Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants

Ethnopharmacologically important highly subsidized Indian medicinal plants: Systematic review on their traditional uses, phytochemistry, pharmacology, quality control, conservation status and future prospective

ETHNOPHARMACOLOGICAL RELEVANCE

India has an extensive reservoir of traditional wisdom and a diverse range of medicinal plants that enrich its heritage. Plants have actively been used for healthcare practices globally since the time immemorial. Medicinal uses of plants have been well recognized in India, evident from plant species documented in different traditional medicinal systems such as Ayurveda (1400-1800 species), Siddha (500-900 species), Unani (400-700 species), Homeopathy (about 372 species), and Sowa-Rigpa (about 250 species), etc. AIM OF THE STUDY: The primary purpose of this review is to provide systematic updated information on thirteen medicinal plants prioritized by the Indian government (providing75 % subsidy on cultivation cost) based on the availability and market demand of these plants. Updated information regarding the traditional uses, phytochemistry, pharmacology, quality control, and conservation status of these plants will help in understanding their pharmacological and commercial importance. This will also help in developing new strategies for their conservation.

MATERIAL AND METHODS

Online databases such as SciFinder, Web of Science, Pubmed, and Google Scholar were used to collect the electronically available literature on targeted thirteen plants. Also, different Indian government official websites such as AYUSH (https://www.ayush.gov.in); NMPB (National Medicinal Plants Board) (https://nmpb.nic.in); e.charak (https://echarak.in) were used for collecting information related to the amount of subsidy, trade and price related information of these plants.

RESULTS

To promote medicinal plant cultivation, the Indian government provides subsidies for cultivating some traditionally important medicinal plants. These plants are divided into three categories according to the subsidy provided to farmers, i.e., 30%, 50%, and 75% of the cost of cultivation. Thirteen medicinal plants which are provided 75% subsidy are Aconitum ferox Wall., Aconitum heterophyllum Wall., Aquilaria agallocha Roxb., Berberis aristata DC., Commiphora wightii (Arn.) Bhandari, Nardostachys jatamansi (D.Don) DC., Oroxylum indicum (L.) Benth. ex Kurz, Picrorhiza kurroa Royle ex Benth., Podophyllum hexandrum Royle, Pterocarpus santalinus L.f., Santalum Album L., Saussurea costus (Falc.) Lipsch., and Swertia chirayita (Roxb.) H.Karst. The literature survey reveals the enormous traditional medicinal importance, wide geographical distribution, diverse range of natural products, and broad spectrum of pharmacological activities of these plants.

CONCLUSION

A comprehensive literature survey revealed that although remarkable progress has been made in isolation, bioactivity evaluation, quality assessment, and conservation, there is still a lot of scope for further scientific interventions. Scientific validation of traditionally claimed medicinal potential is lacking for various bioactivities. Some of the bioactivities are performed just on extracts/fractions, so there is a need for proper phytochemical studies to identify active constituents responsible for the specific bioactivity. Further, quality assessment methods using both targeted and non-targeted tools are required to evaluate the quality of these highly-priced medicinal plants and their adulterants. Ultimately, to encourage the cultivation of these endangered medicinal plant species, it is imperative to implement proper legislation and employ in-situ and ex-situ conservation tools.

Natural Products Dereplication: Databases and Analytical Methods

The development of efficient methods for dereplication has been critical in the re-emergence of the research in natural products as a source of drug leads. Current dereplication workflows rapidly identify already known bioactive secondary metabolites in the early stages of any drug discovery screening campaign based on natural extracts or enriched fractions. Two main factors have driven the evolution of natural products dereplication over the last decades. First, the availability of both commercial and public large databases of natural products containing the key annotations against which the biological and chemical data derived from the studied sample are searched for. Second, the considerable improvement achieved in analytical technologies (including instrumentation and software tools) employed to obtain robust and precise chemical information (particularly spectroscopic signatures) on the compounds present in the bioactive natural product samples. This chapter describes the main methods of dereplication, which rely on the combined use of large natural product databases and spectral libraries, alongside the information obtained from chromatographic, UV-Vis, MS, and NMR spectroscopic analyses of the samples of interest.

Analysis of non-volatile metabolites and quantitation of the anti-arthritic alkaloid sinomenine from blood fruit (Haematocarpus validus (Miers) Bakh.f. ex Forman)

Haematocarpus validus (Miers) Bakh. f. ex Forman, a lesser-known fruit and medicinal plant of high nutraceutical and medicinal value, is used as anti-arthritic, hepatoprotective, and anti-inflammatory agents in ethnomedicine. Metabolome studies in H. validus are a virgin area of research and here we report the spectra of non-volatiles present in the methanolic leaf and fruit extract, using high-resolution liquid chromatography-mass spectrometry. Furthermore, the alkaloid sinomenine was quantified using high-performance thin layer chromatography spectrodensitometric analysis owing to its pharmacological importance as anti-arthritic and anti-inflammatory drug. Electrospray ionization with protonation in positive mode was selected for the analysis and the spectral data was interrogated using MassHunter software. A total of 40 compounds were identified from leaf and fruit samples and the major classes of compounds identified were alkaloids, terpenoids, steroids, tripeptides, vitamins, and related compounds. For separation and quantitation of sinomenine, chloroform:methanol:water (60:30:6.5, v/v) was used as the mobile phase and sinomenine hydrochloride as reference compound. The analysis confirmed the presence of sinomenine in both non-defatted and defatted methanolic leaf extract with quantities 45.73 and 26.02 mg/100 g dry weight, respectively. H. validus is a non-conventional source of sinomenine, the anti-arthritic and anti-inflammatory alkaloid. Sinomenine detected in this study supports the ethnomedicinal uses of H. validus as an anti-arthritic agent. Further study is needed to elucidate the underlying molecular mechanism of its anti-arthritic attributes as well as the corresponding structure-activity relationships.

Development of a multianalytical strategy for detection of frauds in Coleus forskohlii supplements

A new multianalytical methodology based on gas chromatography (GC) and liquid chromatography (LC) coupled to mass spectrometry (MS) has been proposed to evaluate frauds affecting the composition of Coleus forskohlii root supplements (FKS). After optimization and validation of chromatographic methods, 24 FKS were analyzed. Forskolin, their main bioactive component, was only found in 50% of the FKS evaluated (in the 0.032-17.1% range), with 27% of these supplements showing concentrations of this bioactive lower than those declared in their labels. Application of this methodology also proved to be successful for the detection of frauds regarding the replacement of C. forskohlii by other vegetable sources (green tea, soy leaves and a plant of the Berberidaceae family) in 17% of supplements analyzed. A study on stability of forskolin under accelerated conditions allowed to rule out its degradation as responsible for the lack of this bioactive or other natural constituents in 25% of FKS evaluated. It can be concluded that the multianalytical methodology here developed is an advantageous alternative to address the wide diversity of frauds affecting these supplements.

Differential Accumulation of Metabolites and Transcripts Related to Flavonoid, Styrylpyrone, and Galactolipid Biosynthesis in Equisetum Species and Tissue Types

Three species of the genus Equisetum (E. arvense, E. hyemale, and E. telmateia) were selected for an analysis of chemical diversity in an ancient land plant lineage. Principal component analysis of metabolomics data obtained with above-ground shoot and below-ground rhizome extracts enabled a separation of all sample types, indicating species- and organ-specific patterns of metabolite accumulation. Follow-up efforts indicated that galactolipids, carotenoids, and flavonoid glycosides contributed positively to the separation of shoot samples, while stryrylpyrone glycosides and phenolic glycosides were the most prominent positive contributors to the separation of rhizome samples. Consistent with metabolite data, genes coding for enzymes of flavonoid and galactolipid biosynthesis were found to be expressed at elevated levels in shoot samples, whereas a putative styrylpyrone synthase gene was expressed preferentially in rhizomes. The current study builds a foundation for future endeavors to further interrogate the organ and tissue specificity of metabolism in the last living genus of a fern family that was prevalent in the forests of the late Paleozoic era.

Evaluation of the Phytochemical, Antioxidant, Enzyme Inhibition, and Wound Healing Potential of Calotropis gigantea (L.) Dryand: A Source of a Bioactive Medicinal Product

Traditionally, plants of the genus Calotropis have been used to cure various common diseases. The present research work explores the chemical and biological characterization of one of the most common species of this genus, i.e., Calotropis gigantea (L.) Dryand (syn. Calotropis gigantea (L.) Dryand.), having multiple folklore applications. The ethanolic extract of leaves of Calotropis gigantea (L.) Dryand was analyzed for the phytochemical composition by determining the total bioactive (total phenolic and total flavonoid) contents and UHPLC-MS secondary metabolites analysis. For phytopharmacological evaluation, in vitro antioxidant (including DPPH, ABTS, FRAP, CUPRAC, phosphomolybdenum, and metal chelation antioxidant assays) activities, enzyme inhibition potential (against AChE, BChE, α-amylase, and tyrosinase enzymes), and in vivo wound healing potential were determined. The tested extract has been shown to contain considerable flavonoid (46.75 mg RE/g extract) and phenolic (33.71 mg GAE/g extract) contents. The plant extract presented considerable antioxidant potential, being the most active for CUPRAC assays. Secondary metabolite UHPLC-MS characterization, in both the positive and negative ionization modes, indicated the tentative presence of 17 different phytocompounds, mostly derivatives of sesquiterpene, alkaloids, and flavonoids. Similarly, the tested extract exhibited considerable inhibitory effects on tyrosinase (81.72 mg KAE/g extract), whereas it showed weak inhibition ability against other tested enzymes. Moreover, in the case of in vivo wound healing assays, significant improvement in wound healing was observed in both the tested models at the doses of 0.5 percent w/w (p < 0.001) and 2.0 percent w/w (p < 0.01) on the 16^th day. The outcomes of the present research work suggested that C. gigantea (L.) Dryand plant extract could be appraised as a potential origin of bioactive molecules having multifunctional medicinal uses.

Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics

High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.

High-Throughput Detection of an Alkaloidal Plant Metabolome in Plant Extracts Using LC-ESI-QTOF-MS

Plant alkaloids represent a diverse group of nitrogen-containing natural products. These compounds are considered valuable in drug discovery and development. High-throughput identification of such plant secondary metabolites in complex plant extracts is essential for drug discovery, lead optimization, and understanding the biological pathway. The present study aims to rapidly identify different classes of alkaloids in plant extracts through the liquid chromatography with electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) approach using 161 isolated and purified alkaloids. These are biologically important unique alkaloids belonging to different sub-classes such as isoquinoline, quinoline, indole, tropane, pyridine, piperidine, quinolizidine, aporphine, steroidal, and terpenoid. The majority of these are not available commercially and are known to manifest valuable biological activities. Four pools of a maximum of 50 phytostandards each were prepared, based on their log P value to minimize co-elution for rapid and cost-effective analyses. MS/MS spectra were acquired in the positive ionization mode by using their [M + H]⁺ and/or [M + Na]⁺ with both the average collisional energy (25.5-62 eV) and individual collisional energies (10, 20, 30, and 40 eV). Accurate mass, high-resolution mass spectrometry (HR-MS) data, MS/MS data, and retention times were curated for each compound. The developed LC-MS/MS method was successfully used to interrogate and fast dereplicate alkaloids in 13 medicinal plant extracts and a herbal formulation. A total of 56 alkaloids were identified based on the reference standard retention times (RTs), HR-MS spectra, and/or MS/MS spectra. The MS data have been submitted to the MetaboLights online database (MTBLS2914). The mass spectrometric and chromatographic data will be useful for the discovery of new congeners and the study of biological pathways of alkaloids in the plant kingdom.

The Botanical, Chemical and Ethnobotanical Diversity of Southern African Lamiaceae

The Lamiaceae is undoubtedly an important plant family, having a rich history of use that spans the globe with many species being used in folk medicine and modern industries alike. Their ability to produce aromatic volatile oils has made them valuable sources of materials in the cosmetic, culinary, and pharmaceutical industries. A thorough account of the taxonomic diversity, chemistry and ethnobotany is lacking for southern African Lamiaceae, which feature some of the region’s most notable medicinal and edible plant species. We provide a comprehensive insight into the Lamiaceae flora of southern Africa, comprising 297 species in 42 genera, 105 of which are endemic to the subcontinent. We further explore the medicinal and traditional uses, where all genera with documented uses are covered for the region. A broad review of the chemistry of southern African Lamiaceae is presented, noting that only 101 species (34%) have been investigated chemically (either their volatile oils or phytochemical characterization of secondary metabolites), thus presenting many and varied opportunities for further studies. The main aim of our study was therefore to present an up-to-date account of the botany, chemistry and traditional uses of the family in southern Africa, and to identify obvious knowledge gaps.

Pharmacometabonomics: data processing and statistical analysis

Individual variations in drug efficacy, side effects and adverse drug reactions are still challenging that cannot be ignored in drug research and development. The aim of pharmacometabonomics is to better understand the pharmacokinetic properties of drugs and monitor the drug effects on specific metabolic pathways. Here, we systematically reviewed the recent technological advances in pharmacometabonomics for better understanding the pathophysiological mechanisms of diseases as well as the metabolic effects of drugs on bodies. First, the advantages and disadvantages of all mainstream analytical techniques were compared. Second, many data processing strategies including filtering, missing value imputation, quality control-based correction, transformation, normalization together with the methods implemented in each step were discussed. Third, various feature selection and feature extraction algorithms commonly applied in pharmacometabonomics were described. Finally, the databases that facilitate current pharmacometabonomics were collected and discussed. All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.

RP-UHPLC-MS Chemical Profiling, Biological and In Silico Docking Studies to Unravel the Therapeutic Potential of Heliotropium crispum Desf. as a Novel Source of Neuroprotective Bioactive Compounds

Heliotropium is one of the most important plant genera to have conventional folklore importance, and hence is a potential source of bioactive compounds. Thus, the present study was designed to explore the therapeutic potential of Heliotropium crispum Desf., a relatively under-explored medicinal plant species. Methanolic extracts prepared from a whole plant of H. crispum were studied for phytochemical composition and possible in vitro and in silico biological properties. Antioxidant potential was assessed via six different assays, and enzyme inhibition potential against key clinical enzymes involved in neurodegenerative diseases (acetylcholinesterase (AChE) and butyrylcholinesterase (BChE)), diabetes (α-amylase and α-glucosidase), and skin problems (tyrosinase) was assayed. Phytochemical composition was established via determination of the total bioactive contents and reverse phase ultra-high performance liquid chromatography mass spectrometry (RP-UHPLC-MS) analysis. Chemical profiling revealed the tentative presence of 50 secondary metabolites. The plant extract exhibited significant inhibition against AChE and BChE enzymes, with values of 3.80 and 3.44 mg GALAE/g extract, respectively. Further, the extract displayed considerable free radical scavenging activity against DPPH and ABTS radicals, with potential values of 43.19 and 41.80 mg TE/g extract, respectively. In addition, the selected compounds were then docked against the tested enzymes, which have shown high inhibition affinity. To conclude, H. crispum was found to harbor bioactive compounds and showed potent biological activities which could be further explored for potential uses in nutraceutical and pharmaceutical industries, particularly as a neuroprotective agent.

Biochemical characterization of acyl activating enzymes for side chain moieties of Taxol and its analogs

Taxol (paclitaxel) is a very widely used anticancer drug, but its commercial sources mainly consist of stripped bark or suspension cultures of members of the plant genus Taxus. Taxol accumulates as part of a complex mixture of chemical analogs, termed taxoids, which complicates its production in pure form, highlighting the need for metabolic engineering approaches for high-level Taxol production in cell cultures or microbial hosts. Here, we report on the characterization of acyl-activating enzymes (AAEs) that catalyze the formation of CoA esters of different organic acids relevant for the N-substitution of the 3-phenylisoserine side chain of taxoids. On the basis of similarities to AAE genes of known function from other organisms, we identified candidate genes in publicly available transcriptome data sets obtained with Taxus × media. We cloned 17 AAE genes, expressed them heterologously in Escherichia coli, purified the corresponding recombinant enzymes, and performed in vitro assays with 27 organic acids as potential substrates. We identified TmAAE1 and TmAAE5 as the most efficient enzymes for the activation of butyric acid (Taxol D side chain), TmAAE13 as the best candidate for generating a CoA ester of tiglic acid (Taxol B side chain), TmAAE3 and TmAAE13 as suitable for the activation of 4-methylbutyric acid (N-debenzoyl-N-(2-methylbutyryl)taxol side chain), TmAAE15 as a highly efficient candidate for hexanoic acid activation (Taxol C side chain), and TmAAE4 as suitable candidate for esterification of benzoic acid with CoA (Taxol side chain). This study lays important groundwork for metabolic engineering efforts aimed at improving Taxol production in cell cultures.

In Vitro Schistosomicidal Activity of the Alkaloid-Rich Fraction from Ruta graveolens L. (Rutaceae) and Its Characterization by UPLC-QTOF-MS

Schistosomiasis is a neglected tropical disease that affects million people worldwide, mostly in developing countries. Ruta graveolens (Rutaceae) is a plant used in folk medicine to treat several diseases, including parasitic infections. In this study, we reported the in vitro schistosomicidal activity of the R. graveolens extract (Rg) and its active fraction (Rg-FAE). Also, the characterization of Rg-FAE by UPLC-ESI-QTOF-MS analysis and its in vitro antileishmanial activity against Leishmania braziliensis were also performed. In vitro schistosomicidal assays were assessed against adult worms of S. mansoni, while cell viability against peritoneal macrophages was measured by MTT assay. Rg (100 μg/mL) exhibited noticeable schistosomicidal activity, causing 100% mortality and decreasing motor activity of all adult male and female schistosomes, but with low activity against L. braziliensis. After chromatographic fractionation of Rg, fraction Rg-FAE was obtained, showing high activity against adult schistosomes. UPLC-ESI-QTOF-MS analysis of Rg-FAE revealed the presence of eleven alkaloids and one furanocoumarin. No significant antileishmanial activity was found for Rg, while Rg-FAE exhibited activity against L. braziliensis promastigotes. We demonstrated, for the first time, that the R. graveolens extract (Rg) and its alkaloid-rich fraction (Rg-FAE) are active against adult worms of S. mansoni, with no significant cytotoxicity on macrophages. Our findings open the route to further antiparasitic studies with the active fraction of R. graveolens and its identified compounds, especially alkaloids.

Identification of small molecules using accurate mass MS/MS search

Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in MS/MS-based annotation of chemical structures is impacted by instrumental settings and requirements, data acquisition modes including data-dependent and data-independent methods, library scoring algorithms, as well as post-curation steps. We critically discuss parameters that influence search results, such as mass accuracy, precursor ion isolation width, intensity thresholds, centroiding algorithms, and acquisition speed. A range of publicly and commercially available MS/MS databases such as NIST, MassBank, MoNA, LipidBlast, Wiley MSforID, and METLIN are surveyed. In addition, software tools including NIST MS Search, MS-DIAL, Mass Frontier, SmileMS, Mass++, and XCMS2 to perform fast MS/MS search are discussed. MS/MS scoring algorithms and challenges during compound annotation are reviewed. Advanced methods such as the in silico generation of tandem mass spectra using quantum chemistry and machine learning methods are covered. Community efforts for curation and sharing of tandem mass spectra that will allow for faster distribution of scientific discoveries are discussed.

Differential induction of polar and non-polar metabolism during wound-induced suberization in potato (Solanum tuberosum L.) tubers

Wound-induced suberin deposition involves the temporal and spatial coordination of phenolic and fatty acid metabolism. Phenolic metabolism leads to both soluble metabolites that accumulate as defense compounds as well as hydroxycinnamoyl derivatives that form the basis of the poly(phenolic) domain found in suberized tissue. Fatty acid metabolism involves the biosynthesis of very-long-chain fatty acids, 1-alkanols, ω-hydroxy fatty acids and α,ω-dioic acids that form a poly(aliphatic) domain, commonly referred to as suberin. Using the abscisic acid (ABA) biosynthesis inhibitor fluridone (FD), we reduced wound-induced de novo biosynthesis of ABA in potato tubers, and measured the impact on the expression of genes involved in phenolic metabolism (StPAL1, StC4H, StCCR, StTHT), aliphatic metabolism (StCYP86A33, StCYP86B12, StFAR3, StKCS6), metabolism linking phenolics and aliphatics (StFHT) or acyl chains and glycerol (StGPAT5, StGPAT6), and in the delivery of aliphatic monomers to the site of suberization (StABCG1). In FD-treated tissue, both aliphatic gene expression and accumulation of aliphatic suberin monomers were delayed. Exogenous ABA restored normal aliphatic suberin deposition in FD-treated tissue, and enhanced aliphatic gene expression and poly(aliphatic) domain deposition when applied alone. By contrast, phenolic metabolism genes were not affected by FD treatment, while FD + ABA and ABA treatments slightly enhanced the accumulation of polar metabolites. These data support a role for ABA in the differential induction of phenolic and aliphatic metabolism during wound-induced suberization in potato.

Biosynthesis of Diterpenoids in Tripterygium Adventitious Root Cultures

Adventitious root cultures were developed from Tripterygium regelii, and growth conditions were optimized for the abundant production of diterpenoids, which can be collected directly from the medium. An analysis of publicly available transcriptome data sets collected with T. regelii roots and root cultures indicated the presence of a large gene family (with 20 members) for terpene synthases (TPSs). Nine candidate diterpene synthase genes were selected for follow-up functional evaluation, of which two belonged to the TPS-c, three to the TPS-e/f, and four to the TPS-b subfamilies. These genes were characterized by heterologous expression in a modular metabolic engineering system in Escherichia coli Members of the TPS-c subfamily were characterized as copalyl diphosphate (diterpene) synthases, and those belonging to the TPS-e/f subfamily catalyzed the formation of precursors of kaurane diterpenoids. The TPS-b subfamily encompassed genes coding for enzymes involved in abietane diterpenoid biosynthesis and others with activities as monoterpene synthases. The structural characterization of diterpenoids accumulating in the medium of T. regelii adventitious root cultures, facilitated by searching the Spektraris online spectral database, enabled us to formulate a biosynthetic pathway for the biosynthesis of triptolide, a diterpenoid with pharmaceutical potential. Considering the significant enrichment of diterpenoids in the culture medium, fast-growing adventitious root cultures may hold promise as a sustainable resource for the large-scale production of triptolide.

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway toward improving our coverage of the plant metabolome.

Plant metabolism, the diverse chemistry set of the future

New technologies are redefining how plant biology will meet societal challenges in health, nutrition, agriculture, and energy. Rapid and inexpensive genome and transcriptome sequencing is being exploited to discover biochemical pathways that provide tools needed for synthetic biology in both plant and microbial systems. Metabolite detection at the cellular and subcellular levels is complementing gene sequencing for pathway discovery and metabolic engineering. The crafting of plant and microbial metabolism for the synthetic biology platforms of tomorrow will require precise gene editing and delivery of entire complex pathways. Plants sustain life and are key to discovery and development of new medicines and agricultural resources; increased research and training in plant science will accelerate efforts to harness the chemical wealth of the plant kingdom.

Integrative Approaches for the Identification and Localization of Specialized Metabolites in Tripterygium Roots

Members of the genus Tripterygium are known to contain an astonishing diversity of specialized metabolites. The lack of authentic standards has been an impediment to the rapid identification of such metabolites in extracts. We employed an approach that involves the searching of multiple, complementary chromatographic and spectroscopic data sets against the Spektraris database to speed up the metabolite identification process. Mass spectrometry-based imaging indicated a differential localization of triterpenoids to the periderm and sesquiterpene alkaloids to the cortex layer of Tripterygium roots. We further provide evidence that triterpenoids are accumulated to high levels in cells that contain suberized cell walls, which might indicate a mechanism for storage. To our knowledge, our data provide first insights into the cell type specificity of metabolite accumulation in Tripterygium and set the stage for furthering our understanding of the biological implications of specialized metabolites in this genus.

The WEIZMASS spectral library for high-confidence metabolite identification

Annotation of metabolites is an essential, yet problematic, aspect of mass spectrometry (MS)-based metabolomics assays. The current repertoire of definitive annotations of metabolite spectra in public MS databases is limited and suffers from lack of chemical and taxonomic diversity. Furthermore, the heterogeneity of the data prevents the development of universally applicable metabolite annotation tools. Here we present a combined experimental and computational platform to advance this key issue in metabolomics. WEIZMASS is a unique reference metabolite spectral library developed from high-resolution MS data acquired from a structurally diverse set of 3,540 plant metabolites. We also present MatchWeiz, a multi-module strategy using a probabilistic approach to match library and experimental data. This strategy allows efficient and high-confidence identification of dozens of metabolites in model and exotic plants, including metabolites not previously reported in plants or found in few plant species to date.

Unambiguous metabolite annotation is a critical, yet problematic step, in mass spectrometry based metabolomics. Here, Shahaf et al. present WEIZMASS, a platform consisting of a diverse spectral library of more than 3500 plant metabolites and software to aid their identification in biological samples.

Kinetics of glucosylated and non-glucosylated aryltetralin lignans in Linum hairy root cultures

Due to their pronounced cytotoxic activity, a number of aryltetralin lignans (ATLs), such as podophyllotoxin (PTOX), are used as antitumor compounds. The production of such molecules from entire plants or plant cell-tissue-organ cultures is thus of interest to the pharmaceutical industry. Hairy root cultures constitute a good tool not only for phytochemical production but also for investigating plant secondary metabolism. This work reports on the growth and ATL biosynthesis in two hairy root cultures of Linum album Kotschy ex Boiss. and Linum flavum. The kinetics of accumulation of the intermediates of MPTOX biosynthesis and of their glucosylated forms are described over a 21-day period of growth. An accumulation of non-glucosylated forms of the ATLs during the exponential phase of the cultures is followed by an accumulation of the glucosylated forms during the stationary phase. Our results show a strong coordination of the biosynthetic paths derived from deoxypodophyllotoxin via deoxypodophyllotoxin 6-hydroxylase and deoxypodophyllotoxin 7-hydroxylase, and a coordinated glucosylation of podophyllotoxin, methoxypodophyllotoxin, and 5'-demethoxymethoxypodophyllotoxin. Furthermore, our results suggest an important role of β-peltatin-6-glucoside formation in the control of ATL accumulation in Linum hairy root cultures.

NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification--Taxane diterpenoids from Taxus × media cell suspension cultures as a case study

Development and testing of Spektraris-NMR, an online spectral resource, is reported for the NMR-based structural identification of plant natural products (PNPs). Spektraris-NMR allows users to search with multiple spectra at once and returns a table with a list of hits arranged according to the goodness of fit between query data and database entries. For each hit, a link to a tabulated alignment of (1)H NMR and (13)C NMR spectroscopic peaks (query versus database entry) is provided. Furthermore, full spectroscopic records and experimental meta information about each database entry can be accessed online. To test the utility of Spektraris-NMR for PNP identification, the database was populated with NMR data (total of 466 spectra) for ∼ 250 taxanes, which are structurally complex diterpenoids (including the anticancer drug taxol) commonly found in the genus Taxus. NMR data generated with metabolites purified from Taxus cell suspension cultures were then used to search Spektraris-NMR, and enabled the identification of eight taxanes with high confidence. A ninth isolated metabolite could be assigned, based on spectral searches, to a taxane skeletal class, but no high confidence hit was produced. Using various spectroscopic methods, this metabolite was characterized as 2-deacetylbaccatin IV, a novel taxane. These results indicate that Spektraris-NMR is a valuable resource for rapid and reliable identification of known metabolites and has the potential to contribute to de-replication efforts in novel PNP discovery.

Open-access metabolomics databases for natural product research: present capabilities and future potential

Various databases have been developed to aid in assigning structures to spectral peaks observed in metabolomics experiments. In this review article, we discuss the utility of currently available open-access spectral and chemical databases for natural products discovery. We also provide recommendations on how the research community can contribute to further improvements.

Analysis of phenolic and cyclic compounds in plants using derivatization techniques in combination with GC-MS-based metabolite profiling

Metabolite profiling has been established as a modern technology platform for the description of complex chemical matrices and compound identification in biological samples. Gas chromatography coupled with mass spectrometry (GC-MS) in particular is a fast and accurate method widely applied in diagnostics, functional genomics and for screening purposes. Following solvent extraction and derivatization, hundreds of metabolites from different chemical groups can be characterized in one analytical run. Besides sugars, acids, and polyols, diverse phenolic and other cyclic metabolites can be efficiently detected by metabolite profiling. The review describes own results from plant research to exemplify the applicability of GC-MS profiling and concurrent detection and identification of phenolics and other cyclic structures.

Chemical taxonomy of tree peony species from China based on root cortex metabolic fingerprinting

The section Moutan of the genus Paeonia consists of eight species that are confined to a small area in China. A wide range of metabolites, including monoterpenoid glucosides, flavonoids, tannins, stilbenes, triterpenoids, steroids, paeonols, and phenols, have been found in the species belonging to section Moutan. However, although previous studies have analyzed the metabolites found in these species, the metabolic similarities that can be used for the chemotaxonomic distinction of section Moutan species are not yet clear. In this study, HPLC-DAD-based metabolic fingerprinting was applied to the classification of eight species: Paeoniasuffruticosa, Paeoniaqiui, Paeoniaostii, Paeoniarockii, Paeoniajishanensis, Paeoniadecomposita, Paeoniadelavayi, and Paeonialudlowii. In total, of the 47 peaks that exhibited an occurrence frequency of 75% in all 23 tree peony samples, 43 of these metabolites were identified according to their retention times and UV absorption spectra, together with combined HPLC-QTOF-MS. These data were compared with reference standard compounds. The 43 isolated compounds included 17 monoterpenoid glucosides, 11 galloyl glucoses, 5 flavonoids, 6 paeonols and 4 phenols. Principal component analysis (PCA), and hierarchical cluster analysis (HCA), showed a clear separation between the species based on metabolomics similarities and four groups were identified. The results exhibited good agreement with the classical classification based on the morphological characteristics and geographical distributions of the subsections Vaginatae F.C. Stern and Delavayanae F.C. Stern with the exception of P. decomposita, which was found to be a transition species between these two subsections. According to their metabolic fingerprinting characteristics, P. ostii and P. suffruticosa can be considered one species, and this result is consistent with the viewpoint of medicinal plant scientists but different from that of classical morphological processing. Significantly large variations were obtained in the metabolic profiles of P. delavayi, whereas no significant difference was found between P. delavayi and P. ludlowii. This indicates that these two species have a close genetic relationship. In conclusion, the combination of HPLC-DAD and multivariate analyses has great potential for guiding future chemotaxonomic studies to examine the potential pharmaceutical value of the effective constituents of tree peony species and appears to be able to clarify the confusion and skepticism associated with the reported morphology- and molecular phylogenetics-based taxonomy of tree peonies.

In vitro metabolism of the alkaloid piplartine by rat liver microsomes

Because piplartine (PPT) has demonstrated biological activities, such as cytotoxic, anxiolytic, antidepressant, antifungal and antiplatelet activities, this molecule is a relevant drug candidate. The metabolic fate of drug candidates is an essential requirement in assessing their safety and efficacy. Based on this requirement, the biotransformation of PPT by cytochrome P450 enzymes (CYP) was investigated for the first time. To determine the in vitro enzymatic kinetic parameters, an HPLC method was developed and validated to quantify PPT. All samples were separated on a reversed-phase C18 column using a mobile phase of acetonitrile:water (40:60, v/v). The method exhibited a linear range of 2.4-157.7 μmol/L, with the following calibration curve: y=0.0934 (±0.0010)x+0.0027, r=0.9975. The lower limit of quantitation was verified to be 2.4 μmol/L, with an RSD below 7%. The precision and accuracy were assessed for both within-day and between-day determinations; neither relative standard (RSD%) deviations nor relative errors (RER) exceeded a value of 15%. The mean absolute recovery was 85%, with an RSD value below 6%. The enzymatic kinetic parameters revealed a sigmoidal profile, with V(max)=4.7±0.3 μmol/mg mL⁻¹/min, h=2.5±0.4, S₅₀=44.7±0.3 μmol/L and CL(max)=0.054 μL/min/mg protein, indicating cooperativity behavior. Employing a mammalian model, PPT metabolism yielded two unreported monohydroxylated products (m/z 334). The identification and structural elucidation of the metabolites were performed by comparing their mass spectra with those spectra of the parent drug. For the first time, the in vitro metabolism studies employing microsomes were demonstrated to be a suitable tool for data regarding enzymatic kinetics and for the metabolites formed in the PPT mammalian metabolism.

Dereplication of microbial extracts and related analytical technologies

Natural products still continue to have an important role as a resource of various biologically active substances. Dereplication is a key process in natural product screening that analyzes the extracts of microbial fermentation broths or plant samples. In this review article, we describe and discuss the analytical techniques of dereplication and related technologies in the following sections: 1. Direct detection from microbial colonies. 2. Ultra high performance liquid chromatography (UHPLC)-MS profiling for library construction. 3. Micro-fractionation to identify active peaks. 4. Quantification of small-amount compounds. 5. Structure identification from small amounts. Using these techniques, the desired compound in the mixture library can be rapidly identified.

Metabolomics for secondary metabolite research

Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.