Perspective on Quantitative Structure–Toxicity Relationship (QSTR) Models to Predict Hepatic Biotransformation of Xenobiotics (original) (raw)
Related papers
The role of cytochrome P450 enzymes in hepatic and extrahepatic human drug toxicity
Pharmacology & Therapeutics, 1995
The human cytochrome P450 enzyme system metabolises a wide array of xenobiotics to pharmacologically inactive metabolites, and occasionally, to toxicologically active metabolites. Impairment of cytochrome P450 activity, which may be either genetic or environmental, may lead ta toxicity caused by the parent compound itself. In practise, this usually only applies to drugs that have a narrow therapeutic index and when their clearance is critically dependent upon the fraction normally metabolised by that pathway. P450 enzymes may also convert the drug to a chemically reactive metabolite, which, if not detoxified, may lead to various forms of hepatic and extrahepatic toxicity, including cellular necrosis, hypersensitivity, teratogenicity, and carcinogenicity, depending on the site of formation and the relative stability of the metabolite, and the cellular macromolecule with which it reacts. Variation in the regulation and expression of the drug metabolising enzymes may play a key role in both interindividual variation in sensitivity to drugltoxicity and tissue-specific damage. Avoidance of toxicity may be possible in ram instances by prediction of individual susceptibility or by designing new chemical entities that are metabolised by a range of enzymes (both cytochromes P450 and others) and do not undergo bioactivation.
Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes
Frontiers in Pharmacology, 2015
The adverse effects to humans and environment of only few chemicals are well known. Absorption, distribution, metabolism, and excretion (ADME) are the steps of pharmaco/toxicokinetics that determine the internal dose of chemicals to which the organism is exposed. Of all the xenobiotic-metabolizing enzymes, the cytochrome P450 (CYP) enzymes are the most important due to their abundance and versatility. Reactions catalyzed by CYPs usually turn xenobiotics to harmless and excretable metabolites, but sometimes an innocuous xenobiotic is transformed into a toxic metabolite. Data on ADME and toxicity properties of compounds are increasingly generated using in vitro and modeling (in silico) tools. Both physics-based and empirical modeling approaches are used. Numerous ligand-based and target-based as well as combined modeling methods have been employed to evaluate determinants of CYP ligand binding as well as predicting sites of metabolism and inhibition characteristics of test molecules. In silico prediction of CYP-ligand interactions have made crucial contributions in understanding (1) determinants of CYP ligand binding recognition and affinity; (2) prediction of likely metabolites from substrates; (3) prediction of inhibitors and their inhibition potency. Truly predictive models of toxic outcomes cannot be created without incorporating metabolic characteristics; in silico methods help producing such information and filling gaps in experimentally derived data. Currently modeling methods are not mature enough to replace standard in vitro and in vivo approaches, but they are already used as an important component in risk assessment of drugs and other chemicals.
Frontiers in pharmacology, 2016
Using oxygen and NADPH, the redox enzymes cytochrome P450 (CYP) and its reductase (CPR) work in tandem to carry out the phase I metabolism of a vast majority of drugs and xenobiotics. As per the erstwhile understanding of the catalytic cycle, binding of the substrate to CYP's heme distal pocket allows CPR to pump electrons through a CPR-CYP complex. In turn, this trigger (a thermodynamic push of electrons) leads to the activation of oxygen at CYP's heme-center, to give Compound I, a two-electron deficient enzyme reactive intermediate. The formation of diffusible radicals and reactive oxygen species (DROS, hitherto considered an undesired facet of the system) was attributed to the heme-center. Recently, we had challenged these perceptions and proposed the murburn ("mured burning" or "mild unrestricted burning") concept to explain heme enzymes' catalytic mechanism, electron-transfer phenomena and the regulation of redox equivalents' consumption. Mur...
Regulatory Toxicology and Pharmacology, 2000
Differences in biotransformation activities may alter the bioavailability or efficacy of drugs, provide protection from certain xenobiotic and environmental agents, or increase toxicity of others. Cytochrome P450 (CYP450) enzymes are responsible for the majority of oxidation reactions of drugs and other xenobiotics and differences in their expression may directly produce interindividual differences in susceptibility to compounds whose toxicity is modulated by these enzymes. To rapidly quantify CYP450 forms in human hepatic microsomes, we developed, and applied, an ELISA to 40 samples of microsomes from adult human organ donors. The procedure was reliable and the results were reproducible within normal limits. Protein content for CYP1A, CYP2E1, and CYP3A positively correlated with suitable marker activities. CYP1A, CYP2B, CYP2C6, CYP2C11, CYP2E1, and CYP3A protein content demonstrated 36-, 13-, 11-, 2-, 12-, and 22-fold differences between the highest and lowest samples and the values were normally distributed. Of the forms examined, CYP3A was expressed in the highest amount and it was the only form whose content was correlated with total CYP450 content. Content of other forms was independent of total CYP450. We further determined the contribution of specific forms to the biotransformation of trichloroethylene as a model substrate. CYP2E1 was strongly correlated with chloral hydrate formation from trichloroethylene; CYP2B displayed the strongest correlation with trichloroethanol formation. These data describing the expression and distribution of these forms in human microsomes can be used to extrapolate in vitro derived metabolic rates for toxicologically important reactions, when form selectivity and specific activity are known. This approach may be applied to refine estimates of human interindividual differences in susceptibility for application in human health risk assessment.
Current Drug Metabolism
Numerous members of the cytochrome P450 (CYP) superfamily are induced after exposure to a variety of xenobiotics in human liver. We have gained considerable mechanistic insights into these processes in hepatocytes and multiple ligand-activated transcription factors have been identified over the past two decades. Families CYP1, CYP2 and CYP3 involved in xenobiotic metabolism are also expressed in a range of extrahepatic tissues (e.g. intestine, brain, kidney, placenta, lung, adrenal gland, pancreas, skin, mammary gland, uterus, ovary, testes and prostate). Since the expression of the majority of the isoforms appears to be very low in the extrahepatic tissues in comparison with predominant expression in adult liver, the role of the enzymes in overall biotransformation and total body clearance is minor. However, basal expression and up-regulation of extrahepatic CYP enzymes can significantly affect local disposition of xenobiotics or endogenous compounds in peripheral tissues and thus modify their pharmacological/toxicological effects or affect absorption of xenobiotics into systemic circulation. The goal of this review is to critically examine our current understanding of molecular mechanisms involved in induction of xenobiotic metabolizing CYP genes of human families CYP1, CYP2 and CYP3 by exogenous chemicals in extrahepatic tissues. We concentrate on organs such as the intestine, kidney, lung, placenta and skin, which are involved in drug distribution and clearance or are in direct contact with environmental xenobiotics. We also discuss single nucleotide polymorphisms (SNPs) of key CYPs, which at the level of transcription affect expression of the genes in the extrahepatic tissues or are associated with some pathophysiological stages or disorders in the organs.
Cross-species analysis of hepatic cytochrome P450 and transport protein expression
Archives of Toxicology, 2020
Most drugs and xenobiotics are metabolized in the liver. Amongst others, different cytochrome P450 (CYP) enzymes catalyze the metabolic conversion of foreign compounds, and various transport proteins are engaged in the excretion of metabolites from the hepatocytes. Inter-species and inter-individual differences in the hepatic levels and activities of drug-metabolizing enzymes and transporters result from genetic as well as from environmental factors, and play a decisive role in determining the pharmacokinetic properties of a compound in a given test system. To allow for a meaningful comparison of results from metabolism studies, it is, therefore, of utmost importance to know about the specific metabolic properties of the test systems, especially about the levels of metabolic enzymes such as the CYPs. Using a targeted proteomics approach, we, therefore, compared the hepatic levels of important CYP enzymes and transporters in different experimental systems in vivo and in vitro, namely...
Murburn precepts for cytochrome P450 mediated drug/xenobiotic metabolism
2020
Herein, we demonstrate why deeming diffusible reactive oxygen species (DROS) as toxic wastes does not afford a comprehensive understanding of cytochrome P450 mediated microsomal xenobiotic metabolism (mXM). Using the recent insights unveiled in mechanistic redox enzymology, we reason out the remaining pieces of the mXM mechanistic chemistry and support our proposals with visual evidence and thermodynamic calculations. Particularly, we elucidate how murburn model better explains- (i) promiscuity of the unique P450-reductase; (ii) prolific activity and inhibitions of CYP3A4; (iii) structure-function correlations of important key CYP2 family isozymes- 2C9, 2D6 and 2E1; and (iv) mutation studies and mechanism-based inactivation of CYPs. In the light of our findings, it is opportune to revamp the methodologies employed for screening potential drug candidate from lead molecules.
Site of metabolism prediction for six biotransformations mediated by cytochromes P450
Bioinformatics, 2009
Motivation: One goal of metabolomics is to define and monitor the entire metabolite complement of a cell, while it is still far from reach since systematic and rapid approaches for determining the biotransformations of newly discovered metabolites are lacking. For drug development, such metabolic biotransformation of a new chemical entity (NCE) is of more interest because it may profoundly affect its bioavailability, activity and toxicity profile. The use of in silico methods to predict the site of metabolism (SOM) in phase I cytochromes P450-mediated reactions is usually a starting point of metabolic pathway studies, which may also assist in the process of drug/lead optimization. Results: This article reports the Cytochromes P450 (CYP450)-mediated SOM prediction for the six most important metabolic reactions by incorporating the use of machine learning and semi-empirical quantum chemical calculations. Non-local models were developed on the basis of a large dataset comprising 1858 m...
Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions
British Journal of Pharmacology, 2009
The cytochromes P450 (CYPs) comprise a vast superfamily of enzymes found in virtually all life forms. In mammals, xenobiotic metabolizing CYPs provide crucial protection from the effects of exposure to a wide variety of chemicals, including environmental toxins and therapeutic drugs. Ideally, the information on the possible metabolism by CYPs required during drug development would be obtained from crystal structures of all the CYPs of interest. For some years only crystal structures of distantly related bacterial CYPs were available and homology modelling techniques were used to bridge the gap and produce structural models of human CYPs, and thereby obtain useful functional information. A significant step forward in the reliability of these models came seven years ago with the first crystal structure of a mammalian CYP, rabbit CYP2C5, followed by the structures of six human enzymes, CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2D6 and CYP3A4, and a second rabbit enzyme, CYP2B4. In this review we describe as a case study the evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism. This work has led directly to the successful design of CYP2D6 mutants with novel activity-including creating a testosterone hydroxylase, converting quinidine from inhibitor to substrate, creating a diclofenac hydroxylase and creating a dextromethorphan O-demethylase. Our modelling-derived hypothesis-driven integrated interdisciplinary studies have given key insight into the molecular determinants of CYP2D6 and other important drug metabolizing enzymes.