Comparative metabolic fingerprinting of Gentiana rhodantha from different geographical origins using LC-UV-MS/MS and multivariate statistical analysis

Multivariate Statistical Analysis of Metabolites in Anisodus tanguticus (Maxim.) Pascher to Determine Geographical Origins and Network Pharmacology

Anisodus tanguticus (Maxim.) Pascher, has been used for the treatment of septic shock, analgesia, motion sickness, and anesthesia in traditional Tibetan medicine for 2,000 years. However, the chemical metabolites and geographical traceability and their network pharmacology are still unknown. A total of 71 samples of A. tanguticus were analyzed by Ultra-Performance Liquid Chromatography Q-Exactive Mass Spectrometer in combination with chemometrics developed for the discrimination of A. tanguticus from different geographical origins. Then, network pharmacology analysis was used to integrate the information of the differential metabolite network to explore the mechanism of pharmacological activity. In this study, 29 metabolites were identified, including tropane alkaloids, hydroxycinnamic acid amides and coumarins. Principal component analysis (PCA) explained 49.5% of the total variance, and orthogonal partial least-squares discriminant analysis (OPLS-DA) showed good discrimination (R2Y = 0.921 and Q2 = 0.839) for A. tanguticus samples. Nine differential metabolites accountable for such variations were identified through variable importance in the projection (VIP). Through network pharmacology, 19 components and 20 pathways were constructed and predicted for the pharmacological activity of A. tanguticus. These results confirmed that this method is accurate and effective for the geographic classification of A. tanguticus, and the integrated strategy of metabolomics and network pharmacology can explain well the "multicomponent--multitarget" mechanism of A. tanguticus.

LC-ESI/LTQOrbitrap/MS Metabolomic Analysis of Fennel Waste (Foeniculum vulgare Mill.) as a Byproduct Rich in Bioactive Compounds

Food industries produce a high amount of waste every year. These wastes represent a source of bioactive compounds to be used to produce cosmetic and nutraceutical products. In this study, the possibility to retrain food waste as a potential source of bioactive metabolites is evaluated. In particular, metabolite profiles of different parts (bulb, leaves, stems and little stems) of fennel waste were investigated by liquid chromatography coupled with mass spectrometry (LC-ESI/LTQ Orbitrap MS). To discriminate the different plant parts, a Multivariate Data Analysis approach was developed. Metabolomic analysis allowed the identification of different metabolites mainly belonging to hydroxycinnamic acid derivatives, flavonoid glycosides, flavonoid aglycons, phenolic acids, iridoid derivatives and lignans. The identification of compounds was based on retention times, accurate mass measurements, MS/MS data, exploration on specific metabolites database and comparison with data reported in the literature for F. vulgare. Moreover, the presence of different oxylipins was relieved; these metabolites for the first time were identified in fennel. Most of the metabolites identified in F. vulgare possess anti-inflammatory, antioxidant and/or immunomodulatory properties. Considering that polyphenols are described to possess antioxidant activity, spectrophotometric tests were performed to evaluate the antioxidant activity of each part of the fennel.

Development and validation of the TGx-HDACi transcriptomic biomarker to detect histone deacetylase inhibitors in human TK6 cells

Transcriptomic biomarkers can be used to inform molecular initiating and key events involved in a toxicant's mode of action. To address the limited approaches available for identifying epigenotoxicants, we developed and assessed a transcriptomic biomarker of histone deacetylase inhibition (HDACi). First, we assembled a set of ten prototypical HDACi and ten non-HDACi reference compounds. Concentration-response experiments were performed for each chemical to collect TK6 human lymphoblastoid cell samples after 4 h of exposure and to assess cell viability following a 20-h recovery period in fresh media. One concentration was selected for each chemical for whole transcriptome profiling and transcriptomic signature derivation, based on cell viability at the 24-h time point and on maximal induction of HDACi-response genes (RGL1, NEU1, GPR183) or cellular stress-response genes (ATF3, CDKN1A, GADD45A) analyzed by TaqMan qPCR assays after 4 h of exposure. Whole transcriptomes were profiled after 4 h exposures by Templated Oligo-Sequencing (TempO-Seq). By applying the nearest shrunken centroid (NSC) method to the whole transcriptome profiles of the reference compounds, we derived an 81-gene toxicogenomic (TGx) signature, referred to as TGx-HDACi, that classified all 20 reference compounds correctly using NSC classification and the Running Fisher test. An additional 4 HDACi and 7 non-HDACi were profiled and analyzed using TGx-HDACi to further assess classification performance; the biomarker accurately classified all 11 compounds, including 3 non-HDACi epigenotoxicants, suggesting a promising specificity toward HDACi. The availability of TGx-HDACi increases the diversity of tools that can facilitate mode of action analysis of toxicants using gene expression profiling.

Characterization of the complete chloroplast genome of Gentiana rhodantha (Gentianaceae)

The first complete chloroplast genome (cp) sequences of Gentiana rhodantha were reported in this study. The cp genome of G. rhodantha was 148,967 bp in size, with two inverted repeat (IR) regions of 25,760 bp, the large single copy (LSC) region of 79,831 bp, and the small single copy (SSC) region of 17,616 bp. The cp genome contained 112 genes, including 78 protein-coding genes, 4 ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 36.4%. Phylogenetic analysis of the cp genomes within the tribe Gentianeae suggests that G. rhodantha is in a sister clade of other subtribe Gentianinae.

Analytical Methods of Phytochemicals from the Genus Gentiana

The genus Gentiana comprises approximately 400 species. Many species have a wide range of pharmacological activities and have been used therapeutically for thousands of years. To provide comprehensive guidance, utilization and quality control of Gentiana species, this review presents updated information concerning the recent application and progress of chemical analysis including phytochemical analysis, sample preparation and chemometrics. Detailed and comprehensive data including number of analytes, extraction/separation methods, analytical techniques and chemometrics are shown as corresponding tables. These data illustrate that the development of newly discovered compounds and therapeutic uses, understanding of the structure-activity relationship and establishment of harmonious and effective medicinal herb standards are the direction of advancement in future research.

Quantitative evaluation and discrimination of wild Paris polyphylla var. yunnanensis (Franch.) Hand.-Mazz from three regions of Yunnan Province using UHPLC-UV-MS and UV spectroscopy couple with partial least squares discriminant analysis

Paris polyphylla var. yunnanensis (Franch.) Hand.-Mazz (PPY) is used widely as an anthelmintic, antimicrobial, and anti-tumor agent. Multiplicate analytical methods have been employed to discriminate PPY from different regions, as well as to identify regions most beneficial to the growing of this species. In this study, a convenient and accurate method was established using ultra high performance liquid chromatography (UHPLC) for simultaneous determination of four steroid saponins (Pa, Pb, polyphyllin VI, and chonglou saponin VII). Partial least squares discriminant analysis (PLS-DA) according to UHPLC and UV spectroscopy was applied to analyze 30 samples of PPY from three regions of Yunnan Province in China, and identify significant peaks. The results indicated that the correlation coefficients (r ²) of all calibration curves were above 0.999, and the inter- and intra-day relative standard deviations (RSD) of retention time and peak areas of common peaks were below 1.78 % and 3.40 %, respectively, with recovery rates of 99.6-103.4 % with RSD ≤2 %. Quantitative analysis implied that the average values of total saponins in PPY from south Yunnan Province (19.9 mg/g) were higher than in the central (8.79 mg/g) district. Thus, further investigation could focus on the southern region to seek high quality PPY. The analysis found that PLS-DA for ultraviolet (UV) spectroscopy, which could separate the samples from three regions, was more appropriate than UHPLC. Retention times during 20-30.75 min of UHPLC, and absorption at 200-300 nm of the UV spectrum were identified as significant peaks for distinguishing PPY from different regions.