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Li XL, Zhang JQ, Shen XJ, Zhang Y, Guo DA. Overview and limitations of database in global traditional medicines: A narrative review. Acta Pharmacol Sin 2024:10.1038/s41401-024-01353-1. [PMID: 39095509 DOI: 10.1038/s41401-024-01353-1] [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: 07/27/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
The study of traditional medicine has garnered significant interest, resulting in various research areas including chemical composition analysis, pharmacological research, clinical application, and quality control. The abundance of available data has made databases increasingly essential for researchers to manage the vast amount of information and explore new drugs. In this article we provide a comprehensive overview and summary of 182 databases that are relevant to traditional medicine research, including 73 databases for chemical component analysis, 70 for pharmacology research, and 39 for clinical application and quality control from published literature (2000-2023). The review categorizes the databases by functionality, offering detailed information on websites and capacities to facilitate easier access. Moreover, this article outlines the primary function of each database, supplemented by case studies to aid in database selection. A practical test was conducted on 68 frequently used databases using keywords and functionalities, resulting in the identification of highlighted databases. This review serves as a reference for traditional medicine researchers to choose appropriate databases and also provides insights and considerations for the function and content design of future databases.
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Affiliation(s)
- Xiao-Lan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Qing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xuan-Jing Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Pérez-Victoria I. Natural Products Dereplication: Databases and Analytical Methods. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2024; 124:1-56. [PMID: 39101983 DOI: 10.1007/978-3-031-59567-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
The development of efficient methods for dereplication has been critical in the re-emergence of the research in natural products as a source of drug leads. Current dereplication workflows rapidly identify already known bioactive secondary metabolites in the early stages of any drug discovery screening campaign based on natural extracts or enriched fractions. Two main factors have driven the evolution of natural products dereplication over the last decades. First, the availability of both commercial and public large databases of natural products containing the key annotations against which the biological and chemical data derived from the studied sample are searched for. Second, the considerable improvement achieved in analytical technologies (including instrumentation and software tools) employed to obtain robust and precise chemical information (particularly spectroscopic signatures) on the compounds present in the bioactive natural product samples. This chapter describes the main methods of dereplication, which rely on the combined use of large natural product databases and spectral libraries, alongside the information obtained from chromatographic, UV-Vis, MS, and NMR spectroscopic analyses of the samples of interest.
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Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de La Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain.
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3
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Sahayasheela VJ, Lankadasari MB, Dan VM, Dastager SG, Pandian GN, Sugiyama H. Artificial intelligence in microbial natural product drug discovery: current and emerging role. Nat Prod Rep 2022; 39:2215-2230. [PMID: 36017693 PMCID: PMC9931531 DOI: 10.1039/d2np00035k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: up to the end of 2022Microorganisms are exceptional sources of a wide array of unique natural products and play a significant role in drug discovery. During the golden era, several life-saving antibiotics and anticancer agents were isolated from microbes; moreover, they are still widely used. However, difficulties in the isolation methods and repeated discoveries of the same molecules have caused a setback in the past. Artificial intelligence (AI) has had a profound impact on various research fields, and its application allows the effective performance of data analyses and predictions. With the advances in omics, it is possible to obtain a wealth of information for the identification, isolation, and target prediction of secondary metabolites. In this review, we discuss drug discovery based on natural products from microorganisms with the help of AI and machine learning.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
| | - Manendra B Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vipin Mohan Dan
- Microbiology Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, Kerala, India
| | - Syed G Dastager
- NCIM Resource Centre, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan
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4
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Liu Z, Tong X, Liu R, Zou L. Metabolome and Transcriptome Profiling Reveal That Four Terpenoid Hormones Dominate the Growth and Development of Sanghuangporus baumii. J Fungi (Basel) 2022; 8:jof8070648. [PMID: 35887404 PMCID: PMC9317858 DOI: 10.3390/jof8070648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Sanghuangporus baumii is a traditional medicinal fungus that produces pharmacological terpenoids, but natural resources are insufficient for applications, and its growth and development mechanisms are poorly understood. Combining metabolomic and transcriptomic analyses, we found four terpenoid hormones and a central gene, isopentenyl diphosphate isomerase (IDI), involved in growth and development. Additionally, an exogenous hormone test was used to further confirm the importance of the four terpenoid hormones. Finally, hormone content determination and qRT−PCR were performed to explore the growth and development mechanism; we found thatcis-zeatin (CZ) plays a major role in the mycelia stage, trans-zeatin (TZ) and gibberellin A4 (GA4) are important in the primordia stage, GA4 is crucial for the fruiting bodies stage, and abscisic acid (ABA) may be a marker of maturity. The IDI gene was also found to affectterpenoid hormone content by regulating the relative gene transcript levels, thereby controlling morphological changes in S. baumii. Our results revealthe growth and development mechanisms of S. baumii and may promote the breeding and utilisation of high-quality varieties.
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Affiliation(s)
| | | | | | - Li Zou
- Correspondence: ; Tel.: +86-0451-86660457
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5
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Differential Accumulation of Metabolites and Transcripts Related to Flavonoid, Styrylpyrone, and Galactolipid Biosynthesis in Equisetum Species and Tissue Types. Metabolites 2022; 12:metabo12050403. [PMID: 35629907 PMCID: PMC9146389 DOI: 10.3390/metabo12050403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Three species of the genus Equisetum (E. arvense, E. hyemale, and E. telmateia) were selected for an analysis of chemical diversity in an ancient land plant lineage. Principal component analysis of metabolomics data obtained with above-ground shoot and below-ground rhizome extracts enabled a separation of all sample types, indicating species- and organ-specific patterns of metabolite accumulation. Follow-up efforts indicated that galactolipids, carotenoids, and flavonoid glycosides contributed positively to the separation of shoot samples, while stryrylpyrone glycosides and phenolic glycosides were the most prominent positive contributors to the separation of rhizome samples. Consistent with metabolite data, genes coding for enzymes of flavonoid and galactolipid biosynthesis were found to be expressed at elevated levels in shoot samples, whereas a putative styrylpyrone synthase gene was expressed preferentially in rhizomes. The current study builds a foundation for future endeavors to further interrogate the organ and tissue specificity of metabolism in the last living genus of a fern family that was prevalent in the forests of the late Paleozoic era.
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6
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Wishart DS, Sayeeda Z, Budinski Z, Guo A, Lee BL, Berjanskii M, Rout M, Peters H, Dizon R, Mah R, Torres-Calzada C, Hiebert-Giesbrecht M, Varshavi D, Varshavi D, Oler E, Allen D, Cao X, Gautam V, Maras A, Poynton EF, Tavangar P, Yang V, van Santen JA, Ghosh R, Sarma S, Knutson E, Sullivan V, Jystad AM, Renslow R, Sumner LW, Linington RG, Cort JR. NP-MRD: the Natural Products Magnetic Resonance Database. Nucleic Acids Res 2021; 50:D665-D677. [PMID: 34791429 PMCID: PMC8728158 DOI: 10.1093/nar/gkab1052] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/15/2022] Open
Abstract
The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites and other biologically derived chemicals. NMR spectroscopy has long been viewed as the ‘gold standard’ for the structure determination of novel natural products and novel metabolites. NMR is also widely used in natural product dereplication and the characterization of biofluid mixtures (metabolomics). All of these NMR applications require large collections of high quality, well-annotated, referential NMR spectra of pure compounds. Unfortunately, referential NMR spectral collections for natural products are quite limited. It is because of the critical need for dedicated, open access natural product NMR resources that the NP-MRD was funded by the National Institute of Health (NIH). Since its launch in 2020, the NP-MRD has grown quickly to become the world's largest repository for NMR data on natural products and other biological substances. It currently contains both structural and NMR data for nearly 41,000 natural product compounds from >7400 different living species. All structural, spectroscopic and descriptive data in the NP-MRD is interactively viewable, searchable and fully downloadable in multiple formats. Extensive hyperlinks to other databases of relevance are also provided. The NP-MRD also supports community deposition of NMR assignments and NMR spectra (1D and 2D) of natural products and related meta-data. The deposition system performs extensive data enrichment, automated data format conversion and spectral/assignment evaluation. Details of these database features, how they are implemented and plans for future upgrades are also provided. The NP-MRD is available at https://np-mrd.org.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.,Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Zinat Sayeeda
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Zachary Budinski
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - AnChi Guo
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Raynard Dizon
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Robert Mah
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | | | | | - Dorna Varshavi
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Dorsa Varshavi
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Dana Allen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Xuan Cao
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Andrew Maras
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ella F Poynton
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Pegah Tavangar
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Vera Yang
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Rajarshi Ghosh
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,MU Metabolomics Center, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Saurav Sarma
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,MU Metabolomics Center, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Eleanor Knutson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Victoria Sullivan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Amy M Jystad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ryan Renslow
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lloyd W Sumner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,MU Metabolomics Center, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - John R Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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7
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Lange BM, Conner CF. Taxanes and taxoids of the genus Taxus - A comprehensive inventory of chemical diversity. PHYTOCHEMISTRY 2021; 190:112829. [PMID: 34329937 PMCID: PMC8393860 DOI: 10.1016/j.phytochem.2021.112829] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/12/2021] [Accepted: 06/02/2021] [Indexed: 05/05/2023]
Abstract
The pseudoalkaloid diterpene Taxol® (paclitaxel) emerged as a best-selling anti-cancer drug in the mid-1990s. The compound attracted considerable interest because of its unique mechanism to stabilize microtubules, thus reducing dynamicity and ultimately promoting mitotic arrest. Taxol was originally isolated from members of the genus Taxus. Over the last 50 years, close to 600 metabolites with taxane scaffolds were isolated from various Taxus species and their structures reported. The present review article provides an overview of the known chemical diversity of taxanes, with an emphasis on the functionalization of diterpene scaffolds. The implications of the occurrence of chemically diverse taxane metabolites for unraveling Taxol biosynthesis and enabling pathway engineering are discussed as well.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA.
| | - Caleb F Conner
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA
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8
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Kikuchi J, Yamada S. The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science. RSC Adv 2021; 11:30426-30447. [PMID: 35480260 PMCID: PMC9041152 DOI: 10.1039/d1ra03008f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022] Open
Abstract
The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.
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Affiliation(s)
- Jun Kikuchi
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8601 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Shunji Yamada
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Prediction Science Laboratory, RIKEN Cluster for Pioneering Research 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
- Data Assimilation Research Team, RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
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9
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Sorokina M, Merseburger P, Rajan K, Yirik MA, Steinbeck C. COCONUT online: Collection of Open Natural Products database. J Cheminform 2021; 13:2. [PMID: 33423696 PMCID: PMC7798278 DOI: 10.1186/s13321-020-00478-9] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net .
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Affiliation(s)
- Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Peter Merseburger
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Mehmet Aziz Yirik
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
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10
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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: 205] [Impact Index Per Article: 51.3] [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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11
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Marchev AS, Yordanova ZP, Georgiev MI. Green (cell) factories for advanced production of plant secondary metabolites. Crit Rev Biotechnol 2020; 40:443-458. [PMID: 32178548 DOI: 10.1080/07388551.2020.1731414] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For centuries plants have been intensively utilized as reliable sources of food, flavoring, agrochemical and pharmaceutical ingredients. However, plant natural habitats are being rapidly lost due to climate change and agriculture. Plant biotechnology offers a sustainable method for the bioproduction of plant secondary metabolites using plant in vitro systems. The unique structural features of plant-derived secondary metabolites, such as their safety profile, multi-target spectrum and "metabolite likeness," have led to the establishment of many plant-derived drugs, comprising approximately a quarter of all drugs approved by the Food and Drug Administration and/or European Medicinal Agency. However, there are still many challenges to overcome to enhance the production of these metabolites from plant in vitro systems and establish a sustainable large-scale biotechnological process. These challenges are due to the peculiarities of plant cell metabolism, the complexity of plant secondary metabolite pathways, and the correct selection of bioreactor systems and bioprocess optimization. In this review, we present an integrated overview of the possible avenues for enhancing the biosynthesis of high-value marketable molecules produced by plant in vitro systems. These include metabolic engineering and CRISPR/Cas9 technology for the regulation of plant metabolism through overexpression/repression of single or multiple structural genes or transcriptional factors. The use of NMR-based metabolomics for monitoring metabolite concentrations and additionally as a tool to study the dynamics of plant cell metabolism and nutritional management is discussed here. Different types of bioreactor systems, their modification and optimal process parameters for the lab- or industrial-scale production of plant secondary metabolites are specified.
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Affiliation(s)
- Andrey S Marchev
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
| | - Zhenya P Yordanova
- Department of Plant Physiology, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Milen I Georgiev
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
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12
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Srividya N, Lange I, Hartmann M, Li Q, Mirzaei M, Lange BM. Biochemical characterization of acyl activating enzymes for side chain moieties of Taxol and its analogs. J Biol Chem 2020; 295:4963-4973. [PMID: 32086380 DOI: 10.1074/jbc.ra120.012663] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/14/2020] [Indexed: 12/24/2022] Open
Abstract
Taxol (paclitaxel) is a very widely used anticancer drug, but its commercial sources mainly consist of stripped bark or suspension cultures of members of the plant genus Taxus. Taxol accumulates as part of a complex mixture of chemical analogs, termed taxoids, which complicates its production in pure form, highlighting the need for metabolic engineering approaches for high-level Taxol production in cell cultures or microbial hosts. Here, we report on the characterization of acyl-activating enzymes (AAEs) that catalyze the formation of CoA esters of different organic acids relevant for the N-substitution of the 3-phenylisoserine side chain of taxoids. On the basis of similarities to AAE genes of known function from other organisms, we identified candidate genes in publicly available transcriptome data sets obtained with Taxus × media. We cloned 17 AAE genes, expressed them heterologously in Escherichia coli, purified the corresponding recombinant enzymes, and performed in vitro assays with 27 organic acids as potential substrates. We identified TmAAE1 and TmAAE5 as the most efficient enzymes for the activation of butyric acid (Taxol D side chain), TmAAE13 as the best candidate for generating a CoA ester of tiglic acid (Taxol B side chain), TmAAE3 and TmAAE13 as suitable for the activation of 4-methylbutyric acid (N-debenzoyl-N-(2-methylbutyryl)taxol side chain), TmAAE15 as a highly efficient candidate for hexanoic acid activation (Taxol C side chain), and TmAAE4 as suitable candidate for esterification of benzoic acid with CoA (Taxol side chain). This study lays important groundwork for metabolic engineering efforts aimed at improving Taxol production in cell cultures.
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Affiliation(s)
- Narayanan Srividya
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Michael Hartmann
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Qunrui Li
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Maryam Mirzaei
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Bernd Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
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Johnson SR, Bhat WW, Bibik J, Turmo A, Hamberger B, Evolutionary Mint Genomics Consortium, Hamberger B. A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). J Biol Chem 2019; 294:1349-1362. [PMID: 30498089 PMCID: PMC6349103 DOI: 10.1074/jbc.ra118.006025] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/12/2018] [Indexed: 12/30/2022] Open
Abstract
Members of the mint family (Lamiaceae) accumulate a wide variety of industrially and medicinally relevant diterpenes. We recently sequenced leaf transcriptomes from 48 phylogenetically diverse Lamiaceae species. Here, we summarize the available chemotaxonomic and enzyme activity data for diterpene synthases (diTPSs) in the Lamiaceae and leverage the new transcriptomes to explore the diTPS sequence and functional space. Candidate genes were selected with an intent to evenly sample the sequence homology space and to focus on species in which diTPS transcripts were found, yet from which no diterpene structures have been previously reported. We functionally characterized nine class II diTPSs and 10 class I diTPSs from 11 distinct plant species and found five class II activities, including two novel activities, as well as a spectrum of class I activities. Among the class II diTPSs, we identified a neo-cleroda-4(18),13E-dienyl diphosphate synthase from Ajuga reptans, catalyzing the likely first step in the biosynthesis of a variety of insect-antifeedant compounds. Among the class I diTPSs was a palustradiene synthase from Origanum majorana, leading to the discovery of specialized diterpenes in that species. Our results provide insights into the diversification of diterpene biosynthesis in the mint family and establish a comprehensive foundation for continued investigation of diterpene biosynthesis in the Lamiaceae.
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Affiliation(s)
- Sean R Johnson
- Departments of Biochemistry and Molecular Biology, East Lansing, Michigan 48824
| | - Wajid Waheed Bhat
- Departments of Biochemistry and Molecular Biology, East Lansing, Michigan 48824; Pharmacology and Toxicology, East Lansing, Michigan 48824
| | - Jacob Bibik
- Departments of Biochemistry and Molecular Biology, East Lansing, Michigan 48824
| | - Aiko Turmo
- Departments of Biochemistry and Molecular Biology, East Lansing, Michigan 48824
| | - Britta Hamberger
- Departments of Biochemistry and Molecular Biology, East Lansing, Michigan 48824
| | | | - Björn Hamberger
- Departments of Biochemistry and Molecular Biology, East Lansing, Michigan 48824.
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14
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Šamec D, Pierz V, Srividya N, Wüst M, Lange BM. Assessing Chemical Diversity in Psilotum nudum (L.) Beauv., a Pantropical Whisk Fern That Has Lost Many of Its Fern-Like Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:868. [PMID: 31354756 PMCID: PMC6629931 DOI: 10.3389/fpls.2019.00868] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/18/2019] [Indexed: 05/10/2023]
Abstract
Members of the Psilotales (whisk ferns) have a unique anatomy, with conducting tissues but lacking true leaves and roots. Based on recent phyogenies, these features appear to represent a reduction from a more typical modern fern plant rather than the persistence of ancestral features. In this study, extracts of several Psilotum organs and tissues were analyzed by Gas Chromatography - Mass Spectrometry (GC-MS) and High Performance Liquid Chromatography - Quadrupole Time of Flight - Mass Spectrometry (HPLC-QTOF-MS). Some arylpyrones and biflavonoids had previously been reported to occur in Psilotum and these metabolite classes were found to be prominent constituents in the present study. Some of these were enriched and further characterized by Nuclear Magnetic Resonance (NMR) spectroscopy. HPLC-QTOF-MS and NMR data were searched against an updated Spektraris database (expanded by incorporating over 300 new arylpyrone and biflavonoid spectral records) to aid significantly with peak annotation. Principal Component Analysis (PCA) with combined GC-MS and HPLC-QTOF-MS data sets obtained with several Psilotum organs and tissues indicated a clear separation of the sample types. The principal component scores for below-ground rhizome samples corresponded to the vectors for carbohydrate monomers and dimers and small organic acids. Above-ground rhizome samples had principal component scores closer to the direction of vectors for arylpyrone glycosides and sucrose (which had high concentrations in above-and below-ground rhizomes). The unique position of brown synangia in a PCA plot correlated with the vector for biflavonoid glycosides. Principal component scores for green and yellow synangia correlated with the direction of vectors for arylpyrone glycosides and biflavonoid aglycones. Localization studies with cross sections of above-ground rhizomes, using Matrix-Assisted Laser Desorption/Ionization - Mass Spectrometry (MALDI-MS), provided evidence for a preferential accumulation of arylpyrone glycosides and biflavonoid aglycones in cells of the chlorenchyma. Our results indicate a differential localization of metabolites with potentially tissue-specific functions in defenses against biotic and abiotic stresses. The data are also a foundation for follow-up work to better understand chemical diversity in the Psilotales and other members of the fern lineage.
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Affiliation(s)
- Dunja Šamec
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- Ruđer Bošković Institute, Zagreb, Croatia
| | - Verena Pierz
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- Chair of Bioanalytics, Institute of Nutritional and Food Sciences, University of Bonn, Bonn, Germany
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Matthias Wüst
- Chair of Bioanalytics, Institute of Nutritional and Food Sciences, University of Bonn, Bonn, Germany
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- *Correspondence: B. Markus Lange,
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15
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Gomes NG, Pereira DM, Valentão P, Andrade PB. Hybrid MS/NMR methods on the prioritization of natural products: Applications in drug discovery. J Pharm Biomed Anal 2018; 147:234-249. [DOI: 10.1016/j.jpba.2017.07.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/17/2022]
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16
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Inabuy FS, Fischedick JT, Lange I, Hartmann M, Srividya N, Parrish AN, Xu M, Peters RJ, Lange BM. Biosynthesis of Diterpenoids in Tripterygium Adventitious Root Cultures. PLANT PHYSIOLOGY 2017; 175:92-103. [PMID: 28751314 PMCID: PMC5580761 DOI: 10.1104/pp.17.00659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/18/2017] [Indexed: 05/22/2023]
Abstract
Adventitious root cultures were developed from Tripterygium regelii, and growth conditions were optimized for the abundant production of diterpenoids, which can be collected directly from the medium. An analysis of publicly available transcriptome data sets collected with T. regelii roots and root cultures indicated the presence of a large gene family (with 20 members) for terpene synthases (TPSs). Nine candidate diterpene synthase genes were selected for follow-up functional evaluation, of which two belonged to the TPS-c, three to the TPS-e/f, and four to the TPS-b subfamilies. These genes were characterized by heterologous expression in a modular metabolic engineering system in Escherichia coli Members of the TPS-c subfamily were characterized as copalyl diphosphate (diterpene) synthases, and those belonging to the TPS-e/f subfamily catalyzed the formation of precursors of kaurane diterpenoids. The TPS-b subfamily encompassed genes coding for enzymes involved in abietane diterpenoid biosynthesis and others with activities as monoterpene synthases. The structural characterization of diterpenoids accumulating in the medium of T. regelii adventitious root cultures, facilitated by searching the Spektraris online spectral database, enabled us to formulate a biosynthetic pathway for the biosynthesis of triptolide, a diterpenoid with pharmaceutical potential. Considering the significant enrichment of diterpenoids in the culture medium, fast-growing adventitious root cultures may hold promise as a sustainable resource for the large-scale production of triptolide.
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Affiliation(s)
- Fainmarinat S Inabuy
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Justin T Fischedick
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Michael Hartmann
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Amber N Parrish
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Meimei Xu
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-1079
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-1079
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
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17
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Kikuchi J, Yamada S. NMR window of molecular complexity showing homeostasis in superorganisms. Analyst 2017; 142:4161-4172. [DOI: 10.1039/c7an01019b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
NMR offers tremendous advantages in the analyses of molecular complexity. The “big-data” are produced during the acquisition of fingerprints that must be stored and shared for posterior analysis and verifications.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science
- Yokohama
- Japan
- Graduate School of Bioagricultural Sciences
- Nagoya University
| | - Shunji Yamada
- RIKEN Center for Sustainable Resource Science
- Yokohama
- Japan
- Graduate School of Bioagricultural Sciences
- Nagoya University
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18
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Lange BM, Fischedick JT, Lange MF, Srividya N, Šamec D, Poirier BC. Integrative Approaches for the Identification and Localization of Specialized Metabolites in Tripterygium Roots. PLANT PHYSIOLOGY 2017; 173:456-469. [PMID: 27864443 PMCID: PMC5210757 DOI: 10.1104/pp.15.01593] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/13/2016] [Indexed: 05/16/2023]
Abstract
Members of the genus Tripterygium are known to contain an astonishing diversity of specialized metabolites. The lack of authentic standards has been an impediment to the rapid identification of such metabolites in extracts. We employed an approach that involves the searching of multiple, complementary chromatographic and spectroscopic data sets against the Spektraris database to speed up the metabolite identification process. Mass spectrometry-based imaging indicated a differential localization of triterpenoids to the periderm and sesquiterpene alkaloids to the cortex layer of Tripterygium roots. We further provide evidence that triterpenoids are accumulated to high levels in cells that contain suberized cell walls, which might indicate a mechanism for storage. To our knowledge, our data provide first insights into the cell type specificity of metabolite accumulation in Tripterygium and set the stage for furthering our understanding of the biological implications of specialized metabolites in this genus.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.);
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Justin T Fischedick
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Malte F Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Dunja Šamec
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Brenton C Poirier
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
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Kobusiak-Prokopowicz M, Marciniak A, Ślusarczyk S, Ściborski K, Stachurska A, Mysiak A, Matkowski A. A suicide attempt by intoxication with Taxus baccata leaves and ultra-fast liquid chromatography-electrospray ionization-tandem mass spectrometry, analysis of patient serum and different plant samples: case report. BMC Pharmacol Toxicol 2016; 17:41. [PMID: 27577698 PMCID: PMC5006531 DOI: 10.1186/s40360-016-0078-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Taxus (yew) is one of the most frequently reported plants causing potentially fatal outcome when taken incidentally or for suicidal reasons. A fast and reliable method of detection of poisonous compounds or their metabolites is critical in life-saving procedures in cases of yew ingestion. Previously, several chromatographic analytical procedures have been described usually taking longer than one hour of total analysis time. CASE PRESENTATION In this report we describe a suicide case study and an ad hoc developed fast method of detection and quantitation of 3,5-dimethoxyphenol - the main taxane metabolite in the blood plasma from the patient as well as the determination of major taxine components in the plant material (Taxus baccata). At present, there is no reasonable alternative for mass spectrometry that could match its high sensitivity and accuracy, and Multiple Reaction Monitoring could be adequate and useful mass spectrometry technique in analyzing and identification of plants material compounds that cause severe poisoning in humans. In the reported case, intensive cardiac care together with the astuteness of the treating physicians not only saved the patient's life, but also allowed for his complete recovery and return to work. CONCLUSIONS The development of ultra fast liquid chromatography tandem mass spectrometry UFLC-MS/MS method provides a fast means to confirm yew alkaloids and their metabolite in various material. The applied analytical procedure allows early detection of main metabolite in patient material as well as comparing to those extracted from the plant. In our study, the taxanes remained undetected, probably due to the time elapsing from the patient admittance and collection of plasma. In cases like those reported in this study, retaining the gastric material should be obligatory to confirm the ingestion of yew. The possibility of using this approach in detection of native taxine compounds in human plasma remains to be verified.
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Affiliation(s)
| | - Anna Marciniak
- Department of Cardiology, Medical University of Wroclaw, ul. Borowska 213, Wroclaw, 50-556, Poland
| | - Sylwester Ślusarczyk
- Department of Pharmaceutical Biology and Botany, Medical University of Wroclaw, Wroclaw, Poland.,Department of Biochemistry, IUNG Institute of Plant Cultivation and Soil Science, Pulawy, Poland
| | - Krzysztof Ściborski
- Department of Cardiology, Medical University of Wroclaw, ul. Borowska 213, Wroclaw, 50-556, Poland
| | - Aneta Stachurska
- Department of Cardiology, Medical University of Wroclaw, ul. Borowska 213, Wroclaw, 50-556, Poland
| | - Andrzej Mysiak
- Department of Cardiology, Medical University of Wroclaw, ul. Borowska 213, Wroclaw, 50-556, Poland
| | - Adam Matkowski
- Department of Pharmaceutical Biology and Botany, Medical University of Wroclaw, Wroclaw, Poland
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20
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Johnson SR, Lange BM. Open-access metabolomics databases for natural product research: present capabilities and future potential. Front Bioeng Biotechnol 2015; 3:22. [PMID: 25789275 PMCID: PMC4349186 DOI: 10.3389/fbioe.2015.00022] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/14/2015] [Indexed: 12/24/2022] Open
Abstract
Various databases have been developed to aid in assigning structures to spectral peaks observed in metabolomics experiments. In this review article, we discuss the utility of currently available open-access spectral and chemical databases for natural products discovery. We also provide recommendations on how the research community can contribute to further improvements.
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Affiliation(s)
- Sean R Johnson
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University , Pullman, WA , USA
| | - Bernd Markus Lange
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University , Pullman, WA , USA
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