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Herbert LA, Bruguière A, Derbré S, Richomme P, Peña-Rodríguez LM. 13C NMR dereplication-assisted isolation of bioactive polyphenolic metabolites from Clusia flava Jacq. Nat Prod Res 2024; 38:1089-1098. [PMID: 36214555 DOI: 10.1080/14786419.2022.2130917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 10/17/2022]
Abstract
Presently it is estimated that many of the approximately 4000 new natural products isolated every year following complicated, long, and expensive isolation processes are already known; because of this, developing new strategies for locating secondary metabolites of interest in complex extracts or fractions is important. Currently, chromatographic and spectroscopic techniques are being used to optimize the isolation and identification of natural products. In this investigation we have used 13C NMR dereplication analyses for the quick identification of a number of triterpenes (friedelin, lupeol, betulinic acid), sterols (euphol, β-sitosterol) and fatty acids (palmitic acid) present in semipurified fractions obtained from the stem bark extract of Clusia flava and to assist in the isolation of the bioactive metabolites trapezifolixanthone and paralycolin A. The complete and correct assignment of the 1H and 13C NMR spectroscopic data for paralycolin A is reported for the first time and the antioxidant and antiAGEs activity of both metabolites is described.
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Affiliation(s)
- Luis A Herbert
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, México
| | - Antoine Bruguière
- Department of Pharmacy, Faculty of Health Sciences, SONAS, EA921, UNIV Angers, SFR QUASAV, Angers, France
| | - Séverine Derbré
- Department of Pharmacy, Faculty of Health Sciences, SONAS, EA921, UNIV Angers, SFR QUASAV, Angers, France
| | - Pascal Richomme
- Department of Pharmacy, Faculty of Health Sciences, SONAS, EA921, UNIV Angers, SFR QUASAV, Angers, France
| | - Luis M Peña-Rodríguez
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, México
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2
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Leong ST, Liew SY, Khaw KY, Ahmad Hassali H, Richomme P, Derbré S, Lee VS, Yahya R, Awang K. 13C NMR-based dereplication using MixONat software to decipher potent anti-cholinesterase compounds in Mesua lepidota bark. Bioorg Chem 2023; 141:106859. [PMID: 37742494 DOI: 10.1016/j.bioorg.2023.106859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/26/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023]
Abstract
A bio-assay guided fractionation strategy based on cholinesterase assay combined with 13C NMR-based dereplication was used to identify active metabolites from the bark of Mesua lepidota. Eight compounds were identified with the aid of the 13C NMR-based dereplication software, MixONat, i.e., sitosterol (1), stigmasterol (2), α-amyrin (3), friedelin (6), 3β-friedelinol (7), betulinic acid (9), lepidotol A (10) and lepidotol B (11). Further bio-assay guided isolation of active compounds afforded one xanthone, pyranojacareubin (12) and six coumarins; lepidotol A (10), lepidotol B (11), lepidotol E (13), lepidotin A (14), and lepidotin B (15), including a new Mammea coumarin, lepidotin C (16). All the metabolites showed strong to moderate butyrylcholinesterase (BChE) inhibition. Lepidotin B (15) exhibited the most potent inhibition towards BChE with a mix-mode inhibition profile and a Ki value of 1.03 µM. Molecular docking and molecular dynamics simulations have revealed that lepidotin B (15) forms stable interactions with key residues within five critical regions of BChE. These regions encompass residues Asp70 and Tyr332, the acyl hydrophobic pocket marked by Leu286, the catalytic triad represented by Ser198 and His438, the oxyanion hole (OH) constituted by Gly116 and Gly117, and the choline binding site featuring Trp82. To gauge the binding strength of lepidotin B (15) and to pinpoint pivotal residues at the binding interface, free energy calculations were conducted using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) approach. This analysis not only predicted a favourable binding affinity for lepidotin B (15) but also facilitated the identification of significant residues crucial for the binding interaction.
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Affiliation(s)
- Sow Tein Leong
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sook Yee Liew
- Chemistry Division, Centre for Foundation Studies in Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Natural Products Research and Drug Discovery (CENAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kooi Yeong Khaw
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500 Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Hazlina Ahmad Hassali
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Medical Technology Division, Malaysian Nuclear Agency, 43000 Kajang, Selangor Darul Ehsan, Malaysia
| | | | | | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ruzanna Yahya
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Khalijah Awang
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Natural Products Research and Drug Discovery (CENAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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Herbert-Doctor LA, Sánchez-Recillas A, Ortiz-Andrade R, Hernández-Núñez E, Araujo-León JA, Coral-Martínez TI, Cob-Calan NN, Segura Campos MR, Estrada-Soto S. Vasorelaxant Activity of Salvia hispanica L.: Involvement of the Nitric Oxide Pathway in Its Pharmacological Mechanism. Molecules 2023; 28:6225. [PMID: 37687053 PMCID: PMC10488739 DOI: 10.3390/molecules28176225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Salvia hispanica L., commonly known as chía, and its seeds have been used since ancient times to prepare different beverages. Due to its nutritional content, it is considered a dietary ingredient and has been reported with many health benefits. Chia seed components are helpful in cardiovascular disease (CVD) by reducing blood pressure, platelet aggregation, cholesterol, and oxidation. Still, its vasodilator effects on the vascular system were not reported yet. The hexanic (HESh), dichloromethanic (DESh), and methanolic (MESh) extracts obtained from chía seeds were evaluated on an aortic ring ex-vivo experimental model. The vasorelaxant efficacy and mechanism of action were determined. Also, phytochemical data was obtained through 13C NMR-based dereplication. The MESh extract showed the highest efficacy (Emax = 87%), and its effect was partially endothelium-dependent. The mechanism of action was determined experimentally, and the vasorelaxant curves were modified in the presence of L-NAME, ODQ, and potassium channel blockers. MESh caused a relaxing effect on KCl 80 mM-induced contraction and was less potent than nifedipine. The CaCl2-induced contraction was significantly decreased compared with the control curve. Phytochemical analysis of MESh suggests the presence of mannitol, previously reported as a vasodilator on aortic rings. Our findings suggest NO-cGMP pathway participation as a vasodilator mechanism of action of S. hispanica seeds; this effect can be attributed, in part, to the mannitol presence. S. hispanica could be used in future research focused on antihypertensive therapies.
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Affiliation(s)
- Luis A. Herbert-Doctor
- Laboratorio de Farmacología, Facultad de Química, Universidad Autónoma de Yucatán, Mérida 97069, Yucatan, Mexico; (L.A.H.-D.); (A.S.-R.)
| | - Amanda Sánchez-Recillas
- Laboratorio de Farmacología, Facultad de Química, Universidad Autónoma de Yucatán, Mérida 97069, Yucatan, Mexico; (L.A.H.-D.); (A.S.-R.)
| | - Rolffy Ortiz-Andrade
- Laboratorio de Farmacología, Facultad de Química, Universidad Autónoma de Yucatán, Mérida 97069, Yucatan, Mexico; (L.A.H.-D.); (A.S.-R.)
| | - Emanuel Hernández-Núñez
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN, Mérida 97310, Yucatán, Mexico;
| | - Jesús Alfredo Araujo-León
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Cinetífica de Yucatán, A.C., Mérida 97205, Yucatan, Mexico;
| | - Tania Isolina Coral-Martínez
- Laboratorio de Cromatografía, Facultad de Química, Universidad Autónoma de Yucatán, Mérida 97069, Yucatan, Mexico;
| | - Nubia Noemi Cob-Calan
- Instituto Tecnológico Superior de Calkiní en el Estado de Campeche, Calkiní 24900, Campeche, Mexico;
| | | | - Samuel Estrada-Soto
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico;
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Meunier M, Bréard D, Awang K, Boisard S, Guilet D, Richomme P, Derbré S, Schinkovitz A. Matrix free laser desorption ionization assisted by 13C NMR dereplication: A complementary approach to LC-MS2 based chemometrics. Talanta 2023. [DOI: 10.1016/j.talanta.2022.123998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Borges RM, Gouveia GJ, das Chagas FO. Advances in Microbial NMR Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:123-147. [PMID: 37843808 DOI: 10.1007/978-3-031-41741-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Confidently, nuclear magnetic resonance (NMR) is the most informative technique in analytical chemistry and its use as an analytical platform in metabolomics is well proven. This chapter aims to present NMR as a viable tool for microbial metabolomics discussing its fundamental aspects and applications in metabolomics using some chosen examples.
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Affiliation(s)
- Ricardo Moreira Borges
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gonçalo Jorge Gouveia
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Fernanda Oliveira das Chagas
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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6
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Silva-Castro LF, Derbré S, Le Ray AM, Richomme P, García-Sosa K, Peña-Rodriguez LM. Using 13 C-NMR dereplication to aid in the identification of xanthones present in the stem bark extract of Calophyllum brasiliense. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:1102-1109. [PMID: 33938065 DOI: 10.1002/pca.3051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
| | - Séverine Derbré
- Department of Pharmacy, Faculty of Health Sciences, University of Angers, SONAS, SFR QUASAV, Angers, France
| | - Anne Marie Le Ray
- Department of Pharmacy, Faculty of Health Sciences, University of Angers, SONAS, SFR QUASAV, Angers, France
| | - Pascal Richomme
- Department of Pharmacy, Faculty of Health Sciences, University of Angers, SONAS, SFR QUASAV, Angers, France
| | - Karlina García-Sosa
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico
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7
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Bruguière A, Derbré S, Bréard D, Tomi F, Nuzillard JM, Richomme P. 13C NMR Dereplication Using MixONat Software: A Practical Guide to Decipher Natural Products Mixtures. PLANTA MEDICA 2021; 87:1061-1068. [PMID: 33957699 DOI: 10.1055/a-1470-0446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Antoine Bruguière
- Univ Angers, SONAS, SFR QUASAV, Faculty of Health Sciences, Dpt Pharmacy, Angers, France
| | - Séverine Derbré
- Univ Angers, SONAS, SFR QUASAV, Faculty of Health Sciences, Dpt Pharmacy, Angers, France
| | - Dimitri Bréard
- Univ Angers, SONAS, SFR QUASAV, Faculty of Health Sciences, Dpt Pharmacy, Angers, France
| | - Félix Tomi
- Université de Corse-CNRS, UMR 6134 SPE, Equipe Chimie et Biomasse, Ajaccio, France
| | | | - Pascal Richomme
- Univ Angers, SONAS, SFR QUASAV, Faculty of Health Sciences, Dpt Pharmacy, Angers, France
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Marques EDJ, Ferraz CG, dos Santos IB, dos Santos II, El-Bachá RS, Ribeiro PR, Cruz FG. Chemical constituents isolated from Clusia criuva subsp. Criuva and their chemophenetics significance. BIOCHEM SYST ECOL 2021. [DOI: 10.1016/j.bse.2021.104293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
The recent revival of the study of organic natural products as renewable sources of medicinal drugs, cosmetics, dyes, and materials motivated the creation of general purpose structural databases. Dereplication, the efficient identification of already reported compounds, relies on the grouping of structural, taxonomic and spectroscopic databases that focus on a particular taxon (species, genus, family, order, etc.). A set of freely available python scripts, CNMR_Predict, is proposed for the quick supplementation of taxon oriented search results from the naturaL prOducTs occUrrences database (LOTUS, lotus.naturalproducts.net) with predicted carbon-13 nuclear magnetic resonance data from the ACD/Labs CNMR predictor and DB software (acdlabs.com) to provide easily searchable databases. The database construction process is illustrated using Brassica rapa as a taxon example.
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Lianza M, Leroy R, Machado Rodrigues C, Borie N, Sayagh C, Remy S, Kuhn S, Renault JH, Nuzillard JM. The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case. Molecules 2021; 26:637. [PMID: 33530604 PMCID: PMC7865595 DOI: 10.3390/molecules26030637] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
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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Affiliation(s)
- Mariacaterina Lianza
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | - Ritchy Leroy
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
| | - Carine Machado Rodrigues
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
| | - Nicolas Borie
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
| | - Charlotte Sayagh
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
| | - Simon Remy
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
| | - Stefan Kuhn
- School of Computer Science and Informatics, De Montfort University, Leicester LE1 9BH, UK;
| | - Jean-Hugues Renault
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
| | - Jean-Marc Nuzillard
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France; (R.L.); (C.M.R.); (N.B.); (C.S.); (S.R.); (J.-H.R.)
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11
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Coste C, Gérard N, Dinh CP, Bruguière A, Rouger C, Leong ST, Awang K, Richomme P, Derbré S, Charreau B. Targeting MHC Regulation Using Polycyclic Polyprenylated Acylphloroglucinols Isolated from Garcinia bancana. Biomolecules 2020; 10:biom10091266. [PMID: 32887413 PMCID: PMC7563419 DOI: 10.3390/biom10091266] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
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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Affiliation(s)
- Chloé Coste
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France; (C.C.); (N.G.)
- SONAS, EA921, University of Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, CEDEX 01, 49045 Angers, France; (C.P.D.); (A.B.); (C.R.); (P.R.)
| | - Nathalie Gérard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France; (C.C.); (N.G.)
| | - Chau Phi Dinh
- SONAS, EA921, University of Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, CEDEX 01, 49045 Angers, France; (C.P.D.); (A.B.); (C.R.); (P.R.)
| | - Antoine Bruguière
- SONAS, EA921, University of Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, CEDEX 01, 49045 Angers, France; (C.P.D.); (A.B.); (C.R.); (P.R.)
| | - Caroline Rouger
- SONAS, EA921, University of Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, CEDEX 01, 49045 Angers, France; (C.P.D.); (A.B.); (C.R.); (P.R.)
| | - Sow Tein Leong
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.L.); (K.A.)
| | - Khalijah Awang
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.L.); (K.A.)
| | - Pascal Richomme
- SONAS, EA921, University of Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, CEDEX 01, 49045 Angers, France; (C.P.D.); (A.B.); (C.R.); (P.R.)
| | - Séverine Derbré
- SONAS, EA921, University of Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, CEDEX 01, 49045 Angers, France; (C.P.D.); (A.B.); (C.R.); (P.R.)
- Correspondence: (S.D.); (B.C.); Tel.: +33-249-180-440 (S.D.); +33-240-087-416 (B.C.); Fax: +33-240-087-411 (B.C.)
| | - Béatrice Charreau
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France; (C.C.); (N.G.)
- Correspondence: (S.D.); (B.C.); Tel.: +33-249-180-440 (S.D.); +33-240-087-416 (B.C.); Fax: +33-240-087-411 (B.C.)
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12
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Bruguière A, Derbré S, Dietsch J, Leguy J, Rahier V, Pottier Q, Bréard D, Suor-Cherer S, Viault G, Le Ray AM, Saubion F, Richomme P. MixONat, a Software for the Dereplication of Mixtures Based on 13C NMR Spectroscopy. Anal Chem 2020; 92:8793-8801. [DOI: 10.1021/acs.analchem.0c00193] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Antoine Bruguière
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Séverine Derbré
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Joël Dietsch
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
- JEOL Europe SAS, 1 Allée de Giverny, 78290 Croissy-sur-Seine, France
| | - Jules Leguy
- LERIA, EA2645, UNIV Angers, SFR MathSTIC, Faculty of Sciences, 2 boulevard Lavoisier, 49045 Angers cedex 01, France
| | - Valentine Rahier
- LERIA, EA2645, UNIV Angers, SFR MathSTIC, Faculty of Sciences, 2 boulevard Lavoisier, 49045 Angers cedex 01, France
| | - Quentin Pottier
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Dimitri Bréard
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Sorphon Suor-Cherer
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Guillaume Viault
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Anne-Marie Le Ray
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
| | - Frédéric Saubion
- LERIA, EA2645, UNIV Angers, SFR MathSTIC, Faculty of Sciences, 2 boulevard Lavoisier, 49045 Angers cedex 01, France
| | - Pascal Richomme
- SONAS, EA921, UNIV Angers, SFR QUASAV, Faculty of Health Sciences, Department of Pharmacy, 16 Bd Daviers, 49045 Angers cedex 01, France
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Kuhn S, Colreavy-Donnelly S, Santana de Souza J, Borges RM. An integrated approach for mixture analysis using MS and NMR techniques. Faraday Discuss 2020; 218:339-353. [PMID: 31114813 DOI: 10.1039/c8fd00227d] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We suggest an improved software pipeline for mixture analysis. The improvements include combining tandem MS and 2D NMR data for a reliable identification of the constituents in an algorithm based on network analysis aiming for a robust and reliable identification routine. An important part of this pipeline is the use of open-data repositories, although it is not totally reliant on them. The NMR identification step emphasizes robustness and is less sensitive towards changes in data acquisition and processing than existing methods. The process starts with LC-ESI-MSMS based molecular network dereplication using data from the GNPS collaborative collection. We identify closely related structures by propagating structure elucidation through edges in the network. Those identified compounds are added on top of a candidate list for the following NMR filtering method that predicts HSQC and HMBC NMR data. The similarity of the predicted spectra of the set of closely related structures to the measured spectra of the mixture sample is taken as one indication of the most likely candidates for its compounds. The other indication is the match of the spectra to clusters built by a network analysis from the spectra of the mixture. The sensitivity gap between NMR and MS is anticipated and it will be reflected naturally by the eventual identification of fewer compounds, but with a higher confidence level, after the NMR analysis step. The contributions of the paper are an algorithm combining MS and NMR spectroscopy and a robust nJCH network analysis to explore the complementary aspects of both techniques. This delivers good results, even if a perfect computational separation of the compounds in the mixture is not possible. All of the scripts are freely available to aid studies such as with plants, marine organisms, and microorganism natural product chemistry and metabolomics, as those are the driving forces for this project.
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Affiliation(s)
- Stefan Kuhn
- De Montfort University, School of Computer Science and Informatics, The Gateway, Leicester LE1 9BH, UK.
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