Liquid chromatography with ultraviolet absorbance-mass spectrometric detection and with nuclear magnetic resonance spectroscopy: a powerful combination for the on-line structural investigation of plant metabolites

A rapid optimization method for Sepbox system separation using HPTLC: an application of Cerbera manghas L. separation

The rapid isolation of natural products and efficient drug screening are pivotal in expediting drug development. Techniques ranging from traditional open column chromatography to medium-pressure liquid chromatography (MPLC), and the latest Sepbox technology, have been developed to accelerate separation processes and streamline drug development timelines. The Sepbox system combines two-dimensional high-performance liquid chromatography (2D-HPLC) and solid-phase extraction (SPE) technologies, coupled with UV and evaporative light scattering detection (ELSD) systems, offering various column options to cater to diverse sample requirements. Furthermore, the Sepbox system automates and expedites sample fractionation into numerous fractions, facilitating subsequent high-throughput screening and analysis. Despite previous emphasis on 2D-HPLC development, optimizing separation conditions with the Sepbox system poses challenges due to the requirement for substantial sample and solvent quantities, limiting its practicality compared to conventional methods. Hence, this study employed eight standard compounds to explore the correlation between retention factor (Rf) values obtained from high-performance thin-layer chromatography (HPTLC) plates and retention times on the Sepbox main column. Mass spectrometry was utilized to confirm the retention times of the standard compounds. The findings yielded a conversion equation between HPTLC Rf values and Sepbox main column retention times, thereby enhancing the separation efficiency of Sepbox 2D-2000 system. Finally, the efficacy of this method was validated using Cerbera manghas leaf crude extracts and its purified compounds, demonstrating the rapid optimization of suitable elution conditions for the Sepbox 2D-2000 system using HPTLC.

Application of Mass Spectrometry for Analysis of Nucleobases, Nucleosides and Nucleotides in Tea and Selected Herbs: A Critical Review of the Mass Spectrometric Data

The main and most commonly known biological function of nucleobases, nucleosides, and nucleotides is usually associated with the fact that they are the building blocks of nucleic acids. However, these compounds also belong to plant secondary metabolites, although in that role they have attracted less attention than the others, e.g., terpenes, phenolics, or alkaloids. The former compounds are also important constituents of the human diet, e.g., as ingredients of tea and herbs, endowing them with specific taste qualities and pharmacological activities. Liquid chromatography-mass spectrometry seems to be the most important analytical method that permits the identification and determination of nucleobases, nucleosides, and nucleotides, along with the other metabolites. The main goal of this review is to discuss in detail the aspects of mass spectrometric detection of nucleobases, nucleosides, and nucleotides in tea and selected herbs. An important conclusion is that the identification of the compounds of interest should be performed not only on the basis of [M + H]+/[M - H]- ions but should also be confirmed by the respective product ions; however, as discussed in detail in this review, it may sometimes be problematic. It also clear that all difficulties that may be encountered when analyzing plant material are caused by the complexity of the analyzed samples and the need to analyze different classes of compounds, and this review absolutely does not debase any of the mentioned papers.

Advanced high-resolution chromatographic strategies for efficient isolation of natural products from complex biological matrices: from metabolite profiling to pure chemical entities

The isolation of pure compounds from extracts represents a key step common to all investigations of natural product (NP) research. Isolation methods have gone through a remarkable evolution. Current approaches combine powerful metabolite profiling methods for compounds annotation with omics mining results and/or bioassay for bioactive NPs/biomarkers priorisation. Targeted isolation of prioritized NPs is performed using high-resolution chromatographic methods that closely match those used for analytical profiling. Considerable progress has been made by the introduction of innovative stationary phases providing remarkable selectivity for efficient NPs isolation. Today, efficient separation conditions determined at the analytical scale using high- or ultra-high-performance liquid chromatography can be optimized via HPLC modelling software and efficiently transferred to the semi-preparative scale by chromatographic calculation. This ensures similar selectivity at both the analytical and preparative scales and provides a precise separation prediction. High-resolution conditions at the preparative scale can notably be granted using optimized sample preparation and dry load sample introduction. Monitoring by ultraviolet, mass spectrometry, and or universal systems such as evaporative light scattering detectors and nuclear magnetic resonance allows to precisely guide the isolation or trigger the collection of specific NPs with different structural scaffolds. Such approaches can be applied at different scales depending on the amounts of NPs to be isolated. This review will showcase recent research to highlight both the potential and constraints of using these cutting-edge technologies for the isolation of plant and microorganism metabolites. Several strategies involving their application will be examined and critically discussed.

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Twenty Years of 1H NMR Plant Metabolomics: A Way Forward toward Assessment of Plant Metabolites for Constitutive and Inducible Defenses to Biotic Stress

Metabolomics has become an important tool in elucidating the complex relationship between a plant genotype and phenotype. For over 20 years, nuclear magnetic resonance (NMR) spectroscopy has been known for its robustness, quantitative capabilities, simplicity, and cost-efficiency. 1H NMR is the method of choice for analyzing a broad range of relatively abundant metabolites, which can be used for both capturing the plant chemical profile at one point in time and understanding the pathways that underpin plant defense. This systematic Review explores how 1H NMR-based plant metabolomics has contributed to understanding the role of various compounds in plant responses to biotic stress, focusing on both primary and secondary metabolites. It clarifies the challenges and advantages of using 1H NMR in plant metabolomics, interprets common trends observed, and suggests guidelines for method development and establishing standard procedures.

Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine

Traditional Chinese Medicine (TCM) is extensively utilized in clinical practice due to its therapeutic and preventative treatments for various diseases. With the development of high-throughput sequencing and systems biology, TCM research was transformed from traditional experiment-based approaches to a combination of experiment-based and omics-based approaches. Numerous academics have explored the therapeutic mechanism of TCM formula by omics approaches, shifting TCM research from the "one-target, one-drug" to "multi-targets, multi-components" paradigm, which has greatly boosted the digitalization and internationalization of TCM. In this review, we concentrated on multi-omics approaches in principles and applications to gain a better understanding of TCM formulas against various diseases from several aspects. We first summarized frequently used TCM quality assessment methods, and suggested that incorporating both chemical and biological ingredients analytical methods could lead to a more comprehensive assessment of TCM. Secondly, we emphasized the significance of multi-omics approaches in deciphering the therapeutic mechanism of TCM formulas. Thirdly, we focused on TCM network analysis, which plays a vital role in TCM-diseases interaction, and serves for new drug discovery. Finally, as an essential source for storing multi-omics data, we evaluated and compared several TCM databases in terms of completeness and reliability. In summary, multi-omics approaches have infiltrated many aspects of TCM research. With the accumulation of omics data and data-mining resources, deeper understandings of the therapeutic mechanism of TCM have been acquired or will be gained in the future.

Metabolite Identification of HIV-1 Capsid Modulators PF74 and 11L in Human Liver Microsomes

PF74 and 11L, as potent modulators of the HIV-1 capsid protein, have been demonstrated to act at both early and late stages in the HIV-1 life cycle. However, their clearance is high in human liver microsomes (HLMs). The main goal of this study was to clarify the metabolism of PF74 and 11L in HLMs, and provide guidance for future structural optimization. To accomplish this, the phase-I metabolites of PF74 and 11L, resulting from in vitro incubation with HLMs, were investigated via ultra-performance liquid chromatography–ultraviolet–high-resolution mass spectrometry (UPLC–UV–HRMS). The results show that 17 phase-I metabolites were putatively annotated for PF74, whereas 16 phase-I metabolites were found for 11L. The main metabolic pathways of PF74 in HLMs were oxidation and demethylation, and the secondary metabolic pathway was hydrolysis; thus, the di-oxidation and demethylation products (M7, M9, M11, and M14) were found to be major metabolites of PF74 in HLMs. In comparison, the main metabolic pathways of 11L in HLMs were oxidation, demethylation, dehydrogenation, and oxidative deamination, with M6′, M11′, M15′, and M16′ as the main metabolites. We suggest that the indole ring and N-methyl group of PF74, and the aniline group, benzene ring R1′, N-methyl, and methoxy group of 11L, were the main metabolic soft spots. Therefore, our research illuminates structural optimization options in seeking improved HIV-1 CA modulators.

NMR and Metabolomics-A Roadmap for the Future

Metabolomics investigates global metabolic alterations associated with chemical, biological, physiological, or pathological processes. These metabolic changes are measured with various analytical platforms including liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). While LC-MS methods are becoming increasingly popular in the field of metabolomics (accounting for more than 70% of published metabolomics studies to date), there are considerable benefits and advantages to NMR-based methods for metabolomic studies. In fact, according to PubMed, more than 926 papers on NMR-based metabolomics were published in 2021-the most ever published in a given year. This suggests that NMR-based metabolomics continues to grow and has plenty to offer to the scientific community. This perspective outlines the growing applications of NMR in metabolomics, highlights several recent advances in NMR technologies for metabolomics, and provides a roadmap for future advancements.

Polyketide Derivatives in the Resistance of Gerbera hybrida to Powdery Mildew

Powdery mildew is a common disease affecting the commercial production of gerbera flowers (Gerbera hybrida, Asteraceae). Some varieties show a certain degree of resistance to it. Our objective was to identify biomarkers of resistance to powdery mildew using an ¹H nuclear magnetic resonance spectroscopy and chemometrics approach in a complex, fully factorial experiment to suggest a target for selection and breeding. Resistant varieties were found to differ from those that were susceptible in the metabolites of the polyketide pathway, such as gerberin, parasorboside, and gerberinside. A new compound probably involved in resistance, 5-hydroxyhexanoic acid 3-O-β-D-glucoside, was described for the first time. A decision tree model was built to distinguish resistant varieties, with an accuracy of 57.7%, sensitivity of 72%, and specificity of 44.44% in an independent test. Our results suggest the mechanism of resistance to powdery mildew in gerbera and provide a potential tool for resistance screening in breeding programs.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC-MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC-MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC-MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC-MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC-MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.

Combining untargeted and targeted metabolomics approaches for the standardization of polyherbal formulations through UPLC-MS/MS

INTRODUCTION

Polyherbal formulations are an integral part of various indigenous medicinal systems such as Traditional Chinese Medicine (TCM) and Ayurveda. The presence of a very large number of compounds makes the quality control of polyherbal formulations very difficult.

OBJECTIVES

To overcome this problem, we have developed a comprehensive strategy for the dereplication of natural products in polyherbal formulations by using Adhatoda vasica as a case study.

METHODS

The strategy is based on five major steps: the collection of plant samples from different locations to observe the effects of environmental variables; LC-ESI-MS/MS-based untargeted metabolite profiling of the plant samples to identify marker compounds using extensive chemometric analysis of the obtained data; the identification of marker compounds in polyherbal products; the isolation, purification and characterization of the marker compounds; and MRM-based quantitative analysis of the isolated marker compounds using LC-ESI-MS/MS.

RESULTS

Using this strategy, we identified a total of 51 compounds in the methanolic extract of A. vasica plants from 14 accessions. Chemical fingerprinting of the plant led to the identification of characteristic peaks that were used to confirm the presence of A. vasica in complex polyherbal formulations. Four quinazoline alkaloids (marker compounds) were isolated, purified and quantified in various herbal formulations containing A. vasica.

CONCLUSION

This method demonstrates a comprehensive strategy based on untargeted and targeted metabolite analysis that can be used for the standardization of complex polyherbal formulations.

Secondary Metabolite Dereplication and Phylogenetic Analysis Identify Various Emerging Mycotoxins and Reveal the High Intra-Species Diversity in Aspergillus flavus

Aspergillus flavus is one of the most important mycotoxigenic species from the genus Aspergillus, due to its ability to synthesize the potent hepatocarcinogen, aflatoxin B₁. Moreover, this fungus is capable of producing several other toxic metabolites from the class of indole-tetramates, non-ribosomal peptides, and indole-diterpenoids. Populations of A. flavus are characterized by considerable diversity in terms of morphological, functional and genetic features. Although for many years A. flavus was considered an asexual fungus, researchers have shown evidence that at best these fungi can exhibit a predominantly asexual existence. We now know that A. flavus contains functional genes for mating, uncovering sexuality as potential contributor for its diversification. Based on our results, we reconfirm that A. flavus is a predominant producer of B-type aflatoxins. Moreover, this fungus can decisively produce AFM₁ and AFM₂. We did not observe any clear relationship between mating-type genes and particular class of metabolites, probably other parameters such as sexual/asexual ratio should be investigated. A dynamic secondary metabolism was found also in strains intended to be used as biocontrol agents. In addition we succeeded to provide mass spectrometry fragmentation spectra for the most important classes of A. flavus metabolites, which will serve as identification cards for future studies. Both, metabolic and phylogenetic analysis proved a high intra-species diversity for A. flavus. These findings contribute to our understanding about the diversity of Aspergillus section Flavi species, raising the necessity for polyphasic approaches (morphological, metabolic, genetic, etc.) when dealing with this type of complex group of species.

Various Dereplication Strategies Using LC-MS for Rapid Natural Product Lead Identification and Drug Discovery

Natural products are the most consistently successful source of drug leads. The rapid identification of known compounds from natural product extracts, or ‘dereplication’, is an important step in an efficiently run drug discovery program. Modern spectroscopic methods have largely revolutionized compound identification and tremendously accelerated the pace at which isolated compounds can be identified. Dereplication strategies use analytical techniques and database searching to determine the identity of an active compound at the earliest possible stage in the discovery process. This prevents wasted effort on samples with no potential for development and allows resources to be focused on the most promising lead. In the past few years, advances in technology have allowed the development of tandem analytical techniques, such as HPLC-PDA, LC-MS, LC-MS-MS, LC-NMR, and LC-NMR-MS. This review describes the principles and performance of a number of hyphenated techniques involving LC-MS that can be used for dereplication of natural products for rapid lead identification.

Antiproliferative Activity of Neem Leaf Extracts Obtained by a Sequential Pressurized Liquid Extraction

Azadirachta indica A. Juss (neem) extracts have been used in pharmaceutical applications as antitumor agents, due to their terpenes and phenolic compounds. To obtain extracts from neem leaves with potential antiproliferative effect, a sequential process of pressurized liquid extraction was carried out in a fixed bed extractor at 25 °C and 100 bar, using hexane (SH), ethyl acetate (SEA), and ethanol (SE) as solvents. Extractions using only ethanol (EE) was also conducted to compare the characteristics of the fractionated extracts. The results obtained by liquid chromatography-electrospray ionization mass spectrometry suggested a higher concentration of terpenes in the SEA extract in comparison to SH, SE, and EE extracts. Therefore, antiproliferative activity showed that SEA extracts were the most efficient inhibitor to human tumor cells MCF-7, NCI-H460, HeLa, and HepG2. Hepatocellular cells were more resistant to SH, SEA, SE, and EE compared to breast, lung, hepatocellular, and cervical malignant cells. Neem fractioned extracts obtained in the present study seem to be more selective for malignant cells compared to the non-tumor cells.

Sensitivity enhancement by chromatographic peak concentration with ultra-high performance liquid chromatography-nuclear magnetic resonance spectroscopy for minor impurity analysis

High performance liquid chromatography can be coupled with nuclear magnetic resonance (NMR) spectroscopy to give a powerful analytical method known as liquid chromatography-nuclear magnetic resonance (LC-NMR) spectroscopy, which can be used to determine the chemical structures of the components of complex mixtures. However, intrinsic limitations in the sensitivity of NMR spectroscopy have restricted the scope of this procedure, and resolving these limitations remains a critical problem for analysis. In this study, we coupled ultra-high performance liquid chromatography (UHPLC) with NMR to give a simple and versatile analytical method with higher sensitivity than conventional LC-NMR. UHPLC separation enabled the concentration of individual peaks to give a volume similar to that of the NMR flow cell, thereby maximizing the sensitivity to the theoretical upper limit. The UHPLC concentration of compound peaks present at typical impurity levels (5.0-13.1 nmol) in a mixture led to at most three-fold increase in the signal-to-noise ratio compared with LC-NMR. Furthermore, we demonstrated the use of UHPLC-NMR for obtaining structural information of a minor impurity in a reaction mixture in actual laboratory-scale development of a synthetic process. Using UHPLC-NMR, the experimental run times for chromatography and NMR were greatly reduced compared with LC-NMR. UHPLC-NMR successfully overcomes the difficulties associated with analyses of minor components in a complex mixture by LC-NMR, which are problematic even when an ultra-high field magnet and cryogenic probe are used.

Review on a Traditional Herbal Medicine, Eurycoma longifolia Jack (Tongkat Ali): Its Traditional Uses, Chemistry, Evidence-Based Pharmacology and Toxicology

Eurycoma longifolia Jack (known as tongkat ali), a popular traditional herbal medicine, is a flowering plant of the family Simaroubaceae, native to Indonesia, Malaysia, Vietnam and also Cambodia, Myanmar, Laos and Thailand. E. longifolia, is one of the well-known folk medicines for aphrodisiac effects as well as intermittent fever (malaria) in Asia. Decoctions of E. longifolia leaves are used for washing itches, while its fruits are used in curing dysentery. Its bark is mostly used as a vermifuge, while the taproots are used to treat high blood pressure, and the root bark is used for the treatment of diarrhea and fever. Mostly, the roots extract of E. longifolia are used as folk medicine for sexual dysfunction, aging, malaria, cancer, diabetes, anxiety, aches, constipation, exercise recovery, fever, increased energy, increased strength, leukemia, osteoporosis, stress, syphilis and glandular swelling. The roots are also used as an aphrodisiac, antibiotic, appetite stimulant and health supplement. The plant is reported to be rich in various classes of bioactive compounds such as quassinoids, canthin-6-one alkaloids, β-carboline alkaloids, triterpene tirucallane type, squalene derivatives and biphenyl neolignan, eurycolactone, laurycolactone, and eurycomalactone, and bioactive steroids. Among these phytoconstituents, quassinoids account for a major portion of the E. longifolia root phytochemicals. An acute toxicity study has found that the oral Lethal Dose 50 (LD50) of the alcoholic extract of E. longifolia in mice is between 1500-2000 mg/kg, while the oral LD50 of the aqueous extract form is more than 3000 mg/kg. Liver and renal function tests showed no adverse changes at normal daily dose and chronic use of E. longifolia. Based on established literature on health benefits of E. longifolia, it is important to focus attention on its more active constituents and the constituents' identification, determination, further development and most importantly, the standardization. Besides the available data, more evidence is required regarding its therapeutic efficacy and safety, so it can be considered a rich herbal source of new drug candidates. It is very important to conserve this valuable medicinal plant for the health benefit of future generations.

Dereplication: racing to speed up the natural products discovery process

Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.

Current perspectives in drug discovery against tuberculosis from natural products

Currently, one third of the world's population is latently infected with Mycobacterium tuberculosis (MTB), while 8.9-9.9 million new and relapse cases of tuberculosis (TB) are reported yearly. The renewed research interests in natural products in the hope of discovering new and novel antitubercular leads have been driven partly by the increased incidence of multidrug-resistant strains of MTB and the adverse effects associated with the first- and second-line antitubercular drugs. Natural products have been, and will continue to be a rich source of new drugs against many diseases. The depth and breadth of therapeutic agents that have their origins in the secondary metabolites produced by living organisms cannot be compared with any other source of therapeutic agents. Discovery of new chemical molecules against active and latent TB from natural products requires an interdisciplinary approach, which is a major challenge facing scientists in this field. In order to overcome this challenge, cutting edge techniques in mycobacteriology and innovative natural product chemistry tools need to be developed and used in tandem. The present review provides a cross-linkage to the most recent literature in both fields and their potential to impact the early phase of drug discovery against TB if seamlessly combined.

Dereplication of known nucleobase and nucleoside compounds in natural product extracts by capillary electrophoresis-high resolution mass spectrometry

Nucleobase and nucleoside compounds exist widely in various organisms. An often occurring problem in the discovery of new bioactive compounds from natural products is reisolation of known nucleobase and nucleoside compounds. To resolve this problem, a capillary electrophoresis-high resolution mass spectrometry (CE-HR-MS) method providing both rapid separation and accurate mass full-scan MS data was developed for the first time to screen and dereplicate known nucleobase and nucleoside compounds in crude extracts of natural products. Instrumental parameters were optimized to obtain optimum conditions for CE separation and electrospray ionization-time-of-flight mass spectrometry (ESI-TOF/MS) detection. The proposed method was verified to be precise, reproducible, and sensitive. Using this method, known nucleobase and nucleoside compounds in different marine medicinal organisms including Syngnathus acus Linnaeus; Hippocampusjaponicus Kaup and Anthopleura lanthogrammica Berkly were successfully observed and identified. This work demonstrates that CE-HR-MS combined with an accurate mass database may be used as a powerful tool for dereplicating known nucleobase and nucleoside compounds in different types of natural products. Rapid dereplication of known nucleobase and nucleoside compounds allows researchers to focus on other leads with greater potential to yield new substances.

High-resolution MS, MS/MS, and UV database of fungal secondary metabolites as a dereplication protocol for bioactive natural products

A major problem in the discovery of new biologically active compounds from natural products is the reisolation of known compounds. Such reisolations waste time and resources, distracting chemists from more promising leads. To address this problem, dereplication strategies are needed that enable crude extracts to be screened for the presence of known compounds before isolation efforts are initiated. In a project to identify anticancer drug leads from filamentous fungi, a significant dereplication challenge arises, as the taxonomy of the source materials is rarely known, and, thus, the literature cannot be probed to identify likely known compounds. An ultraperformance liquid chromatography-photodiode array-high-resolution tandem mass spectrometric (UPLC-PDA-HRMS-MS/MS) method was developed for dereplication of fungal secondary metabolites in crude culture extracts. A database was constructed by recording HRMS and MS/MS spectra of fungal metabolites, utilizing both positive- and negative-ionization modes. Additional details, such as UV-absorption maxima and retention times, were also recorded. Small-scale cultures that showed cytotoxic activities were dereplicated before engaging in the scale-up or purification processes. Using these methods, approximately 50% of the cytotoxic extracts could be eliminated from further study after the confident identification of known compounds. The specific attributes of this dereplication methodology include a focus on bioactive secondary metabolites from fungi, the use of a 10 min chromatographic method, and the inclusion of both HRMS and MS/MS data.

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.

Structure-oriented UHPLC-LTQ Orbitrap-based approach as a dereplication strategy for the identification of isoflavonoids from Amphimas pterocarpoides crude extract

Hyphenated techniques and especially ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) are nowadays widely employed in natural products research. However, the complex nature of plant extracts complicates considerably the analysis and the identification of their constituents. Nevertheless, new MS analyzers with increased resolving power and accuracy such as the orbital trap (Orbitrap) could facilitate drastically this process. The objective of this study is the development of a new structure-oriented approach based on fast UHPLC-high-resolution (HR)MS and HRMS/MS methodologies for the identification of isoflavonoids in crude extracts. In addition, aims to assist dereplication procedures, to decrease the laborious isolation steps and orient the focused isolation of compounds of interest. As a proof of concept, the methanol extract of the stem bark of Amphimas pterocarpoides (Leguminosae) was selected. Based on chromatographic (retention time, polarity) and spectrometric features (ultraviolet spectra, accurate m/z, proposed elemental composition, ring double bond equivalent, and relative isotopic abundance) as well as HRMS/MS spectra, several isoflavonoids were identified. In order to verify the proposed structures, 11 isoflavonoids were selectively isolated and unambiguously identified using 1&2D nuclear magnetic resonance techniques. Moreover, the isolated isoflavonoids were studied in HRMS/MS level, employing electrospray ionization and atmospheric pressure chemical ionization sources, in both modes. Useful information regarding their fragmentation patterns was obtained, and characteristic diagnostic ions were defined for the identification of methoxylated isoflavones, dihydroisoflavones and 5-hydroxylated isoflavonoids. Based on the current results, the proposed dereplication strategy was verified and could comprise a novel approach for the analysis of crude extracts in the future not only for isoflavonoids but also for other chemical classes of natural products.

Chemical dereplication of wine stilbenoids using high performance liquid chromatography-nuclear magnetic resonance spectroscopy

Wine is a major dietary source of numerous potentially health promoting stilbenoids that have been the subject of many qualitative and quantitative studies. However, our initial HPLC-MS analyses of crude wine samples demonstrated the presence of compounds with molecular weights matching characteristic stilbenoid dimers, trimers, and tetramers that were unaccounted for in the literature. Due to the likelihood that these are known compounds, a chemical dereplication method is highly desirable. We developed such a method using LC-DAD-MS monitored fractionation steps, using adsorption and centrifugal partition chromatography (CPC), to obtain fractions rich in stilbenoids for analysis in stopped-flow LC-NMR. (1)H NMR spectra and MS data were cross-referenced with our laboratory database and the literature for identification. This method yielded highly useful structural information, allowing the characterization of previously unidentified stilbenoids in wine, ampelopsin C, isohopeaphenol, quadrangularin A, and E-ω-viniferin. These results demonstrate the usefulness of stop-flow LC-NMR in conjunction with LC-MS guided fractionation for the dereplication of compounds of interest in general, and specifically for expanding the current knowledge of wine chemistry.

An inside to the Better Understanding of the Ethnobotanical Route to Drug Discovery- the Need of the Hour

For pharmaceuticals ranging from Digitalis to vincristine, the ethnobotanical approach to drug discovery has proven successful. The value of ethnobotanical information in drug development is based on several factors, which are discussed. Published ethnomedical information has many strengths and weaknesses relative to the ability to establish a corresponding biological effect in the laboratory. The ability to correlate ethnomedical reports with corresponding scientific studies could lead to improved selection of plants for further scientific studies. The application of NAPRALERT database in this regard is also discussed. An elaborate plant to drug pathway has been traced out for young researchers to make the drug discovery pathway more approachable. Various cautions related to possible errors during the ethnobotanical approach have also been highlighted.

Natural products from Brazilian biodiversity as a source of new models for medicinal chemistry

Natural products are the inspiration for many valuable therapeutic agents and attest to biodiversity being a rich source of new molecular structures. Their value as templates for medicinal chemistry remains undisputed, even after the growth of the combinatorial chemistry era. Tropical environments, such as Brazilian biomes, offer a particularly rich potential for biologically active compounds with unique structures and continue to contribute toward modern drug discovery. Our bioprospecting of plant species of the Cerrado and Atlantic Forest biomes has yielded promising bioactive secondary metabolites, and we describe some of these molecules and semisynthetic derivatives as potential acetylcholinesterase (AChE) inhibitors.

A historical overview of natural products in drug discovery

Historically, natural products have been used since ancient times and in folklore for the treatment of many diseases and illnesses. Classical natural product chemistry methodologies enabled a vast array of bioactive secondary metabolites from terrestrial and marine sources to be discovered. Many of these natural products have gone on to become current drug candidates. This brief review aims to highlight historically significant bioactive marine and terrestrial natural products, their use in folklore and dereplication techniques to rapidly facilitate their discovery. Furthermore a discussion of how natural product chemistry has resulted in the identification of many drug candidates; the application of advanced hyphenated spectroscopic techniques to aid in their discovery, the future of natural product chemistry and finally adopting metabolomic profiling and dereplication approaches for the comprehensive study of natural product extracts will be discussed.

NMR in metabolomics and natural products research: two sides of the same coin

Small molecules are central to biology, mediating critical phenomena such as metabolism, signal transduction, mating attraction, and chemical defense. The traditional categories that define small molecules, such as metabolite, secondary metabolite, pheromone, hormone, and so forth, often overlap, and a single compound can appear under more than one functional heading. Therefore, we favor a unifying term, biogenic small molecules (BSMs), to describe any small molecule from a biological source.

In a similar vein, two major fields of chemical research,natural products chemistry and metabolomics, have as their goal the identification of BSMs, either as a purified active compound (natural products chemistry) or as a biomarker of a particular biological state (metabolomics). Natural products chemistry has a long tradition of sophisticated techniques that allow identification of complex BSMs, but it often fails when dealing with complex mixtures. Metabolomics thrives with mixtures and uses the power of statistical analysis to isolate the proverbial “needle from a haystack”, but it is often limited in the identification of active BSMs. We argue that the two fields of natural products chemistry and metabolomics have largely overlapping objectives: the identification of structures and functions of BSMs, which in nature almost inevitably occur as complex mixtures.

Nuclear magnetic resonance (NMR) spectroscopy is a central analytical technique common to most areas of BSM research. In this Account, we highlight several different NMR approaches to mixture analysis that illustrate the commonalities between traditional natural products chemistry and metabolomics. The primary focus here is two-dimensional (2D) NMR; because of space limitations, we do not discuss several other important techniques, including hyphenated methods that combine NMR with mass spectrometry and chromatography.

We first describe the simplest approach of analyzing 2D NMR spectra of unfractionated mixtures to identify BSMs that are unstable to chemical isolation. We then show how the statistical method of covariance can be used to enhance the resolution of 2D NMR spectra and facilitate the semi-automated identification of individual components in a complex mixture. Comparative studies can be used with two or more samples, such as active vs inactive, diseased vs healthy, treated vs untreated, wild type vs mutant, and so on. We present two overall approaches to comparative studies: a simple but powerful method for comparing two 2D NMR spectra and a full statistical approach using multiple samples. The major bottleneck in all of these techniques is the rapid and reliable identification of unknown BSMs; the solution will require all the traditional approaches of both natural products chemistry and metabolomics as well as improved analytical methods, databases, and statistical tools.

Identification of new natural sweet compounds in wine using centrifugal partition chromatography-gustatometry and Fourier transform mass spectrometry

Sweetness contributes notably to the taste-balance of dry wines and increases during oak-barrel aging owing to the release of natural sweeteners from wood. The search for such taste-active molecules, which are sometimes present at very low concentrations in wine or other complex matrixes, requires both reliable purification tools and powerful identification techniques. Here, we report the development of an original inductive method using centrifugal partition chromatography (CPC) and sensorial analysis. This method, called CPC-gustatometry, was implemented to isolate a sweet fraction with only four compounds from a complex oak wood extract. The recently developed Fourier transform mass spectrometry (FT-MS, Orbitrap analyzer) was used jointly with two-dimensional nuclear magnetic resonance (2D (1)H and (13)C NMR) to obtain the structural elucidation of the purified compounds. The tandem mass spectrometry (MS/MS) spectra obtained with resonant and nonresonant fragmentation modes were compared, thus providing complementary information about the molecular structure. Two oleanane-type triterpenoids substituted with galloyl and glucosyl moieties were identified, one of which exhibits sweet properties. We term these compounds which have never been reported, Quercotriterpenoside I and II.

Application of different modes of thin-layer chromatography and mass spectrometry for the separation and detection of large and small biomolecules

Biomolecules are widespread throughout the world. A biomolecule is any organic molecule produced by a living organism, including large polymeric molecules such as proteins, polysaccharides and nucleic acids. Many sample preparation techniques are used in biomolecule analysis; the method selected depends on the complexity of the sample, the nature of the matrix and the analytes, and the analytical technique available. This review covers the current state of knowledge on thin-layer chromatography and mass spectrometry for qualitative analysis of biomolecules. In the first part of the paper the reader will gain useful information to avoid some problems about performing various modes of thin-layer chromatography combined with mass spectrometry experiments and in the second part he will find useful information for application of these techniques for separation, detection, and qualitative investigation of structures and quantitative determination of biomolecules such as proteins, peptides, oligonucleotides, amino acids, DNA, RNA, and lipids.

Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches

Monitoring molecular dynamics of an organism upon stress is probably the best approach to decipher physiological mechanisms involved in the stress response. Quantitative analysis of proteins and metabolites is able to provide accurate information about molecular changes allowing the establishment of a range of more or less specific mechanisms, leading to the identification of major players in the considered pathways. Such tools have been successfully used to analyze the plant response to cadmium (Cd), a major pollutant capable of causing severe health issues as it accumulates in the food chain. We present a summary of proteomics and metabolomics works that contributed to a better understanding of the molecular aspects involved in the plant response to Cd. This work allowed us to provide a finer picture of general signaling, regulatory and metabolic pathways that appeared to be affected upon Cd stress. In particular, we conclude on the advantage of employing different approaches of global proteome- and metabolome-wide techniques, combined with more targeted analysis to answer molecular questions and unravel biological networks. Finally, we propose possible directions and methodologies for future prospectives in this field, as many aspects of the plant-Cd interaction remain to be discovered.

On-line identification of 4''-isovalerylspiramycin I in the genetic engineered strain of S. spiramyceticus F21 by liquid chromatography with electrospray ionization tandem mass spectrometry, ultraviolet absorbance detection and nuclear magnetic resonance spectrometry

LC-hyphenated techniques were applied to the on-line identification of isovalerylspiramycin I (isp I), a spiramycin-like macrolide in the crude extract of fermentation broth from a genetically engineered strain of S. spiramyceticus F21. In the structural characterization of the large molecular secondary metabolite of isp I, LC-DAD-UV-ESI-MS(n) analysis played a crucial role, and stop-flow LC-(1)H NMR measurement, with bitespiramycin used as reference, was a valuable complement approach. This rational approach proved to be an efficient means for the rapid and accurate structural determination of known microbial secondary metabolites, by which targeted isolation of component(s) of interest can be subsequently performed for further biological and pharmacological studies in drug development.

Steroidal glycosides from the leaves of Ruscus colchicus: isolation and structural elucidation based on a preliminary liquid chromatography-electrospray ionization tandem mass spectrometry profiling

An HPLC-ESIMS(n) method, based on high-performance liquid chromatography coupled to electrospray positive ionisation multistage ion trap mass spectrometry, has been used as an effective tool to rapidly identify and guide the isolation of target saponins from the ethanol extract of the leaves of Ruscus colchicus Y. Yeo. Twenty-two steroidal glycosides, including seventeen furostanol, four spirostanol and one cholestane glycosides, were online identified. Subsequently, compounds were isolated and their structures were established by the extensive use of 1D- and 2D-NMR experiments. The structures identified by MS were fully consistent with those elucidated by NMR data. Sixteen steroidal glycosides, including thirteen furostanol, two spirostanol and one cholestane glycosides, were identified along with four known furostanol and two spirostanol glycosides. The saponin profile shows that the furostanol glycosides are the main constituents of R. colchicus extract, unlike the other Ruscus species, for which the spirostanol derivatives generally are reported as the major compounds. Moreover, for the first time a cholestane glycoside has been isolated from R. colchicus.

Natural products in drug discovery: present status and perspectives

Natural products and their derivatives have been and continue to be rich sources for drug discovery. However, natural products are not drugs. They are produce in nature and through biological assays they are identified as leads, which become candidates for drug development. More than 60% of the drugs that are in the market derive from natural sources. During the last two decades, research aimed at exploiting natural products as a resource has seriously declined. This is in part due to the development of new technologies such as combinatorial chemistry, metagenomics and high-throughput screening. However, the new drug discovery approaches did not fulfilled the initial expectations. This has lead to a renewed interest in natural products, determined by the urgent need for new drugs, in particular to fight against infections caused by multi-resistant pathogens.

Analysis of flavonoids: tandem mass spectrometry, computational methods, and NMR

Due to the increasing understanding of the health benefits and chemopreventive properties of flavonoids, there continues to be significant effort dedicated to improved analytical methods for characterizing the structures of flavonoids and monitoring their levels in fruits and vegetables, as well as developing new approaches for mapping the interactions of flavonoids with biological molecules. Tandem mass spectrometry (MS/MS), particularly in conjunction with liquid chromatography (LC), is the dominant technique that has been pursued for elucidation of flavonoids. Metal complexation strategies have proven to be especially promising for enhancing the ionization of flavonoids and yielding key diagnostic product ions for differentiation of isomers. Of particular value is the addition of a chromophoric ligand to allow the application of infrared (IR) multiphoton dissociation as an alternative to collision-induced dissociation (CID) for the differentiation of isomers. CID, including energy-resolved methods, and nuclear magnetic resonance (NMR) have also been utilized widely for structural characterization of numerous classes of flavonoids and development of structure/activity relationships.The gas-phase ion chemistry of flavonoids is an active area of research particularly when combined with accurate mass measurement for distinguishing between isobaric ions. Applications of a variety of ab initio and chemical computation methods to the study of flavonoids have been reported, and the results of computations of ion and molecular structures have been shown together with computations of atomic charges and ion fragmentation. Unambiguous ion structures are obtained rarely using MS alone. Thus, it is necessary to combine MS with spectroscopic techniques such as ultraviolet (UV) and NMR to achieve this objective. The application of NMR data to the mass spectrometric examination of flavonoids is discussed.

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.