Use of liquid chromatography/time-of-flight mass spectrometry and multivariate statistical analysis shows promise for the detection of drug metabolites in biological fluids

A multivariate data analysis approach for the investigation of in vitro derived metabolites of ACP-105 in comparison with human in vivo metabolites

Selective androgen receptor modulators (SARMs) such as ACP-105 are prohibited in sports due to their anabolic properties. ACP-105 has in previous equine studies shown to undergo extensive metabolism, which makes its metabolite profile important to investigate in humans, since the metabolism is unknown in this species. The aims of the study were to systematically optimize in vitro microsome incubations for improved metabolite yield and to utilize a multivariate data analysis (MVDA) approach to aid the metabolite discovery. Microsomes together with S9 fractions were used at optimal conditions, both with and without phase II additives. Furthermore, the relevance of the in vitro derived metabolites was evaluated as analytical targets in doping control by comparison with results from a human post-administration urine sample collected after a single dose of 100 µg ACP-105. All samples were analyzed with liquid chromatography - Orbitrap mass spectrometry. The use of the systematical optimization and MVDA greatly simplified the search and a total of 18 in vitro metabolites were tentatively identified. The yield of the two main monohydroxylated isomers increased by 24 and 10 times, respectively. In the human urine sample, a total of seven metabolites of ACP-105, formed by a combination of hydroxylations and glucuronic acid conjugations, were tentatively identified. The main metabolites were two monohydroxylated forms that are suggested as analytical targets for human doping control after hydrolysis. All the in vivo metabolites could be detected with the MVDA approach on the in vitro models, demonstrating its usefulness for prediction of the in vivo metabolite profile.

Urine Metabolites and Bioactive Compounds from Functional Food: Applications of Liquid Chromatography Mass Spectrometry

Bioactive compounds in functional foods, medicinal plants and others are considered attractive value-added molecules based on their wide range of bioactivity. It is clear that an important role is occupied by polyphenol, phenolic compounds and others. Urine is an effective biofluid to evaluate and monitor alterations in homeostasis and other processes related to metabolism. The current review provides a detailed description of the formation of urine in human body, various aspects relevant to sampling and analysis of urinary metabolites before presenting recent developments leveraging on metabolite profiling of urine. For the profiling of small molecules in urine, advancement of liquid chromatography mass tandem spectrometry (LC/MS/MS), establishment of standardized chemical fragmentation libraries, computational resources, data-analysis approaches with pattern recognition tools have made it an attractive option. The profiling of urinary metabolites gives an overview of the biomarkers associated with the diet and evaluates its biological effects. Metabolic pathways such as glycolysis, tricarboxylic acid cycle, amino acid metabolism, energy metabolism, purine metabolism and others can be evaluated. Finally, a combination of metabolite profiling with chemical standardization and bioassay in functional food and medicinal plants will likely lead to the identification of new biomarkers and novel biochemical insights.

The Combination of Electrochemistry and Microfluidic Technology in Drug Metabolism Studies

Drugs are metabolized within the liver (pH 7.4) by phase I and phase II metabolism. During the process, reactive metabolites can be formed that react covalently with biomolecules and induce toxicity. Identifying and detecting reactive metabolites is an important part of drug development. Preclinical and clinical investigations are conducted to assess the toxicity and safety of a new drug candidate. Electrochemistry coupled to mass spectrometry is an ideal complementary technique to the current preclinical studies, a pure instrumental approach without any purification steps and tedious protocols. The combination of microfluidics with electrochemistry towards the mimicry of drug metabolism offers portability, low volume of reagents and faster reaction times. This review explores the development of microfluidic electrochemical cells for mimicking drug metabolism.

Graphene-Based Electrochemical Sensors for Psychoactive Drugs

Sensors developed from nanomaterials are increasingly used in a variety of fields, from simple wearable or medical sensors to be used at home to monitor health, to more complicated sensors being used by border customs or aviation industries. In recent times, nanoparticle-based sensors have begun to revolutionize drug-detection techniques, mainly due to their affordability, ease of use and portability, compared to conventional chromatography techniques. Thin graphene layers provide a significantly high surface to weight ratio compared to other nanomaterials, a characteristic that has led to the design of more sensitive and reliable sensors. The exceptional properties of graphene coupled with its potential to be tuned to target specific molecules have made graphene-based sensors one of the most popular and well-researched sensing materials of the past two decades with applications in environmental monitoring, medical diagnostics, and industries. Here, we present a review of developments in the applications of graphene-based sensors in sensing drugs such as cocaine, morphine, methamphetamine, ketamine, tramadol and so forth in the past decade. We compare graphene sensors with other sensors developed from ultrathin two-dimensional materials, such as transition-metal dichalcogenides, hexagonal boron nitrate, and MXenes, to measure drugs directly and indirectly, in various samples.

Biosynthesis-based spatial metabolome of Salvia miltiorrhiza Bunge by combining metabolomics approaches with mass spectrometry-imaging

Defining the spatial distributions of metabolites and their structures are the two key aspects for interpreting the complexities of biosynthesis pathways in plants. As a means of obtaining information on the spatial distribution of metabolites, a strategy is needed that has high sensitivity and allows visualization. Toward this goal, we carried an untargeted metabolomics to obtain detailed metabolic information on different plant parts of Salvia miltiorrhiza, the roots of which are widely used in traditional Chinese medicine. Systematic optimization of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) including parameter selection and sample preparation were carried out to improve the sensitivity of the method for plant samples. Guided by the metabolomics data, the spatial distributions of diverse metabolites, including phenolic acids, flavonoids, tanshinones, carbohydrates, and lipids, were characterized and visualized for both the underground and aerial parts. To integrate the information pertaining to the spatial distribution of metabolites, the flavonoids and phenolic acids (phenylpropanoid metabolic pathway) were chosen as examples for in-depth study the biosynthesis pathways in S. miltiorrhiza. The complementary data obtained from the metabolomics study and mass spectrometry imaging enabled the identification of key reactions involved in flavonoid biosynthesis in flowers, which lead the changes in metabolite distribution. The analysis also identified the core precursor for phenolic acid biosynthesis in Salvia species. Therefore, the powerful combination of metabolomics and mass spectrometry imaging provides a basis for obtaining detailed information on spatial metabolome and constitutes a platform for deep understanding the biosynthesis of bioactive metabolites in plants.

Metabolism of non-steroidal anti-inflammatory drugs by non-target wild-living organisms

The presence of the non-steroidal anti-inflammatory drugs (NSAIDs) in the environment is a fact, and aquatic and soil organisms are chronically exposed to trace levels of these emerging pollutants. This review presents the current state of knowledge on the metabolic pathways of NSAIDs in organisms at various levels of biological organisation. More than 150 publications dealing with target or non-target analysis of selected NSAIDs (mainly diclofenac, ibuprofen, and naproxen) were collected. The metabolites of phase I and phase II are presented. The similarity of NSAIDs metabolism to that in mammals was observed in bacteria, microalgae, fungi, higher plants, invertebrates, and vertebrates. The differences, such as newly detected metabolites, the extracellular metabolism observed in bacteria and fungi, or phase III metabolism in plants, are highlighted. Metabolites detected in plants (conjugates with sugars and amino acids) but not found in any other organisms are described. Selected, in-depth studies with isolated bacterial strains showed the possibility of transforming NSAIDs into assimilable carbon sources. It has been found that some of the metabolites show higher toxicity than their parent forms. The presence of metabolites of NSAIDs in the environment is the cumulative effect of their introduction with wastewaters, their formation in wastewater treatment plants, and their transformation by non-target wild-living organisms.

The Pharmacometabodynamics of Gefitinib after Intravenous Administration to Mice: A Preliminary UPLC-IM-MS Study

The effects of intravenous gefitinib (10 mg/kg), an anilinoquinazoline thymidylate kinase inhibitor (TKI), selective for the epidermal growth factor receptor (EGFR), on the urinary metabotypes of mice were studied. We hypothesized that, in response to the administration of gefitinib, there might be significant changes in the excretion of many endogenous metabolites in the urine, which could be correlated with the plasma pharmacokinetics (PK) of the drug. In order to investigate this conjecture, urine from male C57 BL6 mice was collected before IV dosing (10 mg/kg) and at 0–3, 3–8, and 8–24 h post-dose. The samples were profiled by UPLC/IM/MS and compared with the profiles obtained from undosed control mice with the data analyzed using multivariate statistical analysis (MVA). This process identified changes in endogenous metabolites over time and these were compared with drug and drug metabolite PK and excretion. While the MVA of these UPLC/IM/MS data did indeed reveal time-related changes for endogenous metabolites that appeared to be linked to drug administration, this analysis did not highlight the presence of either the drug or its metabolites in urine. Endogenous metabolites affected by gefitinib administration were identified by comparison of mass spectral, retention time and ion mobility-derived collision cross section data (compared to authentic standards wherever possible). The changes in endogenous metabolites resulting from gefitinib administration showed both increases (e.g., tryptophan, taurocholic acid, and the dipeptide lysyl-arginine) and decreases (e.g., deoxyguanosine, 8-hydroxydeoxyguanosine, and asparaginyl-histidine) relative to the control animals. By 8–24 h, the post-dose concentrations of most metabolites had returned to near control values. From these studies, we conclude that changes in the amounts of endogenous metabolites excreted in the urine mirrored, to some extent, the plasma pharmacokinetics of the drug. This phenomenon is similar to pharmacodynamics, where the pharmacological effects are related to the drug concentrations, and by analogy, we have termed this effect “pharmacometabodynamics”.

Considerations to Be Taken When Carrying Out Medicinal Plant Research-What We Learn from an Insight into the IC50 Values, Bioavailability and Clinical Efficacy of Exemplary Anti-Inflammatory Herbal Components

Medicinal plants represent a big reservoir for discovering new drugs against all kinds of diseases including inflammation. In spite the large number of promising anti-inflammatory plant extracts and isolated components, research on medicinal plants proves to be very difficult. Based on that background this review aims to provide a summarized insight into the hitherto known pharmacologically active concentrations, bioavailability, and clinical efficacy of boswellic acids, curcumin, quercetin and resveratrol. These examples have in common that the achieved plasma concentrations were found to be often far below the determined IC50 values in vitro. On the other hand demonstrated therapeutic effects suggest a necessity of rethinking our pharmacokinetic understanding. In this light this review discusses the value of plasma levels as pharmacokinetic surrogates in comparison to the more informative value of tissue concentrations. Furthermore the need for new methodological approaches is addressed like the application of combinatorial approaches for identifying and pharmacokinetic investigations of active multi-components. Also the physiological relevance of exemplary in vitro assays and absorption studies in cell-line based models is discussed. All these topics should be ideally considered to avoid inaccurate predictions for the efficacy of herbal components in vivo and to unlock the "black box" of herbal mixtures.

Applications of Metabolomics in Forensic Toxicology and Forensic Medicine

Forensic toxicology and forensic medicine are unique among all other medical fields because of their essential legal impact, especially in civil and criminal cases. New high-throughput technologies, borrowed from chemistry and physics, have proven that metabolomics, the youngest of the “omics sciences”, could be one of the most powerful tools for monitoring changes in forensic disciplines. Metabolomics is a particular method that allows for the measurement of metabolic changes in a multicellular system using two different approaches: targeted and untargeted. Targeted studies are focused on a known number of defined metabolites. Untargeted metabolomics aims to capture all metabolites present in a sample. Different statistical approaches (e.g., uni- or multivariate statistics, machine learning) can be applied to extract useful and important information in both cases. This review aims to describe the role of metabolomics in forensic toxicology and in forensic medicine.

The Effect of Pedal Peptide-Type Neuropeptide on Locomotor Behavior and Muscle Physiology in the Sea Cucumber Apostichopus japonicus

Neuropeptides are endogenous active substances that are present in nervous tissues and participate in behavioral and physiological processes of the animal system. Locomotor behavior is basic to predation, escape, reproduction in animals, and neuropeptides play an important role in locomotion. In this study, the function of pedal peptide-type neuropeptide (PDP) in the process of locomotor behavior of the sea cucumber Apostichopus japonicus was evaluated. The locomotor behavior of A. japonicus was recorded by infrared camera before and after PDP administration, and muscle physiology was studied by ultra performance liquid chromatography and quadrupole time-off-light mass spectrometry (UPLC-Q-TOF-MS) to clarify the potential physiological mechanisms. The results showed that PDP enhanced the cumulative duration of moving significantly at the 7th h after injection, and reduced the mean and maximum velocity by 16.90 and 14.22% in A. japonicus. The data of muscle metabolomics suggested that some significantly changed metabolites were related to locomotor behavior of sea cucumbers. The decreases of phosphatidylethanolamine (PE) and phosphatidylcholine (PC) might result in the increases of lysophosphatidylcholines (lysoPC) and lysophosphatidylethanolamine (lysoPE), and suggested the change of fluidity and permeability in the muscle cell membrane, which would affect the physiology and function of muscle cells, and finally alter the locomotor behavior. In addition, the increased level of arachidonic acid (ARA) might activate K⁺ ion channels and then affect the signaling of muscle cells, or promote the sensitivity of muscle cells to Ca²⁺ and then result in the contractility of longitudinal muscles in sea cucumbers. ARA was also involved in the linoleic acid metabolism which was the only pathway that disturbed significantly after PDP administration. In conclusion, PDP participated in the regulation of locomotor behavior in the sea cucumber, and the decreased PE and PC, increased lysoPC, lysoPE and ARA might be the potential physiological mechanisms that responsible for behavioral effects of PDP in A. japonicus.

Metabolomic insights into the lasting impacts of early-life exposure to BDE-47 in mice

Early-life exposure to toxicants may have lasting effects that adversely impact later development. Thus, although the production and use of a toxicant have been banned, the risk to previously exposed individuals may continue. BDE-47, a component of commercial penta-BDEs, is a persistent organic pollutant with demonstrated neurotoxicity. To investigate the persistent effects of BDE-47 and the mechanisms thereof, we employed a metabolomics approach to analyze the brain, blood and urine of mice exposed to BDE-47 for 28 days and then 3 months post-exposure. In the brain, BDE-47 was detectable just after exposure but was below the limit of detection (LOD) 3 months later. However, the metabolomic alterations caused by early-life exposure to BDE-47 persisted. Potential biomarkers related to these alterations included phosphatidylcholine, lysophosphatidylcholine, sphingomyelin and several amino acids and biogenic amines. The metabolic pathways involved in the response to BDE-47 in the brain were mainly those related to glycerophospholipid metabolism, sphingomyelin metabolism and neurotransmitter regulation. Thus, our study demonstrates the utility of metabolomics, as the omics most closely reflecting the phenotype, in exploring the mechanisms underlying the lasting effects induced by early-life BDE-47 exposure.

Pharmacokinetics of T0901317 in mouse serum and tissues using a validated UFLC-IT-TOF/MS method

T0901317, a liver X receptors (LXRs) agonist with high-affinity, is widely used to explore the functions of LXRs in various diseases such as atherosclerosis and Alzheimer's disease. However, there is currently little information available about the pharmacokinetics (PK) behavior of T0901317. Here we established a novel ultrafast liquid chromatography-high resolution mass spectrometry method to quantify the concentration of T0901317 in serum, liver, and brain. The chromatographic separation was attained on a C18 (2.1 × 100 mm, 1.8 μm) column using acetonitrile and 0.1 % of formic acid in water as mobile phase operated in gradient elution mode. The mass detection was carried out using negative ions m/z 479.9809 and 322.0882 for T0901317 and internal standard, respectively. The proposed method was fully validated according to the FDA guidelines, and it generally provides good results in terms of linearity (r² > 0.99), precision (RSD < 18 % and 12 % for LLOQ and other QC levels, respectively), accuracy (between 92.30 % and 108.16 %), and matrix effect (between 86.56 % and 113.81 %). We then for the first time determined and computed the PK parameters of T0901317 in mouse after intraperitoneal administration of a 20 mg/kg dosage. The peak times (T_max) in serum, liver, and brain were 1.5, 1.5, and 4 h, respectively, while the half-lives (t_1/2) were 4.9, 3.3, and 4.5 h, respectively. Taken together, our results provide a significant choice to study the PK property of T0901317, from which the design of the dosing and sampling protocols of LXRs receptor-antagonist experiments employing T0901317 can also benefit.

On the benefits of using multivariate analysis in mass spectrometric studies of combustion-generated aerosols

The intricate chemistry of the carbonaceous particle surface layer (which drives their reactivity, environmental and health impacts) results in complex mass spectra. In this respect, detailed molecular-level analysis of combustion emissions may be challenging even with high-resolution mass spectrometry. Building on a recently proposed comprehensive methodology (encompassing all stages from sampling to data reduction), we propose herein a comparative analysis of soot particles produced by three different sources: a miniCAST standard generator, a laboratory diffusion flame and a single cylinder internal combustion engine. The surface composition is probed by either laser or secondary ion mass spectrometry. Two examples of multivariate analysis, Principal component analysis and hierarchical clustering analysis proved their efficiency in both identifying general trends and evidencing subtle differences that otherwise would remain unnoticed in the plethora of data generated during mass spectrometric analyses. Chemical information extracted from these multivariate statistical procedures contributes to a better understanding of fundamental combustion processes and also opens to practical applications such as the tracing of engine emissions.

In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation

In liquid chromatography-mass spectrometry (LC-MS) metabolomics, data matrices with up to thousands of variables for each ion peak are subjected to multivariate analysis (MVA) to assess the homogeneity between samples. The large dimensions of LC/MS datasets hinder the identification of the discriminant or the metabolic markers. In the present study, the molecular network (MN) approach and two in silico annotation tools, network annotation propagation (NAP) and the hierarchical chemical classification method, ClassyFire, were used to annotate the metabolites of three Zanthoxylum species, Z. bungeanum, Z. schinifolium and Z. piperitum. The in silico annotation results of the MN nodes and the MVA variables were combined and visualized in loading plots. This approach helped intuitive detection of the variables that greatly contributed to the separation of the samples in the score plot as discriminant or metabolic markers, thereby allowing rapid annotation of two flavanone derivatives.

Review of approaches and examples for monitoring biotransformation in protein and peptide therapeutics by MS

Biotherapeutic drugs have emerged in quantity in pharmaceutical pipelines, and increasingly diverse biomolecules are progressed through preclinical and clinical development. As purification, separation, mass spectrometer detection and data processing capabilities improve, there is opportunity to monitor drug concentration by traditional ligand-binding assay or MS measurement and to monitor metabolism, catabolism or other biomolecular mass variants present in circulation. This review highlights approaches and examples of monitoring biotransformation of biotherapeutics by MS as these techniques are poised to add value to drug development in years to come. The increased use of such approaches, and the successful quantitation of biotherapeutic structural modifications, will provide insightful data for the benefit of both researchers and patients.

Non-targeted metabolomics-guided sildenafil metabolism study in human liver microsomes

Metabolomics combined with high-resolution mass spectrometry (HR-MS) and multivariate data analysis has broad applications in the study of xenobiotic metabolism. Although information about xenobiotic metabolism is essential to understand toxic mechanisms, pharmacokinetic parameters and excretion pathways, it is limited to predict all generated metabolites in biological fluids. Here, we revisited sildenafil metabolism in human liver microsomes using a metabolomics approach to achieve a global picture of sildenafil phase 1 metabolism. Finally, 12 phase 1 metabolites were identified in human liver microsomes; M1-M5 were previously known metabolites. The chemical structures of the novel metabolites were elucidated by MS² fragmentation using an HR-MS system as follows: M6, reduced sildenafil; M7, N,N-deethylation and mono-oxidation; M8, demethanamine, N,N-deethylation and mono-hydroxylation; M9, demethanamine and N,N-deethylation; M10 and M11, mono-oxidation in the piperazine ring after N-demethylation; and M12, mono-oxidation. All metabolites, except M1, were formed by CYP3A4 and CYP3A5. In conclusion, we successfully updated the metabolic pathway of sildenafil in human liver, including 7 novel metabolites using metabolomics combined with HR-MS and multivariate data analysis.

Post-acquisition data mining techniques for LC–MS/MS-acquired data in drug metabolite identification

Metabolite identification is a crucial part of the drug discovery process. LC–MS/MS-based metabolite identification has gained widespread use, but the data acquired by the LC–MS/MS instrument is complex, and thus the interpretation of data becomes troublesome. Fortunately, advancements in data mining techniques have simplified the process of data interpretation with improved mass accuracy and provide a potentially selective, sensitive, accurate and comprehensive way for metabolite identification. In this review, we have discussed the targeted (extracted ion chromatogram, mass defect filter, product ion filter, neutral loss filter and isotope pattern filter) and untargeted (control sample comparison, background subtraction and metabolomic approaches) post-acquisition data mining techniques, which facilitate the drug metabolite identification. We have also discussed the importance of integrated data mining strategy.

Metabolic profiling identification of metabolites formed in Mediterranean mussels (Mytilus galloprovincialis) after diclofenac exposure

Despite the growing concern on the presence of pharmaceutically active compounds in the environment, few studies have been conducted on their metabolism in marine organisms. In this study, a non-targeted strategy based on the generation of chemical profiles generated by liquid chromatography combined with high resolution mass spectrometry was used to highlight metabolite production by the Mediterranean mussel (Mytilus galloprovincialis) after diclofenac exposure. This method allowed revealing the production of 13 metabolites in mussel tissues. Three of them were phase I metabolites, including 4'-hydroxy-diclofenac and 5-hydroxy-diclofenac. The remaining 10 were phase II metabolites, including sulfate and amino acids conjugates. Among all of the metabolites highlighted, 5 were reported for the first time in an aquatic organism exposed to diclofenac.

Revisiting the Metabolism and Bioactivation of Ketoconazole in Human and Mouse Using Liquid Chromatography-Mass Spectrometry-Based Metabolomics

Although ketoconazole (KCZ) has been used worldwide for 30 years, its metabolic characteristics are poorly described. Moreover, the hepatotoxicity of KCZ limits its therapeutic use. In this study, we used liquid chromatography–mass spectrometry-based metabolomics to evaluate the metabolic profile of KCZ in mouse and human and identify the mechanisms underlying its hepatotoxicity. A total of 28 metabolites of KCZ, 11 of which were novel, were identified in this study. Newly identified metabolites were classified into three categories according to the metabolic positions of a piperazine ring, imidazole ring, and N-acetyl moiety. The metabolic characteristics of KCZ in human were comparable to those in mouse. Moreover, three cyanide adducts of KCZ were identified in mouse and human liver microsomal incubates as “flags” to trigger additional toxicity study. The oxidation of piperazine into iminium ion is suggested as a biotransformation responsible for bioactivation. In summary, the metabolic characteristics of KCZ, including reactive metabolites, were comprehensively understood using a metabolomics approach.

Mass spectrometric based approaches in urine metabolomics and biomarker discovery

Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.

Effects of hypoxia in the gills of the Manila clam Ruditapes philippinarum using NMR-based metabolomics

Coastal hypoxia affects the survival, behavior, and reproduction of individual local marine organisms, and the abundance, biomass, and biodiversity of coastal ecosystems. In this study, we investigated the chronic effects of hypoxia on the metabolomics in the gills of Ruditapes (R.) philippinarum. The results indicated significant alterations in the metabolite profiles in the gills of the hypoxia-treated clams, in comparison with those maintained under normoxia. The levels of betaine, taurine, glycine, isoleucine, and alanine were significantly reduced, suggesting a disturbance of osmotic balance associated with hypoxia. Meanwhile, metabolites involved in energy metabolism, such as alanine and succinate, were also affected. Dramatic histopathological changes were observed in the gills and hepatopancreases of R. philippinarum grown in hypoxic waters, demonstrating tissue damages apparently caused by long-term exposure to hypoxia. Our findings suggest that hypoxia significantly affects the physiology of R. philippinarum, even at a sub-lethal level, and impedes health of the clams.

Development of a Rapid Microbore Metabolic Profiling Ultraperformance Liquid Chromatography-Mass Spectrometry Approach for High-Throughput Phenotyping Studies

A rapid gradient microbore ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) method has been developed to provide a high-throughput analytical platform for the metabolic phenotyping of urine from large sample cohorts. The rapid microbore metabolic profiling (RAMMP) approach was based on scaling a conventional reversed-phase UPLC-MS method for urinary profiling from 2.1 mm × 100 mm columns to 1 mm × 50 mm columns, increasing the linear velocity of the solvent, and decreasing the gradient time to provide an analysis time of 2.5 min/sample. Comparison showed that conventional UPLC-MS and rapid gradient approaches provided peak capacities of 150 and 50, respectively, with the conventional method detecting approximately 19 000 features compared to the ∼6 000 found using the rapid gradient method. Similar levels of repeatability were seen for both methods. Despite the reduced peak capacity and the reduction in ions detected, the RAMMP method was able to achieve similar levels of group discrimination as conventional UPLC-MS when applied to rat urine samples obtained from investigative studies on the effects of acute 2-bromophenol and chronic acetaminophen administration. When compared to a direct infusion MS method of similar analysis time the RAMMP method provided superior selectivity. The RAMMP approach provides a robust and sensitive method that is well suited to high-throughput metabonomic analysis of complex mixtures such as urine combined with a 5-fold reduction in analysis time compared with the conventional UPLC-MS method.

Pharmacokinetics and metabolism study of firocoxib in camels after intravenous administration by using high-resolution bench-top orbitrap mass spectrometry

In this study, we developed a high-resolution liquid chromatography mass spectrometry method for the pharmacokinetic study of firocoxib followed by full method validation. Following a solid-phase extraction, the firocoxib and internal standard (celecoxib) were separated on an Agilent Zorbax ZDB C18 column (50 mm × 2.1 mm i.d., 3.5 μm) with a gradient elution using methanol and 0.1% aqueous formic acid. Data acquisition was performed at 25,000 resolution with the automatic gain set to 1,000,000 and the maximum injection time of 100 ms. Data were acquired in full-scan mode over a mass range of 100-550 Da in positive electrospray mode. Linear calibration curves were obtained over the concentration ranges of 0.5-200 ng/mL and no interfering peaks were detected at the retention time of firocoxib and internal standard in blank camel plasma samples. The mean extraction recoveries of firocoxib at three concentrations of 5, 25 and 75 ng/mL ranged from 92 to 104%. Coefficient of variation of intra-day and inter-day precision were both <10%. The accuracy of the method ranged from 95 to 107%. The validated method was then successfully applied in evaluating the pharmacokinetics and metabolism of firocoxib in camels (Camelus dromedarus) (n=5) following intravenous (i.v.) administration of a dose of 0.1 mgkg/body weight. The results obtained (mean ± SD) were as follows: the terminal elimination half-life (t₁/₂β) was 5.75 ± 2.26 h, and total body clearance (ClT) was 354.1 ± 82.6 mL/kg/h. The volume of distribution at steady state (VSS) was 2344.4 ± 238.7 mL/kg. One metabolite of firocoxib was tentatively identified as desalkyl firocoxib (m/z 283). Firocoxib could be detected in plasma 3-5 days following i.v. administration in camels using a sensitive liquid chromatography high-resolution orbitrap mass spectrometry method.

Plasma metabolic profiling of normal and dysmenorrhea syndrome rats and the effects of Xiang-Fu-Si-Wu Decoction intervention

CONTEXT

Primary dysmenorrhea (PDM), a common, clinically heterogeneous endocrine disorder affecting young women, is associated with endocrinopathy and metabolic abnormalities. The Xiang-Fu-Si-Wu Decoction (XFSWD) is a traditional Chinese medicine preparation used to treat PDM.

OBJECTIVE

In the current study, a plasma metabonomics method based on the ultra-high-performance liquid chromatography-quantitative time-of-flight-mass spectrometry (UHPLC-Q-TOF-MS) system was employed to examine the mechanism of XFSWD action in PDM.

MATERIALS AND METHODS

Estradiol benzoate (0.01 g/kg/d) and oxytocin (5 mL/kg) were used to create the dysmenorrhea rat model. Based on the chromatographic data of plasma samples at different time-points following oral administration of XFSWD mixed in water (37.8 g crude herbs/kg) on day 7, partial least square (PLS) and discriminate analysis (DA) were applied to visualize group differentiation and marker selection.

RESULTS

Systemic changes occurring in PDM reflect alterations in not only uterus function but also whole-body metabolism. The XFSWD was effective as a therapeutic agent for PDM by reflect metabolic pathway. Prostaglandins and lysophospholipids were identified as two marker types for oxytocin-induced dysmenorrhea syndrome, including LysoPC(18:4), LysoPE(22:2/0:0), LysoPC(17:0), PGJ₂, 11-deoxy-11-methylene-PGD₂, 15-deoxy-δ-12,14-PGJ₂, LysoPC(20:3), etc. Specifically, the concentrations of prostaglandins compounds (PGJ₂, 11-deoxy-11-methylene-PGD₂, 15-deoxy-δ-12,14-PGJ₂) were increased while those of lysophospholipid compounds [lysoPC(18:4), LysoPE(22:2/0:0), LysoPC(17:0)] were decreased to a significant extent (p < 0.05) in dysmenorrheal rats. Upon treatment with the XFSWD at 12 h, the concentrations of lysophospholipids showed no significant differences (P > 0.05) between the model and normal groups. The lysophospholipid levels were restored. Lysophospholipids were the key factors in phospholipid metabolism. Thus, disruption of phospholipids metabolism appears critical for the development of dysmenorrhea. The XFSWD exerted its effects by interfering with the sphingolipid metabolic pathway.

DISCUSSION AND CONCLUSIONS

The metabonomics method presents a promising tool to treat PDM in animal models, and may be applicable for clinical treatment of the human disease in the future.

LC-MS-based metabolomics: an update

Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics can have a major impact in multiple research fields, especially when combined with other technologies, such as stable isotope tracers and genetically modified mice. This review highlights recent applications of metabolomic technology in the study of xenobiotic metabolism and toxicity, and the understanding of disease pathogenesis and therapeutics. Metabolomics has been employed to study metabolism of noscapine, an aryl hydrocarbon receptor antagonist, and to determine the mechanisms of liver toxicities of rifampicin and isoniazid, trichloroethylene, and gemfibrozil. Metabolomics-based insights into the pathogenesis of inflammatory bowel disease, alcohol-induced liver diseases, non-alcoholic steatohepatitis, and farnesoid X receptor signaling pathway-based therapeutic target discovery will also be discussed. Limitations in metabolomics technology such as sample preparation and lack of LC-MS databases and metabolite standards, need to be resolved in order to improve and broaden the application of metabolomic studies.

Differential metabolic responses of clam Ruditapes philippinarum to Vibrio anguillarum and Vibrio splendidus challenges

Clam Ruditapes philippinarum is one of the important marine aquaculture species in North China. However, pathogens can often cause diseases and lead to massive mortalities and economic losses of clam. In this work, we compared the metabolic responses induced by Vibrio anguillarum and Vibrio splendidus challenges towards hepatopancreas of clam using NMR-based metabolomics. Metabolic responses suggested that both V. anguillarum and V. splendidus induced disturbances in energy metabolism and osmotic regulation, oxidative and immune stresses with different mechanisms, as indicated by correspondingly differential metabolic biomarkers (e.g., amino acids, ATP, glucose, glycogen, taurine, betaine, choline and hypotaurine) and altered mRNA expression levels of related genes including ATP synthase, ATPase, glutathione peroxidase, heat shock protein 90, defensin and lysozyme. However, V. anguillarum caused more severe oxidative and immune stresses in clam hepatopancreas than V. splendidus. Our results indicated that metabolomics could be used to elucidate the biological effects of pathogens to the marine clam R. philippinarum.

Metabolomic analysis revealed the differential responses in two pedigrees of clam Ruditapes philippinarum towards Vibrio harveyi challenge

Manila clam Ruditapes philippinarum is an important marine aquaculture shellfish. This species has several pedigrees including White, Zebra, Liangdao Red and Marine Red distributing in the coastal areas in North China. In this work, we studied the metabolic differences induced by Vibrio harveyi in hepatopancreas from White and Zebra clams using NMR-based metabolomics. Metabolic responses (e.g., amino acids, glucose, glycogen, ATP and succinate) and altered mRNA expression levels of related genes (ATP synthase, heat shock protein 90, defensin and lysozyme) suggested that V. harveyi induced clear disruption in energy metabolism and immune stresses in both White and Zebra clam hepatopancreas. However, V. harveyi caused obvious osmotic stress in Zebra clam hepatopancreas, which was not observed in V. harveyi-challenged White clams samples. In addition, V. harveyi challenge induced more severe disruption in energy metabolism and immune stress in White clams than in Zebra clams. Overall, our results indicated that the biological differences between different pedigrees of R. philippinarum should be considered in immunity studies.

Mass spectrometry techniques in the survey of steroid metabolites as potential disease biomarkers: a review

Mass spectrometric approaches have been fundamental to the identification of metabolites associated with steroid hormones, yet this topic has not been reviewed in depth in recent years. To this end, and given the increasing relevance of liquid chromatography-mass spectrometry (LC-MS) studies on steroid hormones and their metabolites, the present review addresses this subject. This review provides a timely summary of the use of various mass spectrometry-based analytical techniques during the evaluation of steroidal biomarkers in a range of human disease settings. The sensitivity and specificity of these technologies are clearly providing valuable new insights into breast cancer and cardiovascular disease. We aim to contribute to an enhanced understanding of steroid metabolism and how it can be profiled by LC-MS techniques.

Use of the local false discovery rate for identification of metabolic biomarkers in rat urine following Genkwa Flos-induced hepatotoxicity

Metabolomics is concerned with characterizing the large number of metabolites present in a biological system using nuclear magnetic resonance (NMR) and HPLC/MS (high-performance liquid chromatography with mass spectrometry). Multivariate analysis is one of the most important tools for metabolic biomarker identification in metabolomic studies. However, analyzing the large-scale data sets acquired during metabolic fingerprinting is a major challenge. As a posterior probability that the features of interest are not affected, the local false discovery rate (LFDR) is a good interpretable measure. However, it is rarely used to when interrogating metabolic data to identify biomarkers. In this study, we employed the LFDR method to analyze HPLC/MS data acquired from a metabolomic study of metabolic changes in rat urine during hepatotoxicity induced by Genkwa flos (GF) treatment. The LFDR approach was successfully used to identify important rat urine metabolites altered by GF-stimulated hepatotoxicity. Compared with principle component analysis (PCA), LFDR is an interpretable measure and discovers more important metabolites in an HPLC/MS-based metabolomic study.

Investigation of in vivo metabolic profile of Abelmoschus Manihot based on pattern recognition analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Abelmoschus manihot (L.) Medik. var. manihot is one of the most commonly used Chinese medicines and has played an important role in treating chronic glomerulonephritis and diabetic nephropathy.

AIM OF THE STUDY

Metabolites identification of traditional Chinese medicine (TCM) is a complex and time-consuming process due to the complicity of TCM and subsequent large number of detected ions. In this paper, UPLC-MS combined with pattern recognition analysis approach were used to simplify and quicken the identification of the metabolites of Abelmoschus Manihot.

MATERIALS AND METHODS

Rat urine samples were collected before (as control sample) and after Abelmoschus Manihot administration. Pattern recognition analysis method was used to differentiate components between Abelmoschus Manihot-treated group and its controlled comparison. These components could be considered as Abelmoschus Manihot-related metabolites in vivo.

RESULTS

LC-MS based metabolomics could be an advanced tool to help us find metabolites with regards to its capacity of processing large datasets, differentiating and classifying of sample groups, as well as its indiscriminative nature of biomarker and metabolite identification. Using this method, seven metabolites were identified, which are flavonoid aglycone glucuronidation, sulfatation, and methylation metabolites.

CONCLUSION

Our results showed that UPLC-MS based- pattern recognition analysis approach can be used to quickly identify Abelmoschus Manihot related metabolites in biological fluids. Furthermore, this work demonstrates the potential application of combining the UPLC-MS approach with the metabolomics approach in identifying the metabolites of TCM.

Towards polypharmacokinetics: pharmacokinetics of multicomponent drugs and herbal medicines using a metabolomics approach

Determination of pharmacokinetics (PKs) of multicomponent pharmaceuticals and/or nutraceuticals (polypharmacokinetics, poly-PKs) is difficult due to the vast number of compounds present in natural products, their various concentrations across a wide range, complexity of their interactions, as well as their complex degradation dynamics in vivo. Metabolomics coupled with multivariate statistical tools that focus on the comprehensive analysis of small molecules in biofluids is a viable approach to address the challenges of poly-PK. This paper discusses recent advances in the characterization of poly-PK and the metabolism of multicomponent xenobiotic agents, such as compound drugs, dietary supplements, and herbal medicines, using metabolomics strategy. We propose a research framework that integrates the dynamic concentration profile of bioavailable xenobiotic molecules that result from in vivo absorption and hepatic and gut bacterial metabolism, as well as the human metabolic response profile. This framework will address the bottleneck problem in the pharmacological evaluation of multicomponent pharmaceuticals and nutraceuticals, leading to the direct elucidation of the pharmacological and molecular mechanisms of these compounds.

The role of metabolic biomarkers in drug toxicity studies

ABSTRACT Metabolic profiling is a technique that can potentially provide more sensitive and specific biomarkers of toxicity than the current clinical measures benefiting preclinical and clinical drug studies. Both nuclear magnetic resonance (NMR) and mass spectrometry (MS) platforms have been used for metabolic profiling studies of drug toxicity. Not only can both techniques provide novel biomarker(s) of toxicity but the combination of both techniques gives a broader range of metabolites evaluated. Changes in metabolic patterns can provide insight into mechanism(s) of toxicity and help to eliminate a potentially toxic new chemical entity earlier in the developmental process. Metabolic profiling offers numerous advantages in toxicological research and screening as sample collection and preparation are relatively simple. Further, sample throughput, reproducibility, and accuracy are high. The area of drug toxicity of therapeutic compounds has already been impacted by metabolic profiling studies and will continue to be impacted as new, more specific biomarker(s) are found. In order for a biomarker or pattern of biomarkers to be accepted, it must be shown that they originate from the target tissue of interest. Metabolic profiling studies are amenable to any biofluid or tissue sample making it possible to link the changes noted in urine for instance as originating from renal injury. Additionally, the ease of sample collection makes it possible to follow a single animal or subject over time in order to determine whether and when the toxicity resolves itself. This review focuses on the advantages of metabolic profiling for drug toxicity studies.

Integrated quantitative and qualitative workflow for in vivo bioanalytical support in drug discovery using hybrid Q-TOF-MS

Background: UHPLC coupled with orthogonal acceleration hybrid quadrupole-TOF (Q-TOF)-MS is an emerging technique offering new strategies for the efficient screening of new chemical entities and related molecules at the early discovery stage within the pharmaceutical industry. In the first part of this article, we examine the main instrumental parameters that are critical for the integration of UHPLC–Q-TOF technology to existing bioanalytical workflows, in order to provide simultaneous quantitative and qualitative bioanalysis of samples generated following in vivo studies. Material & Methods: Three modern Q-TOF mass spectrometers, including Bruker maXis™, Agilent 6540 and Sciex TripleTOF™ 5600, all interfaced with UHPLC systems, are evaluated in the second part of the article. The scope of this work is to demonstrate the potential of Q-TOF for the analysis of typical small molecules, therapeutic peptides (molecular weight <6000 Da), and enzymatically (i.e., trypsin, chymotrypsin and pepsin) cleaved peptides from larger proteins. Results & Discussion: This work focuses mainly on full-scan TOF data obtained under ESI conditions, the major mode of TOF operation in discovery bioanalytical research, where the compounds are selected based on their pharmacokinetic/pharmacodynamic behaviors using animal models prior to selecting a few desirable candidates for further development. Finally, important emerging TOF technologies that could potentially benefit bioanalytical research in the semi-quantification of metabolites without synthesized standards are discussed. Particularly, the utility of captive spray ionization coupled with TripleTOF 5600 was evaluated for improving sensitivity and providing normalized MS response for drugs and their metabolites. The workflow proposed compromises neither the efficiency, nor the quality of pharmacokinetic data in support of early drug discovery programs.

Metabolomics in the fields of oncology: a review of recent research

The study of all endogenously produced metabolites, known as metabolomics, is the youngest of the "omics" sciences. It is becoming increasingly clear that, of all of the "omics" techniques, metabolomic approaches will become increasingly useful in disease diagnosis and have potential power to improve our understanding of the underlying mechanisms of cancer. The primary aim of the review is to discuss the relationship between metabolomics and tumors are elucidated in detail. Then the review is also to introduce the technologies of metabolomics, especially emphasizing the application of metabolomics in the fields of oncology.

NMR-based metabolomic investigations on the differential responses in adductor muscles from two pedigrees of Manila clam Ruditapes philippinarum to Cadmium and Zinc

Manila clam Ruditapes philippinarum is one of the most important economic species in shellfishery in China due to its wide geographic distribution and high tolerance to environmental changes (e.g., salinity, temperature). In addition, Manila clam is a good biomonitor/bioindicator in "Mussel Watch Programs" and marine environmental toxicology. However, there are several pedigrees of R. philippinarum distributed in the marine environment in China. No attention has been paid to the biological differences between various pedigrees of Manila clams, which may introduce undesirable biological variation in toxicology studies. In this study, we applied NMR-based metabolomics to detect the biological differences in two main pedigrees (White and Zebra) of R. philippinarum and their differential responses to heavy metal exposures (Cadmium and Zinc) using adductor muscle as a target tissue to define one sensitive pedigree of R. philippinarum as biomonitor for heavy metals. Our results indicated that there were significant metabolic differences in adductor muscle tissues between White and Zebra clams, including higher levels of alanine, glutamine, hypotaurine, phosphocholine and homarine in White clam muscles and higher levels of branched chain amino acids (valine, leucine and isoleucine), succinate and 4-aminobutyrate in Zebra clam muscles, respectively. Differential metabolic responses to heavy metals between White and Zebra clams were also found. Overall, we concluded that White pedigree of clam could be a preferable bioindicator/biomonitor in marine toxicology studies and for marine heavy metals based on the relatively high sensitivity to heavy metals.

Mass spectrometry-based holistic analytical approaches for metabolite profiling in systems biology studies

Metabonomics and metabolomics represent one of the three major platforms in systems biology. To perform metabolomics it is necessary to generate comprehensive "global" metabolite profiles from complex samples, for example, biological fluids or tissue extracts. Analytical technologies based on mass spectrometry (MS), and in particular on liquid chromatography-MS (LC-MS), have become a major tool providing a significant source of global metabolite profiling data. In the present review we describe and compare the utility of the different analytical strategies and technologies used for MS-based metabolomics with a particular focus on LC-MS. Both the advantages offered by the technology and also the challenges and limitations that need to be addressed for the successful application of LC-MS in metabolite analysis are described. Data treatment and approaches resulting in the detection and identification of biomarkers are considered. Special emphasis is given to validation issues, instrument stability, and QA/quality control (QC) procedures.

Benzo(a)pyrene-induced metabolic responses in Manila clam Ruditapes philippinarum by proton nuclear magnetic resonance ((1)H NMR) based metabolomics

Benzo(a)pyrene is an important polycyclic aromatic hydrocarbon (PAH) which causes carcinogenic, teratogenic and mutagenic effects in various species and the level of contamination of this toxic agent in the marine environment is of great concern. In this study, metabolic responses induced by two doses (0.02 and 0.2μM) of BaP were characterized in the gill tissues of Manila clam Ruditapes philippinarum after exposure for 24, 48 and 96h. The high dose (0.2μM) of BaP induced the disturbances in energy metabolism and osmotic regulation based on the metabolic biomarkers such as succinate, alanine, glucose, glycogen, branched chain amino acids, betaine, taurine, homarine, and dimethylamine in clam gills after 24h of exposure. In addition, hormesis induced by BaP was found in clams exposed to both doses of BaP. Overall, our results demonstrated the applicability of metabolomics for the elucidation of toxicological effects of marine environmental contaminants in a selected bioindicator species such as the Manila clam.

Xenobiotic metabolomics: major impact on the metabolome

Xenobiotics are encountered by humans on a daily basis and include drugs, environmental pollutants, cosmetics, and even components of the diet. These chemicals undergo metabolism and detoxication to produce numerous metabolites, some of which have the potential to cause unintended effects such as toxicity. They can also block the action of enzymes or receptors used for endogenous metabolism or affect the efficacy and/or bioavailability of a coadministered drug. Therefore, it is essential to determine the full metabolic effects that these chemicals have on the body. Metabolomics, the comprehensive analysis of small molecules in a biofluid, can reveal biologically relevant perturbations that result from xenobiotic exposure. This review discusses the impact that genetic, environmental, and gut microflora variation has on the metabolome, and how these variables may interact, positively and negatively, with xenobiotic metabolism.

Metabolic responses in gills of Manila clam Ruditapes philippinarum exposed to copper using NMR-based metabolomics

Copper is an important heavy metal contaminant with high ecological risk in the Bohai Sea. In this study, the metabolic responses in the bioindicator, Manila clam (Ruditapes philippinarum), to the environmentally relevant copper exposures were characterized using NMR-based metabolomics. The significant metabolic changes corresponding to copper exposures were related to osmolytes, intermediates of the Krebs cycle and amino acids, such as the increase in homarine, branched chain amino acids and decrease in succinate, alanine and dimethylamine in the copper-exposed clam gills during 96 h exposure period. Overall, Cu may lead to the disturbances in osmotic regulation and energy metabolism in clams during 96 h experimental period. These results demonstrate that NMR-based metabolomics is applicable for the discovery of metabolic biomarkers which could be used to elucidate the toxicological mechanisms of marine heavy metal contaminants.

From known knowns to known unknowns: predicting in vivo drug metabolites

'It is better to be useful than perfect'. This review attempts to critically cover and assess the currently available approaches and tools to answer the crucial question: Is it possible (and if it is, to what extent is it possible) to predict in vivo metabolites and their abundances on the basis of in vitro and preclinical animal studies? In preclinical drug development, it is possible to produce metabolite patterns from a candidate drug by virtual means (i.e., in silico models), but these are not yet validated. However, they may be useful to cover the potential range of metabolites. In vitro metabolite patterns and apparent relative abundances are produced by various in vitro systems employing tissue preparations (mainly liver) and in most cases using liquid chromatography-mass spectrometry analytical techniques for tentative identification. The pattern of the metabolites produced depends on the enzyme source; the most comprehensive source of drug-metabolizing enzymes is cultured human hepatocytes, followed by liver homogenate fortified with appropriate cofactors. For specific purposes, such as the identification of metabolizing enzyme(s), recombinant enzymes can be used. Metabolite data from animal in vitro and in vivo experiments, despite known species differences, may help pinpoint metabolites that are not apparently produced in in vitro human systems, or suggest alternative experimental approaches. The range of metabolites detected provides clues regarding the enzymes attacking the molecule under study. We also discuss established approaches to identify the major enzymes. The last question, regarding reliability and robustness of metabolite extrapolations from in vitro to in vivo, both qualitatively and quantitatively, cannot be easily answered. There are a number of examples in the literature suggesting that extrapolations are generally useful, but there are only a few systematic and comprehensive studies to validate in vitro-in vivo extrapolations. In conclusion, extrapolation from preclinical metabolite data to the in vivo situation is certainly useful, but it is not known to what extent.