Identification of natural products using HPLC-SPE combined with CapNMR

NMR-Based Chromatography Readouts: Indispensable Tools to “Translate” Analytical Features into Molecular Structures

Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head of an NMR spectrometer has therefore been pursued for more than three decades. The purpose of this review article was to demonstrate that, while it is possible to use mass spectrometry and similar methods to differentiate, group, and often assign the differentiating variables to entities that can be recognized as single molecules, the structural characterization of these putative biomarkers usually requires the use of NMR spectroscopy.

NMR technique and methodology in botanical health product analysis and quality control

Botanicals have played an important role in maintaining human health and well-being throughout history. During the past few decades in particular, the use of botanical health products has gained more popularity. Whereas, quality, safety and efficacy concerns have continuously been critical issues due to the intrinsic chemical complexity of botanicals. Chemical analytical technologies play an imperative role in addressing these issues. Nuclear magnetic resonance (NMR) spectroscopy has proven to be a powerful and useful tool for the investigation of botanical health products. In this review, NMR techniques and methodologies that have been successfully applied to the research and development of botanical health products in all stages, from plants to products, are discussed and summarized. Furthermore, applications of NMR together with other analytical techniques in a variety of domains of botanical health products investigation, such as plant species differentiation, adulteration detection, and bio-activity evaluation, are discussed and illustrated with typical examples. This article provides an overview of the potential uses of NMR techniques and methodologies in an attempt to further promote their recognition and utilization in the field of botanical health products analysis and quality control.

Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum

An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea (Posidonia oceanica) was studied in order to identify its antimicrobial constituents and further characterize the composition of its metabolome. It was identified as Fusarium petroliphilum by in-depth phylogenetic analyses. The ethyl acetate extract of that strain exhibited antimicrobial activities and an ability to inhibit quorum sensing of Staphylococcus aureus. To perform this study with a few tens of mg of extract, an innovative one-step generic strategy was devised. On one side, the extract was analyzed by UHPLC-HRMS/MS molecular networking for dereplication. On the other side, semi-preparative HPLC using a similar gradient profile was used for a single-step high-resolution fractionation. All fractions were systematically profiled by ¹H-NMR. The data were assembled into a 2D contour map, which we call “pseudo-LC-NMR,” and combined with those of UHPLC-HRMS/MS. This further highlighted the connection within structurally related compounds, facilitated data interpretation, and provided an unbiased quantitative profiling of the main extract constituents. This innovative strategy led to an unambiguous characterization of all major specialized metabolites of that extract and to the localization of its bioactive compounds. Altogether, this approach identified 22 compounds, 13 of them being new natural products and six being inhibitors of the quorum sensing mechanism of S. aureus and Pseudomonas aeruginosa. Minor analogues were also identified by annotation propagation through the corresponding HRMS/MS molecular network, which enabled a consistent annotation of 27 additional metabolites. This approach was designed to be generic and applicable to natural extracts of the same polarity range.

Rapid Structure Determination of Bioactive 4″-Tetrahydrofurfuryl Macrozone Reaction Mixture Components by LC-SPE/Cryo NMR and MS

LC-SPE/cryo NMR and MS methodologies have been developed and employed for a rapid structure determination of 4″-tetrahydrofurfuryl macrozone reaction mixture components. Macrozones, novel conjugates of azithromycin, and thiosemicarbazones have shown very good in vitro antibacterial activities against susceptible and some resistant bacterial strains and are promising agents for further development. The post-column multiple trapping of the chromatographically separated reaction mixture components on the SPE cartridges increased the sensitivity and together with cryogenically cooled NMR probe made it possible to identify and structurally characterize main 4″-tetrahydrofurfuryl macrozone reaction mixture compounds including those present at very low concentration level. This approach has several advantages over a classical off-line procedure, efficiency and low solvent consumption being the two most important ones. All identified components were process-related. It has been demonstrated that two different kinds of compounds with respect to structure were identified, i.e., macrolide-related and thiosemicarbazone-related ones. This methodology can serve as a platform for reliable and effective macrolides reaction components structure profiling, serving as both isolation and identification tools.

Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.

From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites

Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.

The application of combined 1H NMR-based metabolomics and transcriptomics techniques to explore phenolic acid biosynthesis in Salvia miltiorrhiza Bunge

Salvia miltiorrhiza Bunge is a traditional Chinese medicine, and its water-soluble phenolic acid active compounds have very important medicinal value; however, the synthesis pathways of the main active ingredients remain unknown. Here, we employed nuclear magnetic resonance (NMR)-based metabolomics and transcriptomics techniques to study the biosynthesis mechanism of salvianolic acids. High-performance liquid chromatography (HPLC) combined with NMR showed an improvement over traditional techniques, and 54 metabolites were detected. The results of the multivariate statistical analysis showed that salvianolic acid B (SAB), rosmarinic acid (RA), caffeic acid, succinate, and citrate were among the multiple compounds that were increased in the methyl jasmonate (MeJA)-elicited group; the levels of sucrose, fructose, glutamine, and tyrosine were decreased. Combined with the differentially expressed genes (DEGs) found by transcriptome sequencing, we speculate that the synthesis of RA after MeJA treatment mostly occurred through caffeic acid and bypassed 4-hydroxyphenyllactic acid. This provides useful information for the study of salvianolic acids synthesis.

What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs’ Species Origin, Druglikeness, Target and Pathway

Background:

Despite the substantial contribution of natural products to the FDA drug approval list, the discovery of anti-cancer drugs from the huge amount of species on the planet remains looking for a needle in a haystack. Objective: Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.

Objective:

Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.

Methods:

In this study, 260 anti-cancer drugs approved in the past 70 years were comprehensively analyzed by hierarchical clustering of phylogenetic distribution.

Results:

207 out of these 260 drugs were derived from or inspired by the natural products isolated from 58 species. Phylogenetic distribution of those drugs further revealed that nature-derived anti-cancer drugs originated mostly from drug-productive families that tend to be clustered rather than scattered on the phylogenetic tree. Moreover, based on their productivity, drug-producing species were categorized into productive (CPS), newly emerging (CNS) and lessproductive (CLS). Statistical significances in druglikeness between drugs from CPS and CLS were observed, and drugs from CNS were found to share similar drug-like properties to those from CPS.

Conclusion:

This finding indicated a great raise in drug approval standard, which suggested us to focus bioprospecting on the species yielding multiple drugs and keeping productive for long period of time.

Ti(II) and Rh(I) Complexes as Reagents toward a Thapsigargin Core

A novel approach toward the [5-7]fused bicyclic core of thapsigargin, a subnanomolar inhibitor of the endo/sarcoplasmic calcium ATPase (SERCA), is presented. The synthetic route includes an original Ti(II)-mediated hydroxy-directed reductive coupling of an enantiomerically enriched propargylic alcohol and an intramolecular Rh(I)-catalyzed cyclocarbonylation reaction as key steps. Interestingly, through the first experiments of titanocene-mediated reductive cyclization of a 1,8-enyne, a seven-membered cycle was isolated as a unique product with a total diastereoselectivity.

Targeted isolation and identification of bioactive compounds lowering cholesterol in the crude extracts of crabapples using UPLC-DAD-MS-SPE/NMR based on pharmacology-guided PLS-DA

The anti-hyperlipidemic effects of crude crabapple extracts derived from Malus 'Red jade', Malus hupehensis (Pamp.) Rehd. and Malus prunifolia (Willd.) Borkh. were evaluated on high-fat diet induced obese (HF DIO) mice. The results revealed that some of these extracts could lower serum cholesterol levels in HF DIO mice. The same extracts were also parallelly analyzed by LC-MS in both positive and negative ionization modes. Based on the pharmacological results, 22 LC-MS variables were identified to be correlated with the anti-hyperlipidemic effects using partial least square discriminant analysis (PLS-DA) and independent samples t-test. Further, under the guidance of the bioactivity-correlated LC-MS signals, 10 compounds were targetedly isolated and enriched using UPLC-DAD-MS-SPE and identified/elucidated by NMR together with MS/MS as citric acid(1), p-coumaric acid(2), hyperoside(3), myricetin(4), naringenin(5), quercetin(6), kaempferol(7), gentiopicroside(8), ursolic acid(9) and 8-epiloganic acid(10). Among these 10 compounds, 6 compounds, hyperoside(3), myricetin(4), naringenin(5), quercetin(6), kaempferol(7) and ursolic acid(9), were individually studied and reported to indeed have effects on lowering the serum lipid levels. These results demonstrated the efficiency of this strategy for drug discovery. In contrast to traditional routes to discover bioactive compounds in the plant extracts, targeted isolation and identification of bioactive compounds in the crude plant extracts using UPLC-DAD-MS-SPE/NMR based on pharmacology-guided PLS-DA of LC-MS data brings forward a new efficient dereplicated approach to natural products research for drug discovery.

13C Metabolomics: NMR and IROA for Unknown Identification

Abstract: Background

Isotopic Ratio Outlier Analysis (IROA) is an untargeted metabolomics method that uses stable isotopic labeling and LC-HRMS for identification and relative quantification of metabolites in a biological sample under varying experimental conditions.

Objective

We demonstrate a method using high-sensitivity ¹³C NMR to identify an unknown metabolite isolated from fractionated material from an IROA LC-HRMS experiment.

Methods

IROA samples from the nematode Caenorhabditis elegans were fractionated using LC-HRMS using 5 repeated injections and collecting 30 sec fractions. These were concentrated and analyzed by ¹³C NMR.

Results

We isotopically labeled samples of C. elegans and collected 2 adjacent LC fractions. By HRMS, one contained at least 2 known metabolites, phenylalanine and inosine, and the other contained tryptophan and an unknown feature with a monoisotopic mass of m/z 380.0742 [M+H]⁺. With NMR, we were able to easily verify the known compounds, and we then identified the spin system networks responsible for the unknown resonances. After searching the BMRB database and comparing the molecular formula from LC-HRMS, we determined that the fragments were a modified anthranilate and a glucose modified by a phosphate. We then performed quantum chemical NMR chemical shift calculations to determine the most likely isomer, which was 3’-O-phospho-β-D-glucopyranosyl-anthranilate. This compound had previously been found in the same organism, validating our approach.

Conclusion

We were able to dereplicate previously known metabolites and identify a metabolite that was not in databases by matching resonances to NMR databases and using chemical shift calculations to determine the correct isomer. This approach is efficient and can be used to identify unknown compounds of interest using the same material used for IROA.

Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects

Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways. This review covers the approximate period of 2000 to 2014, and highlights specific examples of the discovery and characterization of novel genes and enzymes associated with the biosynthesis of natural products such as flavonoids, glucosinolates, terpenoids, and alkaloids. Additional examples of the integration of metabolomics with genome-based functional characterizations of plant natural products that are important to modern pharmaceutical technology are also reviewed. This article also provides a substantial review of recent technical advances in mass spectrometry imaging, nuclear magnetic resonance imaging, integrated LC-MS-SPE-NMR for metabolite identifications, and X-ray crystallography of microgram quantities for structural determinations. The review closes with a discussion on the future prospects of metabolomics related to crop species and herbal medicine.

The application of HPLC and microprobe NMR spectroscopy in the identification of metabolites in complex biological matrices

Nuclear magnetic resonance (NMR)-based metabolomics can be used directly to identify a variety of metabolites in biological fluids and tissues. Metabolite analysis is an important part of life science and metabolomics research. However, the identification of some metabolites using NMR spectroscopy remains a big challenge owing to low abundance or signal overlap. It is important to develop a method to measure these compounds accurately. Two-dimensional NMR spectroscopy, metabolite prediction software packages, and spike-in experiments with authentic standards are often used to solve these problems, but they are costly and time-consuming. In this study, methods were developed to identify metabolites in complex biological mixtures using both high-performance liquid chromatography (HPLC) and off-line microprobe NMR spectroscopy. With use of these methods, 83 and 73 metabolites were identified in Sprague Dawley rat urine and feces, respectively. Among them, 40 and 45 metabolites, respectively, could not be identified with traditional NMR methods. Our research revealed that the combination of HPLC and NMR techniques could significantly improve the accuracy of trace and overlapped metabolite identification, while offering an effective and convenient approach to identify potential biomarkers in complex biological systems.

Beneficial mycorrhizal symbionts affecting the production of health-promoting phytochemicals

Fresh fruits and vegetables are largely investigated for their content in vitamins, mineral nutrients, dietary fibers, and plant secondary metabolites, collectively called phytochemicals, which play a beneficial role in human health. Quantity and quality of phytochemicals may be detected by using different analytical techniques, providing accurate quantification and identification of single molecules, along with their molecular structures, and allowing metabolome analyses of plant-based foods. Phytochemicals concentration and profiles are affected by biotic and abiotic factors linked to plant genotype, crop management, harvest season, soil quality, available nutrients, light, and water. Soil health and biological fertility play a key role in the production of safe plant foods, as a result of the action of beneficial soil microorganisms, in particular of the root symbionts arbuscular mycorrhizal fungi. They improve plant nutrition and health and induce changes in secondary metabolism leading to enhanced biosynthesis of health-promoting phytochemicals, such as polyphenols, carotenoids, flavonoids, phytoestrogens, and to a higher activity of antioxidant enzymes. In this review we discuss reports on health-promoting phytochemicals and analytical methods used for their identification and quantification in plants, and on arbuscular mycorrhizal fungi impact on fruits and vegetables nutritional and nutraceutical value.

An overview of methods using (13)C for improved compound identification in metabolomics and natural products

Compound identification is a major bottleneck in metabolomics studies. In nuclear magnetic resonance (NMR) investigations, resonance overlap often hinders unambiguous database matching or de novo compound identification. In liquid chromatography-mass spectrometry (LC-MS), discriminating between biological signals and background artifacts and reliable determination of molecular formulae are not always straightforward. We have designed and implemented several NMR and LC-MS approaches that utilize (13)C, either enriched or at natural abundance, in metabolomics applications. For LC-MS applications, we describe a technique called isotopic ratio outlier analysis (IROA), which utilizes samples that are isotopically labeled with 5% (test) and 95% (control) (13)C. This labeling strategy leads to characteristic isotopic patterns that allow the differentiation of biological signals from artifacts and yield the exact number of carbons, significantly reducing possible molecular formulae. The relative abundance between the test and control samples for every IROA feature can be determined simply by integrating the peaks that arise from the 5 and 95% channels. For NMR applications, we describe two (13)C-based approaches. For samples at natural abundance, we have developed a workflow to obtain (13)C-(13)C and (13)C-(1)H statistical correlations using 1D (13)C and (1)H NMR spectra. For samples that can be isotopically labeled, we describe another NMR approach to obtain direct (13)C-(13)C spectroscopic correlations. These methods both provide extensive information about the carbon framework of compounds in the mixture for either database matching or de novo compound identification. We also discuss strategies in which (13)C NMR can be used to identify unknown compounds from IROA experiments. By combining technologies with the same samples, we can identify important biomarkers and corresponding metabolites of interest.

NMR-based metabolomics: from sample preparation to applications in nutrition research

Metabolomics is the study of metabolites present in biological samples such as biofluids, tissue/cellular extracts and culture media. Measurement of these metabolites is achieved through use of analytical techniques such as NMR and mass spectrometry coupled to liquid chromatography. Combining metabolomic data with multivariate data analysis tools allows the elucidation of alterations in metabolic pathways under different physiological conditions. Applications of NMR-based metabolomics have grown in recent years and it is now widely used across a number of disciplines. The present review gives an overview of the developments in the key steps involved in an NMR-based metabolomics study. Furthermore, there will be a particular emphasis on the use of NMR-based metabolomics in nutrition research.

Acetylcholinesterase immobilized capillary reactors coupled to protein coated magnetic beads: a new tool for plant extract ligand screening

The use of immobilized capillary enzyme reactors (ICERs) and enzymes coated to magnetic beads ((NT or CT)-MB) for ligand screening has been adopted as a new technique of high throughput screening (HTS). In this work the selected target was the enzyme acetylcholinesterase (AChE), which acts on the central nervous system and is a validated target for the treatment of Alzheimer's disease, as well as for new insecticides. A new approach for the screening of plant extracts was developed based on the ligand fishing experiments and zonal chromatography. For that, the magnetic beads were used for the ligand fishing experiments and capillary bioreactors for the activity assays. The latter was employed also under non-linear conditions to determine the affinity constants of known ligands, for the first time, as well as for the active fished ligand.

Semi-preparative LC-SPE-cryoflow NMR for impurity identifications: use of mother liquor as a better source of impurities

Unambiguous structural elucidation of active pharmaceutical ingredients (API) impurities is a particularly challenging necessity of pharmaceutical development, particularly if the impurities are low level (0.1% level). In many cases, this requires acquiring high-quality NMR data on a pure sample of each impurity. High-quality, high signal-to-noise (S/N) one- and two-dimensional NMR data can be obtained using liquid chromatography-solid phase extraction-cryoflow NMR (LC-SPE-cryoflow NMR) with a combination of semi-preparative column for separation and mother liquor as a source of concentrated impurities. These NMR data, in conjunction with mass spectrometry data, allowed for quick and unambiguous structural elucidations of four impurities found at low level in the crystallized API but found at appreciable levels in the mother liquor that was used as the source for these impurities. These data show that semi-preparative columns can be used at lower than ideal flow rates to facilitate trapping of HPLC components for LC-SPE-cryoflow NMR analysis without compromising chromatographic resolution. Also, despite the complex chromatography encountered with the use of mother liquor as a source of impurities, acceptably pure analytes were obtained for acquiring NMR data for unambiguous structure elucidations.

Mass spectrometry and NMR spectroscopy: modern high-end detectors for high resolution separation techniques--state of the art in natural product HPLC-MS, HPLC-NMR, and CE-MS hyphenations

Current natural product research is unthinkable without the use of high resolution separation techniques as high performance liquid chromatography or capillary electrophoresis (HPLC or CE respectively) combined with mass spectrometers (MS) or nuclear magnetic resonance (NMR) spectrometers. These hyphenated instrumental analysis platforms (CE-MS, HPLC-MS or HPLC-NMR) are valuable tools for natural product de novo identification, as well as the authentication, distribution, and quantification of constituents in biogenic raw materials, natural medicines and biological materials obtained from model organisms, animals and humans. Moreover, metabolic profiling and metabolic fingerprinting applications can be addressed as well as pharmacodynamic and pharmacokinetic issues. This review provides an overview of latest technological developments, discusses the assets and drawbacks of the available hyphenation techniques, and describes typical analytical workflows.

Using NMR to identify and characterize natural products

Over the past 28 years there have been several thousand publications describing the use of 2D NMR to identify and characterize natural products. During this time period, the amount of sample needed for this purpose has decreased from the 20-50 mg range to under 1 mg. This has been due to both improvements in NMR hardware and methodology. This review will focus on mainly methodology improvements, particularly in pulse sequences, acquisition and processing methods which are particularly relevant to natural product research, with lesser discussion of hardware improvements.

Development of antibiotic activity profile screening for the classification and discovery of natural product antibiotics

Despite recognition of the looming antibiotic crisis by healthcare professionals, the number of new antibiotics reaching the clinic continues to decline sharply. This study aimed to establish an antibiotic profiling strategy using a panel of clinically relevant bacterial strains to create unique biological fingerprints for all major classes of antibiotics. Antibiotic mode of action profile (BioMAP) screening has been shown to effectively cluster antibiotics by structural class based on these fingerprints. Using this approach, we have accurately predicted the presence of known antibiotics in natural product extracts and have discovered a naphthoquinone-based antibiotic from our marine natural product library that possesses a unique carbon skeleton. We have demonstrated that bioactivity fingerprinting is a successful strategy for profiling antibiotic lead compounds and that BioMAP can be applied to the discovery of new natural product antibiotics leads.

Liquid chromatography-nuclear magnetic resonance coupling as alternative to liquid chromatography-mass spectrometry hyphenations: curious option or powerful and complementary routine tool?

Combining the most powerful separation techniques, i.e. liquid chromatography (LC) or capillary electrophoresis (CE) with a information rich detection system - the mass spectrometer or the nuclear magnetic resonance (NMR) spectrometer - has been pursued for more than three decades. This compilation shall provide an overview of the advantages and limitations of the LC-NMR hyphenation in the light of its most valued application-the unequivocal analyte identification. Especially the post LC trapping of analytes with an in-line solid phase extraction (SPE) device prior to transferring the analyte of interest to the NMR spectrometer (LC-SPE-NMR) proved to be a robust installation allowing a significant cut-down of the amount of analyte needed for the generation of high quality heteronuclear NMR shift correlation data. Different available technical realizations will be discussed and typical application examples from natural product research and from industrial settings will be given.

LC-SPE-NMR-MS: a total analysis system for bioanalysis

Liquid chromatography (LC)-solid-phase extraction (SPE)-nuclear magnetic resonance (NMR)-mass spectrometry (MS) coupling is a key technology for fast and thorough structure elucidation of valuable mass-limited samples. Laborious serial isolation and purification procedures of metabolites, byproducts or impurities from complex biomatrices, natural product extracts or other mixtures of several components can be circumvented by the use of this integrated modular system. This combination of high-end analytical technology significantly accelerates the structure-elucidation process for valuable samples present in minute quantities in mixtures. The information depth is significantly increased by the concurrent availability of NMR and MS data of one chromatographic peak. Thus, this flexible technique is well on its way to becoming the gold standard in analytical chemistry of mixtures. LC-SPE-NMR-MS overcomes the limitations of directly coupled LC-NMR. Full flexibility regarding chromatographic conditions and NMR acquisition is gained by this modular technique. LC-SPE-NMR-MS allows for a rapid structure-elucidation process that would not be possible on the basis of MS or NMR data alone.

NMR-based plant metabolomics: where do we stand, where do we go?

NMR-based metabolomics is an important tool for studying biological systems and has been applied in various organisms, including animals, plants and microbes. NMR is able to provide a 'holistic view' of the metabolites under certain conditions, and thus is advantageous for metabolomic studies. To maximize the use of the information obtained, it is also important to create a platform to measure, store and share data. Public databases for storing and sharing information are still lacking for NMR-based metabolomic analysis in plants. Such databases are urgently needed to make metabolic profiling a real omics technology. In addition, to understand metabolic processes in depth, single-cell analysis and the turnover of metabolites in pathways (fluxomics) should be measured.

Important roles of the hyphenated HPLC-DAD-MS-SPE-NMR technique in metabonomics

Metabolite identification is a key step for metabonomics study. A fully automated hyphenation of HPLC-diode-array detector (DAD) mass spectrometry (MS) solid phase extraction (SPE)-NMR spectroscopy (HPLC-DAD-MS-SPE-NMR) is one of the most efficient methods to determine the structure of a given unknown metabolite in a complex mixture (metabonome) and hence represents one of the most important analytical techniques for the further development of metabonomics. In this review, some recent applications of this technique in identifying novel and trace metabolites in plant extracts and drug metabolism have been discussed. Modification of this hyphenated technique, enabling multiple trappings of strong polar metabolites for biofluids, needs further development.

Accelerated dereplication of crude extracts using HPLC-PDA-MS-SPE-NMR: quinolinone alkaloids of Haplophyllum acutifolium

Direct hyphenation of analytical-scale high-performance liquid chromatography, photo-diode array detection, mass spectrometry, solid-phase extraction and nuclear magnetic resonance spectroscopy (HPLC-PDA-MS-SPE-NMR) has been used for accelerated dereplication of crude extract of Haplophyllum acutifolium (syn. Haplophyllum perforatum). This technique allowed fast on-line identification of six quinolinone alkaloids, named haplacutine A-F, as well as of acutine, haplamine, eudesmine, and 2-nonylquinolin-4(1H)-one. Acutine and haplacutine E, isolated by preparative-scale HPLC, showed moderate antiplasmodial activity with IC(50) values of 2.17+/-0.22 microM and 3.79+/-0.24 microM, respectively (chloroquine-sensitive Plasmodium falciparum 3D7 strain).

Nuclear magnetic resonance and liquid chromatography-mass spectrometry combined with an incompleted separation strategy for identifying the natural products in crude extract

NMR and LC-MS combined with an incompleted separation strategy were proposed to the simultaneous structure identification of natural products in crude extracts, and a novel method termed as NMR/LC-MS parallel dynamic spectroscopy (NMR/LC-MS PDS) was developed to discover the intrinsic correlation between retention time (Rt), mass/charge (m/z) and chemical shift (delta) data of the same constituent from mixture spectra by the co-analysis of parallelly visualized multispectroscopic datasets from LC-MS and (1)H NMR. The extracted ion chromatogram (XIC) and (1)H NMR signals deriving from the same individual constituent were correlated through fraction ranges and intensity changing profiles in NMR/LC-MS PDS spectrum due to the signal amplitude co-variation resulted from the concentration variation of constituents in a series of incompletely separated fractions. NMR/LC-MS PDS was applied to identify 12 constituents in an active herbal extract including flavonol glycosides, which was separated into a series of fractions by flash column chromatography. The complementary spectral information of the same individual constituent in the crude extract was discovered simultaneously from mixture spectra. Especially, two groups of co-eluted isomers were identified successfully. The results demonstrated that NMR/LC-MS PDS combined with the incompleted separation strategy achieved the similar function of on-line LC-NMR-MS analysis in off-line mode and had the potential for simplifying and accelerating the analytical routes for structure identification of constituents in herbs or their active extracts.

Microscale LC-MS-NMR platform applied to the identification of active cyanobacterial metabolites

An LC-MS-NMR platform is demonstrated, which combines two innovations in microscale analysis, nanoSplitter LC-MS and microdroplet NMR, for the identification of unknown compounds found at low concentrations in complex sample matrixes as frequently encountered in metabolomics or natural products discovery. The nanoSplitter provides the high sensitivity of nanoelectrospray MS while allowing 98% of the HPLC effluent from a large-bore LC column to be collected and concentrated for NMR. Microdroplet NMR is a droplet microfluidic NMR loading method providing severalfold higher sample efficiency than conventional flow injection methods. Performing NMR offline from LC-UV-MS accommodates the disparity between MS and NMR in their sample mass and time requirements, as well as allowing NMR spectra to be requested retrospectively, after review of the LC-MS data. Interpretable 1D NMR spectra were obtained from analytes at the 200-ng level, in 1 h/well automated NMR data acquisitions. The system also showed excellent intra- and interdetector reproducibility with retention time RSD values less than 2% and sample recovery on the order of 93%. When applied to a cyanobacterial extract showing antibacterial activity, the platform recognized several previously known metabolites, down to the 1% level, in a single 30-mug injection, and prioritized one unknown for further study.

Screening of tobacco smoke condensate for nicotinic acetylcholine receptor ligands using cellular membrane affinity chromatography columns and missing peak chromatography

This manuscript reports an approach to the screening of natural product extracts for compounds which are active at membrane-bound receptors, ion channels and transporters. The technique is based upon cellular membrane affinity chromatography (CMAC) columns created through the immobilization of cellular membrane fragments on liquid chromatography stationary phases. In this study a CMAC(nAChR(+)) column was created out of membranes from a transfected cell line expressing the alpha3beta4 neuronal nicotinic acetylcholine receptor (nAChR) and the column was used to screen tobacco smoke condensates. A strategy involving parallel screening with a CMAC column created from a non-transfected form of the same cell line, CMAC(nAChR(-)) was adopted. The condensate was chromatographed on both columns, timed fractions collected and concentrated. Each fraction was analyzed on a C18 column in order to establish a chromatographic fingerprint of each fraction and a differential elution profile of each compound. Comparison of the elution profiles from the CMAC(nAChR(+)) and CMAC(nAChR(-)) columns identified patterns that could be associated with high affinity ligands and with low-affinity/non-binding compounds. Known strong ligands ((S)-nicotine, (R,S)-anatabine, N'-nitrosonornicotine), weak ligands ((R,S)-nornicotine, anabasine) as well as known non-ligands (N-methyl-gamma-oxo-3-pyridinebutanamide, (1'S,2'S)-nicotine 1'-oxide) have been identified in the complex extract. The results demonstrate that CMAC-based screens can be used in the identification of compounds within natural product extracts that bind to membrane-based targets.

Evolving trends in the dereplication of natural product extracts: new methodology for rapid, small-scale investigation of natural product extracts

The use of an HPLC bioactivity profiling/microtiter plate technique in conjunction with capillary probe NMR instrumentation and access to appropriate databases effectively short-circuits conventional dereplication procedures, necessarily based on multimilligram extracts, to a single, more rapid submilligram operation. This approach to dereplication is illustrated using fungal or bacterial extracts that contain known compounds. In each case the dereplication steps were carried out on microgram quantities of extract and demonstrate the discriminating power of (1)H NMR spectroscopy as a definitive dereplication tool.

Optimized liquid chromatography-mass spectrometry approach for the isolation of minor stress biomarkers in plant extracts and their identification by capillary nuclear magnetic resonance

A LC-MS approach is presented for the isolation of minor key plant biomarkers, in view of their characterization by NMR at the microgram scale. Due to the complexity of plant extracts, the purification of metabolites present in low concentrations is critical. The strategy used relies on the optimization of the chromatographic analysis using ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOF-MS), thanks to modelling software. The optimized method is then transferred to semi-preparative LC conditions with MS detection. The approach is illustrated by the isolation of wound-induced jasmonate derivatives revealed by a metabolomic study in Arabidopsis thaliana leaves and their subsequent characterization by capillary NMR (CapNMR).

Limitations in the deduction of carbon NMR spectra from the f1 dimension of standard 2D heteronuclear experiments when applied to natural products

The structure elucidation of a natural product requires a set of NMR spectra that includes both carbon observe experiments, such as 1D carbon and DEPT, and proton observe experiments, such as HSQC, HMBC, and COSY. Because NMR probes are optimized for either proton or carbon observe experiments, but not both, this often results in some experiments being acquired at a very suboptimal level of efficiency. An alternative is to deduce the carbon spectrum from the indirect, or f 1, dimension of the heteronuclear 2D experiments. This approach is sometimes being employed for the structure elucidation of newly isolated natural products in cases where the amount of material available precludes carbon observe experiments. However whether this approach is reliable in every case has not yet been established. This study applies the "indirect dimension" approach to a representative set of known natural products. The results are mixed. Analysis of E-HSQC spectra, in conjunction with COSY spectra, reliably defines the carbon spectra of the methyl, methylene, and methine carbons present. However, due to limits in resolution in the f 1 dimension of standard HMBC experiments, the presence and chemical shift positions of some quaternary carbons are fairly frequently obscured by those of other carbons. Thus it is often necessary to acquire a 1D carbon NMR spectrum to support the structure elucidation of a natural product.

Natural products as a screening resource

Natural products have been the most productive source of leads for new drugs, but they are currently out of fashion with the pharmaceutical industry. New approaches to sourcing novel compounds from untapped areas of biodiversity coupled with the technical advances in analytical techniques (such as microcoil NMR and linked LC-MS-NMR) have removed many of the difficulties in using natural products in screening campaigns. As the 'chemical space' occupied by natural products is both more varied and more drug-like than that of combinatorial chemical collections, synthetic and biosynthetic methods are being developed to produce screening libraries of natural product-like compounds. A renaissance of drug discovery inspired by natural products can be predicted.