Multicommutated Flow Analysis System for Determination of Horseradish Peroxidase and Its Inhibitors.

A fully mechanized multicommutated flow analysis (MCFA) system dedicated to determining horseradish peroxidase (HRP) activity was developed. Detection was conducted using a flow-through optoelectronic detector-constructed of paired LEDs operating according to the paired emitter-detector diode (PEDD) principle. The PEDD-MCFA system is dedicated to monitoring the enzyme-catalyzed oxidation of p-phenylenediamine (pPD) by a hydrogen peroxide. Under optimized conditions, the presented bioanalytical system was characterized by a linear response range (33.47-200 U/L) with a detection limit at 10.54 U/L HRP activity and 1.66 mV·L/U sensitivity, relatively high throughput (12 signals recordings per hour), and acceptable precision (RSD below 6%). Additionally, the utility of the developed PEDD-MCFA system for the determination of HRP inhibitors allowing the detection of selected thiols at micromolar levels, is demonstrated. The practical utility of the flow system was illustrated by the analysis of some dietary supplements containing L-cysteine, N-acetylcysteine, and L-glutathione.

Inhibitors in Commercially Available 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonate) Affect Enzymatic Assays.

ABTS, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate), is a common chromogenic substrate for peroxidase enzymes, which are widely used in biochemical research and diagnostic tests. We discovered that impurities in the commercially available ABTS significantly affect the results of peroxidase activity assays. We show that the impurities inhibit the activity of the peroxidases and the influence varies for different batches of ABTS from the same source. The inhibition of horseradish peroxidase (HRP) is uncompetitive for the substrate H2O2 while it is competitive for the substrate ABTS. By using high-resolution mass spectrometry, potential inhibitors were identified to be precursors or analogs of ABTS. The inhibitors are also capable of inhibiting the GOx-catalyzed reduction of the ABTS radical cation by glucose in anaerobic conditions. As the inhibition is found to be pH-dependent, diagnostic applications, such as ELISA tests based on the peroxidase-H2O2-ABTS system, should be carried out at pH 4.4 to minimize the inhibitory effect of potentially present impurities.

Implication and Inhibition Boolean Logic Gates Mimicked with Enzyme Reactions.

The enzyme system mimicking Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates has been designed. The same enzyme system was used to operate as the IMPLY or INHIB gate simply by reformulating the input signals. The optical analysis of the logic operation confirmed the output generation as expected for the studied logic gates. The conceptual approach to the IMPLY and INHIB logic gates allows their construction with many other enzymes operating in a similar way.

DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules.

It is challenging to incorporate stereochemical diversity and topographic complexity into DNA-encoded libraries (DELs) because DEL syntheses cannot fully exploit the capabilities of modern synthetic organic chemistry. Here, we describe the design, construction, and validation of DOS-DEL-1, a library of 107 616 DNA-barcoded chiral 2,3-disubsituted azetidines and pyrrolidines. We used stereospecific C-H arylation chemistry to furnish complex scaffolds primed for DEL synthesis, and we developed an improved on-DNA Suzuki reaction to maximize library quality. We then studied both the structural diversity of the library and the physicochemical properties of individual compounds using Tanimoto multifusion similarity analysis, among other techniques. These analyses revealed not only that most DOS-DEL-1 members have "drug-like" properties, but also that the library more closely resembles compound collections derived from diversity synthesis than those from other sources (e.g., commercial vendors). Finally, we performed validation screens against horseradish peroxidase and carbonic anhydrase IX, and we developed a novel, Poisson-based statistical framework to analyze the results. A set of assay positives were successfully translated into potent carbonic anhydrase inhibitors (IC50 = 20.1-68.7 nM), which confirmed the success of the synthesis and screening procedures. These results establish a strategy to synthesize DELs with scaffold-based stereochemical diversity and complexity that does not require the development of novel DNA-compatible chemistry.

Interference of carbidopa and other catechols with reactions catalyzed by peroxidases.

BACKGROUND: A number of compounds, including ascorbic acid, catecholamines, flavonoids, p-diphenols and hydrazine derivatives have been reported to interfere with peroxidase-based medical diagnostic tests (Trinder reaction) but the mechanisms of these effects have not been fully elucidated. METHODS: Reactions of bovine myeloperoxidase with o-dianisidine, bovine lactoperoxidase with ABTS and horseradish peroxidase with 4-aminoantipyrine/phenol in the presence of carbidopa, an anti-Parkinsonian drug, and other catechols, including l-dopa, were monitored spectrophotometrically and by measuring hydrogen peroxide consumption. RESULTS: Chromophore formation in all three enzyme/substrate systems was blocked in the presence of carbidopa and other catechols. However, the rates of hydrogen peroxide consumption were not much affected. Irreversible enzyme inhibition was also insignificant. CONCLUSIONS: Tested compounds reduced the oxidation products or intermediates of model substrates thus preventing chromophore formation. This interference may affect interpretation of results of diagnostic tests in samples from patients with Parkinson's disease treated with carbidopa and l-dopa. GENERAL SIGNIFICANCE: This mechanism allows prediction of interference in peroxidase-based diagnostic tests for other compounds, including drugs and natural products.

Genetically-encoded fragment-based discovery of glycopeptide ligands for DC-SIGN.

We have employed genetically-encoded fragment-based discovery to identify novel glycopeptides with affinity for the dendritic cell receptor DC-SIGN. Starting from libraries of 108 mannose-conjugated peptides, we identified glycopeptides that exhibited up to a 650-fold increase in multivalent binding affinity for DC-SIGN, which is also preserved in cells. Monovalently, our most potent glycopeptides have a similar potency to a Man3 oligosaccharide, representing a 15-fold increase in activity compared to mannose. These compounds represent the first examples of glycopeptide ligands that target the CRD of DC-SIGN. The natural framework of glycopeptide conjugates and the simplicity of orthogonal conjugation to make these glycopeptides anticipates a promising future for development of DC-SIGN-targeting moieties.

Molecular docking and two-dimensional quantitative structure-activity relationship studies of synthetic flavonoids on horseradish peroxidase compounds (I, II, and III).

For the first time, the enzymatic inhibition activity of 13 synthetic flavonoids was assessed by quantitative structure-activity relationship (QSAR) modeling and molecular docking with the three states of the enzyme horseradish peroxidase (HRP). The results show that apigenin, quercetin, kaempferol, fisetin, tricetin, and luteolin exerted a high competitive inhibition on HRP (Ki between 0.14 and 1.74 mM) compared with other flavonoids. The QSAR model of enzymatic activity (R2 = 0.95, RMSE = 5.48) showed that Ghose-Crippen octanol-water partition coefficient (Alog P) and lowest unoccupied molecular orbital's energy (εlumo ) correlated with 0.65 and 0.17, respectively, with Ki values. According to the docking results using Molegro Virtual Docker program, all the flavonoids have shown great binding affinity towards peroxidase. Apigenin has the largest MolDock score in the three states of HRP noting an increased affinity of these flavonoids between compound I and compound II by 2.26%. However, these affinities strongly decrease between compound II and compound III by 28.43% especially for luteolin whose MolDock score decreased by 74.7%. With the results of docking, the affinities of the flavonoids tested and translated by their Ki values are much more presentative of the inhibition of the first reaction states of HRP because their inhibitory effect is important.

Structure-activity relationships and molecular docking of thirteen synthesized flavonoids as horseradish peroxidase inhibitors.

For the first time, the structure-activity relationships of thirteen synthesized flavonoids have been investigated by evaluating their ability to modulate horseradish peroxidase (HRP) catalytic activity. Indeed, a modified spectrophotometrically method was carried out and optimized using 4-methylcatechol (4-MC) as peroxidase co-substrate. The results show that these flavonoids exhibit a great capacity to inhibit peroxidase with Ki values ranged from 0.14±0.01 to 65±0.04mM. Molecular docking has been achieved using Auto Dock Vina program to discuss the nature of interactions and the mechanism of inhibition. According to the docking results, all the flavonoids have shown great binding affinity to peroxidase. These molecular modeling studies suggested that pyran-4-one cycle acts as an inhibition key for peroxidase. Therefore, potent peroxidase inhibitors are flavonoids with these structural requirements: the presence of the hydroxyl (OH) group in 7, 5 and 4' positions and the absence of the methoxy (O-CH3) group. Apigenin contributed better in HRP inhibitory activity. The present study has shown that the studied flavonoids could be promising HRP inhibitors, which can help in developing new molecules to control thyroid diseases.

Advantages of an Electrochemical Method Compared to the Spectrophotometric Kinetic Study of Peroxidase Inhibition by Boroxine Derivative.

In this study, boroxine derivative (K2[B3O3F4OH]) was tested as an inhibitor of horseradish peroxidase (HRP) by spectrophotometric and electrochemical methods. The activity of horseradish peroxidase was first studied under steady-state kinetic conditions by a spectrophotometric method which required the use of guaiacol as a second substrate to measure guaiacol peroxidation. The results of this method have shown that, by changing the concentration of guaiacol as the literature suggests, a different type of inhibition is observed than when changing the concentration of hydrogen peroxide as the substrate. This suggests that guaiacol interferes with the reaction in some way. The electrochemical method involves direct electron transfer of HRP immobilized in Nafion nanocomposite films on a glassy carbon (GC) electrode, creating a sensor with an electro-catalytic response to the reduction of hydrogen peroxide. The electrochemical method simplifies kinetic assays by removing the requirement of reducing substrates.

Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles.

Enzymatic inhibition by product molecules is an important and widespread phenomenon. We describe an approach to study product inhibition at the single-molecule level. Individual HRP molecules are trapped within surface-tethered lipid vesicles, and their reaction with a fluorogenic substrate is probed. While the substrate readily penetrates into the vesicles, the charged product (resorufin) gets trapped and accumulates inside the vesicles. Surprisingly, individual enzyme molecules are found to stall when a few tens of product molecules accumulate. Bulk enzymology experiments verify that the enzyme is noncompetitively inhibited by resorufin. The initial reaction velocity of individual enzyme molecules and the number of product molecules required for their complete inhibition are broadly distributed and dynamically disordered. The two seemingly unrelated parameters, however, are found to be substantially correlated with each other in each enzyme molecule and over long times. These results suggest that, as a way to counter disorder, enzymes have evolved the means to correlate fluctuations at structurally distinct functional sites.

Enzymatic assay for Cu(II) with horseradish peroxidase and its application in colorimetric logic gate.

We report an ultrasensitive and colorimetric assay for Cu(II) via enzymatic amplification strategy. The enzymatic activity of horseradish peroxidase (HRP) is strongly inhibited by Cu(I), which can be used indirectly to assay Cu(II). The limit of detection (LOD) is 0.37 nM, and the detection of 20 nM Cu(II) in solution can be achieved with naked eyes. This assay can be used to construct a colorimetric logic gate.

Effects of cytochrome P450 inhibitors on peroxidase activity.

OBJECTIVES: Of several enzymes metabolizing xenobiotics, cytochrome P450 (CYP) and peroxidase enzymes seem to be most important. One of the major challenges in studies investigating metabolism of xenobiotics is to resolve which of these two groups of enzymes is predominant to metabolize individual xenobiotic compounds. Utilization of selective inhibitors of CYP and peroxidase enzymes might be a useful tool to identify the contribution of these enzymes to metabolism of xenobiotics in samples, where both types of enzymes are present. The aim of this study was to investigate specificities of several known CYP inhibitors to these enzymes; whether they inhibit only the CYP enzymes and do not inhibit peroxidases. METHODS: Since the oxidation of o-anisidine catalyzed by a model peroxidase used, horseradish peroxidase (HRP), is a two-substrate reaction, the inhibition potential of tested chemicals was studied with respect to both peroxidase substrates, o-anisidine and hydrogen peroxide. Initial velocities of o-anisidine oxidation by HRP under various conditions were determined spectrophotometrically. RESULTS: The CYP inhibitors metyrapone, troleandomycine, disulfiram, sulfaphenazole, quinidine and 1-aminobenzotriazole do not inhibit o-anisidine oxidation catalyzed by HRP. In contrast, ketoconazole, diethyldithiocarbamate, ellipticine, α-naphtoflavone, proadifen SKF525A, piperonylbutoxide, were found to inhibit not only the CYPs, but also the HRP-mediated oxidation of o-anisidine. Interestingly, α-naphtoflavone inhibits oxidation of o-anisidine by HRP with respect to H2O2, but not with respect to o-anisidine. Diethyldithiocarbamate is the most potent peroxidase inhibitor of o-anisidine oxidation with Ki with respect to o-anisidine of 10 µM and Ki with respect to H2O2 of 60 µM, being even the better peroxidase inhibitor than the classical "peroxidase inhibitor" - propyl gallate (Ki with respect to o-anisidine of 60 µM and Ki with respect to H2O2 of 750 µM). CONCLUSIONS: The results of the present study demonstrate that 1-aminobenzotriazole, a potent inhibitor of various CYP enzymes, seems to be the best candidate suitable for utilization in studies evaluating participation of CYP enzymes in metabolism of xenobiotics in various complex biological materials containing both CYP and peroxidase enzymes. Moreover, precaution to prevent misinterpretation of results is necessary in cases when proadifen SKF525A, piperonylbutoxide, diethyldithiocarbamate, ketoconazole, α-naphtoflavone and ellipticine are used in similar studies (as CYP inhibitors in various complex biological materials containing both CYP and peroxidase enzymes), since these chemicals can except of CYP enzymes inhibit also peroxidase-mediated reactions.

Partial uncompetitive inhibition of horseradish peroxidase by a water-miscible ionic liquid [BMIM][MeSO4].

The ionic liquid, 1-butyl-3-methylimidazolium methylsulfate ([BMIM][MeSO(4)]), was used to investigate the catalytic mechanism of horseradish peroxidase (HRP). The ionic liquid decreased both K(m) and k(cat) values for the HRP-catalyzed oxidation of guaiacol (2-methoxyphenol) by H(2)O(2). These studies imply that [BMIM][MeSO(4)] inhibits the enzyme in an uncompetitive manner. The incorporation of substrate stabilization effects measured by a thermodynamic method into the partial uncompetitive inhibition scheme successfully describes HRP-catalysis in the presence of [BMIM][MeSO(4)], which participates as the inhibitor. The inhibition constant of the ionic liquid was 0.051 M. The turn-over number of the native HRP was almost 14-times higher than that of the HRP-ionic liquid complex indicating that [BMIM][MeSO(4)] does not form a dead-end complex with HRP.

The inhibition mechanism of luteolin on peroxidase based on multispectroscopic techniques.

Luteolin, a plant-derived flavonoid, was found to exert effective inhibitory effect to peroxidase activity in a non-competitive manner with an IC50 of (6.62 ± 0.45) × 10-5 mol L-1. The interaction between luteolin and peroxidase induced the formation of a static complex with a binding constant (Ksv) of 7.31 × 103 L mol-1 s-1 driven by hydrogen bond and hydrophobic interaction. Further, the molecular interaction between luteolin and peroxidase resulted in intrinsic fluorescence quenching, structural and conformational alternations which were determined by multispectroscopic techniques combined with computational molecular docking. Molecular docking results revealed that luteolin bound to peroxidase and interacted with relevant amino acid residues in the hydrophobic pocket. These results will provide information for screening additional peroxidase inhibitors and provide evidence of luteolin's potential application in preservation and processing of fruit and vegetables and clinical disease remedy.

Hydroxyapatite nanoarray-based cyanide biosensor.

Here we report a simple, biomolecular-friendly protocol for the fabrication of a hydroxyapatite nanowires array (HANWA) biosensor of spatial positioning, large surface area, and abundant adsorbing sites and its application to cyanide sensing. The fabrication of HANWA is performed by template-assisted electrodeposition. The well-aligned hydroxyapatite nanoarray is composed of vertical nanowires with a diameter of approximately 200 nm and an average length of 1 microm. The electrochemical biosensor for the determination of cyanide through its inhibitory effect on horseradish peroxidase (HRP) encapsulated by chitosan (CHIT) on the platform of HANWA is demonstrated. The current organic-inorganic hybrid nanostructure provides excellent enzyme-substrate contact with enzyme activity well maintained. The densely distributed HANWA with large surface area and abundant adsorbing sites can provide a favorable electrochemical interface for the construction of electrochemical biosensor. A sensitive detection limit of 0.6 ng ml(-1) was obtained for cyanide. The proposed CHIT-HRP/HANWA biosensor has the advantages of spatial resolution, high sensitivity, rapid regeneration, and fast response associated with individual nanowires. It broadens the possible applications of chemosensors and biosensors, and it offers an alternative method for toxic substance determination. The new device holds great promise for environmental and food industrial monitoring of toxins.

Amperometric determination of heavy metal using an HRP inhibition biosensor based on ITO nanoparticles-ruthenium (III) hexamine trichloride composite: Central composite design optimization.

A novel horseradish peroxidase (HRP) enzyme inhibition biosensor based on indium tin oxide (ITO) nanoparticles, hexaammineruthenium (III) chloride (RUT), and chitosan (CH) modified glassy carbon electrode (GCE) was developed. The biosensor fabrication process was investigated using scanning electron microscopy, energy-dispersive X-ray spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The amounts of ITO nanoparticles and RUT were optimized using a 22 central composite design for the optimization of electrode composition. The detection limits were determined as 8 nM, 3 nM, and 1 nM for Pb2+, Ni2+, and Cd2+, respectively. The inhibition calibration curves of the biosensor were found to be within the range of 0.009-0.301 µM with a sensitivity of 11.97 µA µM-1 cm-2 (0.85 µA µM-1) for Pb2+, 0.011-0.368 µM with a sensitivity of 10.84 µA µM-1 cm-2 (0.77 µA µM-1) for Ni2+, and 0.008-0.372 µM with a sensitivity of 10.99 µA µM-1 cm-2 (0.78 µA µM-1) for Cd2+. The type of HRP inhibition by Pb2+, Ni2+ and Cd2+ was investigated by the Dixon and Cornish-Bowden plots. The effects of possible interfering species on the biosensor response were examined. The analysis of Pb2+, Ni2+, and Cd2+ in tap water was demonstrated using the HRP/ITO-RUT-CH/GCE with satisfactory experimental results. The proposed method agreed with the atomic absorption spectrometry results.

Tuning of peroxidase activity by covalently tethered DNA oligonucleotides.

We report on the modulation of the peroxidase activity of hybrid catalysts, comprising short DNA oligonucleotides and heme enzymes by means of sequence variation of tethered oligonucleotides. In particular, binary mixtures of native heme (protophorphyrin IX) and single-stranded DNA oligonucleotides as well as the analogous covalent heme-oligonucleotide conjugates were compared with DNA-enzyme conjugates, prepared by reconstitution of apo-myoglobin or apo-horseradisch peroxidase, using the aforementioned covalent heme-oligonucleotide conjugates. In all systems, it was clearly evident that the implemented oligonucleotides markedly influence the catalytic activity in a sequence-dependent matter. Greater than 100-fold changes in catalytic constants were observed, depending on which oligonucleotide was incorporated in the hybrid catalyst. We also observed that the tethered oligomers affect the inhibition of HRP-mediated peroxidation by means of small molecule inhibitors. On the basis of the quantitative description of this phenomenon and consideration of the current state of knowledge, we hypothesize that distinct interactions, such as hydrogen bonding or electrostatic contacts, occur between the oligonucleotides and the heme-containing catalyst, which account for the effects observed.

Alleviated Inhibition of Single Enzyme in Confined and Crowded Environment.

Most proteins perform functions in intracellular milieu. The crowding, compartmentalized cytosol environment affects the protein structure, folding, conformational stability, substrate diffusion, and substrate-enzyme binding. Moreover, enzymes are available at single or very low copy numbers in a cell, and thus the conformation fluctuations of a single enzyme in a crowding environment could also greatly influence its kinetics. However, the crowding effect is poorly understood in the kinetical aspect of enzymatic reactions. In the present study, individual horseradish peroxidase (HRP) is encapsulated in a liposome containing crowding reagents as mimics of viscous cytosol. The confined crowding environment possesses a profound influence on both the catalytic activity and the product inhibition of enzymes. By analyzing the correlation between product generation and product inhibition, we find that the allosteric noncompetitive inhibition of HRP is alleviated in the crowded and confined milieu. Small-angle X-ray scattering experiments provide straightforward proofs of structural changes of enzymes in crowding environments, which are responsible for the reduced enzyme activity and increased enzyme-substrate affinity. We expect that this work may deepen the understanding of correlations between enzymatic conformations and activity performance in real cellular environments.

Condensed and hydrolysable tannins as antioxidants influencing the health.

Natural polyphenols are a wide class of secondary plant metabolites and represent an abundant antioxidant component of human diet. An important, but often neglected group of natural polyphenols, are tannins. This review offers a general description of chemistry of both hydrolysable and condensed tannins (proanthocyanidins), the mechanisms of their antioxidation action, like free radical scavenging activity, chelation of transition metals, inhibition of prooxidative enzymes and lipid peroxidation. The mechanisms of action of antibacterial, antiviral, anticarcinogenic, cardiovascular system preventing, and antiinflammatory effects as well as the absorption, metabolic fate and positive in vivo effects of tannins are enclosed.

Activation and inactivation of horseradish peroxidase by cobalt ions.

The effect of cobalt ions (Co2+) on horseradish peroxidase (HRP) was studied in vitro by enzymatic activity assay, electronic absorption spectra, intrinsic fluorescence spectra and 8-anilo-1-naphthalenesulfonate(ANS)-binding fluorescence spectra. Co2+ at concentrations below 0.1 mM mildly increased the HRP activity, whereas higher concentrations of Co2+ significantly inactivated HRP in a time and concentration-dependent manner. Steady-state kinetic studies show that Co2+ was a noncompetitive inhibitor of o-dianisidine oxidation by HRP. The Ki value dropped as the incubation time increased. Furthermore, Co2+ was found to be an uncompetitive inhibitor of H2O2. These results suggested that Co2+ would slowly bind to the enzyme and progressively induce conformational changes. Spectroscopic analysis showed that even for high Co2+ concentrations, the structure of HRP as a whole only changed slightly; however, there were significant conformational changes near or in the active site of HRP. Based on the above results, we suggest that Co2+ may bind with some amino acids near or in the active site of HRP and the conformational changes of HRP induced by such binding should be the main reason for activation and inactivation effect of Co2+. The potential binding sites of Co2+ were also proposed.