An Enzyme Assay Using pM

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

Enzyme assays with supramolecular chemosensors - the label-free approach

Enzyme activity measurements are essential for many research areas, e.g., for the identification of inhibitors in drug discovery, in bioengineering of enzyme mutants for biotechnological applications, or in bioanalytical chemistry as parts of biosensors. In particular in high-throughput screening (HTS), sensitive optical detection is most preferred and numerous absorption and fluorescence spectroscopy-based enzyme assays have been developed, which most frequently require time-consuming fluorescent labelling that may interfere with biological recognition. The use of supramolecular chemosensors, which can specifically signal analytes with fluorescence-based read-out methods, affords an attractive and label-free alternative to more established enzyme assays. We provide herein a comprehensive review that summarizes the current state-of-the-art of supramolecular enzyme assays ranging from early examples with covalent chemosensors to the most recent applications of supramolecular tandem enzyme assays, which utilize common and often commercially available combinations of macrocyclic host molecules (e.g. cyclodextrins, calixarenes, and cucurbiturils) and fluorescent dyes as self-assembled reporter pairs for assaying enzyme activity.

Ready-to-Use Colorimetric Platform for Versatile Enzyme Assays through Copper Ion-Mediated Catalysis

A low cost and versatile colorimetric platform is developed for selective detections of various enzymes. Similar to peroxidases, free copper ion catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H₂O₂ and turns TMB into a blue product. Bindings from ligands toward copper ions inhibit this catalysis. Enzymes catalyze the reactions of related substrates with generation or consumption the ligands for the binding and thus in turn alter the color changes as responses toward the enzymes. With suitable substrates, exemplary enzymes, including trypsin, acid phosphatase, and tyrosinase, can be sensitively measured, with limits of detection of 0.003 μg/mL, 0.004 U/L, and 0.02 U/mL, respectively. This platform is built with directly available reagents, and the signals can be obtained with inexpensive photometers or visual observations. The low cost and convenience make it suitable for cases where complicated instrumentations are not available, such as point-of-care testing.

A new strategy for calibrating indicator displacement assay (IDA)-based sensor systems

A novel strategy for calibrating Indicator Displacement Assay (IDA)-based sensors is presented herein. The main idea is to replace the instrumental measurement responses by the equilibrium concentration of spectroscopically active species which can be obtained by the Classical Least Squares (CLS) method. Also, coupling the Indirect Hard Modelling (IHM) and CLS methods for the calibration model resulted in a reduction of matrix effects. According to Beer's law, the measured multivariate spectrum of a mixture is the sum of contributions of all spectroscopically active components via their concentrations and pure spectra. Concentrations of a few components are usually the fundamental variables in a measured spectrum in several sensors or wavelengths. In IDA systems, the equilibrium concentrations of indicator and indicator-receptor species are the fundamental variables that can be an alternative for instrumental responses as the input data for regression methods. These fundamental variables can be exploited from the recorded spectra of the mixtures when the pure spectra of the active species are known. Using dramatically reduced number of input variables without the need for any variable selection method is the main advantage of this idea over conventional calibration methods that use variable selected spectroscopic signals. This strategy can be applied for systems in which the active species are known. Accordingly, for IDA-based sensors with determined pure response to indicator and indicator-receptor complex, the free concentrations of active species can be resolved by the Classical Least Squares (CLS) method. The pure analytical responses are altered in mixtures due to the intermolecular interactions caused by matrix effect in real experimental dataset. So, the free concentrations of spectroscopically active species are not resolved correctly by the CLS method. To tackle the issue of nonlinearity of data due to the matrix effect, the Indirect Hard Modelling (IHM) can be applied to correctly resolve the fundamental variables. The applicability of the presented idea is successfully validated by simulated and real sensor array systems.

Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications

Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.

Sonication-induced molecular gels based on mono-cholesterol substituted quinacridone derivatives

A series of monocholesterol substituted quinacridone derivatives MCC(n) (n = 4, 6, 8) has been designed and synthesized. Compounds MCC(6) and MCC(8) can gelate a wide range of organic solvents upon ultrasound irradiation and afford intriguing well-defined nanostructures composed of three-dimensional sponge-like superstructures or fibrous networks. Interestingly, the gel produced from MCC(6) is sensitive to thermo-, aniline, and formic acid stimulus, giving obviously different aggregation behaviors as well as physical properties. Time-dependent spectroscopic data and theoretical calculation results provided explanation for the possible molecular aggregation mode during the formation of the gels.

Screening systems

Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.

A screening system for active and enantioselective amidase based on its acyl transfer activity

A novel enantioselective amidase screening system was developed and proved to be efficient and accurate. This screening system employed acyl transfer activity of amidase in the presence of hydroxylamine, leading to the formation of hydroxamic acids, followed by spectrophotometric quantification of hydroxamic acid/iron(III) complexes. The enantioselectivities of amidase were evaluated by employing (R, S)-2, 2-dimethyl cyclopropanecarboxamide (1), (S)-2, 2-dimethyl cyclopropanecarboxamide and their mixture as substrates concurrently under the same conditions. To prove the accuracy of the screening system, enantioselectivity of acyl transfer reaction (E (T)) and that of hydrolytic reaction (E (H)) was compared. With this method, we obtained eight microorganism strains with enantioselective amidase from 523 isolates, two of which showed R-stereospecific avtivity for (R, S)-1.

A turn-on fluorescent indicator for citrate with micromolar sensitivity

A turn-on fluorescent indicator for citric acid (citrate) has been developed, displaying high emission enhancement (+1500%) and low interference by other carboxylates. The sensor is based on the non-emissive copper(II) complex of a fluorescent amino amide, which, upon addition of citrate decomplexates to yield the emissive ligand. The detection limit estimated for this new chemosensing system is about 0.5 microM. This novel approach to the analysis of citrate constitutes an alternative ca. 10(2)-10(3) times more sensitive than the standard method based on the enzyme citrate lyase.

Cp*Rh-Based Indicator-Displacement Assays for the Identification of Amino Sugars and Aminoglycosides

Indicator-displacement assays based on the organometallic complex [{Cp*RhCl2}2] (Cp*=pentamethylcyclopentadienyl) and the dye gallocyanine were used to sense amino sugars and aminoglycosides in buffered aqueous solution by conducting UV-visible spectroscopy. The data of three assays at pH 7.0, 8.0, and 9.0 were sufficient to distinguish between the amino sugars galactosamine, glucosamine, mannosamine and the aminoglycosides kanamycin A, kanamycin B, amikacin, apramycin, paromomycin, and streptomycin. Furthermore, the assays were used to characterize mixtures of aminoglycosides and obtain quantitative information about the respective analytes.

Self-Assembled Fluorescent Chemosensors

Self-assembling and self-organizing methodologies are powerful tools for the "bottom-up" approach for the realization of complex structure with functional properties. Recently, this concept has been extended to the design of fluorescent chemosensors providing new exciting potentialities for the development of innovative sensing systems. This Concept Article deals mainly with this new approach and discusses its evolution, applications, and limitations.

A High-Throughput, Low-Volume Enzyme Assay on Solid Support

A high-throughput enzyme assay is described that uses 1 microL or less of enzyme solution for each test. Enzyme solutions are deposited by robotic handling in a throughput of over 1000 tests/h on the surface of silica gel plates that have been preimpregnated with fluorogenic substrates. The reaction is quantitated by fluorescence. The method is compatible with water-insoluble substrates (lipases), water-soluble substrates (glycosidases), whole-protein substrates (proteases), and enzyme inhibition measurements. Hydrolytically labile umbelliferyl esters can be used to assay lipases in this format without background hydrolysis. High throughput and reproducibility were tested by fingerprint analysis of lipases and esterases against 37 different fluorogenic ester substrates. A set of eight fluorogenic unbelliferyl esters was selected for optimal activity screening of lipases and esterases on silica gel plates.

Recent advances in enzyme assays

Enzyme assays for high-throughput screening and enzyme engineering, which are often based on derivatives of coumarin, nitrophenol, fluorescein, nitrobenzofurazane or rhodamine dyes, can be divided into two categories: those that depend on labelled substrates, and those that depend on sensing the reactions of unmodified substrates. Labelled substrates include, for example, fluorogenic and chromogenic substrates that generate a reporter molecule by beta-elimination, fluorescence resonance energy transfer (FRET) substrates and isotopic labels for enantioselectivity screening. By contrast, endpoint sensing can be done using amine reagents, fluorescent affinity labels for phosphorylated proteins, or synthetic multifunctional pores. Sensing assays can also be done in real time by using, for example, aldehyde trapping to follow vinyl ester acylation in organic solvent or calcein-copper fluorescence for sensing amino acids. The current trend is to assemble many such assays in parallel for enzyme profiling and enzyme fingerprinting.

Synthesis of Ether Oligomers

[structure: see text] Hydroxyaromatic aldehydes and ketones were used as building blocks to prepare ether oligomers. An iterative two-step protocol involving Mitsunobu coupling and carbonyl reduction provided a protecting-group-free route with high yields. Activity screening of an 84-member library against proteases led to the discovery of micromolar inhibitors for trypsin, chymotrypsin, and subtilisin.

Iterative Oxime Bond Chemistry Leads to Protease Inhibitors

[structure: see text] In the present paper, we have looked at iterative coupling as a strategy to form new druglike molecules. We have developed an iterative coupling chemistry based on oxime bond formation between hydroxyaromatic aldehyde building blocks to form linear oxime oligomers. The strategy is validated by the discovery of micromolar protease inhibitors.

A green fluorescent chemosensor for amino acids provides a versatile high-throughput screening (HTS) assay for proteases

The water soluble fluorescein-based ligand 1 forms a non-fluorescent complex with Cu(2+). This complex serves as a fluorescent sensor for amino acids in the 10(-3) M concentration range. Since the signal response is very fast, the sensor can be used to detect the hydrolytic activity of various proteases (trypsin, chymotrypsin, subtilisin) on bovine serum albumin as a whole protein substrate, and more generally to follow reactions releasing or removing free amino acids, in real time.

The use of enzyme immunoassays for the detection of abzymatic activities. Application to an enantioselective thioacetal hydrolysis activity

Relying on the particularly high specificity displayed by antibodies, enzyme immunoassays have proved to be one of the most efficient tools for early detection of the catalytic activities displayed by antibodies. We took advantage of such an assay, namely the Cat-enzyme-linked immunoassay (EIA) approach developed in our laboratories, both to exhibit and characterise an antibody-catalysed thioacetal hydrolysis. Monoclonal antibody (mAb) H3-32 was thus identified to accelerate the hydrolysis reaction of thioacetal substrate (NC9) to vanillylmandelic acid (VMA), with a k(cat) of 0.148 h(-1) (k(uncat) = 6.85 x 10(-5) h(-1)), and a K(M) of 720 microM. Taking advantage of the enantiomeric discrimination between (R)- and (S)-VMA displayed by some of the anti-H3 monoclonal antibodies, we were also able to determine that (S)-VMA was preferentially formed during this abzymatic hydrolysis with a 47% enantiomeric excess. All these EIA measurements were confirmed through HPLC analyses.

Immunologically driven chemical engineering of antibodies for catalytic activity

We describe a new strategy for the preparation of catalytic antibodies based on a two-step procedure. Firstly, monoclonal antibodies are selected only if displaying the following binding features: binding both the substrate and a reactive group in such a way that the two groups are in a reactive position towards each other. Secondly, the selected monoclonal antibodies (mAbs) are chemically engineered by covalently binding the reactive group into the binding pocket of the antibody. Using previously isolated monoclonal antibodies, we have focused our studies on the control of this second step.

High-throughput screening for biocatalysts

Recent progress in high-throughput enzyme assays includes new examples of fluorogenic and chromogenic substrates, fluorescence resonance energy transfer substrates, and applications of the pH and pM indicator methods. Recent developments of Horeau's pseudo-enantiomer derivatisation method to screen enantioselectivities in high-throughput have also been reported.