Molecular modelling and quantitative structure-activity relationship studies on the interaction of omeprazole with cytochrome P450 isozymes

[Modeling of drug-drug interactions between omeprazole and erythromycin with cytochrome P450 3A4 in vitro assay]

In the present study the electrochemical system based on recombinant cytochrome P450 3A4 (CYP3A4) was used for the investigation of potential drug-drug interaction between medicinal preparations employed for Helicobacter pylori eradication therapy. Drug interactions were demonstrated in association of omeprazole as a proton pump inhibitor (PPI) and macrolide antibiotic erythromycin during cytochrome P450 3A4-mediated metabolism. It was shown that in the presence of omeprazole the rate of N-demethylase activity of CYP3A4 to erythromycin measured by means of product (formaldehyde) formation decreased. Mass-spectrometry analysis of omeprazole sulfone as a CYP3A4-mediated metabolite demonstrated the absence of erythromycin influence on CYP3A4-dependent omeprazole metabolism. This phenomenon may be explained by lower spectral dissociation constant of CYP3A4-omeprazole complex (Kd = 18±2 μM) than that of CYP3A4-erythromycin complex (Kd = 52 μM). Using the electrochemical model of electrochemically-driven drug metabolism it is possible to register CYP3A4-mediated catalytic conversion of certain drugs. In vitro experiments of potential CYP3A4-mediated drug-drug interactions are in accordance with in silico modeling with program PASS and PoSMNA descriptors in the case of omeprazole/erythromycin combinations.

Inhibition of cytochrome P450 3A by acetoxylated analogues of resveratrol in in vitro and in silico models

Many dietary compounds, including resveratrol, are potent inhibitors of CYP3A4. Here we examined the potential to predict inhibition capacity of dietary polyphenolics using an in silico and in vitro approaches and synthetic model compounds. Mono, di, and tri-acetoxy resveratrol were synthesized, a cell line of human intestine origin and microsomes from rat liver served to determine their in vitro inhibition of CYP3A4, and compared to that of resveratrol. Docking simulation served to predict the affinity of the synthetic model compounds to the enzyme. Modelling of the enzyme’s binding site revealed three types of interaction: hydrophobic, electrostatic and H-bonding. The simulation revealed that each of the examined acetylations of resveratrol led to the loss of important interactions of all types. Tri-acetoxy resveratrol was the weakest inhibitor in vitro despite being the more lipophilic and having the highest affinity for the binding site. The simulation demonstrated exclusion of all interactions between tri-acetoxy resveratrol and the heme due to distal binding, highlighting the complexity of the CYP3A4 binding site, which may allow simultaneous accommodation of two molecules. Finally, the use of computational modelling may serve as a quick predictive tool to identify potential harmful interactions between dietary compounds and prescribed drugs.

Interactions between CYP3A4 and Dietary Polyphenols

The human cytochrome P450 enzymes (P450s) catalyze oxidative reactions of a broad spectrum of substrates and play a critical role in the metabolism of xenobiotics, such as drugs and dietary compounds. CYP3A4 is known to be the main enzyme involved in the metabolism of drugs and most other xenobiotics. Dietary compounds, of which polyphenolics are the most studied, have been shown to interact with CYP3A4 and alter its expression and activity. Traditionally, the liver was considered the prime site of CYP3A-mediated first-pass metabolic extraction, but in vitro and in vivo studies now suggest that the small intestine can be of equal or even greater importance for the metabolism of polyphenolics and drugs. Recent studies have pointed to the role of gut microbiota in the metabolic fate of polyphenolics in human, suggesting their involvement in the complex interactions between dietary polyphenols and CYP3A4. Last but not least, all the above suggests that coadministration of drugs and foods that are rich in polyphenols is expected to stimulate undesirable clinical consequences. This review focuses on interactions between dietary polyphenols and CYP3A4 as they relate to structural considerations, food-drug interactions, and potential negative consequences of interactions between CYP3A4 and polyphenols.

QSAR of cytochrome inhibitors

Cytochrome P450 (CYP450) enzymes are predominantly involved in the Phase I metabolism of xenobiotics. Metabolic inhibition and induction can give rise to clinically important drug-drug interactions. Metabolic stability is a prerequisite for sustaining the therapeutically relevant concentrations, and very often drug candidates are sacrificed due to poor metabolic profiles. Computational tools such as quantitative structure-activity relationships are widely used to study different metabolic end points successfully to accelerate the drug discovery process. There are a lot of computational studies on clinically important CYPs already reported in recent years. But other clinically significant families are to yet be explored computationally. Powerfulness of quantitative structure-activity relationship will drive computational chemists to develop new potent and selective inhibitors of different classes of CYPs for the treatment of different diseases with least drug-drug interactions. Furthermore, there is a need to enhance the accuracy, interpretability and confidence in the computational models in accelerating the drug discovery pathways.

Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling

The metabolism mechanism of (S)-N-[1-(3-morpholin-4ylphenyl)ethyl]-3-phenylacrylamide, mediated by CYP3A4 Cytochrome has been investigated by density functional QM calculations aided with molecular mechanics/molecular dynamics simulations. Two different orientations of phenyl ring for substrate approach toward oxyferryl center, imposing two subsequent rearrangement pathways have been investigated. Starting from sigma-complex in perpendicular orientation enzymatic mechanism involves consecutive proton shuttle intermediate, which further leads to the formation of alcohol and ketone. Parallel conformation leads solely to ketone product by 1,2 hydride shift. Although parallel and perpendicular sigma-complexes are energetically equivalent both for the gas phase or PCM solvent model, molecular dynamics studies in full CYP3A4 environment show that perpendicular conformation of the sigma-complex should be privileged, stabilized by hydrophobic interactions of phenylacrylamide chain. After assessing probability of the two conformations we postulate that the alcohol, accessible with the lowest energy barriers should be the major metabolite for studied substrate and CYP3A4 enzyme.

Quantitative structure-activity relationships (QSARs) within the cytochrome P450 system: QSARs describing substrate binding, inhibition and induction of P450s

Quantitative structure-activity relationships (QSARs) within substrates, inducers and inhibitors of cytochromes P450 involved in xenobiotic metabolism are reported, together with QSARs associated with induction, inhibition and metabolic rate. The importance of frontier orbitals and shape descriptors, such as planarity (estimated by the area/depth(2) parameter) and rectangularity (estimated by the length/width parameter) is discussed, particularly in the context of the COMPACT system which discriminates between several P450 families associated with the activation and detoxication of xenobiotics. The use of parameters, particularly those derived from homology modelling of mammalian (especially human) P450s that are involved in exogenous metabolism, in generating QSARs for P450 substrates is discussed in the context of explaining differences in the binding affinities of human P450 substrates which are pharmacologically active.

Benzimidazole drugs and modulation of biotransformation enzymes

Benzimidazole drugs (e.g., anthelmintics albendazole, fenbendazole, oxfenbendazole, thiabendazole, mebendazole; inhibitors of proton pump omeprazole, lansoprasole, pantoprasole) represent substances used in both human and veterinary medicine; however, from the point of view of induction and inhibition of biotransformation enzymes, research has been carried out mainly due to the initiative of human pharmacologists. The purpose of the present review is to inform about inductive and inhibitive effects of benzimidazole drugs in man, animals and cell cultures. Pharmacological and toxicological consequences of modulation of biotransformation enzymes are discussed and the significance of studies in the field of modulation of biotransformation enzymes in food-producing animals is explained. Since the modulating effect of benzimidazoles strongly varies depending on structure of the individual substances, the particular attention is paid to structure-modulation relationships.

Modelling human cytochromes P450 involved in drug metabolism from the CYP2C5 crystallographic template

A historical background to homology modelling of human P450s involved in drug metabolism is outlined, showing that the progress in crystallographic studies of bacterial forms of enzyme and, latterly, determination of a mammalian P450 crystal structure, has enabled the production of increasingly satisfactory models of human P450 enzymes. The methodology for the generation of P450 models by homology with crystallographic template structures is summarized, and recent results of CYP2C5-constructed models of P450s are described. These indicate that selective substrates are able to fit within the putative active sites of each enzyme, where key contacts with complementary amino acid residues are largely consistent with the results of site-directed mutagenesis experiments and metabolic studies. Consequently, the CYP2C5 crystal structure can be regarded at the current paradigm for homology modelling of the drug metabolizing P450s, especially those from the CYP2 family.

Computer systems for the prediction of xenobiotic metabolism

The aim of pharmaceutical research and development is to ensure a continuing pipeline of new chemical entities (NCEs) displaying high therapeutic efficacy with few or no side effects. Failure of promising lead candidates late in the drug discovery processes is regarded as commercially unacceptable in today's increasingly competitive business environment. An inappropriate ADME/Toxicity profile in humans is the major cause of failure of lead candidates in late clinical stages of drug development. Combinatorial chemistry techniques coupled with high throughput screening protocols means that pharmaceutical companies are now dealing with an unprecedented number of NCEs on an annual basis. As a consequence, screening for undesirable ADME/Toxicity properties in the early stages of drug development, preferably pre-synthesis, is now considered the essential paradigm. In silico assessment of NCEs is rapidly emerging as the next wave of technology for early ADME/Toxicity prediction. In this review, we discuss the major commercially available products for the assessing the potential metabolic activity of xenobiotic substances in mammalian systems.

Summary of information on human CYP enzymes: human P450 metabolism data

This chapter is an update of the data on substrates, reactions, inducers, and inhibitors of human CYP enzymes published previously by Rendic and DiCarlo (1), now covering selection of the literature through 2001 in the reference section. The data are presented in a tabular form (Table 1) to provide a framework for predicting and interpreting the new P450 metabolic data. The data are formatted in an Excel format as most suitable for off-line searching and management of the Web-database. The data are presented as stated by the author(s) and in the case when several references are cited the data are presented according to the latest published information. The searchable database is available either as an Excel file (for information contact the author), or as a Web-searchable database (Human P450 Metabolism Database, www.gentest.com) enabling the readers easy and quick approach to the latest updates on human CYP metabolic reactions.

Application of in silico approaches to predicting drug--drug interactions

In an environment driven to find the next blockbuster drug, failure years into a project should not be an option. Recent studies have shown that poor absorption, distribution, metabolism, and excretion (ADME), and the related properties of toxicity and pharmacokinetics are responsible for a large proportion of failures. One way to understand and potentially predict molecules likely to be successful in humans as drugs from an ADME point of view is to use simulations. Such simulations may include simple rule-based approaches, structure--activity relationships, three-dimensional quantitative structure--activity relationships (3D-QSAR), and pharmacophores. All of these represent useful tools in understanding metabolism by the cytochromes P450, predicting drug--drug interactions (DDIs), and other pharmacokinetic parameters. The present paper briefly reviews the application of some computational tools applied to predicting DDIs and will provide the reader with an idea of their utility.

On the recognition of mammalian microsomal cytochrome P450 substrates and their characteristics: towards the prediction of human p450 substrate specificity and metabolism

The characteristics of mammalian microsomal P450 xenobiotic substrates are described, particularly with reference to the major P450 isoforms associated with drug metabolism in humans. It is further reported that a relatively small number of molecular, electronic, and physico-chemical properties are required to discriminate between chemicals that exhibit specificity for human P450 isoforms: CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A4. Molecular templates of superimposed substrates are shown to be complementary with the putative active sites of the relevant enzymes, thus enabling a possible prediction of P450 specificity from structure. Factors contributing to metabolic clearance and binding affinity are also discussed, and methods for their calculation are described.

Structural characteristics of human P450s involved in drug metabolism: QSARs and lipophilicity profiles

The factors with human P450 substrate selectivity are reviewed, together with extensive tabulation of quantitative relationships between structure and activity for many species of P450 substrates, inducers and inhibitors. In addition, the physicochemical characteristics (logP and pK(a) values) of heptic microsomal P450 substrates are collated, such that comparisons can be made on the grounds of compound lipophilicities.

Molecular modelling of CYP1 family enzymes CYP1A1, CYP1A2, CYP1A6 and CYP1B1 based on sequence homology with CYP102

Molecular modelling of a number of CYP1 family enzymes from rat, plaice and human is described based on amino acid sequence homology with the haemoprotein domain of CYP102, a unique bacterial P450 of known structure. The interaction of various substrates and inhibitors within the putative active sites of rat CYP1A1, human CYP1A2, a fish CYP1 enzyme CYP1A6 (from plaice) and human CYP1B1, is shown to be consistent with P450-mediated oxidation in each example or, in the case of inhibitors, mechanism of inhibition. It is reported that relatively small changes between the enzymes' active site regions assist in the rationalization of CYP1 enzyme preferences for particular substrate types, and a template of superimposed CYP1A2 substrates is shown to fit the putative active site of the human CYP1A2 enzyme.

Homology modelling of human cytochromes P450 involved in xenobiotic metabolism and rationalization of substrate selectivity

Molecular modelling of human cytochrome P450 (CYP) isoforms is described, based on amino acid sequence homology with a unique bacterial P450 (CYP102) of known crystal structure. It is found that for the human hepatic P450s involved in the metabolism of xenobiotics, ie. CYPIA2, CYP 1A6, CYP2B6, CYP2C9, CYP2C 19, CYP2D6, CYP2E1 and CYP3A4, there is a satisfactory agreement between specific substrate characteristics and topographical features of the putative active sites, including complementarity with key amino acid residues in the P450 haem environments. A combination of homology model interactions with substrates and certain molecular properties of the compounds themselves provides a methodology for the evaluation of potential P450 selectivity in new chemical entities (NCEs).

The role of cisapride in the treatment of pediatric gastroesophageal reflux. The European Society of Paediatric Gastroenterology, Hepatology and Nutrition

BACKGROUND

Cisapride is a gastrointestinal prokinetic agent that is used worldwide in the treatment of gastrointestinal motility-related disorders in premature infants, full-term infants, and children. Efficacy data suggest that it is the most effective commercially available prokinetic drug.

METHODS

Because of recent concerns about safety, a critical and in-depth analysis of all reported adverse events was performed and resulted in the conclusions and recommendations that follow.

RESULTS

Cisapride should only be administered to patients in whom the use of prokinetics is justified according to current medical knowledge. If cisapride is given to pediatric patients who can be considered healthy except for their gastrointestinal motility disorder, and the maximum dose does not exceed 0.8 mg/kg per day in 3 to 4 administrations of 0.2 mg/kg (not exceeding 40 mg/d), no special safety procedures regarding potential cardiac adverse events are recommended. However, if cisapride is prescribed for patients who are known to be or are suspected of being at increased risk for drug-associated increases in QTc interval, certain precautions are advisable. Such patients include those:(1) with a previous history of cardiac dysrhythmias, (2) receiving drugs known to inhibit the metabolism of cisapride and/or adversely affect ventricular repolarisation, (3) with immaturity and/or disease causing reduced cytochrome P450 3A4 activity, or (4) with electrolyte disturbances. In such patients, ECG monitoring to quantitate the QTc interval should be used before initiation of therapy and after 3 days of treatment to ascertain whether a cisapride-induced cardiac adverse effect is present.

CONCLUSIONS

With rare exceptions, the total daily dose of cisapride should not exceed 0.8 mg/kg divided into 3 or 4 approximately equally spaced doses. If higher doses than this are given, the precautions above are advisable. In any patient in whom a prolonged QTc interval is found, the dose of cisapride should be reduced or the drug discontinued until the ECG normalizes. If the QTc interval returns to normal after withdrawal of cisapride, and the administration of cisapride is considered to be justified because of its efficacy and absence of alternative treatment options, cisapride can be restarted at half dose with control of the QTc interval. Unfortunately, at present, normal ranges of QTc interval in children are unknown. However, a critical analysis of the literature suggests that a duration of less than 450 milliseconds can be considered to be within the normal range and greater than 470 milliseconds as outside it.