Establishing a systematic framework to characterise in vitro methods for human hepatic metabolic clearance

Systematic health risks assessment of chiral fungicide famoxadone: Stereoselectivities in ferroptosis-mediated cytotoxicity and metabolic behavior

Famoxadone is a chiral fungicide frequently found in the environment and agricultural products. However, the health risks of famoxadone enantiomers are not well understood. This study investigated the stereoselective cytotoxicity and metabolic behavior of famoxadone enantiomers in mammals. Results showed that R-famoxadone was 1.5 times more toxic to HepG2 cells than S-famoxadone. R-famoxadone induced more pronounced ferroptosis compared to S-famoxadone. It caused greater upregulation of genes related to iron transport and lipid peroxidation, and greater downregulation of genes related to peroxide clearance. Furthermore, R-famoxadone induced more severe lipid peroxidation and reactive oxygen species (ROS) accumulation through ACSL4 activation and GPX4 inhibition. Additionally, the bioavailability of R-famoxadone in mice was six times higher than that of S-famoxadone. Liver microsome assays, cytochrome P450 (CYP450) inhibition assays, human recombinant CYP450 assays, and molecular docking suggested that the lower binding affinities of CYP2C8, CYP2C19, and CYP2E1 for R-famoxadone caused its preferential accumulation. Overall, R-famoxadone poses a higher risk than S-famoxadone due to its greater cytotoxicity and persistence. This study provides the first evidence of ferroptosis-induced stereoselective toxicity, offering insights for the comprehensive health risk assessment of chiral famoxadone and valuable references for the application of high-efficiency, low-risk pesticide enantiomers.

In Vitro Hepatic Clearance Evaluations of Per- and Polyfluoroalkyl Substances (PFAS) across Multiple Structural Categories

Toxicokinetic (TK) assays and in vitro-in vivo extrapolation (IVIVE) models are New Approach Methods (NAMs) used to translate in vitro points of departure to exposure estimates required to reach equivalent blood concentrations. Per- and polyfluoroalkyl substances (PFAS) are a large chemical class with wide-ranging industrial applications for which only limited toxicity data are available for human health evaluation. To address the lack of TK data, a pooled primary human hepatocyte suspension model was used with targeted liquid chromatography-mass spectrometry to investigate substrate depletion for 54 PFAS. A median value of 4.52 μL/(min x million cells) was observed across those that showed significant clearance, with 35 displaying no substrate depletion. Bayesian modeling propagated uncertainty around clearance values for use in IVIVE models. Structural evaluations showed the fluorotelomer carboxylic acids were the only PFAS carboxylates showing appreciable clearance, and per- and polyfluorosulfonamides were more readily metabolized than other PFAS sulfonates. Biotransformation product prediction, using the chemical transformation simulator, suggested hydrolysis of PFAS sulfonamides to more stable sulfonic acids, which is an important consideration for exposure modeling. This effort greatly expands the PFAS in vitro toxicokinetic dataset, enabling refined TK modeling, in silico tool development, and NAM-based human health evaluations across this important set of emerging contaminants.

Assessing environmental and human health risks: Insight from the enantioselective metabolism and degradation of fenpropidin

Fenpropidin (FPD), a widely employed chiral fungicide, is frequently detected in diverse environments. In an in vitro rat liver microsomes cultivation (RLMs), the metabolism exhibited the order of R-FPD > S-FPD, with respective half-lives of 10.42 ± 0.11 and 12.06 ± 0.15 min, aligning with kinetic analysis results. CYP3A2 has been demonstrated to be the most significant oxidative enzyme through CYP450 enzyme inhibition experiments. Molecular dynamics simulations unveiled the enantioselective metabolic mechanism, demonstrating that R-FPD forms hydrogen bonds with the CYP3A2 protein, resulting in a higher binding affinity (-6.58 kcal mol-1) than S-FPD. Seven new metabolites were identified by Liquid chromatography time-of-flight high-resolution mass spectrometry, which were mainly generated through oxidation, reduction, hydroxylation, and N-dealkylation reactions. The toxicity of the major metabolites predicted by the TEST procedure was found to be stronger than the predicted toxicity of FPD. Moreover, the enantioselective fate of FPD was studied by examining its degradation in three soils with varying physical and chemical properties under aerobic, anaerobic, and sterile conditions. Enantioselective degradation of FPD occurred in soils without enantiomeric transformation, displaying a preference for R-FPD degradation. R-FPD is a low-risk stereoisomer both in the environment and in mammals. The research presented a systematic and comprehensive method for analyzing the metabolic and degradation system of FPD enantiomers. This approach aids in understanding the behavior of FPD in the environment and provides valuable insights into their potential risks to human health.

Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance

In vitro-in vivo extrapolation is a commonly applied technique for liver clearance prediction. Various in vitro models are available such as hepatocytes, human liver microsomes, or recombinant cytochromes P450. According to the free drug theory, only the unbound fraction (fu) of a chemical can undergo metabolic changes. Therefore, to ensure the reliability of predictions, both specific and nonspecific binding in the model should be accounted. However, the fraction unbound in the experiment is often not reported. The study aimed to provide a detailed repository of the literature data on the compound's fu value in various in vitro systems used for drug metabolism evaluation and corresponding human plasma binding levels. Data on the free fraction in plasma and different in vitro models were supplemented with the following information: the experimental method used for the assessment of the degree of drug binding, protein or cell concentration in the incubation, and other experimental conditions, if different from the standard ones, species, reference to the source publication, and the author's name and date of publication. In total, we collected 129 literature studies on 1425 different compounds. The provided data set can be used as a reference for scientists involved in pharmacokinetic/physiologically based pharmacokinetic modelling as well as researchers interested in Quantitative Structure-Activity Relationship models for the prediction of fraction unbound based on compound structure. Database URL: https://data.mendeley.com/datasets/3bs5526htd/1.

Metabolites in the regulatory risk assessment of pesticides in the EU

A large majority of chemicals is converted into metabolites through xenobiotic-metabolising enzymes. Metabolites may present a spectrum of characteristics varying from similar to vastly different compared with the parent compound in terms of both toxicokinetics and toxicodynamics. In the pesticide arena, the role of metabolism and metabolites is increasingly recognised as a significant factor particularly for the design and interpretation of mammalian toxicological studies and in the toxicity assessment of pesticide/metabolite-associated issues for hazard characterization and risk assessment purposes, including the role of metabolites as parts in various residues in ecotoxicological adversities. This is of particular relevance to pesticide metabolites that are unique to humans in comparison with metabolites found in in vitro or in vivo animal studies, but also to disproportionate metabolites (quantitative differences) between humans and mammalian species. Presence of unique or disproportionate metabolites may underlie potential toxicological concerns. This review aims to present the current state-of-the-art of comparative metabolism and metabolites in pesticide research for hazard and risk assessment, including One Health perspectives, and future research needs based on the experiences gained at the European Food Safety Authority.

Identifying xenobiotic metabolites with in silico prediction tools and LCMS suspect screening analysis

Understanding the metabolic fate of a xenobiotic substance can help inform its potential health risks and allow for the identification of signature metabolites associated with exposure. The need to characterize metabolites of poorly studied or novel substances has shifted exposure studies towards non-targeted analysis (NTA), which often aims to profile many compounds within a sample using high-resolution liquid-chromatography mass-spectrometry (LCMS). Here we evaluate the suitability of suspect screening analysis (SSA) liquid-chromatography mass-spectrometry to inform xenobiotic chemical metabolism. Given a lack of knowledge of true metabolites for most chemicals, predictive tools were used to generate potential metabolites as suspect screening lists to guide the identification of selected xenobiotic substances and their associated metabolites. Thirty-three substances were selected to represent a diverse array of pharmaceutical, agrochemical, and industrial chemicals from Environmental Protection Agency's ToxCast chemical library. The compounds were incubated in a metabolically-active in vitro assay using primary hepatocytes and the resulting supernatant and lysate fractions were analyzed with high-resolution LCMS. Metabolites were simulated for each compound structure using software and then combined to serve as the suspect screening list. The exact masses of the predicted metabolites were then used to select LCMS features for fragmentation via tandem mass spectrometry (MS/MS). Of the starting chemicals, 12 were measured in at least one sample in either positive or negative ion mode and a subset of these were used to develop the analysis workflow. We implemented a screening level workflow for background subtraction and the incorporation of time-varying kinetics into the identification of likely metabolites. We used haloperidol as a case study to perform an in-depth analysis, which resulted in identifying five known metabolites and five molecular features that represent potential novel metabolites, two of which were assigned discrete structures based on in silico predictions. This workflow was applied to five additional test chemicals, and 15 molecular features were selected as either reported metabolites, predicted metabolites, or potential metabolites without a structural assignment. This study demonstrates that in some-but not all-cases, suspect screening analysis methods provide a means to rapidly identify and characterize metabolites of xenobiotic chemicals.

Impact of chemical structure on the in vitro hydrolysis of fatty esters of 2-ethylhexanoic acid or 2-ethylhexanol and extrapolation to the in vivo situation

Fatty esters of 2-ethylhexanoic acid (EHA) and 2-ethylhexanol (EH) are commonly used in cosmetics. Human liver and skin S9 and human plasma were used to determine the in vitro rates of clearance (CL_int) of a series of compounds, with a range of 2-11 carbons on the acid or alcohol moiety and branching at the C2 position. The impact of carbon chain length on in vitro CL_int was most prominent for the liver metabolism of esters of EH, while for in vitro skin metabolism it was greater for esters of EHA. The position of the branching also impacted the liver hydrolysis rates, especially for the C3, C4, and C5 esters with lower CL_{int in vitro} rates for esters of EHA relative to those of EH. When the in vitro intrinsic clearance rates were scaled to in vivo rates of hepatic clearance, all compounds approximated the rate for hepatic blood flow, mitigating this dependence of metabolism on structure. This work shows how structural changes to the molecule can affect in vitro metabolism and, furthermore, allows for an estimation of the in vivo metabolism.

Using liver models generated from human-induced pluripotent stem cells (iPSCs) for evaluating chemical-induced modifications and disease across liver developmental stages

The liver is a pivotal organ regulating critical developmental stages of fetal metabolism and detoxification. Though numerous studies have evaluated links between prenatal/perinatal exposures and adverse health outcomes in the developing fetus, the central role of liver to health disruptions resulting from these exposures remains understudied, especially concerning early development and later-in-life health outcomes. While numerous in vitro methods for evaluating liver toxicity have been established, the use of iPSC-derived hepatocytes appears to be particularly well suited to contribute to this critical research gap due to their potential to model a diverse range of disease phenotypes and different stages of liver development. The following key aspects are reviewed: (1) an introduction to developmental liver toxicity; (2) an introduction to embryonic and induced pluripotent stem cell models; (3) methods and challenges for deriving liver cells from stem cells; and (4) applications for iPSC-derived hepatocytes to evaluate liver developmental stages and their associated responses to insults. We conclude that iPSC-derived hepatocytes have great potential for informing liver toxicity and underlying disease mechanisms via the generation of patient-specific iPSCs; implementing large-scale drug and chemical screening; evaluating general biological responses as a potential surrogate target cell; and evaluating inter-individual disease susceptibility and response variability.

Advances in computational methods along the exposure to toxicological response paradigm

Human health risk assessment is a function of chemical toxicity, bioavailability to reach target biological tissues, and potential environmental exposure. These factors are complicated by many physiological, biochemical, physical and lifestyle factors. Furthermore, chemical health risk assessment is challenging in view of the large, and continually increasing, number of chemicals found in the environment. These challenges highlight the need to prioritize resources for the efficient and timely assessment of those environmental chemicals that pose greatest health risks. Computational methods, either predictive or investigative, are designed to assist in this prioritization in view of the lack of cost prohibitive in vivo experimental data. Computational methods provide specific and focused toxicity information using in vitro high throughput screening (HTS) assays. Information from the HTS assays can be converted to in vivo estimates of chemical levels in blood or target tissue, which in turn are converted to in vivo dose estimates that can be compared to exposure levels of the screened chemicals. This manuscript provides a review for the landscape of computational methods developed and used at the U.S. Environmental Protection Agency (EPA) highlighting their potentials and challenges.

Non-specific binding of compounds in in vitro metabolism assays: a comparison of microsomal and hepatocyte binding in different species and an assessment of the accuracy of prediction models

Non-specific binding in in vitro metabolism systems leads to an underestimation of the true intrinsic metabolic clearance of compounds being studied. Therefore in vitro binding needs to be accounted for when extrapolating in vitro data to predict the in vivo metabolic clearance of a compound. While techniques exist for experimentally determining the fraction of a compound unbound in in vitro metabolism systems, early in drug discovery programmes computational approaches are often used to estimate the binding in the in vitro system.Experimental fraction unbound data (n = 60) were generated in liver microsomes (fu_mic) from five commonly used pre-clinical species (rat, mouse, dog, minipig, monkey) and humans. Unbound fraction in incubations with mouse, rat or human hepatocytes was determined for the same 60 compounds. These data were analysed to determine the relationship between experimentally determined binding in the different matrices and across different species. In hepatocytes there was a good correlation between fraction unbound in human and rat (r²=0.86) or mouse (r²=0.82) hepatocytes. Similar correlations were observed between binding in human liver microsomes and microsomes from rat, mouse, dog, Göttingen minipig or monkey liver microsomes (r² of >0.89, n = 51 - 52 measurements in different species). Physicochemical parameters (logP, pKa and logD) were predicted for all evaluated compounds. In addition, logP and/or logD were measured for a subset of compounds.Binding to human hepatocytes predicted using 5 different methods was compared to the measured data for a set of 59 compounds. The best methods evaluated used measured microsomal binding in human liver microsomes to predict hepatocyte binding. The collated physicochemical data were used to predict the human fu_mic using four different in silico models for a set of 53-60 compounds. The correlation (r²) and root mean square error between predicted and observed microsomal binding was 0.69 & 0.20, 0.47 & 0.23, 0.56 & 0.21 and 0.54 & 0.26 for the Turner-Simcyp, Austin, Hallifax-Houston and Poulin models, respectively. These analyses were extended to include measured literature values for binding in human liver microsomes for a larger set of compounds (n=697). For the larger dataset of compounds, microsomal binding was well predicted for neutral compounds (r²=0.67 - 0.70) using the Poulin, Austin, or Turner-Simcyp methods but not for acidic or basic compounds (r²<0.5) using any of the models. While the lipophilicity-based models can be used, the in vitro binding should be measured for compounds where more certainty is needed, using appropriately calibrated assays and possibly established weak, moderate, and strong binders as reference compounds to allow comparison across databases.

Scientific Opinion of the Scientific Panel on Plant Protection Products and their Residues (PPR Panel) on testing and interpretation of comparative in vitro metabolism studies

EFSA asked the Panel on Plant Protection Products and their residues to deliver a Scientific Opinion on testing and interpretation of comparative in vitro metabolism studies for both new active substances and existing ones. The main aim of comparative in vitro metabolism studies of pesticide active substances is to evaluate whether all significant metabolites formed in the human in vitro test system, as a surrogate of the in vivo situation, are also present at comparable level in animal species tested in toxicological studies and, therefore, if their potential toxicity has been appropriately covered by animal studies. The studies may also help to decide which animal model, with regard to a particular compound, is the most relevant for humans. In the experimental strategy, primary hepatocytes in suspension or culture are recommended since hepatocytes are considered the most representative in vitro system for prediction of in vivo metabolites. The experimental design of 3 × 3 × 3 (concentrations, time points, technical replicates, on pooled hepatocytes) will maximise the chance to identify unique (UHM) and disproportionate (DHM) human metabolites. When DHM and UHM are being assessed, test item-related radioactivity recovery and metabolite profile are the most important parameters. Subsequently, structural characterisation of the assigned metabolites is performed with appropriate analytical techniques. In toxicological assessment of metabolites, the uncertainty factor approach is the first alternative to testing option, followed by new approach methodologies (QSAR, read-across, in vitro methods), and only if these fail, in vivo animal toxicity studies may be performed. Knowledge of in vitro metabolites in human and animal hepatocytes would enable toxicological evaluation of all metabolites of concern, and, furthermore, add useful pieces of information for detection and evaluation of metabolites in different matrices (crops, livestock, environment), improve biomonitoring efforts via better toxicokinetic understanding, and ultimately, develop regulatory schemes employing physiologically based or physiology-mimicking in silico and/or in vitro test systems to anticipate the exposure of humans to potentially hazardous substances in plant protection products.

Determination of in vitro metabolic hepatic clearance of valproic acid (VPA) and five analogues by UPLC-MS-QTOF, applicable in alternatives to animal testing

Laboratory measurements of intrinsic clearance support the development of TK models, with potential relevance to weight of evidence toxicity assessments of xenobiotics, including read-across, the concept of predictive estimation by data extrapolation between chemicals of similar structure (analogues). In this work a procedure with analytical method for determination of in vitro hepatic metabolic clearance, relevant to biotransformation toxicokinetic (TK) modelling, is presented. Cryopreserved primary human hepatocytes represent a suitable cells, due to their biological characteristics, for providing an in vitro model for simulating in vivo metabolic clearance. The experimental part considered an adequate sequential time-frame for collecting samples and controls for all chemicals tested, including centrifugation and aliquoting of the corresponding fractions until the instrumental session. For the first time, in vitro hepatocyte intrinsic clearance was measured for six analogue test chemicals: valproic acid, 2-ethyl caproic acid, octanoic acid, valeric acid, 2-methyl butyric acid and 2-trans pentenoic acid, during incubated cell culture exposure up to 2 h or 3.5 h. The time dependence of any metabolism was determined from analysis of the supernatant at intervals using a new developed analytical method for UPLC coupled with QTOF mass spectrometer. The chemicals could then be ranked by their relative intrinsic clearance. The analyses were reproducible, with coherence of the calculated in vitro intrinsic clearance between experiments.

Stereostructure-activity mechanism of cyproconazole by cytochrome P450 in rat liver microsomes: A combined experimental and computational study

Cyproconazole (CPZ), representing the chiral triazole fungicides, is widely used in the pharmaceutical and agricultural fields. To clarify its potential adverse effects on the generalized CYP-mediated processes within mammalian, a comparative experimental and computational approach was employed to investigate the CYP-mediated metabolism processes of CPZ stereoisomers in rat liver microsomes (RLMs). The depletion rate of CPZ stereoisomers in vitro incubation system with RLMs followed the order RR-> SS-> SR-> RS-CPZ. The results of kinetic assays were in line with the depletion rate results. Further inhibition assay confirmed the stereoselective metabolism of CPZ stereoisomers by different CYP isoforms. Molecular dynamics (MD) simulation revealed the stereoselective metabolism mechanism. Several hydrogen bonds and π-stacking restrict the position of CPZ isomers in the active cavity of CYPs so that the 4'-nitrogen on the triazole ring can bind closely to the heme of CYP, which results in the metabolism of CPZ isomers. By combining the computational and experimental approaches, the structure-activity relationship of CPZ and CYP was elucidated, and this method can be further applied to predict the degree of uncertainty in the process of xenobiotic biotransformation of triazole fungicides and serve as a basis for risk assessment.

In vitro metabolism of lidocaine in subcellular post-mitochondrial fractions and precision cut slices from cattle liver

In vitro models are widely used to study the biotransformation of xenobiotics and to provide input parameters to physiologically based kinetic models required to predict the kinetic behavior in vivo. For farm animals this is not common practice yet. The use of slaughterhouse-derived tissue material may provide opportunities to study biotransformation reactions in farm animals. The goal of the present study was to explore the potential of slaughterhouse-derived bovine liver S9 (S9) and precision cut liver slices (PCLSs) to capture observed biotransformation reactions of lidocaine in cows. The in vitro data obtained with both S9 and PCLSs confirm in vivo findings that 2,6-dimethylaniline (DMA) is an important metabolite of lidocaine in cows, being for both PCLSs and S9 the end-product. In case of S9, also conversion of lidocaine to lidocaine-N-oxide and monoethylglycinexylidine (MEXG) was observed. MEGX is considered as intermediate for DMA formation, given that this metabolite was metabolized to DMA by both PLCSs and S9. In contrast to in vivo, no in vitro conversion of DMA to 4-OH-DMA was observed. Further work is needed to explain this lack of conversion and to further evaluate the use of slaughterhouse-derived tissue materials to predict the biotransformation of xenobiotics in farm animals.