Prediction of cytochrome P450 3A4, 2D6, and 2C9 inhibitors and substrates by using support vector machines

Statistical learning methods have been used in developing filters for predicting inhibitors of two P450 isoenzymes, CYP3A4 and CYP2D6. This work explores the use of different statistical learning methods for predicting inhibitors of these enzymes and an additional P450 enzyme, CYP2C9, and the substrates of the three P450 isoenzymes. Two consensus support vector machine (CSVM) methods, "positive majority" (PM-CSVM) and "positive probability" (PP-CSVM), were used in this work. These methods were first tested for the prediction of inhibitors of CYP3A4 and CYP2D6 by using a significantly higher number of inhibitors and noninhibitors than that used in earlier studies. They were then applied to the prediction of inhibitors of CYP2C9 and substrates of the three enzymes. Both methods predict inhibitors of CYP3A4 and CYP2D6 at a similar level of accuracy as those of earlier studies. For classification of inhibitors of CYP2C9, the best CSVM method gives an accuracy of 88.9% for inhibitors and 96.3% for noninhibitors. The accuracies for classification of substrates and nonsubstrates of CYP3A4, CYP2D6, and CYP2C9 are 98.2 and 90.9%, 96.6 and 94.4%, and 85.7 and 98.8%, respectively. Both CSVM methods are potentially useful as filters for predicting inhibitors and substrates of P450 isoenzymes. These methods generally give better accuracies than single SVM classification systems, and the performance of the PP-CSVM method is slightly better than that of the PM-CSVM method.     

毛细管电泳序列分析技术用于在线酶分析研究进展

毛细管电泳技术具有操作简单、样品消耗量少、分离效率高和分析速度快等优势,不仅是一种高效的分离分析技术,而且已经发展成为在线酶分析和酶抑制研究的强有力工具。酶反应全程的实时在线监测,可以实现酶反应动力学过程的高时间分辨精确检测,以更准确地获得反应机制和反应速率常数,有助于更好地了解酶反应机制,从而更全面深入地认识酶在生物代谢中的功能。此外,准确、快速的在线酶抑制剂高通量筛选方法的发展,对加快酶抑制类药物的研发以及疾病的临床诊断亦具有重要意义。电泳媒介微分析法（EMMA）和固定化酶微反应器（IMER）是毛细管电泳酶分析技术中常用的在线分析方法。这两种在线酶分析法的进样方式通常为流体动力学进样和电动进样,无法实现酶反应过程中的无干扰序列进样分析。近年来,基于快速序列进样的毛细管电泳序列分析技术已经发展成为在线酶分析的另一种强有力手段,以实现高时间分辨和高通量的酶分析在线检测。该文从快速序列进样的角度,综述了近年来毛细管电泳序列分析技术在线酶分析的研究进展,并着重介绍了各种序列进样方法及其在酶反应和酶抑制反应中的应用,包括光快门进样、流动门进样、毛细管对接的二维扩散进样、流动注射进样、液滴微流控进样等。     

Recent advances in activity-based probes (ABPs) and affinity-based probes (AfBPs) for profiling of enzymes

Activity-based protein profiling (ABPP) is a technique that uses highly selective active-site targeted chemical probes to label and monitor the state of proteins. ABPP integrates the strengths of both chemical and biological disciplines. By utilizing chemically synthesized or modified bioactive molecules, ABPP is able to reveal complex physiological and pathological enzyme–substrate interactions at molecular and cellular levels. It is also able to provide critical information of the catalytic activity changes of enzymes, annotate new functions of enzymes, discover new substrates of enzymes, and allow real-time monitoring of the cellular location of enzymes. Based on the mechanism of probe-enzyme interaction, two types of probes that have been used in ABPP are activity-based probes (ABPs) and affinity-based probes (AfBPs). This review highlights the recent advances in the use of ABPs and AfBPs, and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.

This review highlights the recent advances in the use of activity-based probes (ABPs) and affinity-based probes (AfBPs), and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.     

Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on α-1,6 Mannanases

There is a vast genomic resource for enzymes active on carbohydrates. Lagging far behind, however, are functional chemical tools for the rapid characterization of carbohydrate-active enzymes. Activity-based probes (ABPs) offer one chemical solution to these issues with ABPs based upon cyclophellitol epoxide and aziridine covalent and irreversible inhibitors representing a potent and widespread approach. Such inhibitors for enzymes active on polysaccharides are potentially limited by the requirement for several glycosidic bonds, themselves substrates for the enzyme targets. Here, it is shown that non-hydrolysable trisaccharide can be synthesized and applied even to enzymes with challenging subsite requirements. It was found that incorporation of carbasugar moieties, which was accomplished by cuprate-assisted regioselective trans-diaxial epoxide opening of carba-mannal synthesised for this purpose, yields inactivators that act as powerful activity-based inhibitors for α-1,6 endo-mannanases. 3-D structures at 1.35–1.47 Å resolutions confirm the design rationale and binding to the enzymatic nucleophile. Carbasugar oligosaccharide cyclophellitols offer a powerful new approach for the design of robust endoglycosidase inhibitors, while the synthesis procedures presented here should allow adaptation towards activity-based endoglycosidase probes as well as configurational isosteres targeting other endoglycosidase families.     

Enzymatic methods of analysis: Novel approaches and applications

The results of a series of investigations dealing with the development of enzymatic methods for determination of biologically active compounds, viz., inhibitors, activators, and substrates of native and immobilized enzymes of the oxidoreductase (peroxidases, alcohol dehydrogenases) and hydrolase (alkaline and acid phosphatases) classes isolated from diverse sources are summarized. Novel original approaches, proposed by the authors, for improving the sensitivity, selectivity, and rapidity of the methods are discussed. Numerous examples of application of the developed enzymatic procedures for the analysis of a wide range of samples are given. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 583–597, April, 2007.     

Self-assembled all-inclusive organic-inorganic nanoparticles enable cascade reaction for the detection of glucose

Traditional colorimetric glucose biosensor generally involves complex assay procedures. Free labile enzymes and peroxidase substrates are used separately for triggering a chromogenic reaction. These limits result in inferior enzyme stability and defective enzymatic catalytic efficiency, making it hard to routinely utilize them for the direct and fast test of glucose. In this work, we provide an all-inclusive substrates/enzymes nanoparticle employed 3,3′5,5′-tetramethylbenzidine (TMB) as chromogenic substrates and glucose oxidase (GOx)/horseradish peroxidase (HRP) as signal amplifier enzymes (TMB-GH NPs) by the molecule self-assembly technique. The “all-inclusive” nanoparticles can realize the tandem colorimetric reactions, and the oxidation product of TMB (ox-TMB) exhibits a strong NIR laser-driven photothermal effect, thus allowing quantitative photothermal detection of glucose. Owing to the restriction of the molecular motion of GOx, HRP, and TMB, the distance of mass transfer between substrates was shortened largely, leading to improved catalytic activity for glucose. Overall, our strategy will simplify the analysis procedure, furthermore, these integrated nanoparticles not only display higher stability and activity than that of the free GOx/HRP system and possesses an excellent performance for colorimetric and photothermal bioassay of glucose simultaneously. We believe that this unique technique will give good inspirations to develop simple and precise methods for bioassay.     

Confirming target engagement for reversible inhibitors in vivo by kinetically tuned activity-based probes

The development of small-molecule inhibitors for perturbing enzyme function requires assays to confirm that the inhibitors interact with their enzymatic targets in vivo. Determining target engagement in vivo can be particularly challenging for poorly characterized enzymes that lack known biomarkers (e.g., endogenous substrates and products) to report on their inhibition. Here, we describe a competitive activity-based protein profiling (ABPP) method for measuring the binding of reversible inhibitors to enzymes in animal models. Key to the success of this approach is the use of activity-based probes that show tempered rates of reactivity with enzymes, such that competition for target engagement with reversible inhibitors can be measured in vivo. We apply the competitive ABPP strategy to evaluate a newly described class of piperazine amide reversible inhibitors for the serine hydrolases LYPLA1 and LYPLA2, two enzymes for which selective, in vivo active inhibitors are lacking. Competitive ABPP identified individual piperazine amides that selectively inhibit LYPLA1 or LYPLA2 in mice. In summary, competitive ABPP adapted to operate with moderately reactive probes can assess the target engagement of reversible inhibitors in animal models to facilitate the discovery of small-molecule probes for characterizing enzyme function in vivo.     

Surface analysis of corrosion inhibitor films by XPS and ToFSIMS

In recent years developments in the capabilities of techniques such as XPS and static SIMS have led to wider application of these methods for the characterisation of industrial materials. After a brief discussion of recent key developments of these techniques, this paper presents a selection of results from research work at our laboratory in the characterisation of organic film-forming corrosion inhibitors on a range of metal substrates which illustrate the nature of the information available. The inherent advantage ofsurface sensitivity and the advantages of a multi-technique approach for the evaluation of surface molecular structure from complex organic compounds is discussed. The additional benefits for analysis offered by the latest developments in technique are also demonstrated.     

Identification of selective inhibitors for the glycosyltransferase MurG via high-throughput screening

Nucleotide-glycosyltransferases (NDP-Gtfs) play key roles in a wide range of biological processes. It is difficult to probe the roles of individual glycosyltransferases or their products because, with few exceptions, selective glycosyltransferase inhibitors do not exist. Here, we investigate a high-throughput approach to identify glycosyltransferase inhibitors based on a fluorescent donor displacement assay. We have applied the screen to E. coli MurG, an enzyme that is both a potential antibiotic target and a paradigm for a large family of glycosyltransferases. We show that the compounds identified in the donor-displacement screen of MurG are selective for MurG over other enzymes that use similar or identical substrates, including structurally related enzymes. The donor displacement assay described here should be adaptable to many other NDP-Gtfs and represents a new strategy to identify selective NDP-Gtf inhibitors.     

Exploiting the versatility and selectivity of Mo enzymes with electrochemistry

This article covers recent advances in the electrochemical study of the mononuclear molybdenum enzymes. Virtually all of these enzymes catalyse a coupled 2-electron, O-atom transfer reaction on a substrate of either organic or inorganic origin. There is a remarkable commonality in structure, function and mechanism of the mononuclear Mo enzymes despite the diversity of their substrates; many that are important to environmental monitoring, food quality control and biomedical science. Mo enzymes routinely oxidise or reduce otherwise inert substrates for which there exist no rapid, simple and reliable analytical methods for their determination and as such represent a potentially rich source of proteins that may be applied in electrochemical biosensors.     

An improved total synthesis of UDP-N-acetyl-muramic acid

Biochemical testing for novel inhibitors of Mur ligases requires several commercially unavailable and structurally complex substrates. We describe a modified synthetic strategy for the total chemical synthesis of the MurC ligase substrate UDP-N-acetyl-muramic acid which includes several improvements over published methods, especially with regard to purification procedures. The synthetic strategy is applicable for the synthesis of further Mur ligase substrates.     

Coupling of enzymatic and immunoassay steps to detect E. coli: a new, highly sensitive tandem technique for the analysis of low levels of bacteria

A tandem technique for the detection of very low levels E. coli within about 2 h is demonstrated. The technique couples the widely employed microbial enzymatic detection methods with an immunoassay step. The bacterial marker enzyme, E. coli β-D-galactosidase, was used in conjunction with synthetic enzyme substrates to produce products that could be measured with a highly sensitive enzyme-labelled immunosorbent assay (ELISA). The commercially available 4-methylumbelliferyl-β-D-galactoside and a newly prepared substrate, 4-methylcoumarin-3-propionate-7-O-β-D-galactoside, were used with an ELISA for 7-hydroxy-4-methylcoumarin to demonstrate the detection of low levels of E. coli. The 2 h test indicates that a few viable bacteria cells could be detected by the tandem procedure. The end point of the test is an ELISA with colorimetric measurement step. The novel approach retains the essential features of the microbial enzymatic detection procedures and provides a highly sensitive detection system that can be used for rapid screening or quantification of viable microbial cells in water samples. The tandem test is generic for commonly employed glycosidases and other marker enzymes for which 4-methylumbillerone substrates are available.     

Can immobilized enzymes Be applicable for homogeneous reaction? A novel technique of acetylcholinesterase immobilization for assaying carbaryl pesticide

A novel technique of enzyme immobilization is developed for making the immobilized enzymes capable of further releasing for homogeneous reaction. Water-soluble poly(vinyl alcohol) was used to prepare enzyme-loaded membranes with immobilized acetylcholinesterase (AChE). When used, a piece of enzymecontaining membrane is put into the solution and dissolves quickly. The released AChE is mixed and interacts with substrates and carbaryl inhibitors. The catalytical activity and inhibition sensitivity of released enzyme are comparable to those of free AChE. The values of Michaelis constant and maximum reaction rate for released AChE are also very close to those for free AChE. The experimental conditions such as the concentrations of PVA and acetone, the time of enzymatic reaction and that of AChE inhibition by carbaryl pesticide were optimized. The relative inhibition of AChE activity increased with the carbaryl concentration ranging from 0.1 μg/L to 100 mg/L. When compared to free AChE in solution or solid powder, the prepared PVA-AChE membranes are advantageous with respect to storage and handling. The suggested technique of enzyme immobilization is suitable for the variety of applications, when the enzyme catalysed reactions allows for single-using of the active material and does not require further enzyme recovering.     

Fluorescent assays to quantitate enzymatic activities yielding as end product an aqueous-insoluble indigo-blue dye

Hydrolytic enzymes acting upon indoxyl-derivatized substrates produce a water-insoluble indigo-blue dye. The generation of indigo dye works well in nonquantitative histochemical or diagnostic assays. For quantitative analyses however, the technique is unsuited. In this paper two fluorescent methods are described that permit quantitative measurement of sialidase/neuraminidase activity toward indoxyl-derivatized N-acetyl-neuraminic acid substrates. The first method is based upon the reaction of the sialic/ N-acetyl-neuraminic acid with pyridoxamine and Zn2+ to produce a fluorescent chelate. This method is not sialic acid-specific and could be used for the quantitation of alpha-oxo acids. The optimum conditions for sialic acid fluorescent chelation are described. The second method is based upon the fluorescence of the reaction intermediates, indoxyl- and indigo-white, by arresting their conversion to nonfluorescent indigo-blue. This method is suitable for measuring any enzymatic activity toward indoxyl-derivatized substrates. Enzyme kinetics derived for influenza viral neuraminidase using the two techniques are described in this paper.     

A Direct Fluorescent Activity Assay for Glycosyltransferases Enables Convenient High-Throughput Screening: Application to O-GlcNAc Transferase

Glycosyltransferases carry out important cellular functions in species ranging from bacteria to humans. Despite their essential roles in biology, simple and robust activity assays that can be easily applied to high-throughput screening for inhibitors of these enzymes have been challenging to develop. Herein, we report a bead-based strategy to measure the group-transfer activity of glycosyltransferases sensitively using simple fluorescence measurements, without the need for coupled enzymes or secondary reactions. We validate the performance and accuracy of the assay using O-GlcNAc transferase (OGT) as a model system through detailed Michaelis–Menten kinetic analysis of various substrates and inhibitors. Optimization of this assay and application to high-throughput screening enabled screening for inhibitors of OGT, leading to a novel inhibitory scaffold. We believe this assay will prove valuable not only for the study of OGT, but also more widely as a general approach for the screening of glycosyltransferases and other group-transfer enzymes.     

Simple and rapid methods for on-site determination of radon and thoron in soil-gases for seismic studies

The determination of soil-gas anomalies especially ²²²Rn anomalies, are important to precisely locate fault traces, as well as to investigate earthquake precursors. In this paper, we have studied and compared new rapid methods for on site determinations of radon (²²²Rn), thoron (²²⁰Rn) and total radon (²²²Rn+²²⁰Rn) in soil-gas. These new techniques pump the soil-gas continuously from the soil through a simple sampling tube to the counting cell for one-minute with discarding the excess. Then, either four one-minute counting periods (5-minute technique) or nine one-minute counting intervals (10-minute technique) are followed immediately. In all the methods, conversely to Morse"s method, the first counting period (C1) was not employed for calculations. Three calculation methods for the five-minute technique, two for the ten-minute technique and a modified Morse"s method are compared with theoretical values and different real soil-gases with different radon/thoron ratios. The affect of different flow rates of soil-gases into the counting cell was also investigated. Finally, the ten-minute technique seems to be a little more accurate, but the 5-minute technique is much more suitable for seismic field studies when a much larger number of determinations are required in a short time.     

On-line-Bestimmung von Enzymen in der Bioproze?analytik unter Berücksichtigung von Probenahme und Flie?injektionstechnik

Summary The on-line determination of enzymes in biotechnical processes becomes an important factor with regard to process development and optimization. At present, most commonly enzymes are determined off-line in the laboratory after withdrawal of a separate sample. Wet chemical methods dominate in this respect, mainly because enzymes have to be measured according to the reaction schemes which are catalyzed by them. For an efficient process monitoring and control the time delay, the limited reliability and the man power needed for analysis of a large number of samples are crucial points. By using the technique of flow injection analysis (FIA) it should in general become easy to develop automatically operated enzyme determination procedures based on reaction schemes which can be used for fast and efficient process monitoring, providing the problems with the coupling of the analyzer at the bioreactor are solved. Continuous sampling in this respect plays a key role in developing on-line measuring techniques. This paper reviews the current status of on-line enzyme analysis, using flow-injection techniques. It is shown that the coupling problems can be solved by using a newly developed sampling module, which is based on membrane filtration. Some examples of on-line enzyme determinations in fermentation as well as in downstream processing illustrate the ease and reliability of the proposed concept for using FIA in connection with membrane separation.     

Synthesis and evaluation of fluorogenic substrates for phospholipase D and phospholipase C

Fluorogenic analogues of phosphatidylcholine and lysophosphatidylcholine, DDPB and lysoDDPB, were synthesized by an enzyme-assisted strategy. The analogues were evaluated as substrates for phospholipases C and D and lysophospholipase D. DDPB was cleaved by bacterial and plant phospholipase D (PLD) enzymes and represents the first direct fluorogenic substrate for real-time measurement of PLD activity. Both fluorogenic substrates have potential in screening for PLD and PC-PLC inhibitors and for monitoring spatiotemporal changes in PLD activity in cells. [structure: see text]     

Chemistry and Biochemistry of Microbial α-Glucosidase Inhibitors

α-Glucosidases are among the most important carbohydrate-splitting enzymes. They catalyze the hydrolysis of α-glucosidic linkages. Their substrates are—depending on their specificity—oligo- and polysaccharides. Microbial inhibitors of α-amylases and other mammalian intestinal carbohydrate-splitting enzymes studied during the last few years have aroused medical interest in the treatment of metabolic diseases such as diabetes. Moreover, they extend the spectrum of microbial secondary metabolites which comprises an enormous variety of structures. They also contribute considerably to a better understanding of the mechanism of action of α-glucosidases. These inhibitors belong to different classes of substances. Those studied most thoroughly are microbial α-glucosidase inhibitors which are members of a homologous series of pseudooligosaccharides of the general formula (4). They all have a core in common which is essential for their inhibitory action, a pseudodisaccharide residue consisting of an unsaturated cyclitol unit, and a 4-amino-4,6-dideoxy- glucose unit. The—in many respects—most interesting representative of this homologous series is acarbose (5), a pseudotetrasaccharide exhibiting a very pronounced inhibitory effect on intestinal α-glucosidases such as sucrase, maltase and glucoamylase. The present paper will review this new field of microbial α-glucosidase inhibitors which has been studied with particular intensity during the past ten years.     

Extending matrix‐assisted laser desorption/ionization triple quadrupole mass spectrometry enzyme screening assays to targets with small molecule substrates

Mass spectrometry (MS)‐based high‐throughput screening (HTS) has tremendous potential as an alternative to current screening methods due to its speed, sensitivity, reproducibility and label‐free readout. We recently reported that a new generation matrix‐assisted laser desorption/ionization triple quadrupole (MALDI‐QqQ) mass spectrometer is ideally suited for a variety of enzyme assays and screening protocols. However, all the targets measured to date had peptide substrates that were easily monitored by selected ion monitoring (SIM) without interference from the MALDI matrix. To further extend the application to enzymes with small molecule, non‐peptide substrates, we evaluated this method for measuring enzyme activity and inhibition of acetylcholinesterase (AChE). Due to the potential of MALDI matrix interference, multiple reaction monitoring (MRM) was investigated for selective MS/MS transitions and to accurately measure the conversion of acetylcholine into choline. Importantly, ionization, detection and MRM transition efficiency differences between the substrate and product can be overcome by pre‐balancing the MRM transitions during method development, thus allowing for a direct readout of the enzyme activity using the ratio of the substrate and product signals. Further validation of the assay showed accurate concentration‐dependent inhibition measurements of AChE with several known inhibitors. Finally, a small library of 1008 drug‐like compounds was screened at a single dose (10 µM) and the top 10 inhibitors from this primary screen were validated in a secondary screen to determine the rank order of inhibitory potency for each compound. Collectively, these data demonstrate that a MALDI‐QqQMS‐based readout platform is amenable to measuring small molecule substrates and products and offers significant advantages over current HTS methods in terms of speed, sensitivity, reproducibility and reagent costs. Copyright © 2009 John Wiley & Sons, Ltd.