramolecularly quenchedones (IQFS) is presented, using the highly fluorescentbifunctional coumarin derivative 7-amino-4-coumarinyl-acetic acid. The key feature of this method is theconjugation of H–Aca–OH through its carboxyl group on theresin, followed by the development of the peptide chainthrough its amino group, using standard Fmoc-derived solidphase peptide synthesis methodology. The 2,4-dinitrophenylgroup was used as quencher and introduced directly to theresin-bound peptides. The IQFSDnp–Lys–Pro–Ile–Cys–Phe–Ile–Lys–Leu–Aca–OH (2) andfour Dnp–X-Lys–Pro–Ile–Cys–Phe–Ile–Lys–Leu–Aca–OH (3–6), where X = Val, Lys, Ser and Glu at P6 position,potential substrates for cathepsin D, were synthesized forproving the utility of the method. The compoundsH–Ile–Lys–Leu–Aca–OH (7),H–Lys–Pro–Ile–Cys–Phe–Ile–Lys–Leu–Aca–OH (8),H–Leu–Aca–OH (9), Dnp–Leu–Aca–OH (10) and Dnp-Leu-OH (11) were also synthesized for comparisonpurposes. The fluorescence properties of compounds 9and 10 were measured.

A general and direct method for the solid phase synthesis of intramolecularly quenched fluorogenic protease substrates using a bifunctional coumarin derivative

A general method for the solid phase preparation offluorogenic peptide substrates or intramolecularly quenchedones (IQFS) is presented, using the highly fluorescentbifunctional coumarin derivative 7-amino-4-coumarinyl-acetic acid. The key feature of this method is theconjugation of H–Aca–OH through its carboxyl group on theresin, followed by the development of the peptide chainthrough its amino group, using standard Fmoc-derived solidphase peptide synthesis methodology. The 2,4-dinitrophenylgroup was used as quencher and introduced directly to theresin-bound peptides. The IQFSDnp–Lys–Pro–Ile–Cys–Phe–Ile–Lys–Leu–Aca–OH (2) andfour Dnp–X-Lys–Pro–Ile–Cys–Phe–Ile–Lys–Leu–Aca–OH (3–6), where X = Val, Lys, Ser and Glu at P6 position,potential substrates for cathepsin D, were synthesized forproving the utility of the method. The compoundsH–Ile–Lys–Leu–Aca–OH (7),H–Lys–Pro–Ile–Cys–Phe–Ile–Lys–Leu–Aca–OH (8),H–Leu–Aca–OH (9), Dnp–Leu–Aca–OH (10) and Dnp-Leu-OH (11) were also synthesized for comparisonpurposes. The fluorescence properties of compounds 9and 10 were measured.

Quenched BODIPY Dye-Labeled Casein Substrates for the Assay of Protease Activity by Direct Fluorescence Measurement

We have prepared casein conjugates of two BODIPY dyes for use as fluorogenic protease substrates in homogeneous assays. Both conjugates are labeled to such an extent that the dyes are efficiently quenched in the protein, yielding virtually nonfluorescent substrate molecules. These fluorogenic substrates release highly fluorescent BODIPY dye-labeled peptides upon protease digestion, with fluorescence increases proportional to enzyme activity. These quenched substrates are suitable for the continuous assay of enzymatic activity using standard fluorometers, filter fluorometers, or fluorescence microplate readers using either fluorescein excitation and emission wavelengths to measure BODIPY FL casein hydrolysis or Texas Red wavelengths to detect proteolysis of BODIPY TR-X casein. Most current techniques for detecting protease activity, such as the fluorescein thiocarbamoyl casein (FTC–casein) protease assay, require extensive manipulation, including separation steps, and are therefore labor intensive and error-prone. In comparison, we found the BODIPY dye-labeled casein protease assays to be simple and precise and to have greater sensitivity and a broader dynamic range of detection than the FTC-casein assay. We were able to sensitively detect the activities of a wide variety of enzymes with these new substrates, including serine, acid, sulfhydryl, and metalloproteases. We also found the assay suitable for quantitating protease inhibitor concentrations and for real-time analysis of proteolysis.

Internally quenched fluorogenic protease substrates: Solid-phase synthesis and fluorescence spectroscopy of peptides containing ortho-aminobenzoyl/dinitrophenyl groups as donor-acceptor pairs

A general procedure, using the commonly employed solid-phase peptide synthesis methodology for obtaining internally quenched fluorogenic peptides with ortho-aminobenzoyl/dinitrophenyl groups as donor-acceptor pairs, is presented. The essential feature of this procedure is the synthesis of an Nα-Boc or-Fmoc derivative of glutamic acid with the α-carboxyl group bound to N-(2,4-dinitrophenyl)-ethylenediamine (EDDnp), which provides the quencher moiety attached to the C-terminus of the substrate. The fluorescent donor group, ortho-aminobenzoic acid (Abz), is incorporated into the resin-bound peptide in the last coupling cycle. Depending on the resin type used, Abz-peptidyl-Gln-EDDnp or Abz-peptidyl-Glu-EDDnp is obtained. Using the procedure described above, substrates for human renin and tissue kallikreins were synthesised. Spectrofluorimetric measurements of Abz bound to the α-amino group of proline showed that strong quenching of Abz fluorescence occurs in the absence of any acceptor group.

Multiple Column Synthesis of Quenched Solid-Phase Bound Fluorogenic Substrates for Characterization of Endoprotease Specificity

A method for multiple column peptide synthesis of resin-bound fluorogenic protease substrates, which are subsequently used in a solid-phase assay for the complete subsite mapping of the active site of endoproteases, is described. Substrate libraries containing anthranilic acid and 3-nitrotyrosine as an efficient donor-acceptor pair for long-range resonance energy transfer were synthesized on kieselguhr-supported polyamide resin and on PEG-polyamide resin, both permitting proteases to diffuse into the interior. The synthesis was performed in a manual library generator that allows simple wet-mixing of the beads and parallel washing procedures. The library was treated with the proteolytic enzyme subtilisin Carlsberg, and fluorescent beads on a background of dark beads were collected manually. The preferred sequences, their scissile bonds, and semi-quantitative estimations of their turnover were determined by sequence analysis of the resin-bound peptides. For each subsite, a statistical distribution of preferred amino acids was obtained. Amino acid sequences that could not be hydrolyzed by extensive treatment with subtilisin Carlsberg were also identified.

Automated synthesis of fluorogenic protease substrates: design of probes for alzheimer's disease-associated proteases

A facile automated solid phase method for the synthesis of internally quenched, fluorogenic protease substrates is described. Substrates specifically tailored to represent putative cleavage sites for the normal secretory processing pathway and the amyloidogenic processing pathway(s) of the Alzheimer's disease amyloid precursor protein (APP) have been prepared by this method, and utilized to identify neural protease activities in normal and Alzheimer's disease brain tissue.

A general method for the preparation of internally quenched fluorogenic protease substrates using solid-phase peptide synthesis.

A general scheme for obtaining a fluorescent donor/acceptor peptide substrate via solid-phase synthesis methodology is presented. The key feature of this method is the design of a glutamic acid derivative that has been modified on the carboxyl side chain with a 5-[(2'-aminoethyl)-amino]naphthelenesulfonic acid (EDANS) to create a fluorescent donor moiety that can be incorporated near the C-terminus of the peptide substrate. The corresponding fluorescent acceptor group containing a 4-[[4-(dimethylamino)phenyl]azo]benzoic acid (DABCYL) can then be attached to the resin-bound peptide at the N-terminus while all side-chain groups are still fully protected. Substrates for renin and HIV proteinase are synthesized as examples.

Evidence for the involvement of metalloendoproteases in the acrosome reaction in sea urchin sperm.

An essential initial step in fertilization in the sea urchin Strongylocentrotus purpuratus is an intracellular membrane fusion event in the sperm known as the acrosome reaction. This Ca2+-dependent, exocytotic process involves fusion of the membrane of the acrosomal vesicle and the plasma membrane. Recently, metalloendoproteases requiring divalent metals have been implicated in several Ca2+-dependent membrane fusion events in other biological systems. In view of the suggested involvement of Zn2+ in the sea urchin sperm acrosome reaction (Clapper, D.L., Davis, J.A., Lamothe, P.J., Patton, C., and Epel, D. (1985) J. Cell Biol. 100, 1817-1824) and the fact that Zn2+ is a metal cofactor for metalloendoproteases, we investigated the potential role of this protease in the acrosome reaction. A soluble metalloendoprotease was demonstrated and characterized in sperm homogenates using the fluorogenic protease substrate succinyl-alanine-alanine-phenylalanine-4-aminomethylcoumarin. The protease was inhibited by the metal chelators EDTA and 1,10-phenanthroline, and activity of the inactive apoenzyme could be reconstituted with Zn2+. The metalloendoprotease substrate and inhibitors blocked the acrosome reaction induced either by egg jelly coat or by ionophore, but had no effect on the influx of Ca2+. These observations suggest that inhibition occurs at a step independent of Ca2+ entry. Overall, the results of this study provide strong indirect evidence that the acrosome reaction requires the action of metalloendoprotease.

Isoelectric focusing (IEF) and band detection with fluorogenic protease substrates.

In a previous paper, combined dye histochemistry and analytical isoelectric focusing (IEF) of supernatants from organ homogenates have been shown to yield good results for the detection of protease isoenzymes. Difficulties arise when the protease to be studied is partially or completely inhibited by diazonium salts and when synthetic peptide substrates different from 4-methoxy-2-naphthylamine (MNA) amino acids and peptides are to be used. In this paper a technique is described in which cellulose acetate foils impregnated with MNA, 7-amino-4-methyl-coumarin (AMC) and 7-amino-4-trifluoromethylcoumarin (AFC) substrates are overlaid on electrophoresis strips after IEF. After incubation, the foils are viewed with an UV-lamp and photographed. The MNA, AMC and AFC peptides are equally suitable for fluorescence band detection. Using this technique, occasionally protease isoenzymes are found which are more sensitive towards diazonium salts, e.g. aminopeptidase A and M. Sometimes it is also possible to detect thiolproteases which is not the case when employing dye histochemistry.

Rat myoblast fusion requires metalloendoprotease activity

The calcium-dependent fusion of cultured rat myoblasts to multinucleate myotubes appears to require the activity of a neutral metalloendoprotease at the time of fusion. Metalloendoprotease inhibitors and synthetic dipeptide substrates prevent myoblast fusion when added to fusion-competent myoblasts with the addition of calcium. Metalloendoprotease activity has been identified and partially characterized in myoblast membranes with a fluorogenic protease substrate, and is inhibited by the same compounds that prevent fusion.