Mass spectrometry-based ginsenoside profiling: Recent applications, limitations, and perspectives.

Ginseng, the roots of Panax species, is an important medicinal herb used as a tonic. As ginsenosides are key bioactive components of ginseng, holistic chemical profiling of them has provided many insights into understanding ginseng. Mass spectrometry has been a major methodology for profiling, which has been applied to realize numerous goals in ginseng research, such as the discrimination of different species, geographical origins, and ages, and the monitoring of processing and biotransformation. This review summarizes the various applications of ginsenoside profiling in ginseng research over the last three decades that have contributed to expanding our understanding of ginseng. However, we also note that most of the studies overlooked a crucial factor that influences the levels of ginsenosides: genetic variation. To highlight the effects of genetic variation on the chemical contents, we present our results of untargeted and targeted ginsenoside profiling of different genotypes cultivated under identical conditions, in addition to data regarding genome-level genetic diversity. Additionally, we analyze the other limitations of previous studies, such as imperfect variable control, deficient metadata, and lack of additional effort to validate causation. We conclude that the values of ginsenoside profiling studies can be enhanced by overcoming such limitations, as well as by integrating with other -omics techniques.

Correction: Genetic and chemical markers for authentication of three Artemisia species: A. capillaris, A. gmelinii, and A. fukudo.

[This corrects the article DOI: 10.1371/journal.pone.0264576.].

Comparative transcriptome and metabolome analyses of four Panax species explore the dynamics of metabolite biosynthesis.

Background: The genus Panax in the Araliaceae family has been used as traditional medicinal plants worldwide and is known to biosynthesize ginsenosides and phytosterols. However, genetic variation between Panax species has influenced their biosynthetic pathways is not fully understood. Methods: Simultaneous analysis of transcriptomes and metabolomes obtained from adventitious roots of two tetraploid species (Panax ginseng and P. quinquefolius) and two diploid species (P. notoginseng and P. vietnamensis) revealed the diversity of their metabolites and related gene expression profiles. Results: The transcriptome analysis showed that 2,3-OXIDOSQUALENE CYCLASEs (OSCs) involved in phytosterol biosynthesis are upregulated in the diploid species, while the expression of OSCs contributing to ginsenoside biosynthesis is higher in the tetraploid species. In agreement with these results, the contents of dammarenediol-type ginsenosides were higher in the tetraploid species relative to the diploid species. Conclusion: These results suggest that a whole-genome duplication event has influenced the triterpene biosynthesis pathway in tetraploid Panax species during their evolution or ecological adaptation. This study provides a basis for further efforts to explore the genetic variation of the Panax genus.

Wearable Surface-Lighting Micro-Light-Emitting Diode Patch for Melanogenesis Inhibition.

Wearable light-emitting diode (LED)-based phototherapeutic devices have recently attracted attention as skin care tools for wrinkles, acne, and hyperpigmentation. However, the therapeutic effectiveness and safety of LED stimulators are still controversial due to their inefficient light transfer, high heat generation, and non-uniform spot irradiation. Here, a wearable surface-lighting micro-LED (SµLED) photostimulator is reported for skin care and cosmetic applications. The SµLEDs, consisting of a light diffusion layer (LDL), 900 thin film µLEDs, and polydimethylsiloxane (PDMS), achieve uniform surface-lighting in 2 × 2 cm2 -sized area with 100% emission yields. The SµLEDs maximize photostimulation effectiveness on the skin surface by uniform irradiation, high flexibility, and thermal stability. The SµLED's effect on melanogenesis inhibition is evaluated via in vitro and in vivo experiments to human skin equivalents (HSEs) and mouse dorsal skin, respectively. The anti-melanogenic effect of SµLEDs is confirmed by significantly reduced levels of melanin contents, melan-A, tyrosinase, and microphthalmia-associated transcription factor (MITF), compared to a conventional LED (CLED) stimulator.

Simultaneous emulation of synaptic and intrinsic plasticity using a memristive synapse.

Neuromorphic computing targets the hardware embodiment of neural network, and device implementation of individual neuron and synapse has attracted considerable attention. The emulation of synaptic plasticity has shown promising results after the advent of memristors. However, neuronal intrinsic plasticity, which involves in learning process through interactions with synaptic plasticity, has been rarely demonstrated. Synaptic and intrinsic plasticity occur concomitantly in learning process, suggesting the need of the simultaneous implementation. Here, we report a neurosynaptic device that mimics synaptic and intrinsic plasticity concomitantly in a single cell. Threshold switch and phase change memory are merged in threshold switch-phase change memory device. Neuronal intrinsic plasticity is demonstrated based on bottom threshold switch layer, which resembles the modulation of firing frequency in biological neuron. Synaptic plasticity is also introduced through the nonvolatile switching of top phase change layer. Intrinsic and synaptic plasticity are simultaneously emulated in a single cell to establish the positive feedback between them. A positive feedback learning loop which mimics the retraining process in biological system is implemented in threshold switch-phase change memory array for accelerated training.

Genetic and chemical markers for authentication of three Artemisia species: A. capillaris, A. gmelinii, and A. fukudo.

The genus Artemisia is an important source of medicines in both traditional and modern pharmaceutics, particularly in East Asia. Despite the great benefits of herbal medicine, quality assessment methods for these medicinal herbs are lacking. The young leaves from Artemisia species are generally used, and most of the species have similar morphology, which often leads to adulteration and misuse. This study assembled five complete chloroplast genomes of three Artemisia species, two accessions of A. gmelinii and A. capillaris, and one A. fukudo. Through comparative analysis, we revealed genomic variations and phylogenetic relationships between these species and developed seven InDel-based barcode markers which discriminated the tested species from each other. Additionally, we analyzed specialized metabolites from the species using LC-MS and suggested chemical markers for the identification and authentication of these herbs. We expect that this integrated and complementary authentication method would aid in reducing the misuse of Artemisia species.

Assessing the genetic and chemical diversity of Taraxacum species in the Korean Peninsula.

The genetic relationship between Taraxacum species, also known as the dandelion, is complicated because of asexual and mixed sexual apomictic reproduction. The usage of Taraxacum species in traditional medicines make their specialized metabolism important, but interspecific chemical difference has rarely been reported for the genus. In this study, we assembled the chloroplast genome and 45S rDNA of six Taraxacum species that occur in Korea (T. campylodes, T. coreanum, T. erythrospermum, T. mongolicum, T. platycarpum, and T. ussuriense), and performed a comparative analysis, which revealed their phylogenetic relationships and possible natural hybridity. We also performed a liquid chromatography-mass spectrometry-based phytochemical analysis to reveal interspecific chemical diversity. The comparative metabolomics analysis revealed that Taraxacum species could be separated into three chemotypes according to their major defensive specialized metabolites, which were the sesquiterpene lactones, the phenolic inositols, and chlorogenic acid derivatives. The CP DNA- and 45S rDNA-based phylogenetic trees showed a tangled relationship, which supports the notion of ongoing hybridization of wild Taraxacum species. The untargeted LC-MS analysis revealed that each Taraxacum plant exhibits species-specific defensive specialized metabolism. Moreover, 45S rDNA-based phylogenetic tree correlated with the hierarchical cluster relied on metabolite compositions. Given the coincidence between these analyses, we represented that 45S rDNA could well reflect overall nuclear genome variation in Taraxacum species.

Glucose Uptake-Stimulating Galloyl Ester Triterpenoids from Castanopsis sieboldii.

Using molecular networking-guided isolation, three new galloyl ester triterpenoids (1-3), two new hexahydroxydiphenic acid-conjugated triterpenoids (6 and 7), and four known compounds (4, 5, 8, and 9) were isolated from the fruits and leaves of Castanopsis sieboldii. The chemical structures of 1-3, 6, and 7 were elucidated on the basis of interpreting their NMR, HRESIMS, and ECD spectra. All compounds (1-9) were evaluated for their glucose uptake-stimulating activities in differentiated adipocytes using 2-deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-d-glucose as a fluorescent-tagged glucose probe. Compounds 2 and 9 resulted in a 1.5-fold increase in glucose uptake. Among them, compound 2 from the fruits showed an upregulation of p-AMPK/AMPK ratio in differentiated C2C12 myoblasts to support the mechanism proposed of glucose uptake stimulation.

Combined MS/MS-NMR Annotation Guided Discovery of Iris lactea var. chinensis Seed as a Source of Viral Neuraminidase Inhibitory Polyphenols.

In this study, the chemical diversity of polyphenols in Iris lactea var. chinensis seeds was identified by combined MS/MS-NMR analysis. Based on the annotated chemical profile, the isolation of stilbene oligomers was conducted, and consequently, stilbene oligomers (1-10) were characterized. Of these, compounds 1 and 2 are previously undescribed stilbene dimer glycoside (1) and tetramer glycoside (2), respectively. Besides, to evaluate this plant seed as a rich source of stilbene oligomers, we quantified three stilbene oligomers of I. lactea var. chinensis seeds. The contents of three major stilbene oligomers-trans-ε-viniferin (3), vitisin A (6), and vitisin B (9)-in I. lactea var. chinensis seeds were quantified as 2.32 (3), 4.95 (6), and 1.64 (9) mg/g dry weight (DW). All the isolated compounds were tested for their inhibitory activities against influenza neuraminidase. Compound 10 was found to be active with the half maximal inhibitory concentration (IC50) values at 4.76 µM. Taken together, it is concluded that I. lactea var. chinensis seed is a valuable source of stilbene oligomers with a human health benefit.

Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow.

Alnus spp. (Betulaceae) have been used for treatments of hemorrhage, burn injuries, antipyretic fever, diarrhea, and alcoholism in traditional medicines. In this study, a digitized LC-MS/MS data analysis workflow was applied to provide an overview on chemical diversity of 15 Alnus extracts prepared from bark, twigs, leaves, and fruits of A. japonica, A. firma, A. hirsuta, and A. hirsuta var. sibirica. Most of the MS/MS spectra could be putatively annotated based on library matching, in silico fragmentation, and substructural topic modeling. The putative annotation allowed us to discriminate the extracts into three chemotypes based on dominant chemical scaffolds: diarylheptanoids, flavonoids or tannins. This high-throughput chemical annotation was correlated with α-glucosidase inhibition data of extracts, and it allowed us to identify gallic acid as the major active compound of A. firma.

A new phenolic compound from Phedimus middendorffianus with antiproliferative activity.

A new phenolic compound (1) and together with 12 known compounds-eight flavonoids (2 ∼ 9), two phenolic compounds (10 and 11) and two benzoic acid (12 and 13)-were isolated from Phedimus middendorffianus (Maxim.). The structures of all compound were determined on the basis of spectroscopic (MS and NMR) analyses. Compounds 4, 5, 7 and 11 ∼ 13 were showed anti-proliferative activities against MCF-7 than PC-3 cell line. Also compound 12 and 13 showed the significant cytotoxic activities against two cancer cell lines, PC-3 and MCF-7.

Exploring novel secondary metabolites from natural products using pre-processed mass spectral data.

Many natural product chemists are working to identify a wide variety of novel secondary metabolites from natural materials and are eager to avoid repeatedly discovering known compounds. Here, we developed liquid chromatography/mass spectrometry (LC/MS) data-processing protocols for assessing high-throughput spectral data from natural sources and scoring the novelty of unknown metabolites from natural products. This approach automatically produces representative MS spectra (RMSs) corresponding to single secondary metabolites in natural sources. In this study, we used the RMSs of Agrimonia pilosa roots and aerial parts as models to reveal the structural similarities of their secondary metabolites and identify novel compounds, as well as isolation of three types of nine new compounds including three pilosanidin- and four pilosanol-type molecules and two 3-hydroxy-3-methylglutaryl (HMG)-conjugated chromones. Furthermore, we devised a new scoring system, the Fresh Compound Index (FCI), which grades the novelty of single secondary metabolites from a natural material using an in-house database constructed from 466 representative medicinal plants from East Asian countries. We expect that the FCIs of RMSs in a sample will help natural product chemists to discover other compounds of interest with similar chemical scaffolds or novel compounds and will provide insights relevant to the structural diversity and novelty of secondary metabolites in natural products.

Molecular Networking Reveals the Chemical Diversity of Selaginellin Derivatives, Natural Phosphodiesterase-4 Inhibitors from Selaginella tamariscina.

Selaginellins are unique pigments found in the genus Selaginella, the largest genus of Lycopodiophyta. Recent studies reported that some selaginellin analogues have potent phosphodiesterase-4 (PDE4) inhibitory activity. In this study, the chemical diversity of natural selaginellin derivatives was revealed by an MS/MS molecular networking-based dereplication of the Selaginella tamariscina extract. It led to the prioritization of chromatographic peaks predicted as previously unknown selaginellin derivatives. Targeted isolation of these compounds afforded two unusual selaginellin analogues with a 1H,3H-dibenzo[de,h]isochromene skeleton, namely, selariscins A (1) and B (2), along with eight new diarylfluorene derivatives, selaginpulvilins M-T (3-10), and five known analogues, 11-15. The absolute configurations of 1, 2, and 8-10 were elucidated by spectroscopic data analyses including computational electronic circular dichroism data. Compounds 1 and 3-10 showed PDE4 inhibitory activity with IC50 values in the range of 2.8-33.8 µM, and their binding modes are suggested by a molecular docking study.

Multiple Targets of 3-Dehydroxyceanothetric Acid 2-Methyl Ester to Protect Against Cisplatin-Induced Cytotoxicity in Kidney Epithelial LLC-PK1 Cells.

Chronic exposure to cisplatin, a potent anticancer drug, causes irreversible kidney damage. In this study, we investigated the protective effect and mechanism of nine lupane- and ceanothane-type triterpenoids isolated from jujube (Ziziphus jujuba Mill., Rhamnaceae) on cisplatin-induced damage to kidney epithelial LLC-PK1 cells via mitogen-activated protein kinase (MAPK) and apoptosis pathways. Cisplatin-induced LLC-PK1 cell death was most significantly reduced following treatment with 3-dehydroxyceanothetric acid 2-methyl ester (3DC2ME). Additionally, apoptotic cell death was significantly reduced. Expression of c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK), and p38 was markedly suppressed by 3DC2ME, indicating inhibition of the MAPK pathway. Treatment with 3DC2ME also significantly reduced expression of active caspase-8 and -3, Bcl-2-associated X protein (Bax), and B cell lymphoma 2 (Bcl-2), indicating the inhibition of apoptosis pathways in the kidneys. We also applied the network pharmacological analysis and identified multiple targets of 3DC2ME related to MAPK signaling pathway and apoptosis.

Expedient Synthesis of Alphitolic Acid and Its Naturally Occurring 2- O-Ester Derivatives.

The expedient synthesis of alphitolic acid (1) as well as its natural C-3-epimer and 2- O-ester derivatives was accomplished in a few steps from the readily commercially available betulin (9). A Rubottom oxidation delivered an α-hydroxy group in a stereo- and chemoselective manner. The diastereoselective reduction of the α-hydroxy ketone was key to accessing the 1,2-diol moiety of this class of natural products. Our concise and stereoselective synthetic protocol allowed the gram-scale synthesis of these natural products, which will facilitate future biological evaluations.

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae.

Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped the diversity of specialized metabolites, which then drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating the diversity of specialized metabolites in an evolutionary context have been limited by the impossibility of identifying chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites and apply it to over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5% based on spectral library matches alone to 42.6% of total MS/MS molecular features, extending annotations from well-known plant compound classes into dark plant metabolomics. To gain insights into substructural diversity within this plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations for the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.

Lignan Dimers from Forsythia viridissima Roots and Their Antiviral Effects.

Six new dimeric lignans (1-6) and one new lignan glycoside (16) were isolated from Forsythia viridissima roots along with nine known lignans (7-15). Spectroscopic analyses and chemical methods were used to determine these new structures and their absolute configurations. Among these compounds, dimatairesinol (1) and viridissimaols A-E (2-6) were assigned as dimers of dibenzylbutyrolactone analogues. Furthermore, the isolated compounds were evaluated for their antiviral activities against coxsackievirus B3 (CVB3) and human rhinovirus 1B (HRV1B). In these tests, compounds 12 and 15 showed antiviral effects against CVB3 infection with IC50 values of 15.4 and 36.4 µM, respectively, while 2, 3, 8, and 9 showed activities against HRV1B with IC50 values of 45.7, 47.5, 13.0, and 43.2 µM, respectively.

Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication.

The integration of LC-MS/MS molecular networking and in silico MS/MS fragmentation is an emerging method for dereplication of natural products. In the present study, a targeted isolation of natural products using a new in silico-based annotation tool named Network Annotation Propagation (NAP) is described. NAP improves accuracy of in silico fragmentation analyses by reranking candidate structures based on the network topology from MS/MS-based molecular networking. Annotation for the MS/MS spectral network of the Sageratia theezans twig extract was performed using NAP, and most molecular families within the network, including the known triterpenoids 1-7, could be putatively annotated, without relying on any previous reports of molecules from this species. Based on the in silico dereplication results, molecules were prioritized for isolation. In total, six dicoumaroyl 8- O-4' neolignans (8-13) and three dicoumaroyl lignans (14-16) were isolated from the twigs of S. theezans and structurally characterized by spectroscopic analyses. Isolates were evaluated for their neuroprotective activity, and compounds 14-16 showed potent protective effects against glutamate-induced oxidative stress in mouse HT22 cells at a concentration of 12.5 µM.

Chemical and genomic diversity of six Lonicera species occurring in Korea.

Lonicera spp. (Caprifoliaceae) are important not only as a common medicinal herb in East Asia but also as one of the most problematic invasive species in North America. In the present study, we performed a systemic analysis of genomic and chemical diversity among six Lonicera species occurring in Korea, L. japonica, L. maackii, L. insularis, L. sachalinensis, L. praeflorens, and L. vesicaria, using chloroplast DNA whole genome shotgun (WGS) sequencing and LC-MS analyses. The phylogenetic and phylochemical relationships did not coincide with each other, but partial consistency could be found among them. InDel-based cDNA marker for authentication was developed based on the genome sequences. Flavonoids, iridoids, and organic acids were identified in the LC-MS analyses, and their inter-species distribution and localization were also revealed.

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng.

Ginsenosides are dammarane-type or triterpenoidal saponins that contribute to the various pharmacological activities of the medicinal herb Panax ginseng. The putative biosynthetic pathway for ginsenoside biosynthesis is known in P. ginseng, as are some of the transcripts and enzyme-encoding genes. However, few genes related to the UDP-glycosyltransferases (UGTs), enzymes that mediate glycosylation processes in final saponin biosynthesis, have been identified. Here, we generated three replicated Illumina RNA-Seq datasets from the adventitious roots of P. ginseng cultivar Cheongsun (CS) after 0, 12, 24, and 48 h of treatment with methyl jasmonate (MeJA). Using the same CS cultivar, metabolomic data were also generated at 0 h and every 12-24 h thereafter until 120 h of MeJA treatment. Differential gene expression, phylogenetic analysis, and metabolic profiling were used to identify candidate UGTs. Eleven candidate UGTs likely to be involved in ginsenoside glycosylation were identified. Eight of these were considered novel UGTs, newly identified in this study, and three were matched to previously characterized UGTs in P. ginseng. Phylogenetic analysis further asserted their association with ginsenoside biosynthesis. Additionally, metabolomic analysis revealed that the newly identified UGTs might be involved in the elongation of glycosyl chains of ginsenosides, especially of protopanaxadiol (PPD)-type ginsenosides.