A population approach to enzyme characterization and identification: application to phenacetin O-deethylation

The Utility of Mixed Effects Models in the Evaluation of Complex Genomic Traits In Vitro

In pharmacogenomic studies, the use of human liver microsomes as a model system to evaluate the impact of complex genomic traits (i.e., linkage-disequilibrium patterns, coding, and non-coding variation, etc.) on efficiency of drug metabolism is challenging. To accurately predict the true effect size of genomic traits requires large richly sampled datasets representative of the study population. Moreover, the acquisition of this data can be labor-intensive if the study design or bioanalytical methods are not high throughput, and it is potentially unfeasible if the abundance of sample needed for experiments is limited. To overcome these challenges, we developed a novel strategic approach using non-linear mixed effects models (NLME) to determine enzyme kinetic parameters for individual liver specimens using sparse data. This method can facilitate evaluation of the impact that complex genomic traits have on the metabolism of xenobiotics in vitro when tissue and other resources are limited. In addition to facilitating the accrual of data, it allows for rigorous testing of covariates as sources of kinetic parameter variability. In this in silico study, we present a practical application of such an approach using previously published in vitro cytochrome P450 (CYP) 2D6 data and explore the impact of sparse sampling, and experimental error on known kinetic parameter estimates of CYP2D6 mediated formation of 4-hydroxy-atomoxetine in human liver microsomes. SIGNIFICANCE STATEMENT: This study presents a novel non-linear mixed effects model (NLME)-based framework for evaluating the impact of complex genomic traits on saturable processes described by a Michaelis-Menten kinetics in vitro using sparse data. The utility of this approach extends beyond gene variant associations, including determination of covariate effects on in vitro kinetic parameters and reduced demand for precious experimental material.

Triple Strategies to Improve Oral Bioavailability by Fabricating Coamorphous Forms of Ursolic Acid with Piperine: Enhancing Water-Solubility, Permeability, and Inhibiting Cytochrome P450 Isozymes

As a BCS IV drug, ursolic acid (UA) has low oral bioavailability mainly because of its poor aqueous solubility/dissolution, poor permeability, and metabolism by cytochrome P450 (CYP) isozymes, such as CYP3A4. Most UA preparations demonstrated a much higher dissolution than that of its crystalline form yet a low drug concentration in plasma due to their lower consideration or evaluation for the permeability and metabolism issues. In the current study, a supramolecular coamorphous system of UA with piperine (PIP) was prepared and characterized by powder X-ray diffraction, differential scanning calorimetry, and scanning electron microscopy. In comparison to crystalline UA and UA in physical mixture, such coamorphous system enhanced solubility (5.3-7-fold in the physiological solution) and dissolution (7-8-fold in the physiological solution within 2 h) of UA and exhibited excellent physical stability under 90-day storage conditions. More importantly, the pharmacokinetic study of coamorphous UA in rats exhibited 5.8-fold and 2.47-fold improvement in AUC0-∞ value, respectively, compared with its free and mixed crystalline counterparts. In order to further explore the mechanism of such improvement, the molecular interactions of a coamorphous system in the solid state were investigated. Fourier transform infrared spectroscopy, solid-state 13C nuclear magnetic resonance spectroscopy, and density functional theory modeling suggested that intermolecular hydrogen bonds with strong interactions newly formed between UA and PIP after coamorphization. The in vitro permeability studies across Caco-2 cell monolayer and metabolism studies by rat hepatic microsomes indicated that free PIP significantly increased the permeability of UA and inhibited the enzymatic metabolism of UA by CYP3A4. However, PIP in the coamorphous combination exhibited a much lower level in the bioenhancing than its free form arising from the synchronized dissolution characteristic of the preparation (only 60% of PIP released in comparison to its free counterpart in 2 h). The in situ loop study in rats proposed that the acid-sensitive dissolution in the stomach of the coamorphous preparation helped to improve the effective free drug concentration, thereby facilitating PIP to play its role in bioenhancing. The current study offers an exploratory strategy to overcome poor solubility/dissolution, poor permeability, and metabolism by cytochrome P450 isozymes of the BCS IV drug to improve its oral bioavailability.

Optimum designs for non-linear mixed effects models in the presence of covariates

In this article, we present a new method for optimizing designs of experiments for non-linear mixed effects models, where a categorical factor with covariate information is a design variable combined with another design factor. The work is motivated by the need to efficiently design preclinical experiments in enzyme kinetics for a set of Human Liver Microsomes. However, the results are general and can be applied to other experimental situations where the variation in the response due to a categorical factor can be partially accounted for by a covariate. The covariate included in the model explains some systematic variability in a random model parameter. This approach allows better understanding of the population variation as well as estimation of the model parameters with higher precision.

Transform-both-sides nonlinear models for in vitro pharmacokinetic experiments

Transform-both-sides nonlinear models have proved useful in many experimental applications including those in pharmaceutical sciences and biochemistry. The maximum likelihood method is commonly used to fit transform-both-sides nonlinear models, where the regression and transformation parameters are estimated simultaneously. In this paper, an analysis of variance-based method is described in detail for estimating transform-both-sides nonlinear models from randomized experiments. It estimates the transformation parameter from the full treatment model and then the regression parameters are estimated conditionally on this estimate of the transformation parameter. The analysis of variance method is computationally simpler compared with the maximum likelihood method of estimation and allows a more natural separation of different sources of lack of fit. Simulation studies show that the analysis of variance method can provide unbiased estimators of complex transform-both-sides nonlinear models, such as transform-both-sides random coefficient nonlinear regression models and transform-both-sides fixed coefficient nonlinear regression models with random block effects.

Nasal cytotoxic and carcinogenic activities of systemically distributed organic chemicals

Toxicity and carcinogenicity in the mucosa of the nasal passages in rodents has been produced by a variety of organic chemicals which are systemically distributed. In this review, 14 such chemicals or classes were identified that produced rodent nasal cytotoxicity, but not carcinogenicity, and 11 were identified that produced nasal carcinogenicity. Most chemicals that affect the nasal mucosa were either concentrated in that tissue or readily activated there, or both. All chemicals with effects in the nasal mucosa that were DNA-reactive, were also carcinogenic, if adequately tested. None of the rodent nasal cytotoxins has been identified as a human systemic nasal toxin. This may reflect the lesser biotransformation activity of human nasal mucosa compared to rodent and the much lower levels of human exposures. None of the rodent carcinogens lacking DNA reactivity has been identified as a nasal carcinogen or other cancer hazard to humans. Some DNA-reactive rodent carcinogens that affect the nasal mucosa, as well as other tissues, have been associated with cancer at various sites in humans, but not the nasal cavity. Thus, findings in only the rodent nasal mucosa do not necessarily predict either a toxic or carcinogenic hazard to that tissue in humans.

Role of pharmacologically active metabolites in drug discovery and development

Pharmacologically active metabolites can contribute significantly to the overall therapeutic and adverse effects of drugs. Therefore, to fully understand the mechanism of action of drugs, it is important to recognize the role of active metabolites. Active metabolites can also be developed as drugs in their own right. Using illustrative examples, this paper discusses a variety of biotransformation reactions that produce active metabolites and their structure-activity relationships. The paper also describes the role and significance of active metabolites in drug discovery and development, various experimental observations that can be used as indicators of their presence, and methods that can be used to assess their biological activities and contribution to the overall therapeutic and adverse effects of drugs.

Validated assays for human cytochrome P450 activities

The measurement of the effect of new chemical entities on human cytochrome P450 marker activities using in vitro experimentation represents an important experimental approach in drug development. In vitro drug interaction data can be used in guiding the design of clinical drug interaction studies, or, when no effect is observed in vitro, the data can be used in place of an in vivo study to claim that no interaction will occur in vivo. To make such a claim, it must be assured that the in vitro experiments are performed with absolute confidence in the methods used and data obtained. To meet this need, 12 semiautomated assays for human P450 marker substrate activities have been developed and validated using approaches described in the GLP (good laboratory practices) as per the code of U.S. Federal Regulations. The assays that were validated are: phenacetin O-deethylase (CYP1A2), coumarin 7-hydroxylase (CYP2A6), bupropion hydroxylase (CYP2B6), amodiaquine N-deethylase (CYP2C8), diclofenac 4'-hydroxylase and tolbutamide methylhydroxylase (CYP2C9), (S)-mephenytoin 4'-hydroxylase (CYP2C19), dextromethorphan O-demethylase (CYP2D6), chlorzoxazone 6-hydroxylase (CYP2E1), felodipine dehydrogenase, testosterone 6 beta-hydroxylase, and midazolam 1'-hydroxylase (CYP3A4 and CYP3A5). High-pressure liquid chromatography-tandem mass spectrometry, using stable isotope-labeled internal standards, has been applied as the analytical method. This analytical approach, through its high sensitivity and selectivity, has permitted the use of very low incubation concentrations of microsomal protein (0.01-0.2 mg/ml). Analytical assay accuracy and precision values were excellent. Enzyme kinetic and inhibition parameters obtained using these methods demonstrated high precision and were within the range of values previously reported in the scientific literature. These methods should prove useful in the routine assessments of the potential for new drug candidates to elicit pharmacokinetic drug interactions via inhibition of cytochrome P450 activities.

Cytochrome P450 inhibition using recombinant proteins and mass spectrometry/multiple reaction monitoring technology in a cassette incubation

Detailed cytochrome P450 (P450) inhibition profiles are now required for the registration of novel molecular entities. This method uses combined substrates (phenacetin, diclofenac, S-mephenytoin, bufuralol, and midazolam) with combined recombinant P450 enzymes (CYP1A2, 2C9, 2C19, 2D6, and 3A4) in an attempt to limit interactions with other more minor P450s and associated reductases. Kinetic analysis of single substrate with single P450 (sP450) yielded apparent Km values of 25, 2, 20, 9, and 3 microM, for CYP1A2, 2C9, 2C19, 2D6, and 3A4, respectively. Combined substrates with combined P450s (cP450) yielded apparent Km values of 65, 4, 19, 7, and 2 microM. Selectivity of the substrates for each P450 isoform was checked. Phenacetin proved to be the least selective substrate. However, the ratio of the various P450s was modified in the final assay such that metabolism of phenacetin by other enzymes was approximately 20% of the metabolism by CYP1A2. IC50 determinations with alpha-naphthoflavone (0.04 microM), sulfaphenazole (0.26 microM), tranylcypromine (9 microM), quinidine (0.02 microM), and ketoconazole (0.01 microM) were similar for sP450 and cP450 enzymes. The assay was further evaluated with 11 literature compounds and 52 in-house new chemical entities, and the data compared with radiometric/fluorescent values. The overall protein level of the assay was reduced from the original starting point, as this led to some artificially high IC50 measurements when compared with existing lower protein assays (radiometric/fluorometric). This method offers high throughput P450 inhibition profiling with potential advantages over current radiometric or fluorometric methods.

The interactions of a selective protein kinase C beta inhibitor with the human cytochromes P450

Studies were performed to determine the cytochromes P450 (P450) responsible for the biotransformation of (S)-13[(dimethylamino)methyl]-10,11,14,15-tetrahydro-4,9:16,21-dimetheno-1H, 13H-dibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadiazacyclohexadecene-1,3(2H)-dione (LY333531) to its equipotent metabolite, N-desmethyl LY333531, and to examine the ability of these two compounds to inhibit P450-mediated metabolism. Kinetic studies indicated that a single enzyme in human liver microsomes was able to form N-desmethyl LY333531 with an apparent K(M) value of approximately 1 microM. The formation rate of N-desmethyl LY333531 was correlated with markers of nine P450s in a bank of 20 human liver microsomes. The only significant correlation observed was with the form-selective activity for CYP3A. Of the nine cDNA-expressed P450s examined, only CYP3A4 and CYP2D6 formed N-desmethyl LY333531. However, CYP3A4 formed N-desmethyl LY333531 at a rate 57-fold greater than that observed with CYP2D6. In incubations with human liver microsomes, quinidine, an inhibitor of CYP2D6, demonstrated little inhibition of metabolite formation while ketoconazole, an inhibitor of CYP3A, demonstrated almost complete inhibition. Thus, CYP3A is responsible for the formation of N-desmethyl LY333531. LY333531 and N-desmethyl LY333531 were also examined for their ability to inhibit metabolism mediated by CYP2D6, CYP2C9, CYP3A, and CYP1A2. LY333531 and N-desmethyl LY333531 were found to competitively inhibit CYP2D6 with calculated K(i) values of 0.17 and 1.0 microM, respectively. Less potent inhibition by these compounds of metabolism mediated by the other three P450s examined was observed. In conclusion, CYP3A is primarily responsible for forming N-desmethyl LY333531. Therefore, alterations in the activity of this enzyme have the potential to affect LY333531 clearance. In addition, LY333531 and its metabolite are predicted to be potential inhibitors of CYP2D6-mediated reactions in vivo.