Electrochemically driven drug metabolism via cytochrome P450 2C9 isozyme microsomes with cytochrome P450 reductase and indium tin oxide nanoparticle composites

We describe herein an electrochemically driven drug metabolism strategy based on nanocomposites that integrate cyt P450 2C9 (CYP2C9) isozyme microsomes with cyt P450 reductase (CPR), indium tin oxide (ITO) nanoparticles and chitosan (CS). This novel bioelectronic system enables monitoring of the drug metabolism and enzyme inhibition.     

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.     

A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building

Summary A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching -helices (C, D, G, I, J, K and L) and -sheets (3/4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, -helices B, B and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val³⁷⁰, Pro³⁷¹, Leu³⁷², Trp³¹⁶, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp¹⁰⁰ or Asp³⁰¹ was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates. These findings are in accordance with a recently published predictive model for substrates of P450 2D6 [Koymans et al., Chem. Res. Toxicol., 5 (1992) 211].     

Modeling of complexes between cytochrome P450 1A2 and substrates

Based on the 2HI4 complex taken from the PDB database, molecular docking of 17 substrates in the cytochrome P450 1A2 cavity is performed using the 3D-QSAR algorithm CiS. The arrangement of substrate molecules in the 1A2 isoform cavity is considered, the orientation of the molecular reaction centers relative to heme is analyzed, and the character of interaction between substrates and active site aminoacid residues is investigated. The structures of the modeled complexes allow us to explain metabolic pathways in demethylation reactions and some reactions of hydroxylation, which enables an application of the CiS algorithm to predict metabolic pathways.     

Surface-enhanced resonance Raman scattering of cytochrome P450-2D6 on coated silver hydrosols

Surface-enhanced resonance Raman scattering (SERRS) from dilute solutions (down to nanomolar concentrations) of human mono-oxygenase CYP2D6 is observed using aqueous dispersions of Ag nanoparticles (hydrosol) coated with self-assembled monolayers (SAMs) of mercaptoalkanoic acids of two different lengths. From a direct comparison with its resonance Raman spectrum in solution, CYP2D6 appears to fully retain its native structure upon adsorption on coated hydrosol through electrostatic interaction, while a structural change in the active site is observed when uncoated citrate-reduced hydrosol is used. Using SERRS on these biocompatible coated hydrosols, the effects of dextromethorphan on the enzyme's active site can be observed, demonstrating that CYP2D6 ability of binding substrates is preserved. Moreover, by tuning the wavelength of the exciting laser away from the main absorption band of the heme, the vibrational bands of the SAM coating are observed and analyzed to see how the presence of the protein affects the SAM structure.     

Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition

A new in silico model is developed to predict cytochrome P450 2D6 inhibition from 2D chemical structure. Using a diverse training set of 100 compounds with published inhibition constants, an ensemble approach to recursive partitioning is applied to create a large number of classification trees, each of which yields a yes/no prediction about inhibition for a given compound. These binary classifications are combined to provide an overall prediction, which answers the yes/no question about inhibition and provides a measure of confidence about that prediction. Compared to single-tree models, the ensemble approach is less sensitive to noise in the experimental data as well as to changes in the training set. Internal validation tests indicated an overall classification accuracy of 75%, whereas predictions applied to an external set of 51 compounds yielded 80% accuracy, with all inhibitors correctly identified. The speed and 2D nature of this model make it appropriate for high-throughput processing of large chemical libraries, and the confidence level provides a continuous scale on which to prioritize compounds.     

Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism

CYP2D6 is an important enzyme that is involved in first pass metabolism and is responsible for metabolizing ~25% of currently marketed drugs. A homology model of CYP2D6 was built using X-ray structures of ligand-bound CYP2C5 complexes as templates. This homology model was used in docking studies to rationalize and predict the site of metabolism of known CYP2D6 substrates. While the homology model was generally found to be in good agreement with the recently solved apo (ligand-free) X-ray structure of CYP2D6, significant differences between the structures were observed in the B′ and F–G helical region. These structural differences are similar to those observed between ligand-free and ligand-bound structures of other CYPs and suggest that these conformational changes result from induced-fit adaptations upon ligand binding. By docking to the homology model using Glide, it was possible to identify the correct site of metabolism for a set of 16 CYP2D6 substrates 85% of the time when the 5 top scoring poses were examined. On the other hand, docking to the apo CYP2D6 X-ray structure led to a loss in accuracy in predicting the sites of metabolism for many of the CYP2D6 substrates considered in this study. These results demonstrate the importance of describing substrate-induced conformational changes that occur upon binding. The best results were obtained using Glide SP with van der Waals scaling set to 0.8 for both the receptor and ligand atoms. A discussion of putative binding modes that explain the distribution of metabolic sites for substrates, as well as a relationship between the number of metabolic sites and substrate size, are also presented. In addition, analysis of these binding modes enabled us to rationalize the typical hydroxylation and O-demethylation reactions catalyzed by CYP2D6 as well as the less common N-dealkylation.     

Label-free genotyping of cytochrome P450 2D6*10 using ligation-mediated strand displacement amplification with DNAzyme-based chemiluminescence detection

Genotyping of cytochrome P450 monooxygenase 2D6*10 (CYP2D6*10) plays an important role in pharmacogenomics, especially in clinical drug therapy of Asian populations. This work reported a novel label-free technique for genotyping of CYP2D6*10 based on ligation-mediated strand displacement amplification (SDA) with DNAzyme-based chemiluminescence detection. Discrimination of single-base mismatch is firstly accomplished using DNA ligase to generate a ligation product. The ligated product then initiates a SDA reaction to produce aptamer sequences against hemin, which can be probed by chemiluminescence detection. The proposed strategy is used for the assay of CYP2D6*10 target and the genomic DNA. The results reveal that the proposed technique displays chemiluminescence responses in linear correlation to the concentrations of DNA target within the range from 1 pM to 1 nM. A detection limit of 0.1 pM and a signal-to-background ratio of 57 are achieved. Besides such high sensitivity, the proposed CYP2D6*10 genotyping strategy also offers superb selectivity, great robustness, low cost and simplified operations due to its label-free, homogeneous, and chemiluminescence-based detection format. These advantages suggest this technique may hold considerable potential for clinical CYP2D6*10 genotyping and association studies.     

Simultaneous chiral analyses of multiple analytes: case studies, implications and method development considerations

The field of chiral separations had a modest beginning some two decades ago. However, due to rapid technological advancement coupled with simultaneous availability of innovative chiral stationary phases and novel chiral derivatization agents, the field of chiral separations has now totally outpaced many other separation fields. Keeping pace with rapid changes in the field of chiral separations, investigators continue to add stereoselective pharmacokinetic, pharmacodynamic, pharmacologic and toxicological data of new and/or marketed racemic compounds to the literature. Examination of the evolution of chiral separations suggests that in the beginning many investigators attempted to separate and quantify a single pair of enantiomers, adopting either direct (separation made on a chiral stationary phase) or indirect (separation made following precolumn conversion of enantiomers to corresponding diastereomers) approaches. However, more recent trends in chiral separations suggest that investigators are attempting to separate and quantify multiple pairs of enantiomers with available technologies. Added to this, some interesting trends have been observed in many of the recently reported chiral applications, including preferences regarding internal standard selection, mobile phase contents and composition, sorting out issues with mass spectrometric detection, determination of elution order, analytical manipulations of metabolite(s) without reference standards and addressing some specificity-related issues. This review mainly focuses on chiral separations involving multiple chiral analytes and attempts to justify the need for such chiral separations involving multiple analytes. In this context, several cases studies are described on the utility and applicability of such chiral separations under discrete headings to provide an account to the readership on the implications of such tasks. The topics of case studies covered in this review include: (a) therapy markers--differentiation from drug abuse and/or applicability in forensics; (b) role in pharmacogenetic/polymorphic evaluation; (c) monitoring and understanding the role of parent and active metabolite(s) in clinical and preclinical investigations; (d) exploration on the pharmacokinetic utility of an active chiral metabolite vis-a-vis the racemic parent moiety; (e) understanding the chirality play in delineating peculiar toxic effects; (f) exploration of chiral inversion phenomenon, and understanding the role of stereoselective metabolism. For the further benefit of readership, some select examples (n = 19) of the separation of multiple chiral analytes with appropriate information on chromatography, detection system, validation parameters and applicable conclusion are also provided. Finally, the review covers some useful considerations for method development involving multiple chiral analytes.     

A comparative molecular field analysis of cytochrome P450 2A5 and 2A6 inhibitors

Structure-activity relationships of 23 P450 2A5 and 2A6 inhibitors were analysed using the CoMFA [1] and GOLPE/GRID with smart region definition (SRD) [2]. The predictive power of the resulting models was validated using five compounds not belonging to the model set. All models have high internal and external predictive power and resulting 3D-QSAR models are supporting each other. Both Sybyl and GOLPE highlight properties near lactone moiety to be important for 2A5 and 2A6 inhibition. Another important feature for pIC₅₀ was the size of the substituent in the 7-positon of coumarin. The models suggest that the 2A5 binding site is larger that that of 2A6 due to larger steric regions in the CoMFA coefficient maps and corresponding GOLPE maps. In addition, the maps reveal that 2A6 disfavours negative charge near the lactone moiety of coumarin.     

Preparation, characterization, and substrate metabolism of gold-immobilized cytochrome P450 2C9

The cytochrome P450 enzymes represent an important class of heme-containing enzymes. There is considerable interest in immobilizing these enzymes on a surface so that interactions between a single enzyme and other species can be studied with respect to electron transfer, homodimer or heterodimer interactions, or for construction of biological-based chips for standardizing cytochrome P450 metabolism or for high-throughput screening of pharmaceutical agents. Previous studies have generally immobilized P450 enzymes in a matrix or on a surface. Here, we have attached CYP2C9 to gold substrates such that the resulting construct maintains the ability to bind and metabolize substrates in the presence of NADPH and cytochrome P450 reductase. The activity of these chips is directly dependent upon the linkers used to attach CYP2C9 and to the presence of key molecules in the active site during enzyme attachment. A novel method to detect substrate-enzyme binding, namely, superconducting quantum interference device (SQUID) magnetometry, was used to monitor the binding of substrates. Most significantly, conditions that allow measurable CYP2C9 metabolism to occur have been developed.     

Mechanistic studies of oxene reactions with organic substrates: Reaction paths on MNDO enthalpy surfaces—models for cytochrome P450 oxidations

In a systematic study, the characteristics of triplet oxene models for alkane, alkene, chloroalkane, and aryl oxidations by the cytochrome P450s have been examined using the semiempirical molecular orbital method MNDO and the formalism of statistical mechanics. Specific model substrates chosen were: methane, ethylene, propene, carbon tetrachloride, chloroform, and toluene. It was found that transition state geometries and activation entropies were reliably predicted, but that an empirical factor was necessary to correct overestimation of activation enthalpies. It was determined that both hydroxylations and epoxidation initiated by a O(³P) atom are nonconcerted; and that oxidations of C? Cl bonds (halosylations) occur by a two-step mechanism similar to hydroxylation. It is shown that the radical mechanisms derived from these studies are consistent with a range of observed properties of cytochrome P450 reactions and provide reasonable explanations for secondary deuterium isotope effects and substituent effects in cytochrome P450 epoxidation of styrenes, suicide inactivation of a P450 enzyme by ethylene, and the characteristics of aerobic CCl₄ and CHCl₃ metabolism. A triplet oxene mechanism for the initial steps of aromatic epoxidation and hydroxylation is also discussed.     

Aromatic hydroxylation by cytochrome P450: model calculations of mechanism and substituent effects

The mechanism and selectivity of aromatic hydroxylation by cytochrome P450 enzymes is explored using new B3LYP density functional theory computations. The calculations, using a realistic porphyrin model system, show that rate-determining addition of compound I to an aromatic carbon atom proceeds via a transition state with partial radical and cationic character. Reactivity is shown to depend strongly on ring substituents, with both electron-withdrawing and -donating groups strongly decreasing the addition barrier in the para position, and it is shown that the calculated barrier heights can be reproduced by a new dual-parameter equation based on radical and cationic Hammett sigma parameters.