Cell-permeable near-infrared fluorogenic substrates for imaging beta-lactamase activity

This communication describes a design of cell-permeable near-infrared fluorogenic substrates for imaging beta-lactamase expression in living mammalian cells. This design is based on fluorescence energy transfer resonance and utilizes a peracetylated d-glucosamine to facilitate the transport of the near-infrared probe across cell membranes. This new type of fluorogenic probe may also be applied to image gene expression in living animals.     

Design and synthesis of highly sensitive fluorogenic substrates for glutathione S-transferase and application for activity imaging in living cells

Here we report the development of fluorogenic substrates for glutathione S-transferase (GST), a multigene-family enzyme mainly involved in detoxification of endogenous and exogenous compounds, including drug metabolism. GST is often overexpressed in a variety of malignancies and is involved in the development of resistance to various anticancer drugs. Despite the medical significance of this enzyme, no practical fluorogenic substrates for fluorescence imaging of GST activity or for high-throughput screening of GST inhibitors are yet available. So, we set out to develop new fluorogenic substrates for GST. In preliminary studies, we found that 3,4-dinitrobenzanilide (NNBA) is a specific substrate for GST and established the mechanisms of its glutathionylation and denitration. Using these results as a basis for off/on control of fluorescence, we designed and synthesized new fluorogenic substrates, DNAFs, and a cell membrane-permeable variant, DNAT-Me. These fluorogenic substrates provide a dramatic fluorescence increase upon GST-catalyzed glutathionylation and have excellent kinetic parameters for the present purpose. We were able to detect nuclear localization of GSH/GST activity in HuCCT1 cell lines with the use of DNAT-Me. These results indicate that the newly developed fluorogenic substrates should be useful not only for high-throughput GST-inhibitor screening but also for studies on the mechanisms of drug resistance in cancer cells.     

Fluorescent detection of carbon-carbon bond formation

We have developed a new spectroscopic system for detecting carbon-carbon bond formation by fluorescence to enhance high-throughput catalyst screening and rapid characterization of catalysts on a small scale. Fluorogenic substrates composed of a fluorophore possessing an amino group are readily prepared as amides of alpha,beta-unsaturated carbonyl compounds and generally exhibit low fluorescence, while Michael or Diels-Alder reactions of these fluorogenic substrates provide products of significantly increased fluorescence. The product's fluorescence is approximately 20- to 100-fold higher than that of the substrate. The assay system was validated by screening potential catalysts of the Michael reaction and in solvent optimization experiments. The covalent combination of fluorophores possessing an amino group with alpha,beta-unsaturated carbonyl compounds should provide a diverse range of fluorogenic substrates that may be used to rapidly screen catalysts and to optimize reaction conditions.     

Development of protein, peptide, and small molecule catalysts using catalysis-based selection strategies

We have developed peptide catalysts and antibody catalysts that catalyze aldol, retro-aldol, and Michael reactions via an enamine mechanism using reaction-based selections with 1,3-diketone derivatives. Nucleophilic amino groups of the catalysts were covalently trapped during the selections. We have also developed fluorogenic substrates that are useful for real-time monitoring of the progress of bond-forming reactions, such as aldol reactions, by an increase in fluorescence. These fluorogenic substrates have been used to monitor peptide-catalyzed, antibody-catalyzed, enzyme-catalyzed, and small molecule-catalyzed reactions. Catalysis-based screening using fluorogenic substrates will accelerate rapid identification of superior catalysts and reaction conditions.     

Bimane fluorogenic substrates for microdetermination of angiotensin converting enzyme level in serum.

The fluorescence of 9,10-dioxa-syn-3,4,6,7-tetramethylbimane (bimane) was found to be quenched in the presence of nitrated aromatic amino acid. Bimane peptides containing nitrated amino acid (1a, b) were shown to be useful fluorogenic substrates for the assay of angiotensin I converting enzyme (ACE) from rabbit lung, similar to bimane substrate containing tryptophan (3) previously reported. Among these bimane substrates, substrate 3 was shown to be a potent fluorogenic substrate for microdetermination of the ACE level in human serum.     

Design, synthesis and evaluation of novel P450 fluorescent probes bearing α-cyanoether

Four α-cyano-containing ethers based on 2-alkoxy-2-naphthylacetonitriles have been designed as a novel structural class of cytochrome P450 fluorescent probes. Their syntheses, fluorescence properties and evaluation in the fluorogenic assay of cytochrome P450 monooxygenase are reported. After P450 enzymatic O-dealkylation, the cyanohydrin metabolite of the four new substrates rearranges to a fluorescent aromatic aldehyde with a larger Stokes shift, and the new substrates exhibit higher specific activities than that of the commercial substrate 7-ethoxyresorufin (ER).     

Novel fluorogenic substrates for phosphodiesterase I

The fluorescence of 9,10-dioxa-syn-3,4,6,7-tetramethylbimane (bimane) was found to be quenched in the presence of guanosine 5'-monophosphate. By using this phenomenon, the bimane system was used for the fluorophor of substrates for phosphodiesterase I. Bimanes were coupled to 5'-guanylic acid and the resulting compounds were shown to be portent fluorogenic substrates for the assay of phosphodiesterase I.     

Fluorogenic probes for aldol reactions: tuning of fluorescence using π-conjugation systems

Fluorogenic aldehydes or probes for monitoring of the progress of aldol reactions have been developed. Fluorescence of benzaldehydes conjugated with aryl groups via a double or triple bond and of their aldol products was evaluated in aqueous solutions. Based on the fluorescence, fluorogenic aldol reaction substrates and retro-aldol reaction substrates were identified. Use of the probe system with optimal fluorescence properties for aldol reactions was demonstrated in assays with purified protein catalysts and with overproduced crude protein catalysts in cell lysates.     

Rapid identification of substrates for novel proteases using a combinatorial peptide library

Fluorogenic substrates for assaying novel proteolytic enzymes could be rapidly identified using an easy, solid-phase combinatorial assay technology. The methodology was validated with leader peptidase of Escherichia coli using a subset of an intramolecularly quenched fluorogenic peptide library. The technique was extended toward the discovery of substrates for a new aspartic protease of pharmaceutical relevance (human napsin A). We demonstrated for the first time known to us that potent fluorogenic substrates can be discovered using extracts of cells expressing recombinant enzyme to screen the peptide library. The straightforward and rapid optimization of protease substrates greatly facilitates the drug discovery process by speeding up the development of high throughput screening assays and thus helps more effective exploitation of the enormous body of information and chemical structures emerging from genomics and combinatorial chemistry technologies.     

Synthesis and characterization of a series of highly fluorogenic substrates for glutathione transferases, a general strategy

Glutathione transferases (GSTs) are used in biotechnology applications as fusion partners for facile purification and are also overexpressed in certain tumors. Consequently, there is a need for sensitive detection of the enzymes. Here we describe a general strategy for the synthesis and characterization of novel fluorogenic substrates for GSTs. The substrates were synthesized by introducing an electrophilic sulfonamide linkage to fluorescent molecules containing an amino group [e.g., 2,4-dinitrobenzenesulfonamide (DNs) derivatives of coumarin, cresyl violet, and rhodamine]. The derivatives were essentially nonfluorescent, and upon GST catalyzed cleavage of the dinitrobenzenesulfonamide, free fluorophore is released (and 1-glutathionyl-2,4-dinitrobenzene + SO(2)). All the coumarin-, cresyl violet- and rhodamine-based fluorogenic probes turned out to be good substrates for most GSTs, especially for GSTA(1-1), in terms of strong fluorescence increases (71-1200-fold), high k(cat)/K(m) values (10(4)-10(7) M(-1) s(-1)) and significant rate enhancements (10(6)-10(9)-fold). The substrates were successfully applied to quantitate very low levels of GST activity in cell extracts and DNs-cresyl violet was also successfully applied to the imaging of microsomal MGST(1) activity in living cells. The cresyl violet stained cells retained their fluorescence after fixation, which is a very useful property. In summary, we describe a general and versatile strategy to generate fluorogenic GST substrates, some of them providing the most sensitive assays so far described for GSTs.     

Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules

A new fluorogenic cyanine dye was synthesized and found to have low fluorescence quantum yield in fluid solution and in the presence of double-stranded DNA but 80-fold enhanced fluorescence in viscous glycerol solution. An RNA aptamer selected for binding to the new dye exhibits K(d) = 87 nM and 60-fold fluorescence enhancement. The dye-aptamer pair is a fluoromodule that can be incorporated into fluorescent sensors and labels.     

Fluorogenic polypropionate fragments for detecting stereoselective aldolases

A series of fluorogenic polypropionate fragments has been prepared. These undergo retroaldolization to an intermediate aldehyde that liberates the fluorescent product umbelliferone by a secondary beta-elimination reaction. leading to a >20-fold increase in fluorescence (lambda(em) = 460 +/- 20 nm, lambdaex = 360 +/- 20 nm). By applying the principle of microscopic reversibility to the reversible aldol reaction, we can use these substrates to detect stereoselective aldolases. Test substrates are available to probe the classical cases of syn- and anti-selective aldolization (11a-d), Cram/ anti-Cram-selective aldolization (10a-d), and double stereoselective aldolization (3a-h). The selectivity of aldolase antibody 38C2 for these substrates is demonstrated as an example. The assay is suitable for high-throughput screening for catalysis in microtiter plates, and therefore provides a convenient tool for the isolation of new stereoselective aldolases from catalyst libraries.     

Terminal phosphate-labeled nucleotides with improved substrate properties for homogeneous nucleic acid assays

Nucleotides with a dye attached to the terminal phosphate with four or more phosphates (tetra- or pentaphosphates) are superior substrates than the corresponding triphosphates for DNA and RNA polymerases. When fluorogenic dyes are directly attached to the terminal phosphate, they can be released by the action of polymerase and alkaline phosphatase. The released dye changes color and fluorescence properties. The fluorescent signal can also be amplified by using multiple labeled nucleotides to detect small amounts of template. We have explored the utility of these nucleotides in a variety of applications including homogeneous SNP detection methods, DNA sequencing, and quantitation of PCR and RCA.     

A Fluorogenic Inhibitor of the Mitochondrial Calcium Uniporter

Inhibitors of the mitochondrial calcium uniporter (MCU) are valuable tools for studying the role of mitochondrial Ca²⁺ in various pathophysiological conditions. In this study, a new fluorogenic MCU inhibitor, RuOCou , is presented. This compound is an analogue of the known MCU inhibitor Ru265 that contains fluorescent axial coumarin carboxylate ligands. Upon aquation of RuOCou and release of the axial coumarin ligands, a simultaneous increase in its MCU-inhibitory activity and fluorescence intensity is observed. The fluorescence response of this compound enabled its aquation to be monitored in both HeLa cell lysates and live HeLa cells. This fluorogenic prodrug represents a potential theranostic MCU inhibitor that can be leveraged for the treatment of human diseases related to MCU activity.     

Continuous Flow Bioconjugations of NIR-AZA Fluorophores via Strained Alkyne Cycloadditions with Intra-Chip Fluorogenic Monitoring**

The importance of bioconjugation reactions continues to grow for cell specific targeting and dual therapeutic plus diagnostic medical applications. This necessitates the development of new bioconjugation chemistries, in-flow synthetic and analytical methods. With this goal, continuous flow bioconjugations were readily achieved with short residence times for strained alkyne substituted carbohydrate and therapeutic peptide biomolecules in reaction with azide and tetrazine substituted fluorophores. The strained alkyne substrates included substituted 2-amino-2-deoxy-α-D-glucopyranose, and the linear and cyclic peptide sequences QIRQQPRDPPTETLELEVSPDPAS-OH and c(RGDfK) respectively. The catalyst and reagent-free inverse electron demand tetrazine cycloadditions proved more favourable than the azide 1,3-dipolar cycloadditions. Reaction completion was achieved with residence times of 5 min at 40 °C for tetrazine versus 10 min at 80 °C for azide cycloadditions. The use of a fluorogenic tetrazine fluorophore, in a glass channelled reactor chip, allowed for intra-chip reaction monitoring by recording fluorescence intensities at various positions throughout the chip. As the Diels-Alder reactions proceeded through the chip, the fluorescence intensity increased accordingly in real-time. The application of continuous flow fluorogenic bioconjugations could offer an efficient translational access to theranostic agents.     

Synthesis and characterization of a new fluorogenic substrate for alpha-galactosidase

Alpha-galactosidase A hydrolyzes the terminal alpha-galactosyl moieties from glycolipids and glycoproteins in lysosomes. Mutations in α-galactosidase cause lysosomal accumulation of the glycosphingolipid, globotriaosylceramide, which leads to Fabry disease. Small-molecule chaperones that bind to mutant enzyme proteins and correct their misfolding and mistrafficking have emerged as a potential therapy for Fabry disease. We have synthesized a red fluorogenic substrate, resorufinyl α-d-galactopyranoside, for a new α-galactosidase enzyme assay. This assay can be measured continuously at lower pH values, without the addition of a stop solution, due to the relatively low pK _a of resorufin (~6). In addition, the assay emits red fluorescence, which can significantly reduce interferences due to compound fluorescence and dust/lint as compared to blue fluorescence. Therefore, this new red fluorogenic substrate and the resulting enzyme assay can be used in high-throughput screening to identify small-molecule chaperones for Fabry disease. Zhen-Dan Shi and Omid Motabar contributed equally to this work     

A fluorogenic ‘click’ reaction of azidoanthracene derivatives

Fluorogenic reactions have broad applications in biolabeling, combinatorial synthesis of fluorescent dyes, and materials development. It was recently reported that the highly selective and efficient Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction can be employed in designing new types of fluorogenic reactions. In this study, we report a fluorogenic reaction using anthracene azides as starting materials. The fluorescence of the anthryl core can be greatly inhibited upon introducing electron-donating azido groups in the proximity. Such weakly fluorescent anthracene azides demonstrate high reactivity with a variety of alkynes under the CuAAC conditions producing a strongly fluorescent triazole product with high quantum yields. This reaction can be used in the synthesis and screening of fluorescent dyes combinatorially. Compared with most existing methods, the fluorogenic CuAAC reaction is a much milder and simpler technique to prepare large libraries of fluorescent dyes without further purification. In order to demonstrate the efficiency of using anthracene azides for biolabeling applications, both small molecules and biomolecules including the multialkyne-derivatized cowpea mosaic virus and tobacco mosaic virus had been studied.     

Bifunctional coumarin derivatives in solution and solid phase synthesis of fluorogenic enzyme substrates

The use of the fluorescent bifunctional compounds 7‐amino‐4‐coumarinyl‐acetic acid 1 , 7‐hydroxy‐4‐coumarinyl‐acetic acid 2 and ethyl 7‐amino‐4‐coumarinyl‐acetate 3 in solution and solid phase synthesis of fluorogenic enzyme substrates was examined. The intramolecularly quenched fluorogenic substrate N‐(7‐amino‐4‐coumarinyl‐acetyl)‐L‐phenylalanyl‐p‐nitroanilide 5 , and the fluorogenic one ethyl 7‐(glutaryl‐L‐phenylalanilamido)‐4‐coumarinyl‐acetate 8 , both suitable for chymotrypsin and/or chymotrypsin like enzymes determination, were prepared in solution. The substrates 7‐oleyloxy‐4‐coumarinyl‐acetic acid 13 and 7‐palmitoyloxy‐4‐coumarinyl‐acetic acid 14 , suitable for the enzymatic study of lipases, were prepared by solid phase technique using 2‐chloro‐chlorotrityl‐resin. The study of the fluorescence properties of the fluorophores 1, 2, 3 , and substrates 5, 8,13,14 showed that the examined bifunctional coumarin derivatives are suitable markers for solution and solid phase synthesis of fluorogenic enzyme substrates.     

Two new fluorogenic substrates for the detection of Penicillin-G-acylase activity

Two fluorogenic substrates are described for the detection of Penicillin-G-acylase (EC 3.5.1.11) activity in coloured cell-containing media and inside single cells. A sensitive enzyme assay is based on the use of 7-phenylacetyl-4-alkylcoumarinylamides. Linear response is obtained in the range 20–300 μU m^?1. After the cells have been made permeable, intracellular enzyme activity can be monitored. It is thus possible to label enzyme-containing cells and to distinguish them from enzyme-free cells by fluorescence microscopy or laser-flow cytometry.