Themes and variations in riboswitch structure and function

The complexity of gene expression control by non-coding RNA has been highlighted by the recent progress in the field of riboswitches. Discovered a decade ago, riboswitches represent a diverse group of non-coding mRNA regions that possess a unique ability to directly sense cellular metabolites and modulate gene expression through formation of alternative metabolite-free and metabolite-bound conformations. Such protein-free metabolite sensing domains utilize sophisticated three-dimensional folding of RNA molecules to discriminate between a cognate ligand from related compounds so that only the right ligand would trigger a genetic response. Given the variety of riboswitch ligands ranging from small cations to large coenzymes, riboswitches adopt a great diversity of structures. Although many riboswitches share structural principles to build metabolite-competent folds, form precise ligand-binding pockets, and communicate a ligand-binding event to downstream regulatory regions, virtually all riboswitch classes possess unique features for ligand recognition, even those tuned to recognize the same metabolites. Here we present an overview of the biochemical and structural research on riboswitches with a major focus on common principles and individual characteristics adopted by these regulatory RNA elements during evolution to specifically target small molecules and exert genetic responses. This article is part of a Special Issue entitled: Riboswitches.

Power of isotopic fine structure for unambiguous determination of metabolite elemental compositions: in silico evaluation and metabolomic application

In mass spectrometry (MS)-based metabolomics studies, reference-free identification of metabolites is still a challenging issue. Previously, we demonstrated that the elemental composition (EC) of metabolites could be unambiguously determined using isotopic fine structure, observed by ultrahigh resolution MS, which provided the relative isotopic abundance (RIA) of (13)C, (15)N, (18)O, and (34)S. Herein, we evaluated the efficacy of the RIA for determining ECs based on the MS peaks of 20,258 known metabolites. The metabolites were simulated with a ≤25% error in the isotopic peak area to investigate how the error size effect affected the rate of unambiguous determination of the ECs. The simulation indicated that, in combination with reported constraint rules, the RIA led to unambiguous determination of the ECs for more than 90% of the tested metabolites. It was noteworthy that, in positive ion mode, the process could distinguish alkali metal-adduct ions ([M+Na](+) and [M+K](+)). However, a significant degradation of the EC determination performance was observed when the method was applied to real metabolomic data (mouse liver extracts analyzed by infusion ESI), because of the influence of noise and bias on the RIA. To achieve ideal performance, as indicated in the simulation, we developed an additional method to compensate for bias on the measured ion intensities. The method improved the performance of the calculation, permitting determination of ECs for 72% of the observed peaks. The proposed method is considered a useful starting point for high-throughput identification of metabolites in metabolomic research.

Residues of the herbicide glyphosate in riparian groundwater in urban catchments

The herbicide glyphosate and its putative metabolite aminomethylphosphonic acid (AMPA) have been found in urban streams, but limited information is available on their presence in urban riparian groundwater. Information is also lacking regarding the source of AMPA in these urban settings (glyphosate metabolite or wastewater), and whether, if present, glyphosate residues in urban riparian groundwater contribute significantly to urban streams. Glyphosate and AMPA were detected in shallow riparian groundwater at 4 of 5 stream sites in urban catchments in Canada and each were found in approximately 1 in 10 of the samples overall. Frequency of observations of glyphosate and AMPA varied substantially between sites, from no observations in a National Park near the Town of Jasper Alberta, to observations of both glyphosate and AMPA in more than half of the samples along two short reaches of streams in Burlington, Ontario. In these two catchments, AMPA was correlated with glyphosate, rather than the artificial sweetener acesulfame, suggesting that the AMPA is derived mainly from glyphosate degradation rather than from wastewater sources. Land use, localized dosage history, depth below ground and other factors likely control the occurrence of detectable glyphosate residues in groundwater.

Plasma metabolomics reveals a potential panel of biomarkers for early diagnosis in acute coronary syndrome

Discovery of new biomarkers is critical for early diagnosis of acute coronary syndrome (ACS). Recent advances in metabolomic technologies have drastically enhanced the possibility of improving the knowledge of its physiopathology through the identification of the altered metabolic pathways. In this study, analyses of peripheral plasma from non-ST segment elevation ACS patients and healthy controls by gas chromatography-mass spectrometry (GC-MC) permitted the identification of 15 metabolites with statistical differences (p < 0.05) between experimental groups. Additionally, validation by GC-MC and liquid chromatography-MC permitted us to identify a potential panel of biomarkers formed by 5-OH-tryptophan, 2-OH-butyric acid and 3-OH-butyric acid. This panel of biomarkers reflects the oxidative stress and the hypoxic state that suffers the myocardial cells and consequently constitutes a metabolomic signature of the atherogenesis process that could be used for early diagnosis of ACS.

Using a simple HPLC approach to identify the enzymatic products of UTL-5g, a small molecule TNF-α inhibitor, from porcine esterase and from rabbit esterase

UTL-5g is a novel small-molecule chemoprotector that lowers hepatotoxicity, nephrotoxicity, and myelotoxicity induced by cisplatin through TNF-α inhibition among other factors. As a prelude to investigating the metabolites of UTL-5g, we set out to identify the enzymatic products of UTL-5g under the treatment of both porcine liver esterase (PLE) and rabbit liver esterase (RLE). First, a number of mixtures made by UTL-5g and PLE were incubated at 25°C. At predetermined time points, individual samples were quenched by acetonitrile, vortexed, and centrifuged. The supernatants were then analyzed by reversed-phase HPLC (using a C18 column). The retention times and UV/vis spectra of individual peaks were compared to those of UTL-5g and its two postulated enzymatic products; thus the enzymatic products of UTL-5g were tentatively identified. Secondly, a different HPLC method (providing different retentions times) was used to cross-check and to confirm the identities of the two enzymatic products. Based on the observations, it was concluded that under the treatment of PLE, the major enzymatic products of UTL-5g were 5-methyliosxazole-3-carboxylic acid (ISOX) and 2,4-dichloroaniline (DCA). Treatment of UTL-5g by RLE also provided the same enzymatic products of UTL-5g from esterase. These results indicate that the peptide bond in UTL-5g was cleaved by PLE/RLE. Michaelis-Menten kinetics showed that the Km values of UTL-5g were 2.07mM with PLE and 0.37mM with RLE indicating that UTL-5g had a higher affinity with RLE. In summary, by a simple HPLC approach, we have concluded that the peptide bond in UTL-5g was cleaved by esterase from either porcine liver or rabbit liver in vitro and afforded DCA (at a mole ratio of 1:1) and ISOX. However, further studies are needed in order to determine whether UTL-5g is metabolized by microsomal enzymes to produce ISOX and DCA.

Ionomic responses and correlations between elements and metabolites under salt stress in wild and cultivated barley

A thorough understanding of ionic detoxification and homeostasis is imperative for improvement of salt tolerance in crops. However, the homeostasis of elements and their relationship to metabolites under salt stress have not been fully elucidated in plants. In this study, Tibetan wild barley accessions, XZ16 and XZ169, differing in salt tolerance, and a salt-tolerant cultivar CM72 were used to investigate ionomic profile changes in tissues in response to 150 and 300 mM NaCl at the germination and seedling stages. At the germination stage, the contents of Ca and Fe significantly decreased in roots, while K and S contents increased, and Ca and Mg contents decreased in shoots, after 10 d of treatment. At the seedling stage, the contents of K, Mg, P and Mn in roots and of K, Ca, Mg and S in shoots decreased significantly after 21 d of treatment. Moreover, Na had a significant negative correlation with metabolites involved in glycolysis, α-ketoglutaric acid, maleic acid and alanine in roots, and metabolites associated with the tricarboxylic acid (TCA) cycle, sucrose, polyols and aspartate in leaves. The salt-tolerant genotypes XZ16 and CM72 showed a lower Na content in tissues, and less reduction in Zn and Cu in roots, of Ca, Mg and S in leaves, and shoot DW than the sensitive genotype XZ169, when exposed to a higher salt level. The results indicated that restriction of Na accumulation and rearrangement of nutrient elements and metabolites in barley tissues are possibly attributable to development of salt tolerance.

Isolation, identification and cyfluthrin-degrading potential of a novel Lysinibacillus sphaericus strain, FLQ-11-1

Strain FLQ-11-1, isolated from sewage sludge, was able to degrade cyfluthrin and was identified as Lysinibacillus sphaericus based on its morphology, 16S rRNA sequence and fatty acid methyl ester (FAME) analyses. This strain could use cyfluthrin as its carbon or nitrogen source. Response surface methodology (RSM) analysis showed that the optimum conditions for degradation were at pH 7.0 and 35 °C, using an inoculum amount with an OD600nm value of 1.6. Under these conditions, approximately 80.4% of cyfluthrin (50 mgl(-1)) was degraded within five days (d) of incubation. Four metabolic compounds were detected during cyfluthrin degradation and identified as methyl-3-(2,2-dichlorovinyl)-2,2-dimethyl-(1-cyclopropane)-carboxylate, 4-fluoro-3-phenoxy-benzoic acid methyl ester, methyl-3-phenoxybenzoate, 3-phenoxy-benzaldehyde by gas chromatography-mass spectrometry (GC-MS) and tandem mass spectrum (MS/MS) analysis and no cyfluthrin was detected after seven days of incubation. A possible degradation pathway was proposed, and our data showed that cyfluthrin could be efficiently degraded by FLQ-11-1, indicating that this strain could potentially be used to eliminate the contamination of pyrethroid herbicides.

Metabolites characterization of chamaechromone in vivo and in vitro by using ultra-performance liquid chromatography/Xevo G2 quadrupole time-of-flight tandem mass spectrometry

ETHNOPHARMACOLOGICAL RELEVANCE

Stellera chamaejasme L. (Thymelaeaceae) was a toxic perennial herb and widely used as pesticide and dermatological agents in China. Chamaechromone was a major component in the dried roots of Stellera chamaejasme with anti-HBV and insecticidal activity. Analysis of metabolic profile in vivo and in vitro plays a pivotal role to unravel how TCM works. And the metabolites of chamaechromone might influence the effects and toxicity of Stellera chamaejasme. Moreover, the metabolic routes of chamaechromone provide an important basis for toxicological safety evaluation. Until now, little is known about the metabolism of chamaechromone. The current study was designed to characterize the whole metabolic pathways of chamaechromone in vitro and in vivo.

MATERIALS AND METHODS

Twenty-four rats were randomly divided into four groups, including two oral administration groups (100mgkg(-1)), one intravenous injection group (5 mgkg(-1)), and one control group. The metabolites in rat urine and feces and bile were identified by UPLC/Q-TOF MS analysis and β-glucuronidase hydrolysis. Moreover, the possible metabolic mechanism was further confirmed by Phase I and Phase II metabolism and catechol-O-methyltransferase methylation in rat liver S9 fraction and degradation in rat intestinal bacteria.

RESULTS

A total of 24 metabolites from chamaechromone were detected and identified in vivo and in vitro, 20 of which were novel. And the major metabolic processes were hydroxylation, methylation, glucuronation, acetylation, dehydroxylation and degradation.

CONCLUSIONS

The present study revealed the whole metabolic pathways of chamaechromone in rat through both in vitro and in vivo experiments for the first time. And chamaechromone could undergo extensive phase I and phase II metabolism in rat. These findings would provide an important basis for the further study and clinical application of chamaechromone. In addition, the results of this work have showed the feasibility of the UPLC/Q-TOF-MS approach for rapid and reliable characterization of metabolites.

Determination of allopurinol and oxypurinol in human plasma and urine by liquid chromatography-tandem mass spectrometry

Allopurinol is used widely for the treatment of gout, but its pharmacokinetics is complex and some patients show hypersensitivity, necessitating careful monitoring and improved detection methods. In this study, a sensitive and reliable liquid chromatography-tandem mass spectrometry method was developed to determine the concentrations of allopurinol and its active metabolite oxypurinol in human plasma and urine using 2,6-dichloropurine as the internal standard (IS). Analytes and the IS were extracted from 0.5ml aliquots of plasma or urine using ethyl acetate and separated on an Agilent Eclipse Plus C18 column using methanol and ammonium formate-formic acid buffer containing 5mM ammonium formate and 0.1% formic acid (95:5, v/v) as the mobile phase (A) for allopurinol or methanol plus 5mM ammonium formate aqueous solution (95:5, v/v) as the mobile phase (B) for oxypurinol. Allopurinol was detected in positive ion mode and the analysis time was about 7min. The calibration curve was linear from 0.05 to 5μg/mL allopurinol in plasma and 0.5-30μg/mL in urine. The lower limit of quantification (LLOQ) was 0.05μg/mL in plasma and 0.5μg/mL in urine. The intra- and inter-day precision and relative errors of quality control (QC) samples were ≤11.1% for plasma and ≤ 8.7% for urine. Oxypurinol was detected in negative mode with an analysis time of about 4min. The calibration curve was linear from 0.05 to 5μg/mL in plasma (LLOQ, 0.05μg/mL) and from 1 to 50μg/mL in urine (LLOQ, 1μg/mL). The intra- and inter-day precision and relative errors were ≤7.0% for plasma and ≤9.6% for urine. This method was then successfully applied to investigate the pharmacokinetics of allopurinol and oxypurinol in humans.

Combined collision-induced dissociation and photo-selected reaction monitoring mass spectrometry modes for simultaneous analysis of coagulation factors and estrogens

Oral estrogens are directly associated with changes in plasma levels of coagulation proteins. Thus, the detection of any variation in protein concentrations due to estrogen contraceptives, by a simultaneous analysis of both coagulation proteins and estrogens, would be a very informative tool. In the present study, the merit of photo-selected reaction monitoring (SRM), a new analytical tool, was evaluated towards estrogens detection in plasma. Then, SRM and photo-SRM detection modes were combined for the simultaneous analysis of estrogen molecules together with heparin co-factor and factor XIIa, two proteins involved in the coagulation cascade. This study shows that photo-SRM could open new multiplexed analytical routes.

The promise of riboswitches as potential antibacterial drug targets

Riboswitches represent promising novel RNA structures for developing compounds that artificially regulate gene expression and, thus, bacterial growth. The past years have seen increasing efforts to identify metabolite-analogues which act on riboswitches and which reveal antibacterial activity. Here, we summarize the current inventory of riboswitch-targeting compounds, their characteristics and antibacterial potential.

Pharmacokinetic study of ginsenoside Rc and simultaneous determination of its metabolites in rats using RRLC-Q-TOF-MS

A rapid resolution liquid chromatography coupled with quadruple-time-of-flight mass spectrometry (RRLC-Q-TOF-MS) method was developed for pharmacokinetic study of ginsenoside Rc and applied in the simultaneous determination of ginsenoside Rc metabolites in rats. The experimental results indicate that the concentration versus time profile of ginsenoside Rc shows a two-compartment pharmacokinetic model after intravenous administration of ginsenoside Rc at a dosage of 0.4mg/kg for rats. In the metabolic study, prototype ginsenoside Rc and its deglycosylated metabolites Mb, Mc, and compound K were characterized by comparing the retention time (tR), accurate mass, and characteristic MS/MS fragment ions with standard compounds. The experiments show that part of the ginsenoside Rc was excreted through urine as prototype and part was metabolized into metabolites Mb and Mc after intravenous administration. In contrast, most of ginsenoside Rc were transformed into Mc and CK in feces after oral administration. The in vivo metabolic pathway of ginsenoside Rc was summarized.

Detection and tentative identification of urinary phase I metabolites of phenylacetylindole cannabimimetics JWH-203 and JWH-251, by GC-MS and LC-MS/MS

The synthetic phenylacetylindole cannabimimetics, JWH-203 and JWH-251, have been identified in 'herbal' smoking mixtures following the widespread legislative control of 'first generation' compounds such as JWH-018 and CP47, 497(C8). N-Alkylindole cannabimimetics (including phenylacetylindoles) undergo extensive metabolism and little or none of the parent compounds are found in urine. Utilizing GC-MS and LC-MS/MS, a series of JWH-203 and JWH-251 urinary metabolites have been tentatively identified. These are products of mono- and dihydroxylation, monohydroxylation combined with formation of carbonyl group on the N-pentyl chain, carboxylation of N-pentyl chain and N-dealkylation combined with monohydroxylation. Additionally, trihydroxylated metabolites were detected for JWH-203. No parent compounds were detected. The monohydroxylated metabolites with the hydroxyl group positioned on the N-pentyl chain were the most abundant and were found to be suitable for establishing ingestion of JWH-203 or JWH-250. Maximum urinary concentrations of chain-monohydroxylated metabolites were observed at 2.5-3h (JWH-203) and 6-10h (JWH-251) following ingestion. These metabolites were observed (GC-MS) for to 10 and 8 days (JWH-203 and JWH-251, respectively).

Rapid sensitive validated UPLC-MS method for determination of venlafaxine and its metabolite in rat plasma: Application to pharmacokinetic study

A new ultra-performance liquid chromatography–electrospray ionization mass spectrometry (UPLC–MS/ESI) method for simultaneous determination of venlafaxine (VEN) and its metabolite O-desmethylvenlafaxine (ODV) in rat plasma has been developed and validated using Venlafaxine d6 as the internal standard. The compounds and internal standard were extracted from plasma by solid phase extraction. The UPLC separation of the analytes was performed on ACQUITY UPLC^® BEH Shield RP18 (1.7 µm, 100 mm×2.1 mm) column, using isocratic elution with mobile phase constituted of water (containing 2 mM ammonium acetate): acetonitrile (20:80, v/v) at a flow rate of 0.3 mL/min. All of the analytes were eluted within 1.5 min. The compounds were ionized in the electrospray ionization (ESI) ion source of the mass spectrometer, operating in multiple reaction monitoring (MRM) and positive ion mode. The precursor to product ion transitions monitored for VEN, ODV and Venlafaxine d6 were m/z 278.3→121.08, 264.2→107.1 and 284.4→121.0, respectively. The developed and validated method was used for the pharmacokinetic study of VEN in rats.

Monitoring of urinary metabolites of JWH-018 and JWH-073 in legal cases

Due to their cannabis-like effects, synthetic cannabinoids have attracted much public attention since 2008. Thus, elucidation of the metabolic pattern and the detection of the intake of these drugs have been of major concern. In order to suggest appropriate urinary biomarkers to prove JWH-018 or JWH-073 intake, we selected the major metabolites of JWH-018 and JWH-073, namely (ω)-, (ω-1)-hydroxy, carboxy and 6-hydroxyindole metabolites, and validated a method for the quantification of these metabolites using solid-phase extraction based on LC-MS/MS analysis. Authentic urine specimens obtained from drug offenders were screened via a synthetic cannabinoid ELISA kit and were analyzed by LC-MS/MS for confirmation. Twenty-one out of a total of 52 samples (40%) were found positive for at least one metabolite of JWH-018 or JWH-073. N-pentyl hydroxy metabolites of JWH-018 and carboxy metabolites of JWH-018 and JWH-073 were detected in all positive samples. However, the rest of the metabolites were either not detected or only a small amount of them were found. A considerable variation was observed in the concentration ratio of (ω) and (ω-1)-hydroxy metabolites of JWH-018. Based on the results, it may have some pitfalls to determine the ingestion of specific synthetic cannabinoids by detecting a few metabolites, considering the continuous emergence of structurally related synthetic cannabinoids. Thus, use of synthetic cannabinoids should be proven carefully through comprehensive investigation of analytical results of biological specimens.

Recent developments in the field of the determination of constituents of TCMs in body fluids of animals and human

Although traditional Chinese medicines (TCMs) play important role in drug discovery and human health, the actual value of TCMs has not been fully recognized worldwide due to its complex components and uncontrollable quality. For the modernization and globalization of TCMs, it is important to establish selective, sensitive and feasible analytical methods for determination and quantification of bioactive components of TCMs in body fluids primarily due to the low concentration, the complex nature of the biological matrices, and multi-components and their metabolites present in biological fluids. The present review summarizes the current extraction techniques, chromatographic separation and spectroscopic (especially mass spectrometric) analysis methods and new trends on the analysis of bioactive components and metabolites of TCMs in biological fluids. In addition, the importance of establishment of pharmacokinetics and bioavailability profiles and simultaneous determination of multi-active components in TCMs is discussed to provide proper examples of analytical methods for pharmacological and clinical studies of TCMs.

Proton magnetic resonance spectroscopy: technique for the neuroradiologist

Magnetic resonance spectroscopy (MRS) provides information on neuronal and axonal viability, energetics of cellular structures, and status of cellular membranes. Proton MRS appeals to clinicians and scientists because its application in the clinical setting can increase the specificity of MR imaging. The objective of this article is to provide descriptive concepts of the technique and its application in vivo for a variety of patient populations. When appropriately incorporating MRS into the neuroradiologic evaluation, this technique produces relevant information to radiologists and clinicians for their understanding of adult and pediatric neurologically based disease processes.

Relative Determination Approach to the Metabolites of Protoberberine Alkaloids in Rat Urine by Liquid Chromatography Tandem Mass Spectrometry for the Comparative Studies on Rhizome coptidis and Zuojinwan Preparation

The lack of authentic standards has limited the quantitative analysis of herbal drugs in biological samples. The present work demonstrated a practicable strategy for the assay of herbs and their metabolites independent of authentic standards. A liquid chromatography- electrospray ionization-mass spectrometry (LC-ESI-MS) method for the qualitative and quantitative determination of the metabolites after oral administration of Rhizome coptidis and Zuojinwan preparation in rat urine has been developed. Urine samples, extracted with a protein precipitation procedure were separated on a C18 column using a mixture of water (containing 0.1% formic acid) and acetonitrile (30:70, v/v) as mobile phase. The detection was performed via MS with electrospray ionization interface in positive selected reaction monitoring (SRM) mode. One urine sample after administration was selected as ‹standard›. The method validation was carried out according to a conventional method which was calibrated by authentic standards. The fully validated method was applied to the pharmacokinetic study of 2,9-demethyljateorhizine-3-sulfate, 13-methoxyjateorhizine-3- glucoronide and 6-methyljateorhizine-5-glucoronide in rat urine. The results could provide evidence to explain the combination of Rhizome coptidis and Evodiae fructus in terms of elimination.

Metabolomics of gastric cancer metastasis detected by gas chromatography and mass spectrometry

AIM: To elucidate the underlying mechanisms of metastasis and to identify the metabolomic markers of gastric cancer metastasis.

METHODS: Gastric tumors from metastatic and non-metastatic groups were used in this study. Metabolites and different metabolic patterns were analyzed by gas chromatography, mass spectrometry and principal components analysis (PCA), respectively. Differentiation performance was validated by the area under the curve (AUC) of receiver operating characteristic curves.

RESULTS: Twenty-nine metabolites were differentially expressed in animal models of human gastric cancer. Of the 29 metabolites, 20 were up-regulated and 9 were down-regulated in metastasis group compared to non-metastasis group. PCA models from the metabolite profiles could differentiate the metastatic from the non-metastatic specimens with an AUC value of 1.0. These metabolites were mainly involved in several metabolic pathways, including glycolysis (lactic acid, alaline), serine metabolism (serine, phosphoserine), proline metabolism (proline), glutamic acid metabolism, tricarboxylic acid cycle (succinate, malic acid), nucleotide metabolism (pyrimidine), fatty acid metabolism (docosanoic acid, and octadecanoic acid), and methylation(glycine). The serine and proline metabolisms were highlighted during the progression of metastasis.

CONCLUSION: Proline and serine metabolisms play an important role in metastasis. The metabolic profiling of tumor tissue can provide new biomarkers for the treatment of gastric cancer metastasis.

Development and validation of a rapid HPLC- fluorescence method for simultaneous determination of venlafaxine and its major metabolites in human plasma

BACKGROUND AND THE PURPOSE OF THE STUDY

To develop a simple, rapid and accurate HPLC method for the measurement of the venlafaxine and its main metabolites, O-desmethylvenlafaxine and O,N-didesmethylvenlafaxine in pharmacokinetic studies and therapeutic drug monitoring.

METHOD

Chromatographic separation was achieved with a ChromolithTM Performance RP-18e 100 mm×4.6 mm column equipped with a Fluorescence detectore (λ(ex) 200 nm/λ(em) 300 nm) The mobile phase of methanol:water (35:65, v/v) adjusted to pH 2.5 by phosphoric acid was passed through the column in an isocratic mode at flow rate of 2 ml/min. The sample preparation involved a simple, one-step, extraction with ethyl acetate.

RESULTS

The calibration curves were linear in the concentration range of 1-300 ng/ml for all analytes (r2>0.998). The lower limit of quantification was 1 ng/ml for all analytes. Within and between day precisions in the measurement of quality control (QC) of samples were in the range of 1.8-14.1% for all analytes.

CONCLUSION

The developed procedure was used to assess the pharmacokinetics of venlafaxine and its main metabolites following oral administration of 75 mg venlafaxine to a healthy subject.