13C-NMR dereplication of Garcinia extracts: Predicted chemical shifts as reliable databases

Bruguière, Antoine; Derbré, Séverine; Coste, Chloé; Bot, Maxime Le; Siegler, Benjamin; Leong, Sow Tein; Sulaiman, Syazreen Nadia; Awang, Khalijah; Richomme, Pascal

doi:10.1016/j.fitote.2018.10.003

Cited by 20 publications

(29 citation statements)

References 24 publications

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“…However, such comprehensive DBs, already shaped to be used with MixONat, are not yet available although researchers usually keep spectral data including δ C in their laboratories and share them through academic publishing. Thus, even if the task is tedious, for given botanical genera or families of interest, using dedicated software or even a simple free text editor (Chart 1), small DBs of NPs associated with their δ C may be manually built [9,10] and ultimately easily shared with the scientific community [21]. As far as volatile compounds from EOs are concerned, such an approach was initiated years ago [22].…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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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 userʼs 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.

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Section: Resultsmentioning

confidence: 99%

“…Using Lamiaceae DB2 (952 NPs | ACD NMR predictors [C, H]), δ C obtained with a high threshold value and a tolerance kept at 1.3 ppm [10,11], 8 monoterpenes reached a perfect score.…”

Section: Chartmentioning

confidence: 99%

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

et al. 2021

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“…The DCM bark extract of Garcinia bancana was prone to contain PPAPs with the selected chemical scaffold as major compounds. After fractionation, a dereplication based on 13 C-NMR experiments confirmed the presence of isomers of garcinol (4), i.e., xanthochymol (2) and guttiferone F (3) as well as derivatives [30,31]. 2 and 3 share very similar structures and were first obtained as a mixture called GX.…”

Section: Phytochemical Analysismentioning

confidence: 97%

Targeting MHC Regulation Using Polycyclic Polyprenylated Acylphloroglucinols Isolated from Garcinia bancana

et al. 2020

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Modulation of major histocompatibility complex (MHC) expression using drugs has been proposed to control immunity. Phytochemical investigations on Garcinia species have allowed the isolation of bioactive compounds such as polycyclic polyprenylated acylphloroglucinols (PPAPs). PPAPs such as guttiferone J (1), display anti-inflammatory and immunoregulatory activities while garcinol (4) is a histone acetyltransferases (HAT) p300 inhibitor. This study reports on the isolation, identification and biological characterization of two other PPAPs, i.e., xanthochymol (2) and guttiferone F (3) from Garcinia bancana, sharing structural analogy with guttiferone J (1) and garcinol (4). We show that PPAPs 1–4 efficiently downregulated the expression of several MHC molecules (HLA-class I, -class II, MICA/B and HLA-E) at the surface of human primary endothelial cells upon inflammation. Mechanistically, PPAPs 1–4 reduce MHC proteins by decreasing the expression and phosphorylation of the transcription factor STAT1 involved in MHC upregulation mediated by IFN-γ. Loss of STAT1 activity results from inhibition of HAT CBP/p300 activity reflected by a hypoacetylation state. The binding interactions to p300 were confirmed through molecular docking. Loss of STAT1 impairs the expression of CIITA and GATA2 but also TAP1 and Tapasin required for peptide loading and transport of MHC. Overall, we identified new PPAPs issued from Garcinia bancana with potential immunoregulatory properties.

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“…A workaround to the lack of experimental spectroscopic data can be found, more or less accurately depending on the analytical technique, by means of computerized prediction tools. Dereplication of NPs based on 13 C-NMR predicted data has been reported and discussed [21,22]. Such predictions may be carried out by various software, including proprietary or free methods, available on local computers or through web interfaces, with possible automated use or not, and with performances that can be difficult to evaluate.…”

Section: Spectroscopymentioning

confidence: 99%

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

et al. 2021

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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.

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13C-NMR dereplication of Garcinia extracts: Predicted chemical shifts as reliable databases

Cited by 20 publications

References 24 publications

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

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

Targeting MHC Regulation Using Polycyclic Polyprenylated Acylphloroglucinols Isolated from Garcinia bancana

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

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