Analysis of activity and inhibition of oxygen-dependent enzymes by optical respirometry on the LightCycler system

There is currently a need for a method capable of measuring the activity and inhibition of biologically relevant oxygenases in a format that enables the convenient, fast, and cost-efficient generation of dose-response information. Here we describe a low-volume luminescence-based assay for the measurement of such oxygen-dependent enzymes. The assay employs a photoluminescent oxygen-sensitive probe and glass capillary microcuvettes measured on the Roche LightCycler detection platform. Three discrete types of oxygen probe were evaluated for this application: (i) solid-state coatings, (ii) soluble macromolecular MitoXpress probe, both phosphorescent porphyrin-based, and (iii) a luminescent Ir(III)-based nanoparticle probe. Measurement parameters were optimised and subsequently applied to the analysis of three biologically relevant oxygenases, namely cytochrome P450 (CYP), monoamine oxygenase (MAO), and cyclooxygenase (COX). CYP enzymes are central players in drug detoxification while specific inhibitors of MAO and COX are important for therapeutic intervention and treatment of neurological and inflammatory diseases, respectively. To determine assay utility, oxygen consumption catalysed by all three enzyme types was measured and the effect of specific inhibitors determined. The panel included the MAO-A/B inhibitors clorgyline, toloxatone, deprenyl, and the COX-1/2 inhibitors niflumic acid, nimesulide, SC-560, ketoprofen, and phenylbutazone. IC₅₀ values were then compared with literature values. The measurement methodology described allows the low-volume analysis of biologically relevant oxygenases and displays the requisite sensitivity and throughput to facilitate routine analysis. It is also applicable to other O₂-dependent enzymes and enzymatic systems.     

Plant cytochrome P450-mediated herbicide metabolism

In the last two decades it has become apparent that enzymes of the P450 monooxygenase (P450) superfamily are responsible for the Phase I metabolism of numerous herbicides representing several classes of organic compounds. The majority of experimental evidence for P450 involvement in herbicide metabolism has been derived from in vitro studies in which the catalytic activity of plant microsomes towards herbicidal substrates was measured in the presence of various P450 inhibitors and activators. While the studies with microsomes elicited much appreciation for the pivotal roles of plant P450s in herbicide metabolism, detailed characterization of these enzymes only became possible after the isolation of genes encoding specific isoforms responsible for herbicide conversion. Several lines of evidence suggest that the development of herbicide resistance in weeds by enhanced detoxification is frequently associated with elevated levels of P450 activity. Enhanced detoxification-based herbicide resistance is particularly difficult to control, because it can involve resistance to multiple, chemically unrelated classes of herbicides. Continued research efforts are aimed at elucidating the role of P450s in the metabolic fates of herbicides in plants and the development of herbicide resistance in weeds. Recent advances made in the isolation and genetic manipulation of P450 enzymes have created new opportunities for their application in engineering herbicide tolerance and bioremediation.     

Plant Cytochrome P450 Monooxygenases

Plant systems utilize a diverse array of cytochrome P450 monooxygenases (P450s) in their biosynthetic and detoxification pathways. The classic forms of these enzymes are heme-dependent mixed function oxidases that utilize NADPH or NADH and molecular oxygen to produce functionalized organic products. The nonclassical forms are monooxygenases that either do not utilize flavoproteins for dioxygen activation or fail to incorporate molecular oxygen into their final product. Biosynthetic P450s play paramount roles in the synthesis of lignin intermediates, sterols, terpenes, flavonoids, isoflavonoids, furanocoumarins, and a variety of other secondary plant products. Other catabolic P450s metabolize toxic herbicides and insecticides into nontoxic products or, conversely, activate nontoxic substances into toxic products. Biochemical and molecular characterizations on a number of plant P450s have indicated that the relationships between these heme proteins and their substrates are at least as complex as those that exist in mammalian systems. Examples now exist of plant P450s that metabolize: a narrow range of substrates to yield different products, a single substrate to yield different products, multiple substrates to yield the same product, or a single substrate sequentially to yield discrete intermediates in the biosynthesis of a single product. Extensive divergence of catalytic site as well as noncatalytic site residues accounts for the high degree of primary structure variation in the P450 gene superfamily and the diverse array of substrates synthesized and/or detoxified by these proteins. Classic P450s still retain a highly conserved F-G-R-C-G motif in their catalytic site and conserved amino acids in their oxygen binding pocket; nonclassical P450s diverge at several of these positions. A broad range of cloning and transient expression strategies are suitable for plant P450 studies and these have allowed for the isolation and characterization of a number of P450 cDNAs and genes. Because many of these sequences have been cloned only recently, much remains to be learned about the substrate specificities of P450 reactions in plants and the mechanisms by which their genes are regulated.     

Autocatalysed oxidative modifications to 2-oxoglutarate dependent oxygenases

Ferrous iron and 2-oxoglutarate-dependent oxygenases and related enzymes catalyse a range of oxidative reactions, possibly the widest of any enzyme family. Their catalytic flexibility is proposed to be related to their nonhaem iron-binding site, which utilizes two or three protein-based ligands. A possible penalty for this flexibility is that they may be more prone to oxidative damage than the P450 oxidases, where the iron is arguably located in a more controlled environment. We review the evidence for autocatalysed oxidative modifications to 2-oxoglutarate-dependent oxygenases, including the recently reported studies on human enzymes, as well as the oxidative fragmentations observed in the case of the plant ethylene-forming enzyme (1-aminocyclopropane-1-carboxylic acid oxidase).     

Cytochrome P450 enzymes: ubiquitous "receptors" for drugs.

Most foreign compounds bind to one or more cytochrome P450 drug-metabolizing isozymes. These heme monooxygenases are most concentrated in the endoplasmic reticulum of liver cells but are present in virtually all biological membranes and in all cells. Some radioligands for known hormone receptors have been found to label, with comparable affinities, specific P450 enzymes. A characteristic feature of P450 enzymes is their broad and overlapping drug specificities, with affinity constants ranging over several orders of magnitude. Because fatty acid derivatives and steroids are endogenous substrates for the P450 enzymes, drugs may interfere with the generation of functional cellular lipids. The functional significance of high-affinity binding of drugs to the oxygenases may, on the one hand, be minimal and reflect extraneous or trivial drug-protein interactions. On the other hand, the drug-P450 union may in other cases mediate the major pharmacological response.     

Lipophilicity Relationships in Inhibitors of CYP2C9 and CYP2C19 Enzymes

Quantitative structure-activity relationships (QSARs) within a series of cytochrome P450 2C9 (CYP2C9) and cytochrome P450 2C19 (CYP2C19) inhibitors are reported. In particular, it is noted that compound lipophilicity, in the form of log P values (where P is the octanol/water partition coefficient), is an important factor in explaining the variation in inhibitory potency within these series of compounds, many of which also act as substrates for the respective enzymes. In addition, there is a role for hydrogen bonding and π-π stacking interactions within the P450 active site which represent secondary factors in the binding processes of these compounds.     

Lipophilicity relationships in inhibitors of CYP2C9 and CYP2C19 enzymes

Quantitative structure-activity relationships (QSARs) within a series of cytochrome P450 2C9 (CYP2C9) and cytochrome P450 2C19 (CYP2C19) inhibitors are reported. In particular, it is noted that compound lipophilicity, in the form of log P values (where P is the octanol/water partition coefficient), is an important factor in explaining the variation in inhibitory potency within these series of compounds, many of which also act as substrates for the respective enzymes. In addition, there is a role for hydrogen bonding and pi-pi stacking interactions within the P450 active site which represent secondary factors in the binding processes of these compounds.     

Quantitative structure-activity relationships (QSARs) for inhibitors and substrates of CYP2B enzymes: importance of compound lipophilicity in explanation of potency differences

The results of quantitative structure-activity relationship (QSAR) studies on inhibitors and substrates of cytochrome P450 2B (CYP2B) subfamily enzymes are reported. It was found that lipophilicity (in the form of log P) is the most important property for explaining the variations in inhibitory activity, and there are similarities between QSARs for both substrates and inhibitors for CYP2B6 (human), and also between those of other CYP2B enzymes, such as CYP2B1 (rat) and CYP2B4 (rabbit). Both linear and quadratic lipophilicity relationships are evidenced in human and other mammalian species, and the particular type of expression found is probably due to the nature of the compounds under investigation, as it is usually the homologous series which tend to show quadratic relationships in log P. The findings from QSAR studies can be rationalized by molecular modelling of the active site interactions with both P450 crystal structures and homology models of CYP2B subfamily enzymes.     

A new format of electrodes for the electrochemical reduction of cytochromes P450

New approach to the electrochemical reduction of cytochromes P450 (P450s, CYPs) at electrodes chemically modified with appropriate substrates for P450s ("reverse" electrodes) was proposed. The method is based on the analysis of cyclic voltammograms, square-wave voltammograms and amperograms with subsequent determination of electrochemical characteristics such as catalytic current and redox potential. The sensitivity of proposed method is 0.2-1 nmol P450/electrode. The changes of maximal current and of redox potentials in square-wave voltammograms as well as the changes of catalytic current in amperometric experiments proved to be informative and reliable. Planar regime of screen-printed electrodes (strip-type sensors) enabled to utilise 20-60 microl of electrolyte volume. The enzyme-substrate pairs P450 2B4/benzphetamine and P450scc/cholesterol were investigated. Electrochemical parameters of electrodes with unspecific P450 substrates differed considerably from electrodes with appropriate substrates.     

Finding homes for orphan cytochrome P450s: CYP4V2 and CYP4F22 in disease states

The cytochrome P450 (CYP) 4 family of enzymes contains several recently identified membersthat are referred to as “orphan P450s” because their endogenous substrates are unknown.Human CYP4V2 and CYP4F22 are two such orphan P450s that are strongly linked to ocular andskin disease, respectively. Genetic analyses have identified a wide spectrum of mutations in the CYP4V2gene from patients suffering from Bietti’s crystalline corneoretinal dystrophy, and mutations in theCYP4F22 gene have been linked to lamellar ichthyosis. The strong gene–disease associations provideunique opportunities for elucidating the substrate specificity of these orphan P450s and unraveling thebiochemical pathways that may be impacted in patients with CYP4V2 and CYP4F22 functional deficits.     

Cytochromes P450 in gibberellin biosynthesis

The gibberellins (GAs) are an important class of plant growth regulators that are active in many aspects of plant growth and development. GAs are synthesized by a complex pathway involving three enzyme classes spanning different subcellular compartments. One of these enzyme classes is the cytochrome P450s which catalyze a number of oxidation steps in the middle part of the pathway. Mutants in these cytochrome P450-mediated steps in a number of species have been crucial in isolating the genes encoding these enzymes and have also played an important role in understanding GA physiology. GAs are also synthesized by fungi, in a biosynthesis pathway largely catalyzed by cytochrome P450s. The fungal pathway appears to have evolved independently to that of higher plants.

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An oxygenase inhibitor study in Solanum lycopersicum combined with metabolite profiling analysis revealed a potent peroxygenase inactivator

Plant genomes contain a vast number of oxygenase genes, but only very few have been functionally characterized. To devise an alternative method for the detection of novel oxygenase-catalysed reactions the effects of the cytochrome P450 oxygenase inhibitors 1-aminobenzotriazole (ABT) and tetcyclacis (TET) have been examined by metabolite profiling analysis in tomato fruit (Solanum lycopersicum). Treatment with TET resulted in significant increases in the levels of certain flavonoids, whereas ABT strongly inhibited their formation during fruit ripening. Injections of buffered solutions of ABT into tomato fruits led rather to an accumulation of 9,12,13-trihydroxy-10(E)-octadecenoic acid probably due to retarded metabolism of the hydroxylated acid, while TET completely repressed its formation. Peroxygenase, a hydroperoxide-dependent hydroxylase involved in the formation of the trihydroxy fatty acid, is strongly inhibited by TET (IC(50) 2.6 μM) as was demonstrated by studies with the recombinant tomato enzyme expressed in yeast. The data show that ABT and TET affect oxygenases differently in tomato fruit and reveal that these enzymes catalyse distinct reactions in different metabolic pathways, among which C(18)-trihydroxy fatty acid and flavonoid metabolism involve novel oxygenase-catalysed reactions. The method is suitable to identify potential substrates and products of ripening-related, putative oxygenases and can support functional analyses of recombinant enzymes.     

Cytochromes P450 as versatile biocatalysts

Cytochromes P450 are ubiquitously distributed enzymes, which were discovered about 50 years ago and which possess high complexity and display a broad field of activity. They are hemoproteins encoded by a superfamily of genes converting a broad variety of substrates and catalysing a variety of interesting chemical reactions. This enzyme family is involved in the biotransformation of drugs, the bioconversion of xenobiotics, the metabolism of chemical carcinogens, the biosynthesis of physiologically important compounds such as steroids, fatty acids, eicosanoids, fat-soluble vitamins, bile acids, the conversion of alkanes, terpenes, and aromatic compounds as well as the degradation of herbicides and insecticides. There is also a broad versatility of reactions catalysed by cytochromes P450 such as carbon hydroxylation, heteroatom oxygenation, dealkylation, epoxidation, aromatic hydroxylation, reduction, dehalogenation (Sono, M., Roach, M.P., Coulter, E.D., Dawson, J.H., 1996. Heme-containing oxygenases. Chem. Rev. 96, 2841-2888), (Werck-Reichhart, D., Feyereisen, R., 2000. Cytochromes P450: a success story. Genome Biol. 1 (REVIEWS3003)), (Bernhardt, R., 2004. Cytochrome P-450. Encyclopedia Biol. Chem. 1, 544-549), (Bernhardt, R., 2004. Optimized chimeragenesis; creating diverse P450 functions. Chem. Biol. 11, 287-288), (Guengerich, F.P., 2004. Cytochrome P450: what have we learned and what are the future issues? Drug Metab. Rev. 36, 159-197). More than 5000 different P450 genes have been cloned up to date (for details see: ). Members of the same gene family are defined as usually having > or =40% sequence identity to a P450 protein from any other family. Mammalian sequences within the same subfamily are always >55% identical. The numbers of individual P450 enzymes in different species differ significantly, showing the highest numbers observed so far in plants. The structure-function relationships of cytochromes P450 are far from being well understood and their catalytic power has so far hardly been used for biotechnological processes. Nevertheless, the set of interesting reactions being catalysed by these systems and the availability of new genetic engineering techniques allowing to heterologously express them and to improve and change their activity, stability and selectivity as well as the increasing interest of the industry in life sciences makes them promising candidates for biotechnological application in the future.     

Modeling and synthesis of novel tight-binding inhibitors of cytochrome P450 2C9

Cytochrome P450 2C9 (2C9) is one of the three major drug metabolizing cytochrome P450 enzymes in human liver. Although the crystal structure of 2C9 has been solved, the important physicochemical properties of substrate-enzyme interactions remain difficult to be determined. This is due in part to the conformational flexibility of mammalian P450 enzymes. Therefore, probing the active-site with high-affinity substrates is important in further understanding substrate-enzyme interactions. Three-dimensional quantitative structure-activity relationships (3D-QSAR) and docking experiments have been shown to be useful tools in correlating biological activity with structure. In particular we have previously reported that the very tight-binding inhibitor benzbromarone can provide important information about the active-site of 2C9. In this study we report the binding affinities and potential substrate-enzyme interactions of 4H-chromen-4-one analogs, which are structurally similar to benzbromarone. The chromenone structures are synthetically accessible inhibitors and give inhibition constants as low as 4.2 nM, comparable with the very tightest-binding inhibitors of 2C9. Adding these compounds to our previous 2C9 libraries for CoMFA models reinforces the important electrostatic and hydrophobic features of substrate binding. These compounds have also been docked in the 2C9 crystal structure and the results indicate that Arg 108 plays significant roles in the binding of chromenone substrates.     

Electrochemical reduction of cytochromes P450 using electrodes containing immobilized substrates

A new approach for the electrochemical reduction of cytochromes P450 (P450, CYPs) with electrodes chemically modified with CYP appropriate substrates (“reverse” electrodes) has been proposed. The method is based on the analysis of cyclic voltammograms, square wave voltammograms, amperograms and determination of such electrochemical characteristics as catalytic current and redox potential. The differences of maximal current and potentials in square wave voltammograms and catalytic current in amperometric measurements are more sensitive and reliable. The planar mode of screen-printed electrodes permits to use 20–60 μl of electrolyte volume. We have investigated P450 2B4-benzphetamine or P450scc-cholesterol enzyme-substrate pairs. Electrochemical parameters of electrodes with nonspecific P450 substrate were differed from the electrodes with appropriate substrates.     

The ferric-hydroperoxo complex of chloroperoxidase

The hydroperoxo-ferric complex, or Compound 0 (Cpd 0), is an unstable transient intermediate common for oxygen activating heme enzymes such as the cytochromes P450, nitric oxide synthases, and heme oxygenases, as well as the peroxidases and catalases which utilize hydrogen peroxide as a source of oxygen and reducing equivalents. Detailed understanding of the mechanism of oxygen activation and formation of the higher valent catalytically active intermediates in heme enzyme catalysis requires the structural and spectroscopic characterization of this immediate precursor, Cpd 0. Using the method of cryoradiolytic reduction of the oxy-ferrous heme complex, we have prepared and characterized hydroperoxo-ferric complex in chloroperoxidase (CPO) and compared this to the same intermediate generated in cytochrome P450 CYP101. Optical absorption spectrum of Cpd 0 in CPO has a Soret band at 449 nm and poorly resolved α, β bands at 576 and 546 nm.     

Homology modeling of plant cytochrome P450s

Plant P450 monooxygenases represent the largest family of plant proteins and the largest collection of P450s available for comparative studies and biotechnological applications. They have been shown to catalyze a diverse array of difficult chemical reactions and have demonstrated potential to be used in pharmacological, agronomic and phytoremediative applications. Central to our use of these catalytically competent enzymes is the need to understand their interactions with substrates. Because most characterized plant P450s are membrane-bound proteins that are resistant to standard X-ray and NMR structure determinations, homology modeling represents a reliable and relatively rapid alternative method for analyzing structure-function relationships and predicting substrates for many P450s that are only now being characterized. These methods, which are being widely used in mammalian P450 structure-function studies, can allow plant biologists to define critical residues interacting with substrates and, in a directed fashion, alter the reactivities of individual monooxygenases. The homology modelings that have been done on a limited number of plant P450s and the site-directed mutations that validate them indicate that current modeling and substrate docking procedures are capable of providing structural explanations for sequence variants as well as for predicting functional characteristics of undefined P450s.     

The oxidases of gibberellin biosynthesis: Their function and mechanism

Gibberellins (GAs) are biosynthesised from the diterpene ent -kaurene by a series of oxidative reactions catalysed by two classes of enzymes. The early steps, involving transformations of highly hydrophobic substrates, are carried out by membrane-associated monooxygenases, probably involving cytochrome P450, whereas the later reactions are catalysed by soluble 2-oxoglutarate-dependent dioxygenases. Some reactions involving substrates, such as GA₁₂ and GA₁₂-aldehyde, that have intermediate polarity are catalysed by enzymes in both classes. The monooxygenases and dioxygenases catalyse the same types of reactions: hydroxylation, desaturation, alcohol and aldehyde oxidation. For both enzyme classes, the oxidant is thought to be an oxyferryl species, depicted as Fe^lv=O, that is derived from molecular oxygen by different mechanisms, the reducing power being supplied by NADPH in the case of cytochrome P450 monooxygenases and by the decarboxylation of 2-oxoglutarate to succinate for the dioxygenases. The recent availability of cDNA clones for several of the dioxygenases and the ability to prepare active enzymes by heterologous expression of cDNAs in Escherichia coli have provided new opportunities for examining the function of these enzymes. They have relatively low substrate specificity and, in many cases, are multifunctional. Consequently, fewer enzymes than expected are required to produce the large number of GA structures encountered in higher plants. In the present review, the major oxygenases of GA biosynthesis are described and their reactions are discussed in an attempt to rationalise this multifunctionality.     

Interactions of substrates at the surface of P450s can greatly enhance substrate potency

Cytochrome P450s are a superfamily of heme containing enzymes that use molecular oxygen and electrons from reduced nicotinamide cofactors to monooxygenate organic substrates. The fatty acid hydroxylase P450BM-3 has been particularly widely studied due to its stability, high activity, similarity to mammalian P450s, and presence of a cytochrome P450 reductase domain that allows the enzyme to directly receive electrons from NADPH without a requirement for additional redox proteins. We previously characterized the substrate N-palmitoylglycine, which found extensive use in studies of P450BM-3 due to its high affinity, high turnover number, and increased solubility as compared to fatty acid substrates. Here, we report that even higher affinity substrates can be designed by acylation of other amino acids, resulting in P450BM-3 substrates with dissociation constants below 100 nM. N-Palmitoyl-l-leucine and N-palmitoyl-l-methionine were found to have the highest affinity, with dissociation constants of less than 8 nM and turnover numbers similar to palmitic acid and N-palmitoylglycine. The interactions of the amino acid side chains with a hydrophobic pocket near R47, as revealed by our crystal structure determination of N-palmitoyl-l-methionine bound to the heme domain of P450BM-3, appears to be responsible for increasing the affinity of substrates. The side chain of R47, previously shown to be important in interactions with negatively charged substrates, does not interact strongly with N-palmitoyl-l-methionine and is found positioned at the enzyme-solvent interface. These are the tightest binding substrates for P450BM-3 reported to date, and the affinity likely approaches the maximum attainable affinity for the binding of substrates of this size to P450BM-3.     

Optimization of an in vivo plant P450 monooxygenase system in Saccharomyces cerevisiae

Cytochrome P450s are heme-thiolate oxygenases involved in a wide number of reactions such as epoxidation, hydroxylation, and demethylation. Heterologously expressed eukaryotic P450s are potentially useful biocatalysts for stereospecific oxygenation reactions under mild conditions. Numerous factors, such as intracellular pH, cytochrome P450, cytochrome P450 reductase, NADPH, and oxygen concentration all influence the in vivo activity. To systematically examine these factors, we selected ferulate 5-hydroxylase (F5H), a plant P450, with the Saccharomyces cerevisiae WAT11 strain as an expression host. Two media compositions and two cultivation procedures were investigated to optimize the in vivo activity of F5H. We modified a previously published selective growth medium (Pompon et al. [1996] Methods Enzymol 272:51-64) that increased the specific growth rate and cell yield of the host strain. A cultivation procedure with separate growth and induction stages that each contained selective media resulted in a 45% increase of whole cell F5H specific activity. In a medium designed for simultaneous growth and induction, we observed a 2.6-fold higher specific F5H activity, but substantially lower cell yield. Surprisingly, in this medium the higher specific F5H activity did not correlate with a higher P450 concentration. The effects of addition of the first committed heme precursor, delta-aminolevulinic acid, and Fe(III) at the beginning of induction period were also studied for our two-stage procedure. A small, but significant (P < 0.05) increase in whole cell F5H activity was observed following ALA addition.