Fluorogenic Enzyme Substrates Research Articles

Self-Immolative Difluorophenyl Ester Linker for Affinity-Based Fluorescence Turn-on Protein Detection.

Currently most fluorogenic probes are developed for the analysis of enzymes, where a bond breaking or rearrangement reaction is required to transform a nonfluorescent enzymatic substrate into a fluorescent product. However, this approach cannot be used for proteins that do not possess enzymatic activities. In this article, we show that fluorogenic probes with a self-immolative difluorophenyl ester linker can mimic the bond disassembly processes of fluorogenic enzyme substrates for the rapid analysis of nonenzymatic proteins. Although numerous self-immolative reagents have shown promising applications in sensors, drug delivery systems, and material chemistry, all of them are triggered by either enzymes or small reactive molecules. In our strategy, the probe binds to the protein via a specific protein-ligand interaction, inducing a chemical reaction between the self-immolative linker and an amino acid of the protein, thereby triggering a cascade reaction that leads to the activation and release of the fluorogenic reporter. In contrast, a phenyl ester linker without the difluoro substituent cannot be triggered to release the fluorogenic reporter. With this probe design, live-cell imaging of extracellular and intracellular endogenous tumor marker proteins can be achieved with high selectivity and sensitivity.

In Vivo Visualization of γ-Glutamyl Transpeptidase Activity with an Activatable Self-Immobilizing Near-Infrared Probe.

γ-Glutamyl transpeptidase (GGT), a type of cell membrane-bound enzyme, is closely involved in a wide range of physiological and pathological processes, and a large number of fluorogenic probes have been developed to detect the activity of GGT. However, the use of these imaging reagents to visualize GGT activity in vivo is largely limited because of rapid diffusion and clearance of activated fluorophores. Herein, by merging quinone methide and a fluorogenic enzyme substrate, we report an activatable self-immobilizing near-infrared probe for the in vitro and in vivo imaging of GGT activity. This probe is initially fluorescently silent, but the selective activation by GGT is able to significantly increase its fluorescence intensity at 714 nm and covalently anchor activated fluorophores at the site of interest. We have shown that this probe induced a much stronger fluorescence on live GGT-overexpressing cells compared to regular fluorogenic probes and allowed wash-free and real-time imaging of enzyme activity. More importantly, the use of this probe in the imaging of GGT activity in U87MG tumor-bearing mice by i.v. administration indicates that this self-immobilizing reagent is capable of efficiently enhancing its retention at the detection target and thus leads to much improved detection sensitivity compared to regular fluorogenic probes. This study demonstrates the advantage of fluorogenic probes with activatable anchors in the noninvasive imaging of enzyme activity in highly dynamic in vivo systems.

Practical Synthesis of the Fluorogenic Enzyme Substrate 4-Methylumbelliferyl α-l-Idopyranosiduronic Acid

A practical and concise synthesis of 4-methylumbelliferyl α-l-idopyranosiduronic acid, a fluorogenic enzyme substrate diagnostic for α-l-iduronidase, was accomplished. It features successive radical bromination and radical reduction of easily accessible methyl 4-methyl­umbelliferyl-2,3,4-tri-O-acetyl-β-d-glucouronate in four steps with 28% overall yield.

Simple and reliable enumeration of Escherichia coli concentrations in wastewater samples by measuring β-d-glucuronidase (GUS) activities via a microplate reader.

Monitoring of Escherichia coli concentrations at wastewater treatment plants (WWTPs) is important to ensure process performance and protect public health. However, conventional E. coli enumeration methods are complicated and time- and labor-consuming. Here, we report a novel simple and reliable method based on β-d-glucuronidase (GUS) activity assay to enumerate E. coli concentrations in wastewater (WW) samples. An aliquot (20μL) of the medium with fluorogenic enzyme substrate for E. coli and 180μL of a WW sample were added to one well of a 96-well microplate. The microplate was placed in a microplate reader at 37°C. To this end, the fluorescence intensity of a fluorogenic enzyme substrate for E. coli was measured every 10min over 3h to determine GUS activity. The linear increase in the fluorescence intensity representing the GUS activities showed a positive correlation with E. coli concentrations in wastewater samples. However, the correlation equations were specific to WWTPs, which could be due to the difference in the E. coli population structures among WWTPs. We observed that the wastewater matrix is not a limitation to measure the GUS activity, and a WWTP-specific correlation equation can be used as a calibration curve to estimate the E. coli concentrations in the samples collected from that site. A comparison of the results with those of culture-dependent Colilert method proved that the current method is simple and useful for the enumeration of E. coli concentrations in wastewater samples reliably.

Paper-based sol-gel thin films immobilized cytochrome P450 for enzyme activity measurement

Cytochrome P450 (CYP450), and in particular CYP3A4, is the most abundantly expressed CYP450 isozyme implicated in many drug-drug and medicinal plant-drug interactions. Therefore, incorporation of CYP3A4 enzyme screening at an early stage of drug discovery is preferable in order to avoid enzymatic interactions. Here we present for the first time a paper-based CYP3A4 immobilized sol-gel-derived a platform using resorufin benzyl ether as a fluorogenic enzyme substrate used to investigate enzyme activity. The fluorescence intensity of the product can be simply quantified by using a handheld digital microscope and an image analysis software. The limit of quantitation was 0.35 μM with good precision (RSDs < 4.1%). Furthermore, the assay of CYP3A4 activity on the developed paper-based device provided comparable results with those obtained from conventional well-plates (p > 0.05), while offering simplicity and lower cost. Kinetic parameters of the immobilized CYP3A4 in sol-gel coated paper were calculated from the Lineweaver-Burk plot, including Michaelis constant (Km) and maximum velocity (Vmax), which were 2.71 ± 0.35 μM and 0.43 ± 0.05 μM/min, respectively. Moreover, a functional test of these devices was conducted by assessments of known CYP3A4 inhibitors (i.e. ketoconazole, itraconazole) and inducers (i.e. phenytoin, carbamazepine). To further demonstrate the broad range of uses, the devices were utilized to assay plant extracts i.e. Areca catechu seeds, Camellia sinensis leaves, Eclipta prostrata aerial part, providing results in good agreement with previous studies. Furthermore, the sol-gel immobilized enzyme stored at 4 °C can increase storage stability, offering the activity of 86.3 ± 0.4% after 3-weeks storage, equivalent to the activity of the free enzyme solution after 1-week storage. The developed paper-based devices offer versatility, portability and low-cost.

Detection of proteinase activated receptor stimulating enzymes in human arthritic knee joint fluids

Purpose: Osteoarthritis (OA) is a major health care burden worldwide. OA can affect all joints but is manifest most often in the knees, hips, big toe hands and spine, and results in joint inflammation, pain and stiffness. There is currently no effective cure or therapeutic interventions for OA. Therefore, there is a need for further studies into mechanisms underlying disease progression and for the identification of novel therapeutic targets. A key feature of OA is the progressive degradation of the cartilage. It is well established that there is an increase in proteolytic enzyme activity that is linked to this damage. We hypothesized that in addition to degrading the extracellular matrix, increased proteolytic activity in the arthritic joint could also signal through the enzymatically activated Proteinase Activated Receptor (PAR) family of G-protein coupled receptors. Methods: To study the hypothesis, twenty human knee joint synovial fluid samples derived from OA patients undergoing realignment osteotomy were screened for PAR cleavage/activity in CHO cells stably transfected with genetically encoded PAR1 or PAR2 sensors (nluc-hPAR1-eYFP and nluc-hPAR2-eYFP). The N-terminal nano-luciferase released upon proteolytic cleavage of the receptor was measured as a luminescence signal in the presence of the substrate furimazine in a 96-well microplate reader. To determine the class/type of enzymes, the test samples were pretreated with enzyme inhibitors and the receptor cleavage was measured using the PAR sensors. In addition, fluorogenic enzyme substrates were used to identify the class of enzymes using a fluorescence microplate reader. Results: PAR activating enzymes were identified at significant levels in the OA synovial fluid samples derived from twenty patients. Through the use of class/type selective enzyme inhibitors and fluorogenic substrates it was found that serine protease class enzymes including thrombin and trypsin-like, and matrix metalloproteinases are present in the inflamed knee joint samples. Further work aimed at identifying the specific enzymes is underway using activity-based probes and mass-spectrometry analysis. Conclusions: It is known that PAR activation is pro-inflammatory and inhibition of these receptors with specific antagonists may be beneficial in treating OA. A better understanding of PAR activators and the pathological signaling pathways triggered by these receptors will guide development of novel therapies to treat joint diseases.

Fluorogenic l-alanylaminopeptidase substrates derived from 6-amino-2-hetarylquinolines and 7-amino-3-hetarylcoumarins and their potential applications in diagnostic microbiology

Six novel fluorogenic enzyme substrates for detecting l-alanylaminopeptidase activity in microorganisms have been prepared and evaluated in Columbia agar media. The substrates are l-alanyl derivatives of 6-amino-2-hetarylquinolines and 7-amino-3-hetarylcoumarins. Both the quinoline and coumarin series of substrates produced fluorescence in the presence of Gram-negative microorganisms. In contrast, fluorescence generation in the presence of the Gram-positive microorganisms and yeasts was limited or absent.

Bridge‐Caging Strategy in Phosphorus‐Substituted Rhodamine for Modular Development of Near‐Infrared Fluorescent Probes

Replacement of the bridging oxygen atom in rhodamine with phosphorus is one of the most efficient ways for bright near-infrared (NIR) fluorophores with wavelengths over 700 nm. However, the organophosphorus bridge is more versatile than just being a spectrum tuner, it is also a profound solubility booster and photostability enhancer, as proved by a series of phosphorus-substituted rhodamines (PRBs). A unique bridge-caging strategy for efficiently manipulating fluorescence has further been innovated in example PRB2. Consistent with theoretical calculations, the formation of organophosphinate by a caging group as a fluorescence-controller locks the spirolactone into a colorless and nonfluorescent form, whereas decaging, a process induced by a specific stimulus, results in a ring-opened form, which yields strong fluorescence. The bridge-caging strategy is feasible for the modular development of NIR probes. Efficient in vivo imaging of photoillumination, hydrogen peroxide, and enzyme have been achieved on the PRB2 scaffold as a photoactivatable fluorophore, PRB2-hν; fluorescent indicator, PRB2-H2 O2 ; and fluorogenic enzyme substrate, PRB2-NTR, respectively.

A latent green fluorescent styrylcoumarin probe for the selective growth and detection of Gram negative bacteria

A novel, green fluorescent β-alanylstyrylcoumarin derivative was synthesized and evaluated for its performance as a fluorogenic enzyme substrate on a range of clinically relevant microorganisms. The substrate was selectively hydrolysed by β-alanyl aminopeptidase producing P. aeruginosa resulting in an on-to-off fluorescent signal. Growth inhibitory effect of the substrate was observed on Gram positive bacteria and yeasts. Meanwhile, Gram negative species, despite their extremely protective cell envelope, showed ready uptake and accumulation of the substrate within their healthy growing colonies displaying intense green fluorescence.

Polymerase-free measurement of microRNA-122 with single base specificity using single molecule arrays: Detection of drug-induced liver injury.

We have developed a single probe method for detecting microRNA from human serum using single molecule arrays, with sequence specificity down to a single base, and without the use of amplification by polymerases. An abasic peptide nucleic acid (PNA) probe—containing a reactive amine instead of a nucleotide at a specific position in the sequence—for detecting a microRNA was conjugated to superparamagnetic beads. These beads were incubated with a sample containing microRNA, a biotinylated reactive nucleobase—containing an aldehyde group—that was complementary to the missing base in the probe sequence, and a reducing agent. When a target molecule with an exact match in sequence hybridized to the capture probe, the reactive nucleobase was covalently attached to the backbone of the probe by a dynamic covalent chemical reaction. Single molecules of the biotin-labeled probe were then labeled with streptavidin-β-galactosidase (SβG), the beads were resuspended in a fluorogenic enzyme substrate, loaded into an array of femtoliter wells, and sealed with oil. The array was imaged fluorescently to determine which beads were associated with single enzymes, and the average number of enzymes per bead was determined. The assay had a limit of detection of 500 fM, approximately 500 times more sensitive than a corresponding analog bead-based assay, with target specificity down to a single base mis-match. This assay was used to measure microRNA-122 (miR-122)—an established biomarker of liver toxicity—extracted from the serum of patients who had acute liver injury due to acetaminophen, and control healthy patients. All patients with liver injury had higher levels of miR-122 in their serum compared to controls, and the concentrations measured correlated well with those determined using RT-qPCR. This approach allows rapid quantification of circulating microRNA with single-based specificity and a limit of quantification suitable for clinical use.

The Synthesis of L-Alanyl and β-Alanyl Derivatives of 2-Aminoacridone and Their Application in the Detection of Clinically-Important Microorganisms.

In clinical microbiology the speed with which pathogenic microorganisms may be detected has a direct impact on patient health. One important strategy used in the laboratory is the growth of cultures in the presence of an enzymatic substrate which, once transformed by the appropriate microbial enzyme, generates a detectable colour or fluorescence output. Such substrates have previously been prepared by our group and others and are available as commercial diagnostic kits, however they all suffer from some degree of diffusion when used in a solid growth medium. This diffusion complicates the detection and differentiation of species in polymicrobial cultures and so we sought to improve on our previous work. In this work we have prepared and evaluated a series of novel fluorogenic enzyme substrates based on N-substituted-2-aminoacridones. All of the prepared substrates were found to be suitable for the detection and differentiation of certain microorganisms, however those based on the 2-amino-10-benzylacridone core in particular showed no apparent diffusion when incorporated into solid growth media. On transformation these substrates generated brightly fluorescent colonies that are clearly contrasted with the background medium due to the difference in emission wavelength (λem 445–450 nm for the substrate, λem 550 nm for the product). Here we have shown that our L-alanyl aminopeptidase substrate, 2-(N-L-alanylamino)-10-benzylacridone, is particularly suited to the detection of Gram-negative bacteria, and our β-alanyl aminopeptidase substrate, 2-(N- β-alanylamino)-10-benzylacridone, to the detection of Pseudomonas aeruginosa and Serratia marcescens when grown on solid media incorporating these substrates. The resulting fluorophore shows no apparent diffusion from the colonies of interest, and the enhanced sensitivity offered by fluorescent emission may allow for the detection of these organisms as microcolonies using automated fluorescence microscopy.

Efficient analysis of a small number of cancer cells at the single-cell level using an electroactive double-well array.

Analysis of the intracellular materials of a small number of cancer cells at the single-cell level is important to improve our understanding of cellular heterogeneity in rare cells. To analyze an extremely small number of cancer cells (less than hundreds of cells), an efficient system is required in order to analyze target cells with minimal sample loss. Here, we present a novel approach utilizing an advanced electroactive double-well array (EdWA) for on-chip analysis of a small number of cancer cells at the single-cell level with minimal loss of target cells. The EdWA consisted of cell-sized trap-wells for deterministic single-cell trapping using dielectrophoresis and high aspect ratio reaction-wells for confining the cell lysates extracted by lysing trapped single cells via electroporation. We demonstrated a highly efficient single-cell arraying (a cell capture efficiency of 96 ± 3%) by trapping diluted human prostate cancer cells (PC3 cells). On-chip single-cell analysis was performed by measuring the intracellular β-galactosidase (β-gal) activity after lysing the trapped single cells inside a tightly enclosed EdWA in the presence of a fluorogenic enzyme substrate. The PC3 cells showed large cell-to-cell variations in β-gal activity although they were cultured under the same conditions in a culture dish. This simple and effective system has great potential for high throughput single-cell analysis of rare cells.

Virginia Orange: A Versatile, Red-Shifted Fluorescein Scaffold for Single- and Dual-Input Fluorogenic Probes.

Fluorogenic molecules are important tools for biological and biochemical research. The majority of fluorogenic compounds have a simple input-output relationship, where a single chemical input yields a fluorescent output. Development of new systems where multiple inputs converge to yield an optical signal could refine and extend fluorogenic compounds by allowing greater spatiotemporal control over the fluorescent signal. Here, we introduce a new red-shifted fluorescein derivative, Virginia Orange, as an exceptional scaffold for single- and dual-input fluorogenic molecules. Unlike fluorescein, installation of a single masking group on Virginia Orange is sufficient to fully suppress fluorescence, allowing preparation of fluorogenic enzyme substrates with rapid, single-hit kinetics. Virginia Orange can also be masked with two independent moieties; both of these masking groups must be removed to induce fluorescence. This allows facile construction of multi-input fluorogenic probes for sophisticated sensing regimes and genetic targeting of latent fluorophores to specific cellular populations.

Evaluation of fluorogenic aminonaphthalenesulfonamides and 6-hydrazinobenz[de]isoquinoline-1,3-diones for the detection of bacteria

New fluorogenic enzyme substrates were synthesized by the coupling of aminonaphthalenesulfonamides or 6-hydrazinobenz[de]isoquinoline-1,3-diones with β-alanine. The 6-hydrazinobenz[de]isoquinoline-1,3-diones were also condensed with a range of aryl aldehydes to give the corresponding hydrazones. The photophysical properties of the synthesized amines and hydrazines and their amide, hydrazide and hydrazone derivatives, were examined and they were also incorporated into Columbia agar in order to determine their potential for the detection of pathogenic bacteria.

ADAM17‐Mediated Shedding of ACE2 in Pancreatic Beta‐Cells

Angiotensin‐converting enzyme 2 (ACE2) hydrolyzes angiotensin II. Our laboratory has previously shown that pancreatic ACE2 levels decrease as diabetes progresses and that pancreatic ACE2 gene therapy counteracts development of hyperglycemia in diabetic animal models. As a disintegrin and metalloprotease 17 (ADAM17) is an enzyme that can cleave enzymatically active ACE2 from the cell to the extracellular environment by so‐called shedding, we hypothesize that increased levels of ADAM17 in pancreatic beta‐cells lead to reduced cellular ACE2 levels. To this end, 832/13 cells (rat insulinoma cells derived from pancreatic beta‐cells) were transfected with expression plasmids for ACE2, ADAM17, and a hydrolytically inactive E406A ADAM17 mutant. Using fluorogenic enzyme substrates, we measured shed ACE2 activity after a 24 h incubation as well as cell‐associated ACE2 and ADAM17 activities. For a wide range of ACE2 expression levels, including the ACE2 expression level observed in pancreatic islets, a 4.6‐fold increase in ADAM17 activity had the following significant effects: shed ACE2 activity was increased 2 – 2.7‐fold, cellular ACE2 activity was decreased 33‐47%, and the ratio of shed ACE2/cellular ACE2 was increased 3.4 – 4.1‐fold. Adjusting for transfection efficiency, we further determined that the cellular ACE2 activity can be described as a power function of the ADAM17 activity with exponent ‐0.29 ±0.04. We conclude that ADAM17‐mediated shedding of ACE2 has the potential to decrease cellular ACE2 levels in pancreatic beta‐cells. More studies are underway to assess the role of this mechanism in diabetes. Support: NIH: GM103424, AHA: 12EIA8030004.

A Sensitive and Robust Enzyme Kinetic Experiment Using Microplates and Fluorogenic Ester Substrates

Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein variants is determined in parallel using a microplate reader, multichannel pipets, serial dilutions, and fluorogenic ester substrates. The utility of this methodology is illustrated by the measurement of differential enzyme activity in microplate volumes in triplicate with small protein samples and low activity enzyme variants. Enzyme kinetic measurements using fluorogenic substrates are, thus, adaptable for use with student-purified enzyme variants and for comparative enzyme kinetics studies. The rapid setup and analysis of these kinetic experiments not only provides advanced undergraduates with experience in a fundamental biochemical technique, but also provide...

Synthesis of 2-arylbenzothiazole derivatives and their application in bacterial detection

A series of 2-arylbenzothiazole derivatives have been prepared as fluorogenic enzyme substrates in order to detect aminopeptidase, esterase, phosphatase and β-galactosidase activity in clinically important Gram-negative and Gram-positive bacteria. Substrates were incorporated into an agar-based culture medium and this allowed growth of intensely fluorescent bacterial colonies based on hydrolysis by specific enzymes. Substrate 20 targeted l-alanine aminopeptidase activity and was hydrolysed exclusively by a range of Gram-negative bacteria and inhibited the growth of a range of Gram-positive bacteria. Substrate 19a targeted β-alanyl aminopeptidase activity and generated fluorescent colonies of selected Gram-negative species including Pseudomonas aeruginosa. Substrate 21b targeted C8-esterase activity and resulted in strongly fluorescent colonies of selected species known to harbour such enzyme activity (e.g., Salmonella and Pseudomonas). Most Gram-negative species produced colonies with an intense blue fluorescence due to hydrolysis of phosphatase substrates 24a–c and substrate 24c was also hydrolysed by strains of Staphylococcus aureus. Compounds 26b and 26c targeted β-galactosidase activity and generated strongly fluorescent colonies with coliform bacteria that produced this enzyme (e.g., Escherichia coli).

Biocatalytic polymer thin films: optimization of the multilayered architecture towards in situ synthesis of anti-proliferative drugs

We report on the assembly of multi-layered polyelectrolyte thin films containing an immobilized enzyme to perform conversion of externally administered prodrugs and achieve delivery of the resulting therapeutics to adhering cells. Towards this goal, multi-layered coatings were assembled using poly(sodium styrene sulfonate) and poly(allylamine hydrochloride). Activity of the incorporated enzyme was quantified as a function of the assembly conditions, position of the enzyme within the multi-layered architecture, concentration of the enzyme in the adsorption solution, and concentration of the administered prodrug. Biocatalytic coatings exhibited sustained levels of enzymatic activity over at least one week of incubation in physiological buffers without signs of loss of activity of the enzyme. Developed enzyme-containing polymer films afforded zero-order release of the in situ synthesized cargo with kinetics of synthesis (nM per hour) covering at least 3 orders of magnitude. Internalization of the synthesized product by adhering cells was visualized using a fluorogenic enzyme substrate. Therapeutic utility of biocatalytic coatings was demonstrated using a myoblast cell line and a prodrug for the anti-proliferative agent, 5-fluorouridine. Taken together, this work presents a novel approach to delivery of small molecule drugs using multi-layered polymer thin films with utility in surface-mediated drug delivery, assembly of therapeutic implantable devices, and tissue engineering.

Single Molecule Enzyme Catalysis: Steps towards Accurate Kinetic Schemes

Single molecule fluorescence spectroscopy provides the unique possibility to study enzymatic reactions with single turnover resolution. using fluorogenic enzyme substrates, the time sequence of enzymatic turnovers can be followed and fluctuations in the turnover rate can be detected. To investigate the possibility of constructing kinetic schemes, we have studied the pH-dependent activity of the enzyme alpha-chymotrypsin.View Large Image | View Hi-Res Image | Download PowerPoint SlideAn accurate construction of kinetic schemes is so far limited, however, by the design of most fluorogenic substrates that carry two enzyme-cleavable bonds per fluorophore. using a typical double-substituted Rhodamine 110-based substrate, the reaction proceeds in two steps involving a mono-substituted intermediate that possesses only 30% of the quantum yield of Rhodamine 110. Despite its low brightness, we are able to specifically detect the intermediate based on its different fluorescence lifetime. At high substrate concentrations the only product formed is the intermediate and a simplified but accurate kinetic scheme can be obtained. Our results show pH-dependent activity of alpha-chymotrypsin but clearly do NOT support stretched exponential kinetics, frequently interpreted as dynamic disorder. We hypothesize that “stretched exponentials” might be data analysis artefacts occurring for low signal-to-noise data.

Advances in the chemistry of small molecule fluorescent probes

Small molecule fluorophores are essential tools for chemical biology. A benefit of synthetic dyes is the ability to employ chemical approaches to control the properties and direct the position of the fluorophore. Applying modern synthetic organic chemistry strategies enables efficient tailoring of the chemical structure to obtain probes for specific biological experiments. Chemistry can also be used to activate fluorophores; new fluorogenic enzyme substrates and photoactivatable compounds with improved properties have been prepared that facilitate advanced imaging experiments with low background fluorescence. Finally, chemical reactions in live cells can be used to direct the spatial distribution of the fluorophore, allowing labeling of defined cellular regions with synthetic dyes.