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You L, Wang T, Li W, Zhang J, Zheng C, Zheng Y, Li S, Shang Z, Lin J, Wang F, Qian Y, Zhou Z, Kong X, Gao Y, Sun X. Xiaozhi formula attenuates non-alcoholic fatty liver disease by regulating lipid metabolism via activation of AMPK and PPAR pathways. JOURNAL OF ETHNOPHARMACOLOGY 2024; 329:118165. [PMID: 38588984 DOI: 10.1016/j.jep.2024.118165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/03/2024] [Accepted: 04/06/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Xiaozhi formula (XZF) is a practical Chinese herbal formula for the treatment of non-alcoholic fatty liver disease (NAFLD), which possesses an authorized patent certificate issued by the State Intellectual Property Office of China (ZL202211392355.0). However, the underlying mechanism by which XZF treats NAFLD remains unclear. PURPOSE This study aimed to explore the main component of XZF and its mechanism of action in NAFLD treatment. METHODS UHPLC-Q-Orbitrap HRMS was used to identify the components of the XZF. A high-fat diet (HFD)-induced NAFLD mouse model was used to demonstrate the effectiveness of XZF. Body weight, liver weight, and white fat weight were recorded to evaluate the therapeutic efficacy of XZF. H&E and Oil Red O staining were applied to observe the extent of hepatic steatosis. Liver damage, lipid metabolism, and glucose metabolism were detected by relevant assay kits. Moreover, the intraperitoneal insulin tolerance test and the intraperitoneal glucose tolerance test were employed to evaluate the efficacy of XZF in insulin homeostasis. Hepatocyte oxidative damage markers were detected to assess the efficacy of XZF in preventing oxidative stress. Label-free proteomics was used to investigate the underlying mechanism of XZF in NAFLD. RT-qPCR was used to calculate the expression levels of lipid metabolism genes. Western blot analysis was applied to detect the hepatic protein expression of AMPK, p-AMPK, PPARɑ, CPT1, and PPARγ. RESULTS 120 compounds were preliminarily identified from XZF by UHPLC-Q-Orbitrap HRMS. XZF could alleviate HFD-induced obesity, white adipocyte size, lipid accumulation, and hepatic steatosis in mice. Additionally, XZF could normalize glucose levels, improve glucolipid metabolism disorders, and prevent oxidative stress damage induced by HFD. Furthermore, the proteomic analysis showed that the major pathways in fatty acid metabolism and the PPAR signaling pathway were significantly impacted by XZF treatment. The expression levels of several lipolytic and β-oxidation genes were up-regulated, while the expression of fatty acid synthesis genes declined in the HFD + XZF group. Mechanically, XZF treatment enhanced the expression of p-AMPK, PPARɑ, and CPT-1 and suppressed the expression of PPARγ in the livers of NAFLD mice, indicating that XZF could activate the AMPK and PPAR pathways to attenuate NALFD progression. CONCLUSION XZF could attenuate NAFLD by moderating lipid metabolism by activating AMPK and PPAR signaling pathways.
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Affiliation(s)
- Liping You
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Tao Wang
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Wenxuan Li
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Jinghao Zhang
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Chao Zheng
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Yanxi Zheng
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Suyin Li
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Zhi Shang
- Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Pestilence Disease Laboratory of Integrated Chinese and Western Medicine, Shanghai Institute of Traditional Chinese Medicine, Shanghai, China
| | - Jiacheng Lin
- Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Fang Wang
- Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Yihan Qian
- Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Zhijia Zhou
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Xiaoni Kong
- Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China.
| | - Yueqiu Gao
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Pestilence Disease Laboratory of Integrated Chinese and Western Medicine, Shanghai Institute of Traditional Chinese Medicine, Shanghai, China.
| | - Xuehua Sun
- Department of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China.
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Castañeta G, Sepulveda B, Areche C. Liquid chromatography-electrospray ionization-mass spectrometry/mass spectrometry characterization of depsides and depsidones from the Chilean lichen Parmotrema perlatum. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2024; 30:125-132. [PMID: 38523368 DOI: 10.1177/14690667241240477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Lichens are recognized by their unique compounds and diverse applications in food, medicines, and cosmetics. Using ultra-high pressure liquid chromatography, coupled with a high-resolution mass spectrometer, metabolomic profiling of the lichen Parmotrema perlatum, from a methanolic extract, was performed. Based on characteristic fragmentation patterns, twenty-five lichenic substances were tentatively identified including 5 depsides, 12 depsidones, 2 diphenyl ethers, 1 aromatic considered as possible artifact, 1 dibenzofuran, 1 carbohydrate, 1 organic acid, and 2 undefined compounds. To the best of our knowledge, this is a more complete report of their phytochemistry from P perlatum. Our findings of the P perlatum profile may contribute and complement the current data of the Parmotrema genus.
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Affiliation(s)
- Grover Castañeta
- Facultad de Ciencias Puras y Naturales, Instituto de Investigaciones Químicas, Universidad Mayor de San Andrés, La Paz, Bolivia
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Beatriz Sepulveda
- Departamento de Ciencias Químicas, Universidad Andrés Bello, Campus Viña del Mar, Viña del Mar, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Mendili M, Khadhri A, Sabatini F, Degano I, Aschi-Smiti S. Parietin, the Vibrant Natural Dye in Xanthoria parietina. Chem Biodivers 2024; 21:e202301357. [PMID: 38072912 DOI: 10.1002/cbdv.202301357] [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: 09/05/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]
Abstract
The use of natural dyes in several areas is regulated by current European and non-European legislation, due to various problems with synthetic dyes. The analysis revealed that the lichen studied: Xanthoria parietina has potential natural dye sources and provides bright colors for extraction solvents. Furthermore, dyed wool and toile fabric have good fastness properties in ammonia fermentation and boiling water, both with and without mordants. The sample dyes with Xanthoria parietina were characterized by several analytical techniques: high-performance liquid chromatography with diode array detection (HPLC-DAD) and electrospray ionization with tandem mass spectrometry (HPLC-ESI-Q-ToF). As compounds from Xanthoria parietina form a complex with mordants and tissues, it is impossible to identify the molecules responsible for coloring using chromatographic techniques. However, we have evaluated the dyeing power of their major molecule, parietin. To further confirm the coloring power of the isolated parietin molecule, we performed a dye test with pure parietin. Thus, CIALAB analyses have shown parietin is the molecule responsible for the coloring obtained by Xanthoria parietina. The utilization of parietin derived from lichens facilitates the development of sustainable dyes for textile coloring, presenting an environmentally friendly alternative to synthetic dyes while simultaneously enriching lichen biodiversity.
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Affiliation(s)
- Mohamed Mendili
- Plant, soil, and environment interactions laboratory, Faculty of Sciences of Tunis, University of El Manar, Campus Academia, 2092, Tunis, Tunisia
| | - Ayda Khadhri
- Plant, soil, and environment interactions laboratory, Faculty of Sciences of Tunis, University of El Manar, Campus Academia, 2092, Tunis, Tunisia
| | - Francesca Sabatini
- Department of Chemistry and Industrial Chemistry, University of Pisa, I-56124, Pisa, Italy
| | - Ilaria Degano
- Department of Chemistry and Industrial Chemistry, University of Pisa, I-56124, Pisa, Italy
| | - Samira Aschi-Smiti
- Plant, soil, and environment interactions laboratory, Faculty of Sciences of Tunis, University of El Manar, Campus Academia, 2092, Tunis, Tunisia
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Bittremieux W, Avalon NE, Thomas SP, Kakhkhorov SA, Aksenov AA, Gomes PWP, Aceves CM, Caraballo-Rodríguez AM, Gauglitz JM, Gerwick WH, Huan T, Jarmusch AK, Kaddurah-Daouk RF, Kang KB, Kim HW, Kondić T, Mannochio-Russo H, Meehan MJ, Melnik AV, Nothias LF, O'Donovan C, Panitchpakdi M, Petras D, Schmid R, Schymanski EL, van der Hooft JJJ, Weldon KC, Yang H, Xing S, Zemlin J, Wang M, Dorrestein PC. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nat Commun 2023; 14:8488. [PMID: 38123557 PMCID: PMC10733301 DOI: 10.1038/s41467-023-44035-y] [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: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
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Affiliation(s)
- Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020, Antwerpen, Belgium.
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sydney P Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sarvar A Kakhkhorov
- Laboratory of Physical and Chemical Methods of Research, Center for Advanced Technologies, Tashkent, 100174, Uzbekistan
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
- Arome Science inc., Farmington, CT, 06032, USA
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Rima F Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, 27701, USA
- Department of Medicine, Duke University, Durham, NC, 27710, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, 27710, USA
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Goyang, 10326, Korea
| | - Todor Kondić
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, 14800-901, Brazil
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexey V Melnik
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
- Arome Science inc., Farmington, CT, 06032, USA
| | - Louis-Felix Nothias
- Université Côte d'Azur, CNRS, ICN, Nice, France
- Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur, Nice, France
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, 72076, Tuebingen, Germany
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92507, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Heejung Yang
- Laboratory of Natural Products Chemistry, College of Pharmacy, Kangwon National University, Chuncheon, 24341, Korea
| | - Shipei Xing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, 92507, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA.
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Khadim A, Yaseen Jeelani SU, Khan MN, Kumari S, Raza A, Ali A, Zareena B, Zaki Shah SM, Musharraf SG. Targeted Analysis of Veterinary Drugs in Food Samples by Developing a High-Resolution Tandem Mass Spectral Library. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12839-12848. [PMID: 37528805 DOI: 10.1021/acs.jafc.3c03715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Veterinary drug residues present in foods can pose severe health threats to the population. The present study aims to develop a high-resolution mass spectral library of 158 veterinary drugs of 16 different classes for their rapid identification in food samples through liquid chromatography-high-resolution electrospray ionization-tandem mass spectrometry (LC-HR-ESI-MS/MS). Standard drugs were pooled according to their log P values and exact masses before analysis. Spectra were collected at system automated collision energy, i.e., of 25-60 eV and four predetermined collision energies (10, 20, 30, and 40 eV) for each compound using a schedule precursor list of [M + H]+, [M + Na]+, and [M + NH4]+ ions. The utility of the developed database was checked by analyzing food samples. A total of 17 veterinary drugs based on the reference standard retention times (RTs), HR-MS spectra, and MS/MS spectra were identified in the analyzed samples. Moreover, five veterinary drugs were selected for quantitative analysis, including doxycycline hyclate, lincomycin, sulfasalazine, moxifloxacin, and diphenoxylate, using liquid chromatography-ion trap mass-spectrometry (LC-IT-MS). Concentrations of the drug were obtained to vary from 0.0805 to 0.9731 mg/kg in food samples and were found to be exceeded in most of the cases as per the maximum residue levels described by Food and Agriculture Organization (FAO)/World Health Organization (WHO). The MS data were submitted to the MetaboLights online database (MTBLS2914). This study will help in the high-throughput screening of multiclass veterinary drugs in foodstuffs.
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Affiliation(s)
- Adeeba Khadim
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Syed Usama Yaseen Jeelani
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Muhammad Noman Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sindhia Kumari
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ali Raza
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Bibi Zareena
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Syed Muhammad Zaki Shah
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Syed Ghulam Musharraf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- T.C.M Hospital, Southwest Medical University, Luzhou, Sichuan 646000, China
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Koopaie M, Karimi H, Sohrabi M, Norouzi H. Cytotoxic, anti-proliferative, and apoptotic evaluation of Ramalina sinensis (Ascomycota, Lecanoromycetes), lichenized fungus on oral squamous cell carcinoma cell line; in-vitro study. BMC Complement Med Ther 2023; 23:296. [PMID: 37608377 PMCID: PMC10463489 DOI: 10.1186/s12906-023-04118-1] [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: 11/07/2022] [Accepted: 08/05/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Scientists and medical professionals are actively striving to improve the efficacy of treatment methods for oral squamous cell carcinoma (OSCC), the most frequently occurring cancer within the oral cavity, by exploring the potential of natural products. The active pharmacological compounds found in lichenized fungi have shown potential for aiding in cancer treatment. Recent research aims to evaluate the impact of the lichenized fungus Ramalina sinensis (R. sinensis) on the cell viability and apoptosis of OSCC cell lines, considering the anti-inflammatory and anti-cancer capabilities of lichens. METHODS Ramalina sinensis (Ascomycota, Lecanoromycetes) was selected for investigation of its effects on a human oral squamous cell carcinoma cell line. Acetone and methanol extracts of R. sinensis on an OSCC cell line (KB cell line, NCBI Code: C152) were investigated. Viability was assessed by MTT assay analysis, and apoptotic cells were measured using flow cytometry analysis. Scratch assay was used to assess cell migration. The chemical composition and metabolic profiling of R. sinensis were investigated. RESULTS The growth and multiplication of KB cells were observed to undergo a gradual but remarkable inhibition when exposed to various concentrations. Specifically, concentrations of 6.25, 12.5, 25, 50, 100, and 200 μg/mL exhibited a significant suppressive effect on the proliferation of KB cells. The inhibition of cell proliferation exhibited a statistically significant difference between the extracts obtained from acetone and methanol. Flow cytometry results show an increase in apoptosis of OSCC cells by acetone extract. R. sinensis exerted a concentration-dependent inhibitory effect on the migration of OSCC cells. The chemical composition of R. sinensis was investigated using liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), and 33 compounds in the acetone and methanol extracts of R. sinensis were detected. CONCLUSION The findings provide evidence supporting the beneficial effects of R. sinensis extract on inducing apoptosis in OSCC cells and exerting anti-cancer properties.
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Affiliation(s)
- Maryam Koopaie
- Department of Oral Medicine, School of Dentistry, Tehran University of Medical Sciences, North Kargar St, P.O. Box: 14395 -433, Tehran, 14399-55991, Iran.
| | - Hanieh Karimi
- Department of Oral Medicine, School of Dentistry, Tehran University of Medical Sciences, North Kargar St, P.O. Box: 14395 -433, Tehran, 14399-55991, Iran
| | - Mohammad Sohrabi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Hooman Norouzi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
- Former graduate student of the Department of Horticultural Sciences, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
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Popov RS, Ivanchina NV, Silchenko AS, Avilov SA, Kalinin VI, Malyarenko TV, Stonik VA, Dmitrenok PS. A Mass Spectrometry Database for Sea Cucumber Triterpene Glycosides. Metabolites 2023; 13:783. [PMID: 37512490 PMCID: PMC10384350 DOI: 10.3390/metabo13070783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Sea cucumber triterpene glycosides are a class of secondary metabolites that possess distinctive chemical structures and exhibit a variety of biological and pharmacological activities. The application of MS-based approaches for the study of triterpene glycosides allows rapid evaluation of the structural diversity of metabolites in complex mixtures. However, the identification of the detected triterpene glycosides can be challenging. The objective of this study is to establish the first spectral library containing the mass spectra of sea cucumber triterpene glycosides using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry. The library contains the electrospray ionization tandem mass spectra and retention times of 191 triterpene glycosides previously isolated from 15 sea cucumber species and one starfish at the Laboratory of the Chemistry of Marine Natural Products of the G.B. Elyakov Pacific Institute of Bioorganic Chemistry. In addition, the chromatographic behavior and some structure-related neutral losses in tandem MS are discussed. The obtained data will accelerate the accurate dereplication of known triterpene glycosides and the annotation of novel compounds, as we demonstrated by the processing of LC-MS/MS data of Eupentacta fraudatrix extract.
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Affiliation(s)
- Roman S Popov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Natalia V Ivanchina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Alexandra S Silchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Sergey A Avilov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Vladimir I Kalinin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Timofey V Malyarenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Valentin A Stonik
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
| | - Pavel S Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospect 100-let Vladivostoku, Vladivostok 690022, Russia
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Ren M, Jiang S, Wang Y, Pan X, Pan F, Wei X. Discovery and excavation of lichen bioactive natural products. Front Microbiol 2023; 14:1177123. [PMID: 37138611 PMCID: PMC10149937 DOI: 10.3389/fmicb.2023.1177123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.
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Affiliation(s)
- Meirong Ren
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Shuhua Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Feng Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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9
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Singh G. Linking Lichen Metabolites to Genes: Emerging Concepts and Lessons from Molecular Biology and Metagenomics. J Fungi (Basel) 2023; 9:jof9020160. [PMID: 36836275 PMCID: PMC9964704 DOI: 10.3390/jof9020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Lichen secondary metabolites have tremendous pharmaceutical and industrial potential. Although more than 1000 metabolites have been reported from lichens, less than 10 have been linked to the genes coding them. The current biosynthetic research focuses strongly on linking molecules to genes as this is fundamental to adapting the molecule for industrial application. Metagenomic-based gene discovery, which bypasses the challenges associated with culturing an organism, is a promising way forward to link secondary metabolites to genes in non-model, difficult-to-culture organisms. This approach is based on the amalgamation of the knowledge of the evolutionary relationships of the biosynthetic genes, the structure of the target molecule, and the biosynthetic machinery required for its synthesis. So far, metagenomic-based gene discovery is the predominant approach by which lichen metabolites have been linked to their genes. Although the structures of most of the lichen secondary metabolites are well-documented, a comprehensive review of the metabolites linked to their genes, strategies implemented to establish this link, and crucial takeaways from these studies is not available. In this review, I address the following knowledge gaps and, additionally, provide critical insights into the results of these studies, elaborating on the direct and serendipitous lessons that we have learned from them.
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Kalra R, Conlan XA, Goel M. Recent advances in research for potential utilization of unexplored lichen metabolites. Biotechnol Adv 2023; 62:108072. [PMID: 36464145 DOI: 10.1016/j.biotechadv.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/28/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.
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Affiliation(s)
- Rishu Kalra
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - Mayurika Goel
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India.
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11
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Metabolomic Profiling, Antioxidant and Enzyme Inhibition Properties and Molecular Docking Analysis of Antarctic Lichens. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228086. [PMID: 36432187 PMCID: PMC9692326 DOI: 10.3390/molecules27228086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/13/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
The lichen species Lecania brialmontii, Pseudephebe pubescens, and Sphaerophorus globosus are part of the prominent lichenoflora of the Antarctic territory. In this work, we report the metabolomic identification of ethanolic extracts of these species, their antioxidant and cholinesterase enzyme inhibitory activity, and conduct a molecular docking analysis with typical compounds. Eighteen compounds were identified by UHPLC-ESI-QTOF-MS in L. brialmontii, 18 compounds in P. pubescens, and 14 compounds in S. globosus. The content of phenolic compounds was variable among the species, ranging from 0.279 to 2.821 mg AG/g, and all three species showed high inhibition potential on the cholinesterase enzymes. Molecular docking showed important interactions between AChE and BChE with the selected compounds. This study evidences the chemical fingerprint of three species of the order Lecanorales that support the continuation of the study of other biological activities and their potential for medical research.
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Bittremieux W, Wang M, Dorrestein PC. The critical role that spectral libraries play in capturing the metabolomics community knowledge. Metabolomics 2022; 18:94. [PMID: 36409434 DOI: 10.1007/s11306-022-01947-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/19/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Spectral library searching is currently the most common approach for compound annotation in untargeted metabolomics. Spectral libraries applicable to liquid chromatography mass spectrometry have grown in size over the past decade to include hundreds of thousands to millions of mass spectra and tens of thousands of compounds, forming an essential knowledge base for the interpretation of metabolomics experiments. AIM OF REVIEW We describe existing spectral library resources, highlight different strategies for compiling spectral libraries, and discuss quality considerations that should be taken into account when interpreting spectral library searching results. Finally, we describe how spectral libraries are empowering the next generation of machine learning tools in computational metabolomics, and discuss several opportunities for using increasingly accessible large spectral libraries. KEY SCIENTIFIC CONCEPTS OF REVIEW This review focuses on the current state of spectral libraries for untargeted LC-MS/MS based metabolomics. We show how the number of entries in publicly accessible spectral libraries has increased more than 60-fold in the past eight years to aid molecular interpretation and we discuss how the role of spectral libraries in untargeted metabolomics will evolve in the near future.
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Affiliation(s)
- Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mingxun Wang
- Department of Computer Science, University of California Riverside, Riverside, CA, 92507, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Kumar TK, Siva B, Anand A, Anusha K, Mohabe S, Reddy AM, Le Devehat F, Tiwari AK, Boustie J, Babu KS. Comprehensive Lichenometabolomic Exploration of Ramalina conduplicans Vain Using UPLC-Q-ToF-MS/MS: An Identification of Free Radical Scavenging and Anti-Hyperglycemic Constituents. Molecules 2022; 27:molecules27196720. [PMID: 36235256 PMCID: PMC9570585 DOI: 10.3390/molecules27196720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
In this study, we propose ultra-performance liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry (UPLC-QToF-MS/MS)-guided metabolite isolation as a choice analytical approach to the ongoing structure−activity investigations of chemical isolates from the edible lichen, Ramalina conduplicans Vain. This strategy led to the isolation and identification of a new depside (5) along with 13 known compounds (1−4, 6−14), most of which being newly described in this lichen species. The structures of the isolates were established by detailed analysis of their spectral data (IR, NMR, and Mass). The acetone extract was further analyzed by UPLC-Q-ToF-MS/MS in a negative ionization mode, which facilitated the identification and confirmation of 18 compounds based on their fragmentation patterns. The antioxidant capacities of the lichen acetone extract (AE) and isolates were measured by tracking DPPH and ABTS free radical scavenging activities. Most isolates displayed marked radical scavenging activities against ABTS while moderate activities were observed against DPPH radical scavenging. Except for atranol (14), oxidative DNA damage was limited by all the tested compounds, with a marked protection for the novel isolated compound (5), as previously noted for the acetone extract (p < 0.001). Furthermore, compound (4) and acetone extract (AE) have inhibited intestinal α-glucosidase enzyme significantly (p < 0.01). Although some phytochemical studies were already performed on this lichen, this study provided new insights into the isolation and identification of bioactive compounds, illustrating interest in future novel analytical techniques.
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Affiliation(s)
- Tatapudi Kiran Kumar
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bandi Siva
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ajay Anand
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Komati Anusha
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Satish Mohabe
- Department of Botany, Yogi Vemana University, Vemanapuram, Kadapa 516003, India
- Faculty of Sciences & IT, Madhyanchal Professional University, Ratibad, Bhopal 462044, India
| | | | - Françoise Le Devehat
- Institut des Sciences Chimiques de Rennes, Université Rennes, CNRS, ISCR-UMR6226, 35000 Rennes, France
| | - Ashok Kumar Tiwari
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Joël Boustie
- Institut des Sciences Chimiques de Rennes, Université Rennes, CNRS, ISCR-UMR6226, 35000 Rennes, France
- Correspondence: (J.B.); (K.S.B.)
| | - Katragadda Suresh Babu
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence: (J.B.); (K.S.B.)
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Ollivier S, Jéhan P, Olivier‐Jimenez D, Lambert F, Boustie J, Lohézic‐Le Dévéhat F, Le Yondre N. New insights into the Van Krevelen diagram: Automated molecular formula determination from HRMS for a large chemical profiling of lichen extracts. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:1111-1120. [PMID: 35789004 PMCID: PMC9796888 DOI: 10.1002/pca.3163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/26/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION In recent years, LC-MS has become the golden standard for metabolomic studies. Indeed, LC is relatively easy to couple with the soft electrospray ionization. As a consequence, many tools have been developed for the structural annotation of tandem mass spectra. However, it is sometimes difficult to do data-dependent acquisition (DDA), especially when developing new methods that stray from the classical LC-MS workflow. OBJECTIVE An old tool from petroleomics that has recently gained popularity in metabolomics, the Van Krevelen diagram, is adapted for an overview of the molecular diversity profile in lichens through high-resolution mass spectrometry (HRMS). METHODS A new method is benchmarked against the state-of-the-art classification tool ClassyFire using a database containing most known lichen metabolites (n ≈ 2,000). Four lichens known for their contrasted chemical composition were selected, and extractions with apolar, aprotic polar, and protic polar solvents were performed to cover a wide range of polarities. Extracts were analyzed with direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) and atmospheric solids analysis probe mass spectrometry (ASAP-MS) techniques to be compared with the chemical composition described in the literature. RESULTS The most common lichen metabolites were efficiently classified, with more than 90% of the molecules in some classes being matched with ClassyFire. Results from this method are consistent with the various extraction protocols in the present case study. CONCLUSION This approach is a rapid and efficient tool to gain structural insight regarding lichen metabolites analyzed by HRMS without relying on DDA by LC-MS/MS analysis. It may notably be of use during the development phase of novel MS-based metabolomic approaches.
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Affiliation(s)
- Simon Ollivier
- CNRS, ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ RennesRennesFrance
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes) ‐ UMR 6226Univ RennesRennesFrance
- Present address:
INRAE, UR BIA, F‐44300 Nantes, France and INRAEPROBE research infrastructure, BIBS facilityF‐44300Nantes, France
| | - Philippe Jéhan
- CNRS, ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ RennesRennesFrance
| | - Damien Olivier‐Jimenez
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes) ‐ UMR 6226Univ RennesRennesFrance
| | - Fabian Lambert
- CNRS, ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ RennesRennesFrance
| | - Joël Boustie
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes) ‐ UMR 6226Univ RennesRennesFrance
| | | | - Nicolas Le Yondre
- CNRS, ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ RennesRennesFrance
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15
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Ollivier S, Jéhan P, Lambert F, Olivier‐Jimenez D, Boustie J, Lohézic‐Le Dévéhat F, Le Yondre N. ASAP-MS and DART-MS as ancillary tools for direct analysis of the lichen metabolome. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:1028-1035. [PMID: 35753311 PMCID: PMC9796614 DOI: 10.1002/pca.3156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Lichens contain unique metabolites that most often need to be characterized from a limited amount of material. While thin layer chromatography is still the preferred analysis method for most lichenologists, liquid chromatography gives a deeper insight in the lichen metabolome, but an extractive step is needed before any analysis. Therefore, ambient ionization mass spectrometry (MS) analysis of lichen samples using Atmospheric Solid Analysis Probe (ASAP) and Direct Acquisition in Real Time (DART) techniques is evaluated. OBJECTIVE We looked for a faster method to screen the metabolome by disrupting the classical workflow of analysis. METHODS Four lichens selected for their metabolic diversity were analyzed with MS; namely Evernia prunastri, Lichina pygmaea, Parmelia saxatilis, and Roccella fuciformis. ASAP and DART analyses were compared against the reference electrospray ionization with a bioinformatic process including Van Krevelen diagrams as well as the multivariate comparison of the ionization methods in positive and negative modes. RESULTS Metabolite profiles obtained from DART and ASAP analyses of lichen samples are consistent with classical analyses of lichen extracts. Through an easy and rapid experiment and without any extraction solvent, a large and informative profile of lichen metabolites is obtained when using complementary ionization modes of these high resolution mass spectrometry methods. CONCLUSION ASAP-MS and DART-MS are two ancillary methods that provide a comprehensive evaluation of the lichen metabolome.
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Affiliation(s)
- Simon Ollivier
- ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ Rennes, CNRSRennesFrance
- ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226Univ Rennes, CNRSRennesFrance
- Present address:
INRAE, UR BIA, F‐44300 Nantes, France and INRAE, PROBE research infrastructure, BIBS facility, F‐44300 NantesFrance
| | - Philippe Jéhan
- ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ Rennes, CNRSRennesFrance
| | - Fabian Lambert
- ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ Rennes, CNRSRennesFrance
| | - Damien Olivier‐Jimenez
- ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226Univ Rennes, CNRSRennesFrance
| | - Joël Boustie
- ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226Univ Rennes, CNRSRennesFrance
| | | | - Nicolas Le Yondre
- ScanMAT UAR 2025, CRMPO (Centre Régional de Mesures Physiques de l'Ouest)Univ Rennes, CNRSRennesFrance
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16
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Srimani S, Schmidt CX, Gómez-Serranillos MP, Oster H, Divakar PK. Modulation of Cellular Circadian Rhythms by Secondary Metabolites of Lichens. Front Cell Neurosci 2022; 16:907308. [PMID: 35813500 PMCID: PMC9260025 DOI: 10.3389/fncel.2022.907308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background Most mammalian cells harbor molecular circadian clocks that synchronize physiological functions with the 24-h day-night cycle. Disruption of circadian rhythms, through genetic or environmental changes, promotes the development of disorders like obesity, cardiovascular diseases, and cancer. At the cellular level, circadian, mitotic, and redox cycles are functionally coupled. Evernic (EA) and usnic acid (UA), two lichen secondary metabolites, show various pharmacological activities including anti-oxidative, anti-inflammatory, and neuroprotective action. All these effects have likewise been associated with a functional circadian clock. Hypothesis/Purpose To test, if the lichen compounds EA and UA modulate circadian clock function at the cellular level. Methods We used three different cell lines and two circadian luminescence reporter systems for evaluating dose- and time-dependent effects of EA/UA treatment on cellular clock regulation at high temporal resolution. Output parameters studied were circadian luminescence rhythm period, amplitude, phase, and dampening rate. Results Both compounds had marked effects on clock rhythm amplitudes and dampening independent of cell type, with UA generally showing a higher efficiency than EA. Only in fibroblast cells, significant effects on clock period were observed for UA treated cells showing shorter and EA treated cells showing longer period lengths. Transient treatment of mouse embryonic fibroblasts at different phases had only minor clock resetting effects for both compounds. Conclusion Secondary metabolites of lichen alter cellular circadian clocks through amplitude reduction and increased rhythm dampening.
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Affiliation(s)
- Soumi Srimani
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Cosima Xenia Schmidt
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Maria Pilar Gómez-Serranillos
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
- *Correspondence: Pradeep K. Divakar
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Agnès SA, Okpekon T, Kouadio YA, Jagora A, Bréard D, Costa EV, da Silva FMA, Koolen HHF, Le Ray-Richomme AM, Richomme P, Champy P, Beniddir MA, Le Pogam P. Implementation of a MS/MS database for isoquinoline alkaloids and other annonaceous metabolites. Sci Data 2022; 9:270. [PMID: 35668110 PMCID: PMC9170680 DOI: 10.1038/s41597-022-01345-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
This data descriptor reports on the upload to a public repository (GNPS) of the IQAMDB, IsoQuinoline and Annonaceous Metabolites Data Base, comprising 320 tandem mass spectra. This project originated from our in-house collection of isoquinolines. The diversity of compounds included in this database was further extended through the contribution of two additional laboratories involved in isoquinoline alkaloids research: University of Angers and University of Manaus. The generated MS/MS data were processed and annotated on an individual basis to promote their straightforward reuse by natural product chemists interested in either the description of new isoquinoline alkaloids or the dereplication of isoquinoline-containing samples. The interest of the current repertoire for dereplication purposes has been validated based on the molecular networking of the well-investigated plant model Annona montana against the IQAMDB‐implemented GNPS. Measurement(s) | electrospray ionization | Technology Type(s) | Ultra High-performance Liquid Chromatography • Tandem Mass Spectrometry |
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Affiliation(s)
- Salemon Akpa Agnès
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.,Laboratoire de Constitution et Réaction de la Matière (LCRM), UFR Sciences des Structures de la Matière et Technologie, Université Félix Houphouët-Boigny, BP 582, Abidjan 22, Côte d'Ivoire
| | - Timothée Okpekon
- Laboratoire de Constitution et Réaction de la Matière (LCRM), UFR Sciences des Structures de la Matière et Technologie, Université Félix Houphouët-Boigny, BP 582, Abidjan 22, Côte d'Ivoire
| | - Yvette Affoué Kouadio
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.,Laboratoire de Constitution et Réaction de la Matière (LCRM), UFR Sciences des Structures de la Matière et Technologie, Université Félix Houphouët-Boigny, BP 582, Abidjan 22, Côte d'Ivoire
| | - Adrien Jagora
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France
| | | | - Emmanoel V Costa
- Departamento de Química, Universidade Federal do Amazonas, Av. Rodrigo Otávio 1200, 69067-005, Manaus, AM, Brazil
| | - Felipe M A da Silva
- Centro de Apoio Multidisciplinar (CAM), Universidade Federal do Amazonas, Av. Rodrigo Otávio 1200, 69067-005, Manaus, Brazil
| | - Hector H F Koolen
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Av. Carvalho Leal 1777, 69065-001, Manaus, Brazil
| | | | | | - Pierre Champy
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France
| | - Pierre Le Pogam
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
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18
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High Diversity of Type I Polyketide Genes in Bacidia rubella as Revealed by the Comparative Analysis of 23 Lichen Genomes. J Fungi (Basel) 2022; 8:jof8050449. [PMID: 35628705 PMCID: PMC9146135 DOI: 10.3390/jof8050449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/21/2022] Open
Abstract
Fungi involved in lichen symbioses produce a large array of secondary metabolites that are often diagnostic in the taxonomic delimitation of lichens. The most common lichen secondary metabolites—polyketides—are synthesized by polyketide synthases, particularly by Type I PKS (TI-PKS). Here, we present a comparative genomic analysis of the TI-PKS gene content of 23 lichen-forming fungal genomes from Ascomycota, including the de novo sequenced genome of Bacidia rubella. Firstly, we identify a putative atranorin cluster in B. rubella. Secondly, we provide an overview of TI-PKS gene diversity in lichen-forming fungi, and the most comprehensive Type I PKS phylogeny of lichen-forming fungi to date, including 624 sequences. We reveal a high number of biosynthetic gene clusters and examine their domain composition in the context of previously characterized genes, confirming that PKS genes outnumber known secondary substances. Moreover, two novel groups of reducing PKSs were identified. Although many PKSs remain without functional assignments, our findings highlight that genes from lichen-forming fungi represent an untapped source of novel polyketide compounds.
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Le Pogam P, Poupon E, Champy P, Beniddir MA. Implementation of an MS/MS Spectral Library for Monoterpene Indole Alkaloids. Methods Mol Biol 2022; 2505:87-100. [PMID: 35732939 DOI: 10.1007/978-1-0716-2349-7_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In less than 10 years, molecular networking (MN) strategy has revolutionized the art of Natural Products (NP) isolation to enter a rational workflow greatly increasing the probabilities of isolating new chemical entities. To pinpoint and streamline the isolation of new Monoterpene Indole Alkaloids (MIAs) in producing plants, we rendered publicly available the MIA database (MIADB), comprising MS2 data for ca. 200 structurally diverse MIA, by uploading it to the Global Natural Products Social Molecular Networking (GNPS) platform. Here, we describe the key experimental aspects underlying data collection, data curation, and their subsequent upload to the GNPS libraries as a database. Practical tips are also provided at the end of this chapter to help optimizing the efficiency of the dereplication of MIA-containing plants against the MIADB-implemented GNPS library.
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Affiliation(s)
- Pierre Le Pogam
- Équipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, Châtenay-Malabry, France
| | - Erwan Poupon
- Équipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, Châtenay-Malabry, France
| | - Pierre Champy
- Équipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, Châtenay-Malabry, France.
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Khadim A, Zareena B, Hussain S, Jeelani SUY, Ali A, Musharraf SG. Pooling strategy to construct in-house high-resolution electrospray ionization tandem mass spectrometry database of drugs. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2021.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Ikeda MA, Nakamura H, Sawada K. Long-chain alkenes and alkadienes of eight lichen species collected in Japan. PHYTOCHEMISTRY 2021; 189:112823. [PMID: 34098255 DOI: 10.1016/j.phytochem.2021.112823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
The hydrocarbons of eight lichen species isolated in Japan were analyzed, and diverse mono-, di-, and tri-unsaturated alkenes were detected. The positions of the double bonds of C17 alkadienes (heptadecadiene) and C17-C20 alkenes were determined by mass spectrometry of their dimethyl disulfide adducts. We found that the six lichens containing green algal photobionts were distinguished by the presence of 1,8-heptadecadiene, 6,9-heptadecadiene, and 8- and 7-heptadecenes. On the other hand, 1-octadecene, 4-octadecene, and 5-nonadecene were the major alkene components of the two lichens with cyanobacterial photobionts. These alkadienes and alkenes were present in large quantities in the lichen samples. In particular, 1,8-heptadecadiene accounted for more than 90% of the total alkenes in all four lichens containing it. Our results provide new insights into the origin of C17 alkadienes and C17-C20 alkenes in environmental and geological samples, and these alkenes can potentially be applied as lichen biomarkers.
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Affiliation(s)
- Masashi A Ikeda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10W8, Kita-ku, Sapporo, 060-0810, Japan.
| | - Hideto Nakamura
- Department of Geosciences, Graduate School of Science, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Ken Sawada
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10W8, Kita-ku, Sapporo, 060-0810, Japan; Department of Earth and Planetary Sciences, Faculty of Science, Hokkaido University, N10W8, Kita-ku, Sapporo, 060-0810, Japan
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Ollivier S, Fanuel M, Rogniaux H, Ropartz D. Molecular Networking of High-Resolution Tandem Ion Mobility Spectra: A Structurally Relevant Way of Organizing Data in Glycomics? Anal Chem 2021; 93:10871-10878. [PMID: 34324299 DOI: 10.1021/acs.analchem.1c01244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Data organization through molecular networks has been used in metabolomics over the past years as a way to efficiently mine the massive amount of structural information produced by tandem mass spectrometry (MS). However, glycomics lags a step behind: carbohydrate structures involve numerous levels of isomerism, making MS and tandem MS blind to many key structural features of glycans. This roadblock can in part be alleviated with gas-phase ion mobility spectrometry (IMS), a method highly sensitive to isomerism. In this work, we propose a novel strategy for structural glycomics: molecular networking of high-resolution IMS/IMS spectra. We combine the cutting-edge strategies of tandem IMS and molecular networking of spectral data. We demonstrate that-when it comes to oligosaccharides and their numerous levels of isomerisms-molecular networks based on IMS/IMS spectra are widely superior to MS/MS-based networks to sort and organize molecules with a high degree of structural relevance.
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Affiliation(s)
- Simon Ollivier
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Mathieu Fanuel
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
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Kim W, Liu R, Woo S, Kang KB, Park H, Yu YH, Ha HH, Oh SY, Yang JH, Kim H, Yun SH, Hur JS. Linking a Gene Cluster to Atranorin, a Major Cortical Substance of Lichens, through Genetic Dereplication and Heterologous Expression. mBio 2021; 12:e0111121. [PMID: 34154413 PMCID: PMC8262933 DOI: 10.1128/mbio.01111-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
The depside and depsidone series compounds of polyketide origin accumulate in the cortical or medullary layers of lichen thalli. Despite the taxonomic and ecological significance of lichen chemistry and its pharmaceutical potentials, there has been no single piece of genetic evidence linking biosynthetic genes to lichen substances. Thus, we systematically analyzed lichen polyketide synthases (PKSs) for categorization and identification of the biosynthetic gene cluster (BGC) involved in depside/depsidone production. Our in-depth analysis of the interspecies PKS diversity in the genus Cladonia and a related Antarctic lichen, Stereocaulon alpinum, identified 45 BGC families, linking lichen PKSs to 15 previously characterized PKSs in nonlichenized fungi. Among these, we identified highly syntenic BGCs found exclusively in lichens producing atranorin (a depside). Heterologous expression of the putative atranorin PKS gene (coined atr1) yielded 4-O-demethylbarbatic acid, found in many lichens as a precursor compound, indicating an intermolecular cross-linking activity of Atr1 for depside formation. Subsequent introductions of tailoring enzymes into the heterologous host yielded atranorin, one of the most common cortical substances of macrolichens. Phylogenetic analysis of fungal PKS revealed that the Atr1 is in a novel PKS clade that included two conserved lichen-specific PKS families likely involved in biosynthesis of depsides and depsidones. Here, we provide a comprehensive catalog of PKS families of the genus Cladonia and functionally characterize a biosynthetic gene cluster from lichens, establishing a cornerstone for studying the genetics and chemical evolution of diverse lichen substances. IMPORTANCE Lichens play significant roles in ecosystem function and comprise about 20% of all known fungi. Polyketide-derived natural products accumulate in the cortical and medullary layers of lichen thalli, some of which play key roles in protection from biotic and abiotic stresses (e.g., herbivore attacks and UV irradiation). To date, however, no single lichen product has been linked to respective biosynthetic genes with genetic evidence. Here, we identified a gene cluster family responsible for biosynthesis of atranorin, a cortical substance found in diverse lichen species, by categorizing lichen polyketide synthase and reconstructing the atranorin biosynthetic pathway in a heterologous host. This study will help elucidate lichen secondary metabolism, harnessing the lichen's chemical diversity, hitherto obscured due to limited genetic information on lichens.
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Affiliation(s)
- Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Rundong Liu
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Sunmin Woo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Young Hyun Yu
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Hyung-Ho Ha
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Ji Ho Yang
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Sung-Hwan Yun
- Department of Medical Sciences, Soonchunhyang University, Asan, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
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Ellis CJ, Asplund J, Benesperi R, Branquinho C, Di Nuzzo L, Hurtado P, Martínez I, Matos P, Nascimbene J, Pinho P, Prieto M, Rocha B, Rodríguez-Arribas C, Thüs H, Giordani P. Functional Traits in Lichen Ecology: A Review of Challenge and Opportunity. Microorganisms 2021; 9:766. [PMID: 33917569 PMCID: PMC8067525 DOI: 10.3390/microorganisms9040766] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 01/29/2023] Open
Abstract
Community ecology has experienced a major transition, from a focus on patterns in taxonomic composition, to revealing the processes underlying community assembly through the analysis of species functional traits. The power of the functional trait approach is its generality, predictive capacity such as with respect to environmental change, and, through linkage of response and effect traits, the synthesis of community assembly with ecosystem function and services. Lichens are a potentially rich source of information about how traits govern community structure and function, thereby creating opportunity to better integrate lichens into 'mainstream' ecological studies, while lichen ecology and conservation can also benefit from using the trait approach as an investigative tool. This paper brings together a range of author perspectives to review the use of traits in lichenology, particularly with respect to European ecosystems from the Mediterranean to the Arctic-Alpine. It emphasizes the types of traits that lichenologists have used in their studies, both response and effect, the bundling of traits towards the evolution of life-history strategies, and the critical importance of scale (both spatial and temporal) in functional trait ecology.
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Affiliation(s)
| | - Johan Asplund
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 5003 NO-1432 Ås, Norway;
| | - Renato Benesperi
- Dipartimento di Biologia, Università di Firenze, Via la Pira, 450121 Florence, Italy; (R.B.); (L.D.N.)
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal; (C.B.); (P.P.); (B.R.)
| | - Luca Di Nuzzo
- Dipartimento di Biologia, Università di Firenze, Via la Pira, 450121 Florence, Italy; (R.B.); (L.D.N.)
| | - Pilar Hurtado
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, 28933 Móstoles, Spain; (P.H.); (I.M.); marí (M.P.); (C.R.-A.)
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, c/Darwin, 2, 28049 Madrid, Spain
| | - Isabel Martínez
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, 28933 Móstoles, Spain; (P.H.); (I.M.); marí (M.P.); (C.R.-A.)
| | - Paula Matos
- MARE—Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
| | - Juri Nascimbene
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum, University of Bologna, I-40126 Bologna, Italy;
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal; (C.B.); (P.P.); (B.R.)
| | - María Prieto
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, 28933 Móstoles, Spain; (P.H.); (I.M.); marí (M.P.); (C.R.-A.)
| | - Bernardo Rocha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal; (C.B.); (P.P.); (B.R.)
| | - Clara Rodríguez-Arribas
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, 28933 Móstoles, Spain; (P.H.); (I.M.); marí (M.P.); (C.R.-A.)
| | - Holger Thüs
- Botany Department, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany;
| | - Paolo Giordani
- DIFAR, University of Genova, Viale Cembrano, 4, I-16148 Genova, Italy;
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Studzińska-Sroka E, Majchrzak-Celińska A, Zalewski P, Szwajgier D, Baranowska-Wójcik E, Żarowski M, Plech T, Cielecka-Piontek J. Permeability of Hypogymnia physodes Extract Component-Physodic Acid through the Blood-Brain Barrier as an Important Argument for Its Anticancer and Neuroprotective Activity within the Central Nervous System. Cancers (Basel) 2021; 13:cancers13071717. [PMID: 33916370 PMCID: PMC8038629 DOI: 10.3390/cancers13071717] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/20/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Central nervous system (CNS) diseases, including tumors such as glioblastomas and neurodegenerative diseases, such as Alzheimer’s disease, are some of the greatest challenges of modern medicine. Therefore, our study aimed to evaluate the anticancer and neuroprotective activity of the extract from a common European lichen Hypogymnia physodes and of its compound-physodic acid. The examined substances were cytotoxic against the glioblastoma cell lines A-172, T98G, and U-138 MG. Both substances strongly inhibited hyaluronidase, and diminished cyclooxygenase-2 activity (H. physodes extract), enzymes expressed in patients with malignant glioma. Furthermore, H. physodes extract inhibited tyrosinase activity, the enzyme linked to neurodegenerative diseases. The tested substances exhibited antioxidant activity, however, acetylcholinesterase and butyrylcholinesterase inhibitory activity were not high. We proved that physodic acid can cross the blood–brain barrier. We conclude that physodic acid and H. physodes extract should be regarded as promising agents with anticancer, chemopreventive, and neuroprotective activities, especially concerning CNS. Abstract Lichen secondary metabolites are characterized by huge pharmacological potential. Our research focused on assessing the anticancer and neuroprotective activity of Hypogymnia physodes acetone extract (HP extract) and physodic acid, its major component. The antitumor properties were evaluated by cytotoxicity analysis using A-172, T98G, and U-138 MG glioblastoma cell lines and by hyaluronidase and cyclooxygenase-2 (COX-2) inhibition. The neuroprotective potential was examined using COX-2, tyrosinase, acetylcholinesterase (AChE), and butyrylcholinesterase (BChE) activity tests. Moreover, the antioxidant potential of the tested substances was examined, and the chemical composition of the extract was analyzed. For physodic acid, the permeability through the blood–brain barrier using Parallel Artificial Membrane Permeability Assay for the Blood–Brain Barrier assay (PAMPA-BBB) was assessed. Our study shows that the tested substances strongly inhibited glioblastoma cell proliferation and hyaluronidase activity. Besides, HP extract diminished COX-2 and tyrosinase activity. However, the AChE and BChE inhibitory activity of HP extract and physodic acid were mild. The examined substances exhibited strong antioxidant activity. Importantly, we proved that physodic acid crosses the blood–brain barrier. We conclude that physodic acid and H. physodes should be regarded as promising agents with anticancer, chemopreventive, and neuroprotective activities, especially regarding the central nervous system diseases.
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Affiliation(s)
- Elżbieta Studzińska-Sroka
- Department of Pharmacognosy, Poznan University of Medical Sciences, Święcicki 4 Str, 60-781 Poznań, Poland; (P.Z.); (J.C.-P.)
- Correspondence:
| | - Aleksandra Majchrzak-Celińska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Święcicki 4 Str, 60-781 Poznań, Poland;
| | - Przemysław Zalewski
- Department of Pharmacognosy, Poznan University of Medical Sciences, Święcicki 4 Str, 60-781 Poznań, Poland; (P.Z.); (J.C.-P.)
| | - Dominik Szwajgier
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8 Str, 20‐704 Lublin, Poland; (D.S.); (E.B.-W.)
| | - Ewa Baranowska-Wójcik
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8 Str, 20‐704 Lublin, Poland; (D.S.); (E.B.-W.)
| | - Marcin Żarowski
- Department of Developmental Neurology, Poznan University of Medical Sciences, Przybyszewski 49 Str, 60-355 Poznań, Poland;
| | - Tomasz Plech
- Department of Pharmacology, Medical University of Lublin, Chodźki 4a Str, Lublin, Poland;
| | - Judyta Cielecka-Piontek
- Department of Pharmacognosy, Poznan University of Medical Sciences, Święcicki 4 Str, 60-781 Poznań, Poland; (P.Z.); (J.C.-P.)
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Vaez M, Javad Davarpanah S. New Insights into the Biological Activity of Lichens: Bioavailable Secondary Metabolites of Umbilicaria decussata as Potential Anticoagulants. Chem Biodivers 2021; 18:e2100080. [PMID: 33773025 DOI: 10.1002/cbdv.202100080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/26/2021] [Indexed: 11/09/2022]
Abstract
This study reports the in vitro anticoagulation activity of acetonic extract (AE) of 42 lichen species and the identification of potential bioavailable anticoagulant compounds from Umbilicaria decussata as a competent anticoagulant lichen species. Lichens' AEs were evaluated for their anticoagulant activity by monitoring activated partial thromboplastin time (APTT) and prothrombin time (PT) assays. A strong, positive correlation was observed between total phenolics concentration (TPC) of species and blood coagulation parameters. U. decussata was the only species with the longest clotting time in both APTT and PT assays. The research was moved forward by performing in vivo assays using rats. The results corroborated the dose-dependent impact of U. decussata's AE on rats' clotting time. Major secondary metabolites of U. decussata and their plasma-related bioavailability were also investigated using LC-ESI-MS/MS. Atranol, orsellinic acid, D-mannitol, lecanoric acid, and evernic acid were detected as possible bioavailable anticoagulants of U. decussata. Our findings suggest that U. decussata might be a potential anticoagulant lichen species that can be used for the prevention or treatment of coagulation-related issues such as cardiovascular diseases (CVDs).
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Affiliation(s)
- Mohsen Vaez
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran, 3313193685
| | - Seyed Javad Davarpanah
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran, 1435917341
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Lee S, Suh YJ, Yang S, Hong DG, Ishigami A, Kim H, Hur JS, Chang SC, Lee J. Neuroprotective and Anti-Inflammatory Effects of Evernic Acid in an MPTP-Induced Parkinson's Disease Model. Int J Mol Sci 2021; 22:2098. [PMID: 33672606 PMCID: PMC7924051 DOI: 10.3390/ijms22042098] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress, mitochondrial dysfunction, and neuroinflammation are strongly associated with the pathogenesis of Parkinson's disease (PD), which suggests that anti-oxidative and anti-inflammatory compounds might provide an alternative treatment for PD. Here, we evaluated the neuroprotective effects of evernic aid (EA), which was screened from a lichen library provided by the Korean Lichen Research Institute at Sunchon National University. EA is a secondary metabolite generated by lichens, including Ramalina, Evernia, and Hypogymnia, and several studies have described its anticancer, antifungal, and antimicrobial effects. However, the neuroprotective effects of EA have not been studied. We found that EA protected primary cultured neurons against 1-methyl-4-phenylpyridium (MPP+)-induced cell death, mitochondrial dysfunction, and oxidative stress, and effectively reduced MPP+-induced astroglial activation by inhibiting the NF-κB pathway. In vivo, EA ameliorated MPTP-induced motor dysfunction, dopaminergic neuronal loss, and neuroinflammation in the nigrostriatal pathway in C57BL/6 mice. Taken together, our findings demonstrate that EA has neuroprotective and anti-inflammatory effects in PD models and suggest that EA is a potential therapeutic candidate for PD.
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Affiliation(s)
- Seulah Lee
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan 46241, Korea; (S.L.); (Y.J.S.); (S.Y.); (D.G.H.)
| | - Yeon Ji Suh
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan 46241, Korea; (S.L.); (Y.J.S.); (S.Y.); (D.G.H.)
| | - Seonguk Yang
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan 46241, Korea; (S.L.); (Y.J.S.); (S.Y.); (D.G.H.)
| | - Dong Geun Hong
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan 46241, Korea; (S.L.); (Y.J.S.); (S.Y.); (D.G.H.)
| | - Akihito Ishigami
- Molecular Regulation of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan;
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, Suncheon 57922, Korea;
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
| | - Seung-Cheol Chang
- Department of Cogno-Mechatronics Engineering, College of Nanoscience and Nanotechnology, Pusan National University, Busan 46241, Korea;
| | - Jaewon Lee
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan 46241, Korea; (S.L.); (Y.J.S.); (S.Y.); (D.G.H.)
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Lagarde A, Mambu L, Mai PY, Champavier Y, Stigliani JL, Beniddir MA, Millot M. Chlorinated bianthrones from the cyanolichen Nephroma laevigatum. Fitoterapia 2021; 149:104811. [PMID: 33359429 DOI: 10.1016/j.fitote.2020.104811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 11/25/2022]
Abstract
While depsidones, depsides or dibenzofuran-like compounds dominate the chemical composition of lichens, the cyanolichen Nephroma laevigatum affords a diversity of quinoid pigments represented by chlorinated anthraquinones derived from emodin and new bianthrones resulting from the homo- or heterodimerization of monomers. Bianthrones were pointed out from the dichloromethane extract by MS/MS-based molecular networking, then isolated and characterized on the basis of extensive spectroscopic analyzes and GIAO NMR shift calculation followed by CP3 analyzes.
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Affiliation(s)
- Aurélie Lagarde
- Departement de Pharmacognosie, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Lengo Mambu
- Departement de Pharmacognosie, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France.
| | - Phuong-Y Mai
- Departement de Pharmacognosie, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Yves Champavier
- Plateforme BISCEm, Université de Limoges, 2 Rue du Pr Descottes, 87025 Limoges Cedex, France.
| | - Jean-Luc Stigliani
- Laboratoire de Chimie de Coordination, UPR CNRS 8241, Université de Toulouse UPS, France.
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles", Université Paris-Saclay, CNRS, BioCIS, 5, rue J.-B. Clément, 92290 Châtenay-Malabry, France.
| | - Marion Millot
- Departement de Pharmacognosie, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France.
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Noël A, Garnier A, Clément M, Rouaud I, Sauvager A, Bousarghin L, Vásquez-Ocmín P, Maciuk A, Tomasi S. Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity. PHYTOCHEMISTRY 2021; 181:112535. [PMID: 33099225 DOI: 10.1016/j.phytochem.2020.112535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Lichens are specific symbiotic organisms harboring various microorganisms in addition to the two classic partners (algae or cyanobacterium and fungus). Although lichens produce many antibiotic compounds such as (+)-usnic acid, their associated microorganisms possess the ability to colonize an environment where antibiosis exists. Here, we have studied the behavior of several lichen-associated bacterial strains in the presence of (+)-usnic acid, a known antibiotic lichen compound. The effect of this compound was firstly evaluated on the growth and metabolism of three bacteria, thus showing its ability to inhibit Gram-positive bacteria. This inhibition was not thwarted with the usnic acid producer strain Streptomyces cyaneofuscatus. The biotransformation of this lichen metabolite was also studied. An ethanolamine derivative of (+)-usnic acid with low antibiotic activity was highlighted with chemical profiling, using HPLC-UV combined with low resolution mass spectrometry. These findings highlight the way in which some strains develop resistance mechanisms. A methylated derivative of (+)-usnic acid was annotated using the molecular networking method, thus showing the interest of this computer-based approach in biotransformation studies.
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Affiliation(s)
- Alba Noël
- Univ Rennes, CNRS, ISCR - UMR 6226, F-35000, Rennes, France
| | | | | | | | | | - Latifa Bousarghin
- INSERM, Univ. Rennes, INRA, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), UMR-1241, Biosit, MRic/ISFR, Rennes, France
| | | | - Alexandre Maciuk
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Sophie Tomasi
- Univ Rennes, CNRS, ISCR - UMR 6226, F-35000, Rennes, France.
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Norouzi H, Azizi A, Gholami M, Sohrabi M, Boustie J. Chemotype variations among lichen ecotypes of Umbilicaria aprina as revealed by LC-ESI-MS/MS: a survey of antioxidant phenolics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:40296-40308. [PMID: 32661964 DOI: 10.1007/s11356-020-10053-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
In the present study, we characterized the phytochemical properties, which were specifically associated with phenolic compounds and antioxidant activities in six distinct ecotypes of Umbilicaria aprina Nyl. from Iran (including Kivarestan, Mishan, Takht-e Nader, Tochal, Sabalan, and Sahand) to detect diversities within the species. Total phenolic concentration (TPC) and radical scavenging capacities of U. aprina ecotypes were evaluated. Moreover, qualitative differences between chemical profiles were surveyed using liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Relatively moderate TPCs (Kivarestan = 36.12 ± 2.1, Mishan = 41.59 ± 2.2, Takht-e Nader = 31.85 ± 1.3, Tochal = 37.55 ± 2.3, Sabalan = 28.91 ± 2.5, and Sahand = 31.59 ± 2.2) were observed for ecotypes, but a very strong correlation (r = -0/842) was obtained between TPCs and IC50 values. Based on the results of LC-ESI-MS/MS, the following chemical substances were identified: orsellinic acid (1), lecanoric acid (2), evernic acid (3), gyrophoric acid (4), umbilicaric acid (5), hiascic acid (6), stictic acid (7) methyl hiascic acid (8), and an unknown substance (9). The MS/MS fragmentation scheme for each substance was determined and proposed. Wide discrepancies were observed in the chemical profiles of lichen ecotypes, which may corroborate the influence of ecological locality conditions, for example, altitude and slope aspects on secondary metabolism of lichen species U. aprina. The north-facing and east-facing ecotypes (Sabalan and Mishan, respectively) lacked depsidones (stictic acid) mainly because they receive the least direct radiation. Mishan ecotype, as the only east-facing ecotype, showed the most different chemical profile.
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Affiliation(s)
- Hooman Norouzi
- Department of Horticultural Sciences, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Ali Azizi
- Department of Horticultural Sciences, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Mansour Gholami
- Department of Horticultural Sciences, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Sohrabi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Joel Boustie
- Institute of Chemistry of Rennes, ISCR, UMR CNRS 6226, University of Rennes 1, 2 Av. du Pr. Leon Bernard, 35043, Rennes Cedex, France
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Devi AP, Duong TH, Ferron S, Beniddir MA, Dinh MH, Nguyen VK, Pham NKT, Mac DH, Boustie J, Chavasiri W, Pogam PL. Salazinic Acid-Derived Depsidones and Diphenylethers with α-Glucosidase Inhibitory Activity from the Lichen Parmotrema dilatatum. PLANTA MEDICA 2020; 86:1216-1224. [PMID: 32819010 DOI: 10.1055/a-1203-0623] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Three new depsidones, parmosidones F - G (1 - 2), and 8'-O-methylsalazinic acid (3), and 3 new diphenylethers, parmetherines A - C (4 - 6), together with 2 known congeners were isolated from the whole thalli of Parmotrema dilatatum, a foliose chlorolichen. Their structures were unambiguously determined by extensive spectroscopic analyses and comparison with literature data. The isolated polyphenolics were assayed for their α-glucosidase inhibitory activities. Newly reported benzylated depsidones 1: and 2: in particular inhibited α-glucosidase with IC50 values of 2.2 and 4.3 µM, respectively, and are thus more potent than the positive control, acarbose.
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Affiliation(s)
- Asshaima Paramita Devi
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Thuc-Huy Duong
- Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Vietnam
| | - Solenn Ferron
- Université Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, Rennes, France
| | - Mehdi A Beniddir
- Équipe «Pharmacognosie-Chimie des Substances Naturelles», BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Minh-Hiep Dinh
- Management Board of Ho Chi Minh City Agricultural Hi-Tech Park, Binh Thanh, Ho Chi Minh City, Vietnam
| | - Van-Kieu Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang, Vietnam
| | | | - Dinh-Hung Mac
- Department of Organic Chemistry, VNU University of Science, Hoan Kiem, Hanoi, Vietnam
| | - Joël Boustie
- Université Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, Rennes, France
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Pierre Le Pogam
- Équipe «Pharmacognosie-Chimie des Substances Naturelles», BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
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N'Tamon AD, Okpekon AT, Bony NF, Bernadat G, Gallard JF, Kouamé T, Séon-Méniel B, Leblanc K, Rharrabti S, Mouray E, Grellier P, Ake M, Amin NC, Champy P, Beniddir MA, Le Pogam P. Streamlined targeting of Amaryllidaceae alkaloids from the bulbs of Crinum scillifolium using spectrometric and taxonomically-informed scoring metabolite annotations. PHYTOCHEMISTRY 2020; 179:112485. [PMID: 32861139 DOI: 10.1016/j.phytochem.2020.112485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Four undescribed alkaloids have been isolated from the bulbs of the previously unstudied Crinum scillifolium. These compounds were targeted following a state-of-the-art molecular networking strategy comprising a dereplication against in silico databases and re-ranking of the candidate structures based on taxonomically informed scoring. The unreported structures span across a variety of Amaryllidaceae alkaloids appendages. Their structures were unambiguously elucidated by thorough interpretation of their HRESIMS and 1D and 2D NMR data, and comparison to literature data. DFT-NMR calculations were performed to support the determined relative configurations of scillitazettine and scilli-N-desmethylpretazettine and their absolute configurations were mitigated by comparison between experimental and theoretically calculated ECD spectra. The lack of a methyl group on the nitrogen atom in the structure of scilli-N-desmethylpretazettine series is highly unusual in the pretazettine/tazettine series but the most original structural feature in it lies in its 11α disposed hydrogen, which is new to pretazettines. The antiplasmodial as well as the cytotoxic activities against the human colon cancer cell line HCT116 were evaluated, revealing mild to null activities.
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Affiliation(s)
- Amon Diane N'Tamon
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France; Département de Chimie Analytique, Minérale et Générale, Technologie Alimentaire, UFR Sciences Pharmaceutiques et Biologiques, Univ. FHB, 06 B. P. 2256, Abidjan 06, Cote d'Ivoire
| | - Aboua Timothée Okpekon
- Laboratoire de Chimie Organique et de Substances Naturelles (LCOSN), UFR Sciences des Structures de la Matière et Technologie, Univ. FHB, 22 BP 582, Abidjan 22, Cote d'Ivoire
| | - Nicaise F Bony
- Département de Chimie Analytique, Minérale et Générale, Technologie Alimentaire, UFR Sciences Pharmaceutiques et Biologiques, Univ. FHB, 06 B. P. 2256, Abidjan 06, Cote d'Ivoire
| | | | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay, 21 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Tapé Kouamé
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France; Laboratoire de Chimie Organique et de Substances Naturelles (LCOSN), UFR Sciences des Structures de la Matière et Technologie, Univ. FHB, 22 BP 582, Abidjan 22, Cote d'Ivoire
| | | | - Karine Leblanc
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Somia Rharrabti
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Elisabeth Mouray
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR7245, CP54, 57, Rue Cuvier, 75005, Paris, France
| | - Philippe Grellier
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR7245, CP54, 57, Rue Cuvier, 75005, Paris, France
| | - Michèle Ake
- Département de Chimie Analytique, Minérale et Générale, Technologie Alimentaire, UFR Sciences Pharmaceutiques et Biologiques, Univ. FHB, 06 B. P. 2256, Abidjan 06, Cote d'Ivoire
| | - N'Cho Christophe Amin
- Département de Chimie Analytique, Minérale et Générale, Technologie Alimentaire, UFR Sciences Pharmaceutiques et Biologiques, Univ. FHB, 06 B. P. 2256, Abidjan 06, Cote d'Ivoire
| | - Pierre Champy
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France.
| | - Pierre Le Pogam
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France.
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Calla-Quispe E, Fuentes-Rivera HL, Ramírez P, Martel C, Ibañez AJ. Mass Spectrometry: A Rosetta Stone to Learn How Fungi Interact and Talk. Life (Basel) 2020; 10:E89. [PMID: 32575729 PMCID: PMC7345136 DOI: 10.3390/life10060089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/08/2023] Open
Abstract
Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, such as soluble compounds that are secreted into the medium and volatile compounds that are chemical mediators over short and long distances. Mass spectrometry (MS) is currently playing a dominant role in mycological studies, mainly due to its inherent sensitivity and rapid identification capabilities of different metabolites. Furthermore, MS has also been used as a reliable and accurate tool for fungi identification (i.e., biotyping). Here, we introduce the readers about fungal specialized metabolites, their role in ecological interactions and provide an overview on the MS-based techniques used in fungal studies. We particularly present the importance of sampling techniques, strategies to reduce false-positive identification and new MS-based analytical strategies that can be used in mycological studies, further expanding the use of MS in broader applications. Therefore, we foresee a bright future for mass spectrometry-based research in the field of mycology.
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Affiliation(s)
- Erika Calla-Quispe
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
| | - Hammerly Lino Fuentes-Rivera
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Germán Amézaga 375, Lima 15081, Peru;
| | - Pablo Ramírez
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Germán Amézaga 375, Lima 15081, Peru;
| | - Carlos Martel
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Arenales 1256, Jesús María 15072, Lima, Peru
| | - Alfredo J. Ibañez
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
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Molecular Network-Guided Alkaloid Profiling of Aerial Parts of Papaver nudicaule L. Using LC-HRMS. Molecules 2020; 25:molecules25112636. [PMID: 32517053 PMCID: PMC7321159 DOI: 10.3390/molecules25112636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022] Open
Abstract
Papaver nudicaule L. (Iceland poppy) is widely used for ornamental purposes. A previous study demonstrated the alleviation of lipopolysaccharide-induced inflammation mediated by P. nudicaule extract through nuclear factor-kappa B and signal transducer and activator of transcription 3 inactivation. As isoquinoline alkaloids are chemical markers and bioactive constituents of Papaver species, the present study investigated the alkaloid profile of aerial parts of five P. nudicaule cultivars with different flower colors and a P. rhoeas cropped for two years. A combination of liquid chromatography high-resolution mass spectrometry and molecular networking was used to cluster isoquinoline alkaloids in the species and highlight the possible metabolites. Aside from the 12 compounds, including rotundine, muramine, and allocryptopine, identified from Global Natural Products Social library and reported information, 46 structurally related metabolites were quantitatively investigated. Forty-two and 16 compounds were proposed for chemical profiles of P. nudicaule and P. rhoeas, respectively. Some species-specific metabolites showed similar fragmentation patterns. The alkaloid abundance of P. nudicaule differed depending on the flower color, and the possible chemical markers were proposed. These results show that molecular networking-guided dereplication allows investigation of unidentified metabolites. The derived chemical profile may facilitate evaluation of P. nudicaule quality for pharmacological applications.
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Sorokina M, Steinbeck C. Review on natural products databases: where to find data in 2020. J Cheminform 2020; 12:20. [PMID: 33431011 PMCID: PMC7118820 DOI: 10.1186/s13321-020-00424-9] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/22/2020] [Indexed: 02/06/2023] Open
Abstract
Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.
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Affiliation(s)
- Maria Sorokina
- University Friedrich-Schiller, Lessing Strasse 8, 07743, Jena, Germany.
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