A new aminopeptidase inhibitor from Streptomyces strain HCCB10043 found by UPLC-MS

The diversity of microbial metabolites has been of interest and concern for a long time, yet a suitable method for discovering these is still unavailable. In the work discussed in this report, ultra-performance liquid chromatography coupled with tandem quadrupole and time of flight high-resolution mass spectrometry (UPLC–Q–TOF-HRMS), with MS data analysis, was set up to study the metabolites of Streptomyces strain HCCB10043. It was found that besides antibacterial substances (A21978C complex) and two anti-aminopeptidase compounds (valistatin and bestatin), this strain can produce a new aminopeptidase inhibitor, identified as 3-amino-2-hydroxy-4-phenylbutanoylvalylisoleucine. This new compound had greater activity than valistatin or bestatin in aminopeptidase N (APN) inhibition assay. The results proved that combination of UPLC–Q–TOF-MS analysis and classic purification and identification steps as complementary strategies can provide a method with high reliability for research on microbial secondary metabolites. Furthermore, it has shown that the study of secondary metabolic profiling might be the key to discovering new drugs.     

Evaluation of in vitro antioxidant activities of soyasaponins from soy hypocotyls in human HepG2 cell line

Soyasaponins were shown to have a wide range of biological activities in previous studies; however, the activities of their monomeric compounds are unclear. The aim of this study was to evaluate the in vitro antioxidant activities of soyasaponins in HepG2 cells. Four soyasaponins were isolated from soy hypocotyls and identified as soyasaponin Aa, Ab, Ba, and Bb. The protective effects of these soyasaponins against production of hydrogen peroxide-induced reactive oxygen species in cells were investigated. The cellular antioxidant activity of soyasaponins was found to be in a dose-dependent manner at concentrations ranging between 25 and 400 μg/mL in 24 h. Finally, based on cell morphology observations, group A soyasaponins showed better cellular antioxidant activity and anti-oxidative enzyme activity than group B ones, with an optimal concentration of 100 μg/mL.     

Genomic and Metabolomic Investigation of a Rhizosphere Isolate Streptomyces netropsis WLXQSS-4 Associated with a Traditional Chinese Medicine

Rhizosphere microorganisms play important ecological roles in promoting herb growth and producing abundant secondary metabolites. Studies on the rhizosphere microbes of traditional Chinese medicines (TCMs) are limited, especially on the genomic and metabolic levels. In this study, we reported the isolation and characterization of a Steptomyces netropsis WLXQSS-4 strain from the rhizospheric soil of Clematis manshurica Rupr. Genomic sequencing revealed an impressive total of 40 predicted biosynthetic gene clusters (BGCs), whereas metabolomic profiling revealed 13 secondary metabolites under current laboratory conditions. Particularly, medium screening activated the production of alloaureothin, whereas brominated and chlorinated pimprinine derivatives were identified through precursor-directed feeding. Moreover, antiproliferative activities against Hela and A549 cancer cell lines were observed for five compounds, of which two also elicited potent growth inhibition in Enterococcus faecalis and Staphylococcus aureus, respectively. Our results demonstrated the robust secondary metabolism of S. netropsis WLXQSS-4, which may serve as a biocontrol agent upon further investigation.     

Relationship between Volatile Composition and Bioactive Potential of Vegetables and Fruits of Regular Consumption—An Integrative Approach

In recent years, there has been a growing interest in studying and exploring the potential health benefits of foods, mainly from vegetables and fruits from regular intake. The presence of secondary metabolites, namely polyphenols, carotenoids and terpenes, in certain food matrices seems to contribute to their functional properties, expressed through an increased prevention in the development of certain chronic diseases, namely coronary heart diseases, neurodegenerative diseases, cancer and diabetes. However, some foods’ volatile secondary metabolites also present important bioactive properties, although this is a poorly scientifically explored field. In this context, and in order to explore the potential bioactivity of volatile metabolites in different vegetables and fruits from regular consumption, the volatile composition was established using a green extraction technique, solid phase microextraction in headspace mode (HS-SPME), combined with gas chromatography tandem mass spectrometry (GC-MS). A total of 320 volatile metabolites, comprising 51 terpenic compounds, 45 organosulfur compounds, 31 aldehydes, 37 esters, 29 ketones, 28 alcohols, 23 furanic compounds, 22 hydrocarbons, 19 benzene compounds, 13 nitrogenous compounds, 9 carboxylic acids, 7 ethers, 4 halogenated compounds and 3 naphthalene derivatives, were positively identified. Each investigated fruit and vegetable showed a specific volatile metabolomic profile. The obtained results revealed that terpenic compounds, to which are associated antimicrobial, antioxidant, and anticancer activities, are the most predominant chemical family in beetroot (61%), orange carrot (58%) and white carrot (61%), while organosulfur compounds (antiviral activity) are dominant in onion, garlic and watercress. Broccoli and spinach are essentially constituted by alcohols and aldehydes (enzyme-inhibition and antimicrobial properties), while fruits from the Solanaceae family are characterized by esters in tamarillo and aldehydes in tomato.     

Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry: A New Tool Complementing Metabolomic Analyses of Polar Metabolites

Mass spectrometry (MS) driven metabolomics is a frequently used tool in various areas of life sciences; however, the analysis of polar metabolites is less commonly included. In general, metabolomic analyses lead to the detection of the total amount of all covered metabolites. This is currently a major limitation with respect to metabolites showing high turnover rates, but no changes in their concentration. Such metabolites and pathways could be crucial metabolic nodes (e.g., potential drug targets in cancer metabolism). A stable-isotope tracing capillary electrophoresis–mass spectrometry (CE-MS) metabolomic approach was developed to cover both polar metabolites and isotopologues in a non-targeted way. An in-house developed software enables high throughput processing of complex multidimensional data. The practicability is demonstrated analyzing [U-¹³C]-glucose exposed prostate cancer and non-cancer cells. This CE-MS-driven analytical strategy complements polar metabolite profiles through isotopologue labeling patterns, thereby improving not only the metabolomic coverage, but also the understanding of metabolism.     

Semi-targeted analysis of metabolites using capillary-flow ion chromatography coupled to high-resolution mass spectrometry

This work describes a novel application of capillary-flow ion chromatography mass spectrometry for metabolomic analysis, and comparison of the technique to octadecyl silica and hydrophilic interaction chromatography (HILIC)-based mass spectrometry. While liquid chromatography/mass spectrometry (LC/MS) is rapidly becoming the standard technique for metabolomic analysis, metabolomic samples are extremely heterogeneous, leading to a requirement for multiple methods of analysis and separation techniques to perform a 'global' metabolomic analysis. While C18 is suitable for hydrophobic metabolites and has been used extensively in pharmaceutical drug metabolism studies, HILIC is, in general, efficient at separating polar metabolites. Phosphorylated species and organic acids are challenging to analyse and effectively quantitate on both systems. There is therefore a requirement for an MS-compatible analytical technique that can separate negatively charged compounds, such as ion-exchange chromatography. Evaluation of capillary flow ion chromatography with electrolytic suppression was performed on a library of metabolite standards and was shown to effectively separate organic acids and sugar di- and tri-phosphates. Limits of detection for these compounds range from 0.01 to 100 pmol on-column. Application of capillary ion chromatography to a comparative analysis of energy metabolism in procyclic forms of the parasitic protozoan Trypanosoma brucei where cells were grown on glucose or proline as a carbon source was demonstrated to be more effective than HILIC for detection of the organic acids that comprise glucose central metabolism and the tricarboxylic acid (TCA) cycle.     

Development of an integrated metabolomic profiling approach for infectious diseases research

Metabolomic profiling offers direct insights into the chemical environment and metabolic pathway activities at sites of human disease. During infection, this environment may receive important contributions from both host and pathogen. Here we apply an untargeted metabolomics approach to identify compounds associated with an E. coli urinary tract infection population. Correlative and structural data from minimally processed samples were obtained using an optimized LC-MS platform capable of resolving ~2300 molecular features. Principal component analysis readily distinguished patient groups and multiple supervised chemometric analyses resolved robust metabolomic shifts between groups. These analyses revealed nine compounds whose provisional structures suggest candidate infection-associated endocrine, catabolic, and lipid pathways. Several of these metabolite signatures may derive from microbial processing of host metabolites. Overall, this study highlights the ability of metabolomic approaches to directly identify compounds encountered by, and produced from, bacterial pathogens within human hosts.     

Compatibility effects of herb pair Phellodendri chinensis cortex and Anemarrhenae rhizoma on benign prostatic hyperplasia using targeted metabolomics

Phellodendri chinensis cortex (P. C. cortex) and Anemarrhenae rhizoma (A. rhizoma) herb pair is a core component of traditional Chinese medicines used to treat inflammation and benign prostatic hyperplasia (BPH). The present study was designed to profile the arachidonic acid (AA) metabolomic characteristics in rat plasma and prostate after being treated with P. C. cortex and A. rhizoma as well as their combination. Plasma and prostate samples from sham group, BPH model group, herb pair group and two single herb groups were collected on days 7, 14, 21 and 28. Then, a systemic metabolomic analysis based on UFLC‐MS/MS was employed to quantify AA and its cyclooxygenase and lipoxygenase pathway metabolites (15‐HETE, 12‐HETE, 5‐HETE, AA, PGI₂, PGF_2α, 8‐HETE, PGD₂, PGE₂ and LTB₄). The results demonstrated that BPH led a significant increase of 10 biomarkers in plasma and tissue (p < 0.05). The clusters of herb pair group and single herb groups showed a tendency to return to the initial space, and the AA and its metabolites from those groups were differently downregulated to a healthier level, with the combination of single herbs most obvious. The present study demonstrated that P. C. cortex–A. rhizoma herb pair might produce synergistic or complementary compatibility effects on suppressing inflammatory processes occurring in BPH.     

Untargeted metabolomic analysis using liquid chromatography quadrupole time-of-flight mass spectrometry for non-volatile profiling of wines

The current study presents a method for comprehensive untargeted metabolomic fingerprinting of the non-volatile profile of the Graciano Vitis vinifera wine variety, using liquid chromatography/electrospray ionization time of flight mass spectrometry (LC–ESI-QTOF). Pre-treatment of samples, chromatographic columns, mobile phases, elution gradients and ionization sources, were evaluated for the extraction of the maximum number of metabolites in red wine. Putative compounds were extracted from the raw data using the extraction algorithm, molecular feature extractor (MFE). For the metabolite identification the WinMet database was designed based on electronic databases and literature research and includes only the putative metabolites reported to be present in oenological matrices. The results from WinMet were compared with those in the METLIN database to evaluate how much the databases overlap for performing identifications. The reproducibility of the analysis was assessed using manual processing following replicate injections of Vitis vinifera cv. Graciano wine spiked with external standards. In the present work, 411 different metabolites in Graciano Vitis vinifera red wine were identified, including primary wine metabolites such as sugars (4%), amino acids (23%), biogenic amines (4%), fatty acids (2%), and organic acids (32%) and secondary metabolites such as phenols (27%) and esters (8%). Significant differences between varieties Tempranillo and Graciano were related to the presence of fifteen specific compounds.     

Dihydro-β-agarofurans from the Australian rainforest plant Denhamia celastroides that inhibit leucine transport in prostate cancer cells

Four new dihydro-β-agarofurans, denhaminols K–N ( 4 – 7 ), along with three known secondary metabolites, denhaminols A–C ( 1 – 3 ) were obtained from the large-scale isolation studies of the leaves of the Australian endemic rainforest plant, Denhamia celastroides. The structures of the previously undescribed compounds were determined by detailed 1D and 2D nuclear magnetic resonance spectroscopy, mass spectrometry, ultraviolet, and infrared data analysis. All compounds were found to inhibit the activity of leucine transport in a human prostate cancer cell line with IC₅₀ values ranging from 5.1–74.9 μM. Dihydro-β-agarofurans 1 – 7 showed better potency than the L-type amino acid transporter family inhibitor, 2-aminobicyclo[2.2.1]-heptane-2-carboxylic acid (BCH).     

Is metabolomics reachable? Different purification strategies of human colon cancer cells provide different CE-MS metabolite profiles

In this work, four different metabolite purification approaches are investigated prior to metabolomics of human HT29 colon cancer cells. Namely, methanol deproteinization, ultrafiltration and two SPE methods using C18 and polymer-based cartridges were studied. The extracts were characterized via a metabolomic approach based on the application of CE TOF MS (CE-MS). CE-MS analysis time was less than 20 min per sample and allowed the simultaneous and reproducible analysis of more than 80 metabolites in a single run with a minimum consumption of sample and reagents. Metabolome analysis revealed in some cases important differences among the studied metabolite purification procedures. No significant differences were observed in the metabolite profile using C18 and polymer-based cartridges, or between ultrafiltration and methanol deproteinization. However, important differences were observed in the metabolomic profiles obtained from SPE and methanol deproteinization samples. These results demonstrate the crucial role of the metabolite purification strategy in metabolomics since it can bias (and in some cases mislead) the conclusions achieved by the metabolomic study.     

The iromycins, a new family of pyridone metabolites from Streptomyces sp. I. Structure, NOS inhibitory activity, and biosynthesis

The iromycins A-D are members of a new family of rare alpha-pyridone metabolites. The isolation and structure elucidation of these microbial secondary metabolites from Streptomyces sp. Dra 17 revealed a N-heterocyclic core structure with two unusual side chains. Iromycins act as inhibitors of nitric oxide synthases (NOS), a protein family, which produces the crucial second messenger nitric oxide (NO). Importantly, these compounds inhibit selectively endothelial NOS rather than neuronal NOS and thus set prospects for both medical therapy and basic research. Feeding experiments with 13C- and 15N -labeled precursors indicated an uncommon type of polyketide biosynthesis and clearly ruled out an isoprenoid origin. A detoxification pathway of a particular secondary metabolite in the host strain is a rare observation and here we demonstrate it with the iromycin family.     

A metabolomic strategy to screen the prototype components and metabolites of Qingkailing injection in rat urine by high‐performance liquid chromatography with tandem mass spectrometry

Xenobiotic metabolome identification of Chinese herbal formula in biological systems is a very challenging task. Qingkailing injection is a typical Chinese herbal injection, which is wildly used clinically in China. However, the holistic metabolic fate of the ingredient from Qingkailing injection remains unclear. In this work, a metabolomic strategy for comprehensively elucidating Qingkailing injection derived prototype components and metabolites in rat urine conducted by hybrid linear ion trap high‐resolution mass spectrometry was developed. High‐performance liquid chromatography coupled with hybrid linear ion trap high‐resolution mass spectrometry was developed to obtain the urine profiling between the control group and Qingkailing injection treated group. Orthogonal partial least squares discriminate analysis was applied to distinguish the exogenous and the endogenous. In the S‐plot, 37 xenobiotics derived from Qingkailing injection were found in urine, including 18 prototype compounds and 19 metabolites. The characterization of the prototype components and metabolites in rat's urine provided essential data for further pharmacological studies of Qingkailing injection. Our results indicated that the metabolomic approach was an effective tool to discover, screen, and analyze the multiple prototype components and their metabolites from complicated traditional Chinese preparations in vivo.     

亲水作用色谱/质谱联用方法用于大肠杆菌代谢组分析

建立了两性离子亲水作用色谱/质谱联用方法用于大肠杆菌胞内极性代谢物的分离分析。选取52个代表性极性物质对方法进行考察,发现此方法有较好的线性范围,且大部分物质最低检测限均在ng/mL数量级。平行制备6份样品进行分析,结果显示85%以上代谢物峰面积的RSD值小于30%。6个内标物质在低、中、高3个浓度下的日内精密度（RSD）均小于20%,大部分物质的相对回收率都在可接受的范围内（70%~130%）。把此方法用于yfcC基因改造的3株大肠杆菌代谢组分析,发现一些小肽、氨基酸、核苷、有机酸、磷脂等物质在基因改造后发生明显变化。此研究结果表明,建立的两性离子亲水作用色谱/质谱方法检测到的物质化学性质分布广,跨越了极性磷脂到小肽的各个范围,且具有良好的重复性、稳定性和适用性。     

High performance liquid chromatographic determination of diazinon, permethrin, DEET (N, N-diethyl-m-toluamide), and their metabolites in rat plasma and urine

A rapid method was developed for the analysis of the insecticide (A) diazinon (O,O-diethyl O-2-isopropyl-6-methylpyridimidinyl) phosphorothioate, its metabolites (B) diazoxon (O,O-diethyl O-2-isopropyl-6-methylpyridimidinyl) phosphate, and (C) 2-isopropyl-6-methyl-4-pyrimidinol, the insecticide (D) permethrin [3-(2,2-dichloro-ethenyl)-2,2-dimethylcyclopropanecarboxylic acid (3-phenoxyphenyl)methylester], its metabolites (E) m-phenoxybenzyl alcohol, and (F) m-phenoxybenzoic acid, the insect repellent (G) DEET (N,N-diethyl-m-toluamide), and its metabolites (H) m-toluamide and (I) m-toluic acid in rat plasma and urine. The method is based on using C18 Sep-Pak cartridges (Waters Corporation, Milford, Mass., U.S.A.) for solid phase extraction and high performance liquid chromatography with a reversed phase C18 column, and absorbance detection at 230 nm for compounds A, B, and C, and at 210 nm for compounds D-I. The compounds were separated using a gradient from 1% to 99% acetonitrile in water (pH 3.0) at a flow rate ranging between 1 and 1.7 mL/min in a period of 17 min. The limits of detection were ranged between 20 and 100 ng/mL, while limits of quantification were 80-200 ng/mL. The relationship between peak areas and concentration was linear over a range of 100-1000 ng/mL. This method was applied to determine the above insecticides and their metabolites following dermal administration in rats.     

Headspace solid-phase microextraction combined with mass spectrometry as a powerful analytical tool for profiling the terpenoid metabolomic pattern of hop-essential oil derived from Saaz variety

Hop (Humulus lupulus L., Cannabaceae family) is prized for its essential oil contents, used in beer production and, more recently, in biological and pharmacological applications. In this work, a method involving headspace solid-phase microextraction and gas chromatography-mass spectrometry was developed and optimized to establish the terpenoid (monoterpenes and sesquiterpenes) metabolomic pattern of hop-essential oil derived from Saaz variety as a mean to explore this matrix as a powerful biological source for newer, more selective, biodegradable and naturally produced antimicrobial and antioxidant compounds. Different parameters affecting terpenoid metabolites extraction by headspace solid-phase microextraction were considered and optimized: type of fiber coatings, extraction temperature, extraction time, ionic strength, and sample agitation. In the optimized method, analytes were extracted for 30 min at 40°C in the sample headspace with a 50/30 μm divinylbenzene/carboxen/polydimethylsiloxane coating fiber. The methodology allowed the identification of a total of 27 terpenoid metabolites, representing 92.5% of the total Saaz hop-essential oil volatile terpenoid composition. The headspace composition was dominated by monoterpenes (56.1%, 13 compounds), sesquiterpenes (34.9%, 10), oxygenated monoterpenes (1.41%, 3), and hemiterpenes (0.04%, 1) some of which can probably contribute to the hop of Saaz variety aroma. Mass spectrometry analysis revealed that the main metabolites are the monoterpene β-myrcene (53.0 ± 1.1% of the total volatile fraction), and the cyclic sesquiterpenes, α-humulene (16.6 ± 0.8%), and β-caryophyllene (14.7 ± 0.4%), which together represent about 80% of the total volatile fraction from the hop-essential oil. These findings suggest that this matrix can be explored as a powerful biosource of terpenoid metabolites.     

Strategy of using microsome-based metabolite production to facilitate the identification of endogenous metabolites by liquid chromatography mass spectrometry

One of the challenges in metabolomic profiling of complex biological samples is to identify new and unknown compounds. Typically, standards are used to help identify metabolites, yet standards cannot be purchased or readily synthesized for many unknowns. In this work we present a strategy of using human liver microsomes (HLM) to metabolize known endogenous human metabolites (substrates), producing potentially new metabolites that have yet to be documented. The metabolites produced by HLM can be tentatively identified based on the associated substrate structure, known metabolic processes, tandem mass spectrometry (MS/MS) fragmentation patterns and, if necessary, accurate mass measurements. Once identified, these metabolites can be used as references for identification of the same compounds in complex biological samples. As a proof of principle, a total of 9 metabolites have been identified from individual HLM incubations using 5 different substrates. Each metabolite was used as a standard. In the analysis of human urine sample by liquid chromatography MS/MS, four spectral matches were found from the 9 microsome-produced metabolite standards. Two of them have previously been documented as endogenous human metabolites, the third is an isomer of a microsome-metabolite and the fourth compound has not been previously reported and is also an isomer of a microsome-metabolite. This work illustrates the feasibility of using microsome-based metabolism to produce metabolites of endogenous human metabolites that can be used to facilitate the identification of unknowns in biological samples. Future work on improving the performance of this strategy is also discussed.     

Isolation and structure elucidation of two new cytotoxic metabolites from red yeast rice

In this study, 10 already described secondary metabolites and 2 unknown metabolites were identified in an extract of Monascus purpureus by high-performance liquid chromatography-diode array detection. The unknown metabolites were isolated and their chemical structures were elucidated. The new metabolites possess the molecular formulas C(21)H(27)NO(4) and C(23)H(31)NO(4). They were named monascopyridines E and F due to their pyridine backbone. The cytotoxicity of the new compounds was studied using immortalised human kidney epithelial cells displaying IC(50) values in the micromolar range.     

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry monitoring of anthocyanins in extracts from Arabidopsis thaliana leaves

Anthocyanins are secondary plant metabolites ubiquitous in the plant kingdom. They have different biological activities, so monitoring their content in plant tissue or in feed/food derived from plants may be an important task in different projects from various fields of molecular biology and biotechnology. Profiling of secondary metabolites with high-performance liquid chromatography/mass spectrometry (HPLC/MS) systems is time-consuming, especially when many samples have to be checked within a defined time frame with a reasonable number of repetitions according to the metabolomic standards. Even application of the advanced ultra-performance liquid chromatography (UPLC)/MS or equivalent systems would require a long time for analysis of numerous samples. We demonstrate the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the assessment of level (concentration) of anthocyanins in leaf tissues of four Arabidopsis thaliana ecotypes grown at normal (20 degrees C/16 degrees C day/night) and decreased (4 degrees C) temperature. The quantitative results were obtained for anthocyanins with MALDI-TOF MS using ferulic acid as a matrix. The amounts of anthocyanins in leaves of A. thaliana varied from 0.3-2.5 microg per gram of leaves for ecotypes Col-0 and C24, respectively, and contents of these markedly increased in plants grown in the cold. The applied analytical method exhibited better repeatability of measurements than obtained with an HPLC/ion trap MS system.     

Simultaneous quantification of differently glycosylated, acetylated, and 2,3-dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one-conjugated soyasaponins using reversed-phase high-performance liquid chromatography with evaporative light scattering detection

A novel method utilizing high-performance liquid chromatography (HPLC) with evaporative light scattering detection (ELSD) and electrospray ionisation mass spectrometry (ESI-MS) was developed for the analysis of soyasaponins, a divers group of triterpenic compounds with one or two sugar side chains, occurring in soy. Group A soyasaponins in different degrees of acetylation, as well as group B soyasaponins in both their 2,3-dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one (DDMP)-conjugated and non-conjugated forms could be separated and quantified using authentic soyasaponin standards, in one single run. The method was tested by the determination of the soyasaponin content and composition of eight soygerm samples of different origin. Differences in the composition and the degree of acetylation of the group A soyasaponins were observed among these samples. The group B soyasaponins showed much less variability and they were mainly present in their DDMP-conjugated form.