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Introduction: Natural deep eutectic solvents (NADES) have emerged as interesting extractants to develop botanical ingredients. They are nontoxic and biodegradable, nonflammable, easy to prepare, and able to solubilize a wide range of molecules. However, NADES extracts remain difficult to analyze because the metabolites of interest stay highly diluted in the nonvolatile viscous NADES matrix., Objective: This study presents a robust analytical workflow for the chemical profiling of NADES extracts. It is applied to Hypericum perforatum aerial parts extracted with the neutral mixture fructose/glycerol/water (3/1/1, w/w/w), and compared to the chemical profiling of a classical dry methanol extract., Methods: Exploiting polarity differences between metabolites, the H. perforatum NADES extract was partitioned in a liquid-liquid solvent system to trap the hydrophilic NADES constituents in the lower phase. The upper phase, containing a diversity of secondary metabolites from H. perforatum, was fractionated by centrifugal partition chromatography. All fractions were chemically investigated using a 13 C NMR dereplication method which involves hierarchical clustering analysis of the whole NMR dataset, a natural metabolite database for metabolite identification, and 2D NMR analyses for validation. Liquid chromatography-mass spectrometry (LC-MS) analyses were also performed to complete the identification process., Results: A range of 21 metabolites were unambiguously identified, including glycosylated flavonols, lactones, catechins, phenolic acids, lipids, and simple sugars, and 15 additional minor extract constituents were annotated by LC-MS based on exact mass measurements., Conclusion: The proposed identification process is rapid and nondestructive and provides good prospects to deeply characterize botanical extracts obtained in nonvolatile and viscous NADES systems., (© 2023 John Wiley & Sons Ltd.)

Introduction: We developed Data Base similarity (DBsimilarity), a user-friendly tool designed to organize structure databases into similarity networks, with the goal of facilitating the visualization of information primarily for natural product chemists who may not have coding experience., Method: DBsimilarity, written in Jupyter Notebooks, converts Structure Data File (SDF) files into Comma-Separated Values (CSV) files, adds chemoinformatics data, constructs an MZMine custom database file and an NMRfilter candidate list of compounds for rapid dereplication of MS and 2D NMR data, calculates similarities between compounds, and constructs CSV files formatted into similarity networks for Cytoscape., Results: The Lotus database was used as a source for Ginkgo biloba compounds, and DBsimilarity was used to create similarity networks including NPClassifier classification to indicate biosynthesis pathways. Subsequently, a database of validated antibiotics from natural products was combined with the G. biloba compounds to identify promising compounds. The presence of 11 compounds in both datasets points to possible antibiotic properties of G. biloba, and 122 compounds similar to these known antibiotics were highlighted. Next, DBsimilarity was used to filter the NPAtlas database (selecting only those with MIBiG reference) to identify potential antibacterial compounds using the ChEMBL database as a reference. It was possible to promptly identify five compounds found in both databases and 167 others worthy of further investigation., Conclusion: Chemical and biological properties are determined by molecular structures. DBsimilarity enables the creation of interactive similarity networks using Cytoscape. It is also in line with a recent review that highlights poor biological plausibility and unrealistic chromatographic behaviors as significant sources of errors in compound identification., (© 2023 John Wiley & Sons Ltd.)

Introduction: This study describes the molecular profile and the potential antiviral activity of extracts from Phyllanthus brasiliensis, a plant widely found in the Brazilian Amazon. The research aims to shed light on the potential use of this species as a natural antiviral agent., Methods: The extracts were analysed using liquid chromatography-mass spectrometry (LC-MS) system, a potent analytical technique to discover drug candidates. In the meantime, in vitro antiviral assays were performed against Mayaro, Oropouche, Chikungunya, and Zika viruses. In addition, the antiviral activity of annotated compounds was predicted by in silico methods., Results: Overall, 44 compounds were annotated in this study. The results revealed that P. brasiliensis has a high content of fatty acids, flavones, flavan-3-ols, and lignans. Furthermore, in vitro assays revealed potent antiviral activity against different arboviruses, especially lignan-rich extracts against Zika virus (ZIKV), as follows: methanolic extract from bark (MEB) [effective concentration for 50% of the cells (EC 50 ) = 0.80 μg/mL, selectivity index (SI) = 377.59], methanolic extract from the leaf (MEL) (EC 50  = 0.84 μg/mL, SI = 297.62), and hydroalcoholic extract from the leaf (HEL) (EC 50  = 1.36 μg/mL, SI = 735.29). These results were supported by interesting in silico prediction, where tuberculatin (a lignan) showed a high antiviral activity score., Conclusions: Phyllanthus brasiliensis extracts contain metabolites that could be a new kick-off point for the discovery of candidates for antiviral drug development, with lignans becoming a promising trend for further virology research., (© 2023 John Wiley & Sons Ltd.)

Introduction: Natural products and metabolomics are intrinsically linked through efforts to analyze complex mixtures for compound annotation. Although most studies that aim for compound identification in mixtures use MS as the main analysis technique, NMR has complementary advances that are worth exploring for enhanced structural confidence., Objective: This review aimed to showcase a portfolio of the main tools available for compound identification using NMR., Materials and Methods: COLMAR, SMART-NMR, MADByTE, and NMRfilter are presented using examples collected from real samples from the perspective of a natural product chemist. Data are also made available through Zenodo so that readers can test each case presented here., Conclusion: The acquisition of 1 H NMR, HSQC, TOCSY, HSQC-TOCSY, and HMBC data for all samples and fractions from a natural products study is strongly suggested. The same is valid for MS analysis to create a bridged analysis between both techniques in a complementary manner. The use of NOAH supersequences has also been suggested and demonstrated to save NMR time., (© 2023 John Wiley & Sons Ltd.)

Introduction: In this era of 'omics' technology in natural products studies, the complementary aspects of mass spectrometry (MS)- and nuclear magnetic resonance (NMR)-based techniques must be taken into consideration. The advantages of using both analytical platforms are reflected in a higher confidence of results especially when using replicated samples where correlation approaches can be used to statistically link results from MS to NMR., Objectives: Demonstrate the use of Statistical Total Correlation (STOCSY) for linking results from MS and NMR data to reach higher confidence in compound identification., Methodology: Essential oil samples of Melaleuca alternifolia and M. rhaphiophylla (Myrtaceae) were used as test objects. Aliquots of 10 samples were collected for GC-MS and NMR data acquisition [proton ( 1 H)-NMR, and carbon-13 ( 13 C)-NMR as well as two-dimensional (2D) heteronuclear single quantum correlation (HSQC), heteronuclear multiple-bond correlation (HMBC), and HSQC-total correlated spectroscopy (TOCSY) NMR]. The processed data was imported to Matlab where STOCSY was applied., Results: STOCSY calculations led to the confirmation of the four main constituents of the sample-set. The identification of each was accomplished using; MS spectra, retention time comparison, 13 C-NMR data, and scalar correlations of the 2D NMR spectra., Conclusion: This study provides a pipeline for high confidence in compound identification using a set of essential oils samples as test objects for demonstration., (© 2022 John Wiley & Sons, Ltd.)

Introduction: Xanthones are metabolites with a variety of biological properties. The Clusiaceae family, which until recently included the genus Calophyllum, is recognised for its production of monohydroxylated and polyhydroxylated xanthones. Presently, C. brasiliense is the only Calophyllum spp. known to occur in the Yucatan peninsula., Objective: To use a combination of traditional phytochemical methods and carbon-13 nuclear magnetic resonance ( 13 C-NMR) dereplication analysis to identify xanthones in the stem bark of C. brasiliense., Material and Methods: Initial fractionation and purification of the stem bark extract of C. brasiliense produced macluraxanthone (1). Additional xanthones, together with chromanones and terpenoids, were identified using 13 C-NMR dereplication analysis in different semipurified fractions obtained from the low and medium polarity fractions of the stem bark extract of C. brasiliense., Results: Initial identification of macluraxanthone (1) was confirmed by 13 C-NMR dereplication analysis; additionally, 13 C-NMR dereplication analysis allowed the identification of a number of monohydroxylated and polyhydroxylated xanthones, together with chromanones and terpenoids., Conclusion: This study confirms C. brasiliense as a rich source of xanthones and the 13 C-NMR dereplication analysis as a suitable method to quickly identify the presence of different families of secondary metabolites in semipurified fractions., (© 2021 John Wiley & Sons, Ltd.)

Introduction: Given the diversity of secondary metabolites produced by species of the genus Erythroxylum, in addition to the many methods that have already been described in the literature, modern screening and identification methodologies, such as dereplication, represent an efficient and quick strategy compared to the classic techniques linked to natural product research., Objective: The objective of the present study was to determine the phenolic profiles obtained from three species of Erythroxylum (Erythroxylum pauferrense Plowman, Erythroxylum pulchrum A.St.-Hil. and Erythroxylum simonis Plowman) by dereplication using liquid chromatography coupled with ESI-MS n and HRESIMS., Material and Methods: Ethyl acetate and n-butanolic fractions from crude ethanolic extract of Erythroxylum species were analyzed by HPLC-ESI-MS n and HPLC-HRESIMS, in order to identify its corresponding compounds. Experiments were performed in negative ionization mode, and the metabolites were provisionally identified based on deprotonated molecules, molecular formulas, fragmentation patterns and literature data. The corresponding isolated compounds were characterized by 1 H and 13 C NMR spectroscopy., Results: According to the dereplication method, it was possible to establish and compare the phenolic profile of the corresponding species by the assignment of 55 compounds, most of which were first described in these species and among which some were also new to the Erytroxylum genus. Additionally, nine compounds were isolated, including biphenyl-3,3',4,4'-tetraol, where the mass spectral data were not sufficient for their identification, and reported for the first time in the Erythroxylaceae family., Conclusion: This research contributes to the phytochemical knowledge of the Erythroxylum genus and demonstrates the importance of the dereplication method regarding the investigation of natural products, enabling accurate identification of the metabolites while avoiding the efforts and material expenses involved in the isolation of known compounds., (© 2021 John Wiley & Sons, Ltd.)

Introduction: Casearia is an essential source of cytotoxic highly oxidised clerodane diterpenes, in addition to phenolics, flavonoids, and glycoside derivatives. Here we identify flavonoid-3-O-glycoside derivatives in the ethyl acetate (EtOAc) fraction of the methanolic extract from leaves C. arborea leaves., Objective: To characterise the EtOAc phase from the methanolic extract of C. arborea leaves using ultra-high-performance liquid chromatography diode array detector high-resolution tandem mass spectrometry (UHPLC-DAD-HRMS/MS) and molecular networking-based dereplication. Methodology We identified compounds not annotated in the GNPS platform by co-injection of standards in HPLC-DAD or by isolation and characterisation of the metabolites using nuclear magnetic resonance (NMR) spectroscopy. A workflow on the GNPS platform aided the organisation of spectral data and dereplication by annotations. We subjected the EtOAc phase to HPLC-DAD analysis using standard compound co-injection to corroborate the GNPS annotations. We isolated unidentified compounds with semi-preparative HPLC-DAD for structural identification using NMR., Results: We annotated a molecular family of flavonoid-3-O-glycosides in the molecular networking created using the GNPS platform. These included avicularin, cacticin, isoquercitrin, quercitrin, rutin, and a quercetin-3-O-pentoside cluster. We confirmed the annotations with standard compounds using HPLC-DAD co-injection analysis, besides identifying quercetin-3-O-robinobioside and kaempferol. We isolated three flavonoid-3-O-pentosides and characterised them using one- and two-dimensional NMR; we identified them as reynoutrin, guaijaverin, and avicularin., Conclusion: This work describes the isolation of kaempferol and nine known flavonoid-3-O-glycosides from the polar fraction of the methanolic extract (EtOAc) from C. arborea leaves using molecular networking to guide the chromatographic procedures. We identified eight compounds for the first time in Casearia that amplify and reinforce the genus' chemotaxonomy with the presence of glycosylated flavonoids., (© 2021 John Wiley & Sons, Ltd.)

Introduction: Plants have been considered a promising source for discovering new compounds with pharmacological activities. The Fabaceae family comprises a large variety of species that produce substances with diverse therapeutic potential, including anti-inflammatory activity. The limitations of current anti-inflammatories generate the need to research new anti-inflammatory structures with higher efficacy as well as develop methods for screening multiple samples, reliably and ethically, to assess such therapeutic properties., Objective: Validate and apply a quantification method for prostaglandin E 2 (PGE 2 ) production from an ex vivo assay in human blood in order to screen anti-inflammatory activity present in many Fabaceae species extracts., Methods: Human blood was incubated with extracts from 47 Fabaceae species. After lipopolysaccharide (LPS)-induced inflammation, PGE 2 was quantified in the plasma by liquid chromatography with tandem mass spectrometry (LC-MS/MS). The extracts that presented PGE 2 production inhibition were further assessed through in vivo assay and then chemically characterised through an analysis of ultra-performance liquid chromatography electrospray ionisation quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-QTOF-MS 2 ) data., Results: The new ex vivo anti-inflammatory assay showed that five out of the 47 Fabaceae species inhibited PGE 2 production. Results from an in vivo assay and the metabolic profile of the active extracts supported the anti-inflammatory potential of four species., Conclusion: The quantification method for PGE 2 demonstrated fast, sensitive, precise, and accurate results. The new ex vivo anti-inflammatory assay comprised a great, reliable, and ethical approach for the screening of a large number of samples before an in vivo bioassay. Additionally, the four active extracts in both ex vivo and in vivo assays may be useful for the development of more efficient anti-inflammatory drugs., (© 2021 John Wiley & Sons, Ltd.)

Introduction: Hyptis verticillata Jacq. (Lamiaceae) is a Mexican medicinal plant for the treatment of skin infections and illness affecting the respiratory and gastrointestinal systems., Objective: To associate the efficient resolution provided by ultra-high-performance liquid chromatography combined to the accuracy of a hybrid Fourier-transform (FT) mass spectrometer in order to dereplicate podophyllotoxin-type lignans in a plant extract., Methods: An ultra-high-performance liquid chromatography-photodiode array-high resolution electrospray ionisation tandem mass spectrometry (UHPLC-PDA-HRESI-MS/MS) method was applied in an Orbitrap hybrid FT spectrometer for dereplication of podophyllotoxin and related cytotoxic lignans in wild bushmint. This procedure included high-resolution mass values for positively charged ions [M + H] + and [M + NH 4 ] + , MS/MS data, and comparison of UV maxima and retention times with pure compounds., Results: Podophyllotoxin in addition to seven aryltetralins, four arylnaphthalenes, and one dibenzylbutyrolactone were dereplicated from the methanol extract in a short-time analysis (5 min). 4'-O-Demethyl-dehydro-deoxypodophyllotoxin was identified as a new natural product., Conclusion: The applied UHPLC-MS/MS dereplication method is suitable for a rapid analysis of podophyllotoxin-type lignans and the resulting chemical fingerprinting could be valuable in quality control of herbal drugs and their phytopharmaceuticals., (© 2019 John Wiley & Sons, Ltd.)

Introduction: Thin layer chromatography (TLC) is frequently used to obtain the fingerprint of a plant extract. Although the retardation factor and the response to visualisation give primary information about compound identification, the direct TLC-mass spectrometry (MS) coupling allows a more detailed characterisation of samples., Objectives: To demonstrate the potential for the flavonoid dereplication using an inorganic matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) method with and without TLC separation., Material and Methods: Samples derived from wine, apple or rose were deposited on an aluminium-backed silica gel TLC sheet compatible with the MS adapter. Unlike the wine sample, for apple and rose samples compound derivatisation was necessary. These two samples were deposited twice and the plate was cut in two parts. One half was oversprayed with Neu-Peg reagent to visualise flavonoids while the inorganic matrix was deposited on each flavonoid zone on the second half for MS ionisation., Results: Mass spectra obtained for samples without plate development showed numerous ions corresponding to glycosylated flavonoids. The lower m/z observed could be due either to aglycone flavonoids or to in-source fragment ions. After plate development, a separation of many spots was observed and each spot was analysed separately leading to a deeper identification of the present flavonoids. Moreover, isobaric flavonoids with different hRf values could be differentiated., Conclusion: TLC-MALDI-TOF-MS using an inorganic matrix enabled the analysis of anthocyanins in positive mode and of flavonols, flavanols, dihydrochalcones and phenolic acids in negative mode, reducing adduct, aggregate forms giving thus simple and reliable spectra for the dereplication approach of flavonoids in complex samples., (© 2018 John Wiley & Sons, Ltd.)

Introduction: Molecular networks are now established as the method of choice for tandem mass spectrometry dereplication and similarity-based structure elucidation. Node identification can be used to start the propagation of the structure elucidation of unknown compounds progressively., Objective: To demonstrate the capabilities of using the LipidXplorer data results along with molecular networking to identify nodes and aid sequential structure elucidation of unknown compounds., Material and Methods: Molecular fragmentation query language (MFQL) files were written to identify glycoalkaloids based on known structures described for Solanum species. A dataset generated from liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis of Solanum pseudoquina sample were submitted to dereplication on both LipidXplorer software and Global Natural Products Social Molecular Network (GNPS) online system. The resulting attribute table from GNPS calculations was merged with the LipidXplorer results and this merged file was used for network visualisation in Cytoscape. Nodes in the molecular network were labelled using the LipidXplorer identifiers, thus assisting the structure elucidation of unidentified compounds., Results: The combination of the LipidXplorer glycoalkaloids list and GNPS analysis was used in Cytoscape to label nodes in the molecular network. The analysis of the network using these labelled starting points triggered the structure elucidation of closely related nodes leading to the identification of 30 compounds using the LipidXplorer output and four purified and structure elucidated compounds, including a new glycoalkaloids identified as 3-O-(β-d-xylopyranosyl)-(20R,25S)-22,26-epimino-16-acetyl-cholesta-5,22(N)-diene., Conclusion: A significant compound identification completely based on molecular formula and fragmentation queries was achieved. This new and effective approach could help researches to expand the identification rate of compounds in dereplication studies using molecular networks., (© 2018 John Wiley & Sons, Ltd.)

Introduction: Dereplication, an approach to sidestep the efforts involved in the isolation of known compounds, is generally accepted as being the first stage of novel discoveries in natural product research. It is based on metabolite profiling analysis of complex natural extracts., Objective: To present the application of LipidXplorer for automatic targeted dereplication of phenolics in plant crude extracts based on direct infusion high-resolution tandem mass spectrometry data., Material and Methods: LipidXplorer uses a user-defined molecular fragmentation query language (MFQL) to search for specific characteristic fragmentation patterns in large data sets and highlight the corresponding metabolites. To this end, MFQL files were written to dereplicate common phenolics occurring in plant extracts. Complementary MFQL files were used for validation purposes., Results: New MFQL files with molecular formula restrictions for common classes of phenolic natural products were generated for the metabolite profiling of different representative crude plant extracts. This method was evaluated against an open-source software for mass-spectrometry data processing (MZMine®) and against manual annotation based on published data., Conclusion: The targeted LipidXplorer method implemented using common phenolic fragmentation patterns, was found to be able to annotate more phenolics than MZMine® that is based on automated queries on the available databases. Additionally, screening for ascarosides, natural products with unrelated structures to plant phenolics collected from the nematode Caenorhabditis elegans, demonstrated the specificity of this method by cross-testing both groups of chemicals in both plants and nematodes., (Copyright © 2018 John Wiley & Sons, Ltd.)

Introduction: Byrsonima species have been used in the treatment of gastrointestinal and gynecological inflammations, skin infections and snakebites. Based on their biological activities, it is important to study other organisms from this genus and to identify their metabolites., Objectives: To determine the metabolic fingerprinting of methanol and ethyl acetate extracts of four Byrsonima species (B. intermedia, B. coccolobifolia, B. verbascifolia and B. sericea) by HPLC-DAD-ESI-MS/MS and evaluate their in vitro antioxidant, anti-glycation, anti-inflammatory and cytotoxic activities., Materials and Methods: Antioxidant activity was determined by DPPH˙, ABTS˙ + and ROO˙ scavenging assays. Anti-glycation activity was evaluated by the ability to inhibit the formation of advanced glycation endproducts (AGEs). Anti-inflammatory activity was evaluated using a murine macrophage cell line (RAW 264-7) in the presence of lipopolysaccharide (LPS). Tumour necrosis factor alpha (TNF-α) and nitrite (NO 2 - ) production were measured by ELISA and the Griess reaction, respectively. The compounds present in the extracts were tentatively identified by HPLC-DAD-ESI-MS/MS., Results: The evaluation of the biological activities showed the potential of the extracts. The activities were assigned to the presence of glycoside flavonoids mainly derived from quercetin, quinic acid derivatives, gallic acid derivatives, galloylquinic acids and proanthocyanidins. Two isomers of sinapic acid-O-hexoside were described for the first time in a Byrsonima species., Conclusion: This research contributes to the study of the genus, it is the first report of the chemical composition of B. sericea and demonstrates the importance of the dereplication process, allowing the identification of known compounds without time-consuming procedures. Copyright © 2017 John Wiley & Sons, Ltd., (Copyright © 2017 John Wiley & Sons, Ltd.)