13C NMR Dereplication Using MixONat Software: A Practical Guide to Decipher Natural Products Mixtures.

The growing use of herbal medicines worldwide requires ensuring their quality, safety, and efficiency to consumers and patients. Quality controls of vegetal extracts are usually undertaken according to pharmacopeial monographs. Analyses may range from simple chemical experiments to more sophisticated but more accurate methods. Nowadays, metabolomic analyses allow a fast characterization of complex mixtures. In the field, besides mass spectrometry (MS), nuclear magnetic resonance spectroscopy (NMR) has gained importance in the direct identification of natural products in complex herbal extracts. For a decade, automated dereplication processes based on 13C-NMR have been emerging to efficiently identify known major compounds in mixtures. Though less sensitive than MS, 13C-NMR has the advantage of being appropriate to discriminate stereoisomers. Since NMR spectrometers nowadays provide useful datasets in a reasonable time frame, we have recently made available MixONat, a software that processes 13C as well as distortionless enhancement by polarization transfer (DEPT)-135 and -90 data, allowing carbon multiplicity (i.e., CH3, CH2, CH, and C) filtering as a critical step. MixONat requires experimental or predicted chemical shifts (δ C) databases and displays interactive results that can be refined based on the user's phytochemical knowledge. The present article provides step-by-step instructions to use MixONat starting from database creation with freely available and/or marketed δ C datasets. Then, for training purposes, the reader is led through a 30 - 60 min procedure consisting of the 13C-NMR based dereplication of a peppermint essential oil.

The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case.

The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from Urceolina peruviana, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources.

Dereplication of Natural Extracts Diluted in Glycerin: Physical Suppression of Glycerin by Centrifugal Partition Chromatography Combined with Presaturation of Solvent Signals in 13C-Nuclear Magnetic Resonance Spectroscopy.

For scientific, regulatory, and safety reasons, the chemical profile knowledge of natural extracts incorporated in commercial cosmetic formulations is of primary importance. Many extracts are produced or stabilized in glycerin, a practice which hampers their characterization. This article proposes a new methodology for the quick identification of metabolites present in natural extracts when diluted in glycerin. As an extension of a 13C nuclear magnetic resonance (NMR) based dereplication process, two complementary approaches are presented for the chemical profiling of natural extracts diluted in glycerin: A physical suppression by centrifugal partition chromatography (CPC) with the appropriate biphasic solvent system EtOAc/CH3CN/water 3:3:4 (v/v/v) for the crude extract fractionation, and a spectroscopic suppression by presaturation of 13C-NMR signals of glycerin applied to glycerin containing fractions. This innovative workflow was applied to a model mixture containing 23 natural metabolites. Dereplication by 13C-NMR was applied either on the dry model mixture or after dilution at 5% in glycerin, for comparison, resulting in the detection of 20 out of 23 compounds in the two model mixtures. Subsequently, a natural extract of Cedrus atlantica diluted in glycerin was characterized and resulted in the identification of 12 metabolites. The first annotations by 13C-NMR were confirmed by two-dimensional NMR and completed by LC-MS analyses for the annotation of five additional minor compounds. These results demonstrate that the application of physical suppression by CPC and presaturation of 13C-NMR solvent signals highly facilitates the quick chemical profiling of natural extracts diluted in glycerin.

Investigation of the glucosinolates in Hesperis matronalis L. and Hesperis laciniata All.: Unveiling 4'-O-ß-d-apiofuranosylglucomatronalin.

The glucosinolate (GSL) profiles of wild-growing plants from the genus Hesperis, i.e. Hesperis laciniata All. (leaf, stem, flower, and root) from Croatia and Hesperis matronalis L. (leaf, stem, flower, seed, and root) from Canada, were established by LC-MS. During this investigation, 5-(methylsulfanyl)pentyl- (3), 6-(methylsulfanyl)hexyl- (4), 6-(methylsulfinyl)hexyl- (6), and 4'-α-l-rhamnopyranosyloxybenzyl- (17) GSLs were identified. In addition, the presence of 7-(methylsulfinyl)heptyl GSL (18), hydroxy-(α-l-rhamnopyranosyloxy)benzyl GSL, and of one d-apiosylated analogue of 17 were suggested. Moreover, one new GSL, 4'-O-ß-d-apiofuranosylglucomatronalin (19) was isolated from H. laciniata (flower, steam and leaf) and characterized by spectroscopic data interpretation. Finally, we report the presence of 3, 4, 6, 19, glucosinalbin (12), and 4-hydroxyglucobrassicin (20) in H. matronalis and hypothesize the presence of glucomatronalin (13) and 3-hydroxy-6-(methylsulfanyl)hexyl GSL (21).

Bioactive metabolites from the leaves of Withania adpressa.

CONTEXT: Withania (Solanaceae) species are known to be a rich source of withanolides, which have shown several biological properties. OBJECTIVE: To identify the compounds responsible for Withania adpressa Coss. antioxidant activity and further test them for their NF-κB inhibition and antiproliferative activity in multiple myeloma cells. MATERIALS AND METHODS: Compounds were obtained from the EtOAc extract of W. adpressa leaves. Structure elucidation was carried out mainly by 1D- and 2D-NMR, and mass spectrometry. Isolated compounds were tested in a dose-response for their in vitro NF-κB inhibition and antiproliferative activity in multiple myeloma cells after 5 and 72 h treatment, respectively. RESULTS: The fractionation resulted in the isolation of a new glycowithanolide named wadpressine (5) together with withanolide F, withaferin A, coagulin L, and nicotiflorin. The latter showed a moderate ability to scavenge free radicals in DPPH (IC50 = 35.3 µM) and NO (IC50 = 41.3 µM) assays. Withanolide F and withaferin A exhibited low µM antiproliferative activity against both multiple myeloma cancer stem cells and RPMI 8226 cells. Furthermore, they inhibited NF-κB activity with IC50 values of 1.2 and 0.047 µM, respectively. The other compounds showed a moderate inhibition of cell proliferation in RPMI 8226 cells, but were inactive against cancer stem cells and did not inhibit NF-κB activity. DISCUSSION AND CONCLUSIONS: One new glycowithanolide and four known compounds were isolated. Biological evaluation data gave further insight on the antitumor potential of withanolides for refractory cancers.

Two new bis-iridoids isolated from Scabiosa stellata and their antibacterial, antioxidant, anti-tyrosinase and cytotoxic activities.

This study presents the chemical profile investigation of a 70% ethanol extract obtained from Scabiosa stellata, a medicinal herbaceous traditionally used to treat heel cracks. A 13C NMR-based dereplication methodology was firstly applied on centrifugal partition chromatography-generated fractions in order to quickly identify the major compounds of the extract. The dereplication process was then completed by semi-preparative high-performance liquid chromatography in order to identify unknown or minor compounds. Two new bis-iridoids, namely 7-O-caffeoyl-sylvestroside I (1) and 7-O-(p-coumaroyl)-sylvestroside I (2), together with ten known compounds (3-12) were isolated. Their structures were elucidated by spectroscopic methods including NMR and HR-ESI-MS. The antibacterial, anti-tyrosinase and DPPH radical scavenging activities of the crude extract, fractions, and isolated compounds were evaluated. A significant antibacterial activity was observed for nine isolated compounds, particularly 1 and 2 which yielded MIC values of 31.2µg/mL against Enterococcus faecalis and 62.5µg/mL against Staphylococcus epidermidis. The cytotoxic activity of these new bis-iridoids was evaluated on a fibrosarcoma cell line (HT1080) and only compound 1 exhibited a moderate cytotoxic activity (IC50 35.9µg/mL).

Computer-Aided 13C NMR Chemical Profiling of Crude Natural Extracts without Fractionation.

A computer-aided, 13C NMR-based dereplication method is presented for the chemical profiling of natural extracts without any fractionation. An algorithm was developed in order to compare the 13C NMR chemical shifts obtained from a single routine spectrum with a set of predicted NMR data stored in a natural metabolite database. The algorithm evaluates the quality of the matching between experimental and predicted data by calculating a score function and returns the list of metabolites that are most likely to be present in the studied extract. The proof of principle of the method is demonstrated on a crude alkaloid extract obtained from the leaves of Peumus boldus, resulting in the identification of eight alkaloids, including isocorydine, rogersine, boldine, reticuline, coclaurine, laurotetanine, N-methylcoclaurine, and norisocorydine, as well as three monoterpenes, namely, p-cymene, eucalyptol, and α-terpinene. The results were compared to those obtained with other methods, either involving a fractionation step before the chemical profiling process or using mass spectrometry detection in the infusion mode or coupled to gas chromatography.

Computer-aided Dereplication and Structure Elucidation of Natural Products at the University of Reims.

Natural product chemistry began in Reims, France, in a pharmacognosy research laboratory whose main emphasis was the isolation and identification of bioactive molecules, following the guidelines of chemotaxonomy. The structure elucidation of new compounds of steadily increasing complexity favored the emergence of methodological work in nuclear magnetic resonance. As a result, our group was the first to report the use of proton-detected heteronuclear chemical shift correlation spectra for the computer-assisted structure elucidation of small organic molecules driven by atom proximity relationships and without relying on databases. The early detection of known compounds appeared as a necessity in order to deal more efficiently with complex plant extracts. This goal was reached by an original combination of mixture fractionation by centrifugal partition chromatography, analysis by 13 C NMR, digital data reduction and alignment, hierarchical data clustering, and computer database search.

Bio-Guided Isolation of Methanol-Soluble Metabolites of Common Spruce (Picea abies) Bark by-Products and Investigation of Their Dermo-Cosmetic Properties.

Common spruce (Picea abies L.) is a fast-growing coniferous tree, widely used in several countries for the production of sawn wood, timber and pulp. During this industrial exploitation, large quantities of barks are generated as waste materials. The aim of this study was the bio-guided investigation and the effective recovery of methanol-soluble metabolites of common spruce bark for the development of new dermo-cosmetic agents. The active methanol extract was initially fractionated by Centrifugal Partition Chromatography (CPC) using a triphasic solvent system in a step-gradient elution mode. All resulting fractions were evaluated for their antibacterial activity, antioxidant activity and their capability to inhibit tyrosinase, elastase and collagenase activity. In parallel, the chemical composition of each fraction was established by combining a 13C-NMR dereplication approach and 2D-NMR analyses. As a result, fourteen secondary metabolites corresponding to stilbene, flavonoid and phenolic acid derivatives were directly identified in the CPC fractions. A high amount (0.93 g) of E-astringin was recovered from 3 g of crude extract in a single 125 min run. E-Astringin significantly induced the tyrosinase activity while E-piceid, taxifolin, and taxifolin-3'-O-glucopyranoside exhibited significant anti-tyrosinase activity. The above compounds showed important anti-collagenase and antimicrobial activities, thus providing new perspectives for potential applications as cosmetic ingredients.

In Vitro Dermo-Cosmetic Evaluation of Bark Extracts from Common Temperate Trees.

Wood residues produced from forestry activities represent an interesting source of biologically active, high value-added secondary metabolites. In this study, 30 extracts from 10 barks of deciduous and coniferous tree species were investigated for their potential dermo-cosmetic use. The extracts were obtained from Fagus sylvatica, Quercus robur, Alnus glutinosa, Prunus avium, Acer pseudoplatanus, Fraxinus excelsior, Populus robusta, Larix decidua, Picea abies, and Populus tremula after three successive solid/liquid extractions of the barks with n-heptane, methanol, and methanol/water. All extracts were evaluated for their radical scavenging capacity, for their elastase, collagenase, and tyrosinase inhibitory activities, as well as for their antibacterial activity against gram-positive Staphylococcus aureus. In parallel, the global metabolite profiles of all extracts were established by 1D and 2D NMR and related to their biological activity. The results showed that the methanol extracts of Q. robur, A. glutinosa, L. decidua, and P. abies barks exhibit particularly high activities on most bioassays, suggesting their promising use as active ingredients in the dermo-cosmetic industry.

Glucosinolate Diversity in Bretschneidera sinensis of Chinese Origin.

The glucosinolate (GL) profile in several plant parts (leaf, branch, bark, root, and fruit) of Bretschneidera sinensis from three geographical regions of the People's Republic of China was established for the first time by HPLC. During this investigation, benzyl GL (1), 4-hydroxybenzyl GL (2), 2-hydroxy-2-methylpropyl GL (3), and 4-methoxybenzyl GL (4) were identified. In addition, one new GL, 3-hydroxy-4-methoxybenzyl GL (5), was isolated in a minor amount from the fruit and characterized by spectroscopic data interpretation. Furthermore, traces of 4-hydroxy-3-methoxyphenylacetonitrile were detected by GC-MS analysis in the fruits, thus confirming the presence of the regioisomeric 4-hydroxy-3-methoxybenzyl GL (6). GLs 1-5 were also quantified for the first time by HPLC in the various plant organs.

Exploiting the Complementarity between Dereplication and Computer-Assisted Structure Elucidation for the Chemical Profiling of Natural Cosmetic Ingredients: Tephrosia purpurea as a Case Study.

The aqueous-ethanolic extract of Tephrosia purpurea seeds is currently exploited in the cosmetic industry as a natural ingredient of skin lotions. The aim of this study was to chemically characterize this ingredient by combining centrifugal partition extraction (CPE) as a fractionation tool with two complementary identification approaches involving dereplication and computer-assisted structure elucidation. Following two rapid fractionations of the crude extract (2 g), seven major compounds namely, caffeic acid, quercetin-3-O-rutinoside, ethyl galactoside, ciceritol, stachyose, saccharose, and citric acid, were unambiguously identified within the CPE-generated simplified mixtures by a recently developed (13)C NMR-based dereplication method. The structures of four additional compounds, patuletin-3-O-rutinoside, kaempferol-3-O-rutinoside, guaiacylglycerol 8-vanillic acid ether, and 2-methyl-2-glucopyranosyloxypropanoic acid, were automatically elucidated by using the Logic for Structure Determination program based on the interpretation of 2D NMR (HSQC, HMBC, and COSY) connectivity data. As more than 80% of the crude extract mass was characterized without need for tedious and labor-intensive multistep purification procedures, the identification tools involved in this work constitute a promising strategy for an efficient and time-saving chemical profiling of natural extracts.

Stepwise elution of a three-phase solvent system in centrifugal partition extraction: a new strategy for the fractionation and phytochemical screening of a crude bark extract.

INTRODUCTION: Tree bark represents an interesting source of bioactive molecules for the discovery of new pharmaceutical agents. However, the detailed screening of secondary metabolites in crude bark extracts is often hampered by the presence of tannins, which are difficult to separate from other plant constituents. OBJECTIVE: In the present study, a new centrifugal partition extraction (CPE) method was developed in order to fractionate a crude bark extract of Anogeissus leiocarpus Guill. & Perr. (Combretaceae). METHODS: A three-phase solvent system composed of n-heptane, methyl tert-butyl ether, acetonitrile and water was optimised for the stepwise elution at 20 mL/min of different phytochemical classes according to their hydrophobicity. Onedimensional and two-dimensional NMR analyses of the simplified fractions were then performed in order to characterise potentially interesting metabolites. RESULTS: In one step, 5 g of the initial crude extract were efficiently fractionated to yield highly simplified fractions that contained triterpenes, ellagic acid derivatives, flavonoids and phenolic compounds. All undesired compounds, that is, the highly abundant water-soluble tannins (78.8%), were totally removed and each run was rapidly achieved in 90 min on a the multi-gram scale and with low solvent volumes. CONCLUSION: Centrifugal partition extraction in the elution mode using a three-phase solvent system can thus be proposed as an efficient and cost-effective alternative for a rapid fractionation of crude bark extracts and for an effective screening of potentially active secondary metabolites.

Cembranolides from the stem bark of the southern African medicinal plant, Croton gratissimus (Euphorbiaceae).

The stem bark of Croton gratissimus (Euphorbiaceae) yielded four cembranolides, including the first reported example of a 2,12-cyclocembranolide, (+)-[1R*,2S*,7S*,8S*,12R*]-7,8-epoxy-2,12-cyclocembra-3E,10Z-dien-20,10-olide, whose structure was confirmed by means of single crystal X-ray analysis. This compound showed moderate activity against the PEO1 and PEO1TaxR ovarian cancer cell lines.

New improvements in automatic structure elucidation using the LSD (Logic for Structure Determination) and the SISTEMAT expert systems.

This article describes the integration of the LSD (Logic for Structure Determination) and SISTEMAT expert systems that were both designed for the computer-assisted structure elucidation of small organic molecules. A first step has been achieved towards the linking of the SISTEMAT database with the LSD structure generator. The skeletal descriptions found by the SISTEMAT programs are now easily transferred to LSD as substructural constraints. Examples of the synergy between these expert systems are given for recently reported natural products.

Strong ion-exchange centrifugal partition chromatography as an efficient method for the large-scale purification of glucosinolates.

The glucosinolates sinalbin and glucoraphanin were purified by strong ion-exchange displacement centrifugal partition chromatography (SIXCPC). The optimized conditions involved the biphasic solvent system ethyl acetate/n-butanol/water (3:2:5, v/v), the lipophilic anion-exchanger Aliquat 336 (trioctylmethylammonium chloride, 160 and 408 mM) and a sodium iodide solution (80 and 272 mM) as displacer. Amounts as high as 2.4 g of sinalbin and 2.6g of glucoraphanin were obtained in one step in 2.5 and 3.5h respectively, starting from 12 and 25 g of mustard and broccoli seed aqueous extracts, using a laboratory scale CPC column (200 mL inner volume).

Novel seco-dibenzopyrrocoline alkaloid from Cryptocarya oubatchensis.

[structure: see text] A novel seco-dibenzopyrrocoline alkaloid, named oubatchensine 6, and five phenanthroindolizidines (1-5) were isolated from Cryptocarya oubatchensis, and their structures were elucidated. Displacement centrifugal partition chromatography was used to purify compounds 1 and 6. Structure determination of the latter was carried out by mass spectrometry, NMR spectroscopy, quantum chemistry, and computer-assisted structure determination. Cytotoxic activity against KB cells was then investigated.

Chrysopentamine, an antiplasmodial anhydronium base from Strychnos usambarensis leaves.

A new derivative of strychnopentamine was isolated from the leaves of Strychnos usambarensis. This compound, named chrysopentamine, was identified by detailed spectroscopic methods (UV, IR, HR-ESI-MS, 1D and 2D NMR). Chrysopentamine presented an original hydroxy substitution on C-14 and an aromatization of the ring D of strychnopentamine leading to anhydronium base properties and exhibited strong antiplasmodial properties (IC (50) less than 1 microM).