Low background FRET-substrates for lipases and esterases suitable for high-throughput screening under basic (pH 11) conditions

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

Supramolecular Assembly with Aggregation-Induced Emission Property for Sensing and Detection

The fabrication of new supramolecular materials for real-time detection of analytes including ions, organic pollutants, gases, biomolecules, and drugs is of pivotal importance in industrial manufacture, clinical treatment, and environmental remediation. Incorporating fluorescent molecules with distinct aggregation-induced emission (AIE) effects into supramolecular assemblies has received much attention over the past two decades, owing to the remarkable performance of the AIE-active supramolecular materials in sensing and detection. In this minireview, we summarize the recent progress of superior detection systems on the basis of supramolecular assemblies accompanied with AIE features. We envision that this minireview will be helpful and timely for relevant researchers to stimulate new thinking for constructing new AIE-based supramolecular materials with advanced architectures for effective sensing and detection.

Profluorescent substrates for the screening of olefin metathesis catalysts

Herein we report on a 96-well plate assay based on the fluorescence resulting from the ring-closing metathesis of two profluorophoric substrates. To demonstrate the validity of the approach, four commercially available ruthenium-metathesis catalysts were evaluated in six different solvents. The results from the fluorescent assay agree well with HPLC conversions, validating the usefulness of the approach.

Synthesis of phospholipids on a glyceric acid scaffold: design and preparation of phospholipase A2 specific substrates

Synthesis of a new series of phospholipid analogues to serve as activity-based probes of secretory phospholipase A₂ enzymes is reported. The synthesis is based upon 1) preparation of long-chain esters and amides of glyceric acid, followed by 2) regioselective derivatization of the diol function of the molecule to achieve phosphorylation at the primary hydroxyl group, and to introduce the incipient sn-2-ester group of the target compounds. The sequence has been shown to allow incorporation of fluorescent, paramagnetic, and redox-active reporter groups, leading to phospholipid analogues applicable to detect and measure enzyme activity, to develop highly specific, real-time spectroscopic assay of phospholipase A₂ enzymes, as well as to track the metabolic fate of the hydrolysis products. The synthetic method has a great deal of flexibility to open the way to the design and synthesis of activity-probes for other phospholipid metabolizing enzymes as well.

A fluorescent light-up probe with “AIE + ESIPT” characteristics for specific detection of lysosomal esterase

Fluorescent light-up probe with “AIE + ESIPT” characteristics for specific detection of lysosomal esterase.

Assay and inhibition of diacylglycerol lipase activity

A series of N-formyl-α-amino acid esters of β-lactone derivatives structurally related to tetrahydrolipstatin (THL) and O-3841 were synthesized that inhibit human and murine diacylglycerol lipase (DAGL) activities. New ether lipid reporter compounds were developed for an in vitro assay to efficiently screen inhibitors of 1,2-diacyl-sn-glycerol hydrolysis and related lipase activities using fluorescence resonance energy transfer (FRET). A standardized thin layer chromatography (TLC) radioassay of diacylglycerol lipase activity utilizing the labeled endogenous substrate [1″-(14)C]1-stearoyl-2-arachidonoyl-sn-glycerol with phosphorimaging detection was used to quantify inhibition by following formation of the initial product [1″-(14)C]2-arachidonoylglycerol and further hydrolysis under the assay conditions to [1-(14)C]arachidonic acid.

Activatable Optical Probes for the Detection of Enzymes

The early detection of many human diseases is crucial if they are to be treated successfully. Therefore, the development of imaging techniques that can facilitate early detection of disease is of high importance. Changes in the levels of enzyme expression are known to occur in many diseases, making their accurate detection at low concentrations an area of considerable active research. Activatable fluorescent probes show immense promise in this area. If properly designed they should exhibit no signal until they interact with their target enzyme, reducing the level of background fluorescence and potentially endowing them with greater sensitivity. The mechanisms of fluorescence changes in activatable probes vary. This review aims to survey the field of activatable probes, focusing on their mechanisms of action as well as illustrating some of the in vitro and in vivo settings in which they have been employed.

Förster resonance energy transfer methods for quantification of protein-protein interactions on microarrays

Methods based on Förster (or fluorescence) resonance energy transfer (FRET) are widely used in various areas of bioanalysis and molecular biology, such as fluorescence microscopy, quantitative real-time polymerase chain reaction (PCR), immunoassays, or enzyme activity assays, just to name a few. In the last years, these techniques were successfully implemented to multiplex biomolecular screening on microarrays. In this review, some fundamental considerations and practical approaches are outlined and it is demonstrated how this very sensitive (and distance-dependent) method can be utilized for microarray-based high-throughput screening (HTS) with a focus on protein microarrays. The advantages and also the demands of this dual-label technique in miniaturized multiplexed formats are discussed with respect to its potential readout modes, such as intensity, dual wavelength, and time-resolved FRET detection.

DNA-polyfluorophore excimers as sensitive reporters for esterases and lipases

DNA-scaffolded oligodeoxyriboside fluorophores (ODFs) were used as the reporters in turn-on sensing of enzymatic bond-cleaving activity. A tetramer ODF of pyrene deoxynucleosides displayed high quenching efficiency when conjugated via ester linkages with a dabcyl quencher, and yielded large signal increases with several enzymes in vitro and in intact human cells.

Enzyme assays

Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.

Luminescent lanthanide complexes as probes for the determination of enzyme activities

The determination of enzyme activities and the screening of enzyme regulators is a major task in clinical chemistry and the development of new drugs. A broad variety of enzymatic reactions is associated with the consumption or formation of small molecules like H(2)O(2), ATP, pyrophosphate, or phosphate. Luminescent lanthanide complexes can be applied to monitor these enzymatic conversions and therefore can serve as probes for the determination of enzyme activities. The utility of this concept will be demonstrated by means of some selected examples including europium and terbium complexes. Accordingly, this new approach could be already implemented for the determination of glucose oxidase, catalase, and peroxidase activity. In particular, enzymes that catalyze phosphorylation or dephosphorylation reactions came to the fore of interest because of their high relevance as drug targets. These include (protein) kinases, adenylyl cyclases, phosphodiesterases, phosphatases, and ATPases. The development and design of fluorescent lanthanide complexes should lead to probes with optimized selectivity and response times that can be applied for high-throughput screening of enzyme inhibitors and for real-time monitoring of enzyme kinetics. In contrast to other assays for enzyme activity determination, this method does not require the use of radioactively labelled substrates or the accomplishment of rather complex and expensive immunoassays.

Fluorogenic substrates for lipases, esterases, and acylases using a TIM-mechanism for signal release

3-Acyloxyl-2-oxopropyl ethers of umbelliferone were investigated as new fluorogenic substrates for lipases and esterases. The aliphatic primary alcohol-leaving group released the fluorescent product umbelliferone by an enolization/beta-elimination reaction similar to the triose phosphate isomerase (TIM) reaction. A similarly designed phenylacetamide provided a fluorescent probe for penicillin G acylase, whereby the enolization/beta-elimination sequence from the intermediate aminoketone was very fast and spontaneous even under acidic conditions. The corresponding epoxyketone was not fluorogenic with epoxide hydrolases (EH). These substrates represent periodate-free Clips-otrade mark substrates.

Recent progress in engineering alpha/beta hydrolase-fold family members

The members of the alpha/beta hydrolase-fold family represent a functionally versatile group of enzymes with many important applications in biocatalysis. Given the technical significance of alpha/beta hydrolases in processes ranging from the kinetic resolution of enantiomeric precursors for pharmaceutical compounds to bulk products such as laundry detergent, optimizing and tailoring enzymes for these applications presents an ongoing challenge to chemists, biochemists, and engineers alike. A review of the recent literature on alpha/beta hydrolase engineering suggests that the early successes of "random processes" such as directed evolution are now being slowly replaced by more hypothesis-driven, focused library approaches. These developments reflect a better understanding of the enzymes' structure-function relationship and improved computational resources, which allow for more sophisticated search and prediction algorithms, as well as, in a very practical sense, the realization that bigger is not always better.

A red-fluorescent substrate microarray for lipase fingerprinting

A lipase substrate microarray was obtained by printing aliphatic C2-C12 monoesters of (5R)- and (5S)-3-(5,6-dihydroxyhexyloxy)benzaldehyde by reductive alkylation on amine-functionalized glass slides coated with bovine serum albumin and a short PEG linker. The microarray features 12 substrates and their 66 possible binary mixtures spotted in a 9 x 36 spot array. Lipase reactions are detected by chemoselective NaIO(4)-oxidation of the 1,2-diol hydrolysis product to form an aldehyde, which is then tagged with the red-fluorescent dye rhodamine B sulfohydrazide . Specific fingerprints are produced by active enzymes. These experiments provide the first example of lipase fingerprinting using microarrays.