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Meena SN, Wajs-Bonikowska A, Girawale S, Imran M, Poduwal P, Kodam KM. High-Throughput Mining of Novel Compounds from Known Microbes: A Boost to Natural Product Screening. Molecules 2024; 29:3237. [PMID: 38999189 PMCID: PMC11243205 DOI: 10.3390/molecules29133237] [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: 06/03/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
Advanced techniques can accelerate the pace of natural product discovery from microbes, which has been lagging behind the drug discovery era. Therefore, the present review article discusses the various interdisciplinary and cutting-edge techniques to present a concrete strategy that enables the high-throughput screening of novel natural compounds (NCs) from known microbes. Recent bioinformatics methods revealed that the microbial genome contains a huge untapped reservoir of silent biosynthetic gene clusters (BGC). This article describes several methods to identify the microbial strains with hidden mines of silent BGCs. Moreover, antiSMASH 5.0 is a free, accurate, and highly reliable bioinformatics tool discussed in detail to identify silent BGCs in the microbial genome. Further, the latest microbial culture technique, HiTES (high-throughput elicitor screening), has been detailed for the expression of silent BGCs using 500-1000 different growth conditions at a time. Following the expression of silent BGCs, the latest mass spectrometry methods are highlighted to identify the NCs. The recently emerged LAESI-IMS (laser ablation electrospray ionization-imaging mass spectrometry) technique, which enables the rapid identification of novel NCs directly from microtiter plates, is presented in detail. Finally, various trending 'dereplication' strategies are emphasized to increase the effectiveness of NC screening.
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Affiliation(s)
- Surya Nandan Meena
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
| | - Anna Wajs-Bonikowska
- Institute of Natural Products and Cosmetics, Faculty of Biotechnology and Food Sciences, Łódz University of Technology, Stefanowskiego Street 2/22, 90-537 Łódz, Poland
| | - Savita Girawale
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
| | - Md Imran
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Preethi Poduwal
- Department of Biotechnology, Dhempe College of Arts and Science, Miramar, Goa 403001, India;
| | - Kisan M. Kodam
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
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Li S, Bohman B, Flematti GR, Jayatilaka D. Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph. J Cheminform 2023; 15:104. [PMID: 37936244 PMCID: PMC10631010 DOI: 10.1186/s13321-023-00776-y] [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: 05/16/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Identifying the molecular formula and fragmentation reactions of an unknown compound from its mass spectrum is crucial in areas such as natural product chemistry and metabolomics. We propose a method for identifying the correct candidate formula of an unidentified natural product from its mass spectrum. The method involves scoring the plausibility of parent candidate formulae based on a parent subformula graph (PSG), and two possible metrics relating to the number of edges in the PSG. This method is applicable to both electron-impact mass spectrometry (EI-MS) and tandem mass spectrometry (MS/MS) data. Additionally, this work introduces the two-dimensional fragmentation plot (2DFP) for visualizing PSGs. RESULTS Our results suggest that incorporating information regarding the edges of the PSG results in enhanced performance in correctly identifying parent formulae, in comparison to the more well-accepted "MS/MS score", on the 2016 Computational Assessment of Small Molecule Identification (CASMI 2016) data set (76.3 vs 58.9% correct formula identification) and the Research Centre for Toxic Compounds in the Environment (RECETOX) data set (66.2% vs 59.4% correct formula identification). In the extension of our method to identify the correct candidate formula from complex EI-MS data of semiochemicals, our method again performed better (correct formula appearing in the top 4 candidates in 20/23 vs 7/23 cases) than the MS/MS score, and enables the rapid identification of both the correct parent ion mass and the correct parent formula with minimal expert intervention. CONCLUSION Our method reliably identifies the correct parent formula even when the mass information is ambiguous. Furthermore, should parent formula identification be successful, the majority of associated fragment formulae can also be correctly identified. Our method can also identify the parent ion and its associated fragments in EI-MS spectra where the identity of the parent ion is unclear due to low quantities and overlapping compounds. Finally, our method does not inherently require empirical fitting of parameters or statistical learning, meaning it is easy to implement and extend upon. SCIENTIFIC CONTRIBUTION Developed, implemented and tested new metrics for assessing plausibility of candidate molecular formulae obtained from HR-MS data.
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Affiliation(s)
- Sean Li
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia.
| | - Björn Bohman
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Gavin R Flematti
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
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Mendonça SC, Simas RC, Reis Simas DL, Leitão SG, Leitão GG. Mass spectrometry as a tool for the dereplication of saponins from Ampelozizyphus amazonicus Ducke bark and wood. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:262-282. [PMID: 32681766 DOI: 10.1002/pca.2972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 06/01/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Mass spectrometry in natural products research has been used as a first step to identify possible chemical structures and to guide subsequent efforts to isolate novel compounds. Preparations of Ampelozizyphus amazonicus Ducke (AA) are known for their high content of saponins, especially dammarane-type triterpenoid aglycones. In the Amazon, where it is known as "saracura-mirá", roots and bark are widely used for the treatment and prevention of malaria, while the wood is discarded. The extract prepared from the wood is also saponin-rich, but its exact chemical composition has not been described. OBJECTIVE This study provides information on the chemical profiling and tentative structural identification of the major compounds (saponins) present in aqueous and ethanol extracts of bark and wood of AA by mass spectrometry. METHODS The strategy used to identify compounds present in all samples was ultra-high-performance liquid chromatography with an ultraviolet detector coupled to tandem mass spectrometry (UHPLC-UV-MS/MS) for the analysis of fragmentation patterns through product ion scan using MZmine 2 software. Also, direct sample injection and electrospray ionisation combined with high-resolution mass spectrometry (DI-ESI-HRMS) measurements were performed. RESULTS The extracts showed chemical similarity, and 95 saponins were tentatively identified in AA wood and bark, including 73 which are described for the first time as tentative structures for this plant species. CONCLUSION This research describes a useful method for the fast and simultaneous tentative identification of major saponins in AA, contributing to the study of the chemical properties of this genus and family. Furthermore, it demonstrates the importance of the qualitative dereplication process, allowing a straightforward way to propose the tentative identification of compounds.
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Affiliation(s)
- Simony C Mendonça
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosineide C Simas
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Suzana G Leitão
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gilda G Leitão
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Hussain A, Hassan QP, Shouche YS. New approaches for antituberculosis leads from Actinobacteria. Drug Discov Today 2020; 25:2335-2342. [PMID: 33069935 DOI: 10.1016/j.drudis.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 09/11/2020] [Accepted: 10/09/2020] [Indexed: 12/31/2022]
Abstract
Bioactive metabolites derived from the phylum Actinobacteria represent many of the existing antimicrobial drugs. Compared with other bacterial pathogens, direct preliminary screening by diffusion assays is a limiting factor against Mycobacterium tuberculosis (Mtb) and different methodologies have been used to improve the search for new molecules. However, the concern remains that most of the previously discovered molecules replicate by conventional procedures. The combination of multidisciplinary approaches with new technologies could advance the discovery of new leads against Mtb like considering the unexplored Actinobacteria jointly with selective and integrative procedures.
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Affiliation(s)
- Aehtesham Hussain
- National Centre for Microbial Resource (NCMR) - National Centre for Cell Science (NCCS), Pune, Maharashtra 411021, India.
| | - Qazi Parvaiz Hassan
- Microbial Biotechnology Division, CSIR - Indian Institute of Integrative Medicine, Jammu & Kashmir 190005, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR) - National Centre for Cell Science (NCCS), Pune, Maharashtra 411021, India
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Ahad H, Jin H, Liu Y, Wang J, Sun G, Liang X, Akber Aisa H. Chemical profiling of spermidines in goji berry by strong cation exchange solid-phase extraction (SCX-SPE) combined with ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS/MS). J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1137:121923. [DOI: 10.1016/j.jchromb.2019.121923] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/20/2019] [Accepted: 12/01/2019] [Indexed: 11/29/2022]
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MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes. Cell Discov 2019; 5:40. [PMID: 31636953 PMCID: PMC6796874 DOI: 10.1038/s41421-019-0107-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/14/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
Isotope-labeling-based mass spectrometry (MS) is widely used in quantitative proteomic studies. With this technique, the relative abundance of thousands of proteins can be efficiently profiled in parallel, greatly facilitating the detection of proteins differentially expressed across samples. However, this task remains computationally challenging. Here we present a new approach, termed Model-based Analysis of Proteomic data (MAP), for this task. Unlike many existing methods, MAP does not require technical replicates to model technical and systematic errors, and instead utilizes a novel step-by-step regression analysis to directly assess the significance of observed protein abundance changes. We applied MAP to compare the proteomic profiles of undifferentiated and differentiated mouse embryonic stem cells (mESCs), and found it has superior performance compared with existing tools in detecting proteins differentially expressed during mESC differentiation. A web-based application of MAP is provided for online data processing at http://bioinfo.sibs.ac.cn/shaolab/MAP.
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Lotfy MM, Hassan HM, Mohammed R, Hetta M, El-Gendy AO, Rateb ME, Zaki MA, Gamaleldin NM. Chemical Profiling and Biological Screening of Some River Nile Derived-Microorganisms. Front Microbiol 2019; 10:787. [PMID: 31037069 PMCID: PMC6476301 DOI: 10.3389/fmicb.2019.00787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/27/2019] [Indexed: 12/03/2022] Open
Abstract
AIMS Chemical and biological studies of the River Nile derived-microorganisms are limited. Hence, this work was carried out to screen the River Nile habitat. Identification of the isolated organisms, chemical profiling of their ethyl acetate extracts as well as screening of their antimicrobial, antileishmanial, antitrypanosomal, and antimalarial activities were investigated. METHODS Identification of the microbial isolates were carried out using bacterial 16S rRNA and fungal 18S rRNA gene sequencing. Chemical profiling of the EtOAc extracts using LC-HRESIMS spectroscopy was carried out. The in vitro antimicrobial screening using the modified version of the CLSI method, antileishmanial and antitrypanosomal activities were screened using Leishmania donovani promastigote assay, L. donovani axenic amastigote assay, Trypanosoma brucei trypamastigotes assay and THP1 toxicity assay. The in vitro antimalarial activities against D6 (chloroquine sensitive) and W2 (chloroquine-resistant) strains of Plasmodium falciparum were evaluated. RESULTS Seven isolated microorganisms were identified as Streptomyces indiaensis, Bacillus safensis, B. anthracis, Bacillus sp., and Aspergillus awamori. Chemical investigation of different extracts showed several bioactive compounds, identified as; nigragillin, 5-caboxybenzofuran and dyramide B from A. awamori and actinopolysporin B from S. indiaensis. On the other hand many nitrogenous compounds with high molecular weights showed no hits that may correspond to new long chain and/or cyclic peptides. The EtOAc extract of B. safensis fermentation broth showed the highest activity against P. falciparum D6 and P. falciparum W2 (IC50 = 25.94 and 27.28 μg/mL, respectively), while two isolates S. indiaensis and Bacillus sp. RN-011 extracts showed the highest antitrypanosomal activity (IC50 = 0.8 and 0.96 μg/mL). CONCLUSION The River Nile could be a new source for production of promising bioactive leading compound where antimicrobial and antiparasitic activities may be correlated.
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Affiliation(s)
- Momen M. Lotfy
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Hossam M. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mona Hetta
- Department of Pharmacognosy, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - Ahmed O. El-Gendy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni- Suef University, Beni-Suef, Egypt
| | - Mostafa E. Rateb
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, United Kingdom
| | - Mohamed A. Zaki
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Noha M. Gamaleldin
- Department of Microbiology, Faculty of Pharmacy, The British University in Egypt (BUE), El-Sherouk, Egypt
- The Center for Drug Research and Development (CDRD), The British University in Egypt (BUE), El-Sherouk, Egypt
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Qualitative and Quantitative Analysis of C-glycosyl-flavones of Iris lactea Leaves by Liquid Chromatography/Tandem Mass Spectrometry. Molecules 2018; 23:molecules23123359. [PMID: 30567397 PMCID: PMC6320948 DOI: 10.3390/molecules23123359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 11/24/2022] Open
Abstract
Iris lactea Pall. var. chinensis (Fisch.) Koidz. is a traditional medicinal plant resource. To make full use of the I. lactea plant resources, constituents of I. lactea leaves were determined by high performance liquid chromatography (HPLC)-quadrupole time-of-flight tandem mass spectrometry and 22 C-glycosylflavones were identified or tentatively identified. Optimal extraction of I. lactea leaves was established via single factor investigations combined with response surface methodology. Then, HPLC coupled with a diode array detector was used to quantitatively analyze the six main components of 14 batches of I. lactea leaves grown in different areas. The results showed the C-glycosylflavones were the main components of I. lactea leaves, and the total contents of detected components were relatively stable for the majority of samples. These results provide a foundation for the development and utilization of I. lactea leaves.
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Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Anal Chem 2018; 91:704-742. [DOI: 10.1021/acs.analchem.8b05112] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | | | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 44035 Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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Cai T, Guo ZQ, Xu XY, Wu ZJ. Recent (2000-2015) developments in the analysis of minor unknown natural products based on characteristic fragment information using LC-MS. MASS SPECTROMETRY REVIEWS 2018; 37:202-216. [PMID: 27341181 DOI: 10.1002/mas.21514] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
Liquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds. This review consists of three parts. Firstly, the methods used to determine unique molecular formula of unknown compounds such as accurate mass measurements, MSn spectra, or relative isotopic abundance information, are introduced. Secondly, the methods improving signal-to-noise ratio of MS/MS spectra by manual-MS/MS or workflow targeting-only signals were elucidated; pure precursor ions can be selected by changing the precursor ion isolated window. Lastly, characteristic fragmentation patterns such as Retro-Diels-Alder (RDA), McLafferty rearrangements, "internal residue loss," and so on, occurring in the molecular ions of natural products are summarized. Classical application of characteristic fragmentation patterns in identifying unknown compounds in extracts and relevant fragmentation mechanisms are presented (RDA reactions occurring readily in the molecular ions of flavanones or isoflavanones, McLafferty-type fragmentation reactions of some natural products such as epipolythiodioxopiperazines; fragmentation by "internal residue loss" possibly involving ion-neutral complex intermediates). © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:202-216, 2018.
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Affiliation(s)
- Tian Cai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ze-Qin Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Xiao-Ying Xu
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhi-Jun Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
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Henkin JM, Ren Y, Soejarto DD, Kinghorn AD. The Search for Anticancer Agents from Tropical Plants. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2018; 107:1-94. [PMID: 30178270 DOI: 10.1007/978-3-319-93506-5_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many of the clinically used anticancer agents in Western medicine are derived from secondary metabolites found in terrestrial microbes, marine organisms, and higher plants, with additional compounds of this type being currently in clinical trials. If plants are taken specifically, it is generally agreed that the prospects of encountering enhanced small organic-molecule chemical diversity are better if tropical rather than temperate species are investigated in drug discovery efforts. Plant collection in tropical source countries requires considerable preparation and organization to conduct in a responsible manner that abides by the provisions of the 1992 Rio Convention of Biological Diversity and the 2010 Nagoya Protocol on Access to Genetic Resources. Correct taxonomic identifications and enhanced procedures for processing and documenting plant samples when collected in often difficult terrain are required. Phytochemical aspects of the work involve solvent fractionation, known compound dereplication, preliminary in vitro testing, and prioritization, leading to "activity-guided fractionation", compound structure determination, and analog development. Further evaluation of lead compounds requires solubility, formulation, preliminary pharmacokinetics, and in vivo testing in suitable models. Covering the work of the authors carried out in two sequential multidisciplinary, multi-institutional research projects, examples of very promising compounds discovered from plants acquired from Africa, Southeast Asia, the Americas, and the Caribbean region, and with potential anticancer activity will be mentioned. These include plant secondary metabolites of the diphyllin lignan, cyclopenta[b]benzofuran, triterpenoid, and tropane alkaloid types.
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Affiliation(s)
- Joshua M Henkin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Yulin Ren
- Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Djaja Djendoel Soejarto
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - A Douglas Kinghorn
- Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA.
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Du WJ, Ji J, Wang L, Lan XY, Li J, Lei JQ, He X, Zhang CF, Huang WZ, Wang ZZ, Xiao W, Wang CZ, Yuan CS. Relationship between the UPLC-Q-TOF-MS fingerprinted constituents from Daphne genkwa and their anti-inflammatory, anti-oxidant activities. Biomed Chromatogr 2017; 31. [PMID: 28543360 DOI: 10.1002/bmc.4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/04/2017] [Accepted: 05/17/2017] [Indexed: 01/06/2023]
Abstract
Daphne genkwa Sieb.et Zucc. is a well-known medicinal plant. This study was designed to apply the ultra-high performance liquid chromatography system to establish a quality control method for D. genkwa. Data revealed that there were 15 common peaks in 10 batches of D. genkwa Sieb. Et Zucc. (Thymelaeaceae) from different provinces of China. On this basis, the fingerprint chromatogram was established to provide references for quality control. Afterwards, the chemical constitutions of these common peaks were analyzed using the UPLC-Q-TOF-MS system and nine of them were identified. In addition, LPS-stimulated RAW264.7 murine macrophages and DPPH assay were used to study the anti-inflammatory and anti-oxidation effects of D. genkwa. Then the fingerprint-efficacy relationships between UPLC fingerprints and pharmacodynamic data were studied with canonical correlation analysis. Analysis results indicated that the anti-inflammatory and anti-oxidation effects differed among the 10 D. genkwa samples owing to their inherent differences of chemical compositions. Taken together, this research established a fingerprint-efficacy relationship model of D. genkwa plant by combining the UPLC analytic technique and pharmacological research, which provided references for the detection of the principal components of traditional Chinese medicine on bioactivity.
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Affiliation(s)
- Wen-Juan Du
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Jun Ji
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ling Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Xin-Yi Lan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Jia Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Jun-Qiu Lei
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Xin He
- School of Pharmacy, Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Chun-Feng Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Wen-Zhe Huang
- Jiangsu Kanion Pharmaceutical Co. Ltd, Lianyungang, China
| | | | - Wei Xiao
- Jiangsu Kanion Pharmaceutical Co. Ltd, Lianyungang, China
| | - Chong-Zhi Wang
- Tang Center of Herbal Medicine Research and Department of Anesthesia and Critical Care, University of Chicago, Chicago, Illinois, USA
| | - Chun-Su Yuan
- Tang Center of Herbal Medicine Research and Department of Anesthesia and Critical Care, University of Chicago, Chicago, Illinois, USA
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Aravind APA, Pandey R, Kumar B, Asha KRT, Rameshkumar KB. Phytochemical Screening of Garcinia travancorica by HPLC-ESI-QTOF Mass Spectrometry and Cytotoxicity Studies of the Major Biflavonoid Fukugiside. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601101216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Qualitative screening of multiclass secondary metabolites present in the fruits, leaves and stem bark extracts of Garcinia travancorica was carried out using HPLC-QTOF-MS analysis. Twenty-three compounds were identified in the fruits, leaves and stem bark, including two acids (hydroxycitric acid and hydroxycitric acid lactone), eight biflavonoids (morelloflavone, GB-1, GB-1a, GB-2, GB-2a, fukugiside, xanthochymusside and GB-1a glucoside), nine xanthones (α-mangostin, γ-mangostin, 1,5-dihydroxy-3-methoxyxanthone, garciniaxanthone E, 4-(1,1-dimethylprop-2-enyl)-1,3,5,8-tetrahydroxy-xanthone, garcinone A, garcinone B, garcinone C and polyanxanthone C) and four polyisoprenylated benzophenones (gambogenone, aristophenone A, garcinol and garciyunnanin A). Cytotoxicity studies of the major biflavonoid fukugiside reported from G. travancorica leaves revealed a dose-dependent cancer cell growth inhibition in A431 and HeLa cells. The antiproliferative effect appears to be due to the ability of fukugiside to induce S-phase arrest and apoptotic cell death. In HeLa cells, fukugiside reduced the expression of MAPKp38 by 26.1% compared with untreated control.
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Affiliation(s)
- Aravindakshanpillai P. Anu Aravind
- Phytochemistry and Phytopharmacology Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram 695562, Kerala, India
| | - Renu Pandey
- Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi-110025, India
| | - Brijesh Kumar
- Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi-110025, India
| | | | - Koranappallil B. Rameshkumar
- Phytochemistry and Phytopharmacology Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram 695562, Kerala, India
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The Applications and Features of Liquid Chromatography-Mass Spectrometry in the Analysis of Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2016; 2016:3837270. [PMID: 27956918 PMCID: PMC5121459 DOI: 10.1155/2016/3837270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023]
Abstract
With increasingly improved separation of complex samples and detection of unknown material capabilities, liquid chromatography coupled with mass spectrometry (LC-MS) has been widely used in traditional Chinese medicine (TCM) research. This article describes the principles of liquid chromatography (LC) and mass spectrometry (MS) and their advantages and disadvantages in qualitative and quantitative analysis of TCM. We retrieved research literatures about the application of LC-MS in TCM published during the past five years at home and abroad. To better guide the analysis of TCM, this review mainly focuses on the applications category of LC-MS, how often different kinds of LC-MS are used, and the qualitative and quantitative ability of various LC-MS in the study of TCM.
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Gorrochategui E, Jaumot J, Lacorte S, Tauler R. Data analysis strategies for targeted and untargeted LC-MS metabolomic studies: Overview and workflow. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.07.004] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Jaegle B, Uroic MK, Holtkotte X, Lucas C, Termath AO, Schmalz HG, Bucher M, Hoecker U, Hülskamp M, Schrader A. A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s. BMC PLANT BIOLOGY 2016; 16:190. [PMID: 27586417 PMCID: PMC5007998 DOI: 10.1186/s12870-016-0880-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/23/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND (Pro)anthocyanidins are synthesized by the flavonoid biosynthesis pathway with multi-layered regulatory control. Methods for the analysis of the flavonoid composition in plants are well established for different purposes. However, they typically compromise either on speed or on depth of analysis. RESULTS In this work we combined and optimized different protocols to enable the analysis of the flavonoid biosynthesis pathway with as little as possible biological material. We chose core substances of this metabolic pathway that serve as a fingerprint to recognize alterations in the main branches of the pathway. We used a simplified sample preparation, two deuterated internal standards, a short and efficient LC separation, highly sensitive detection with tandem MS in multiple reaction monitoring (MRM) mode and hydrolytic release of the core substances to reduce complexity. The method was optimized for Arabidopsis thaliana seeds and seedlings. We demonstrate that one Col-0 seed/seedling is sufficient to obtain a fingerprint of the core substances of the flavonoid biosynthesis pathway. For comparative analysis of different genotypes, we suggest the use of 10 seed(lings). The analysis of Arabidopsis thaliana mutants affecting steps in the pathway revealed foreseen and unexpected alterations of the pathway. For example, HY5 was found to differentially regulate kaempferol in seeds vs. seedlings. Furthermore, our results suggest that COP1 is a master regulator of flavonoid biosynthesis in seedlings but not of flavonoid deposition in seeds. CONCLUSIONS When sample numbers are high and the plant material is limited, this method effectively facilitates metabolic fingerprinting with one seed(ling), revealing shifts and differences in the pathway. Moreover the combination of extracted non-hydrolysed, extracted hydrolysed and non-extracted hydrolysed samples proved useful to deduce the class of derivative from which the individual flavonoids have been released.
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Affiliation(s)
- Benjamin Jaegle
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Miran Kalle Uroic
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Xu Holtkotte
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Christina Lucas
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Andreas Ole Termath
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939 Cologne, Germany
| | - Hans-Günther Schmalz
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939 Cologne, Germany
| | - Marcel Bucher
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Andrea Schrader
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, Zülpicher Str. 47b, 50674 Cologne, Germany
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Henke MT, Kelleher NL. Modern mass spectrometry for synthetic biology and structure-based discovery of natural products. Nat Prod Rep 2016; 33:942-50. [PMID: 27376415 PMCID: PMC4981503 DOI: 10.1039/c6np00024j] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2016In this highlight, we describe the current landscape for dereplication and discovery of natural products based on the measurement of the intact mass by LC-MS. Often it is assumed that because better mass accuracy (provided by higher resolution mass spectrometers) is necessary for absolute chemical formula determination (≤1 part-per-million), that it is also necessary for dereplication of natural products. However, the average ability to dereplicate tapers off at ∼10 ppm, with modest improvement gained from better mass accuracy when querying focused databases of natural products. We also highlight some recent examples of how these platforms are applied to synthetic biology, and recent methods for dereplication and correlation of substructures using tandem MS data. We also offer this highlight to serve as a brief primer for those entering the field of mass spectrometry-based natural products discovery.
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Affiliation(s)
- Matthew T Henke
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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18
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Heiling S, Khanal S, Barsch A, Zurek G, Baldwin IT, Gaquerel E. Using the knowns to discover the unknowns: MS-based dereplication uncovers structural diversity in 17-hydroxygeranyllinalool diterpene glycoside production in the Solanaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:561-77. [PMID: 26749139 DOI: 10.1111/tpj.13119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 05/25/2023]
Abstract
Exploring the diversity of plant secondary metabolism requires efficient methods to obtain sufficient structural insights to discriminate previously known from unknown metabolites. De novo structure elucidation and confirmation of known metabolites (dereplication) remain a major bottleneck for mass spectrometry-based metabolomic workflows, and few systematic dereplication strategies have been developed for the analysis of entire compound classes across plant families, partly due to the complexity of plant metabolic profiles that complicates cross-species comparisons. 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) are abundant defensive secondary metabolites whose malonyl and glycosyl decorations are induced by jasmonate signaling in the ecological model plant Nicotiana attenuata. The multiple labile glycosidic bonds of HGL-DTGs result in extensive in-source fragmentation (IS-CID) during ionization. To reconstruct these IS-CID clusters from profiling data and identify precursor ions, we applied a deconvolution algorithm and created an MS/MS library from positive-ion spectra of purified HGL-DTGs. From this library, 251 non-redundant fragments were annotated, and a workflow to characterize leaf, flower and fruit extracts of 35 solanaceous species was established. These analyses predicted 105 novel HGL-DTGs that were restricted to Nicotiana, Capsicum and Lycium species. Interestingly, malonylation is a highly conserved step in HGL-DTG metabolism, but is differentially affected by jasmonate signaling among Nicotiana species. This MS-based workflow is readily applicable for cross-species re-identification/annotation of other compound classes with sufficient fragmentation knowledge, and therefore has the potential to support hypotheses regarding secondary metabolism diversification.
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Affiliation(s)
- Sven Heiling
- Molecular Ecology Department, Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, 07745, Jena, Germany
| | - Santosh Khanal
- Molecular Ecology Department, Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, 07745, Jena, Germany
| | - Aiko Barsch
- Bruker Daltonics, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Gabriela Zurek
- Bruker Daltonics, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Ian T Baldwin
- Molecular Ecology Department, Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, 07745, Jena, Germany
| | - Emmanuel Gaquerel
- Plant Defense Metabolism Research Group, Centre for Organismal Studies Heidelberg, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
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19
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Li P, AnandhiSenthilkumar H, Wu SB, Liu B, Guo ZY, Fata JE, Kennelly EJ, Long CL. Comparative UPLC-QTOF-MS-based metabolomics and bioactivities analyses of Garcinia oblongifolia. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1011:179-95. [PMID: 26773895 DOI: 10.1016/j.jchromb.2015.12.061] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 11/29/2022]
Abstract
Garcinia oblongifolia Champ. ex Benth. (Clusiaceae) is a well-known medicinal plant from southern China, with edible fruits. However, the phytochemistry and bioactivity of the different plant parts of G. oblongifolia have not been studied extensively. Comparative metabolic profiling and bioactivities of the leaf, branch, and fruit of G. oblongifolia were investigated. A total of 40 compounds such as biflavonoids, xanthones, and benzophenones were identified using UPLC-QTOF-MS and MS(E), including 15 compounds reported for the first time from this species. Heatmap analyses found that benzophenones, xanthones, and biflavonoids were predominately found in branches, with benzophenones present in relatively high concentrations in all three plant parts. Xanthones were found to have limited distribution in fruit while biflavonoids were present at only low levels in leaves. In addition, the cytotoxic (MCF-7 breast cancer cell line) and antioxidant (ABTS and DPPH chemical tests) activities of the crude extracts of G. oblongifolia indicate that the branch extract exhibits greater bioactivity than either the leaf or the fruit extracts. Orthogonal partial least squares discriminate analysis was used to find 12 marker compounds, mainly xanthones, from the branches, including well-known antioxidants and cytotoxic agents. These G. oblongifolia results revealed that the variation in metabolite profiles can be correlated to the differences in bioactivity of the three plant parts investigated. This UPLC-QTOF-MS strategy can be useful to identify bioactive constituents expressed differentially in the various plant parts of a single species.
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Affiliation(s)
- Ping Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Harini AnandhiSenthilkumar
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York 10468, USA; Biochemistry, Biology and Chemistry Ph.D. Programs, The Graduate Center, City University of New York, New York, NY 10016, USA; Department of Biological Sciences, College of Staten Island, Staten Island, New York 10314, USA
| | - Shi-biao Wu
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York 10468, USA
| | - Bo Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Zhi-yong Guo
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Jimmie E Fata
- Biochemistry, Biology and Chemistry Ph.D. Programs, The Graduate Center, City University of New York, New York, NY 10016, USA; Department of Biological Sciences, College of Staten Island, Staten Island, New York 10314, USA
| | - Edward J Kennelly
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China; Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York 10468, USA; Biochemistry, Biology and Chemistry Ph.D. Programs, The Graduate Center, City University of New York, New York, NY 10016, USA.
| | - Chun-lin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China; Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China.
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20
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Johnson AR, Carlson EE. Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation. Anal Chem 2015; 87:10668-78. [PMID: 26132379 DOI: 10.1021/acs.analchem.5b01543] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mass spectrometry is a powerful tool in natural product structure elucidation, but our ability to directly correlate fragmentation spectra to these structures lags far behind similar efforts in peptide sequencing and proteomics. Often, manual data interpretation is required and our knowledge of the expected fragmentation patterns for many scaffolds is limited, further complicating analysis. Here, we summarize advances in natural product structure elucidation based upon the application of collision induced dissociation fragmentation mechanisms.
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Affiliation(s)
- Andrew R Johnson
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University , 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
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21
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Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
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Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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22
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Zheng L, Cong HJ, Wu B, Xue M, Xiang T, Yao ZQ, Lin WH. HPLC–Q-TOF–MS/MS Analysis of the Constituents in the Rat Biological Fluids After Oral Administration of Qing Ru Xiao granules. J Chromatogr Sci 2015; 53:1562-9. [DOI: 10.1093/chromsci/bmv058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Indexed: 01/29/2023]
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23
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Li H, Yu Y, Wang Z, Geng J, Dai Y, Xiao W, Yao X. Chemical profiling of Re-Du-Ning injection by ultra-performance liquid chromatography coupled with electrospray ionization tandem quadrupole time-of-flight mass spectrometry through the screening of diagnostic Ions in MS(E) mode. PLoS One 2015; 10:e0121031. [PMID: 25875968 PMCID: PMC4395252 DOI: 10.1371/journal.pone.0121031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
The broad applications and mechanism explorations of traditional Chinese medicine prescriptions (TCMPs) require a clear understanding of TCMP chemical constituents. In the present study, we describe an efficient and universally applicable analytical approach based on ultra-performance liquid chromatography coupled to electrospray ionization tandem quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q/TOF-MS) with the MSE (E denotes collision energy) data acquisition mode, which allowed the rapid separation and reliable determination of TCMP chemical constituents. By monitoring diagnostic ions in the high energy function of MSE, target peaks of analogous compounds in TCMPs could be rapidly screened and identified. “Re-Du-Ning” injection (RDN), a eutherapeutic traditional Chinese medicine injection (TCMI) that has been widely used to reduce fever caused by viral infections in clinical practice, was studied as an example. In total, 90 compounds, including five new iridoids and one new sesquiterpene, were identified or tentatively characterized by accurate mass measurements within 5 ppm error. This analysis was accompanied by MS fragmentation and reference standard comparison analyses. Furthermore, the herbal sources of these compounds were unambiguously confirmed by comparing the extracted ion chromatograms (EICs) of RDN and ingredient herbal extracts. Our work provides a certain foundation for further studies of RDN. Moreover, the analytical approach developed herein has proven to be generally applicable for profiling the chemical constituents in TCMPs and other complicated mixtures.
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Affiliation(s)
- Haibo Li
- Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, China
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
- State Key Lab of New-Tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
| | - Yang Yu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Zhenzhong Wang
- Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, China
- State Key Lab of New-Tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
| | | | - Yi Dai
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Wei Xiao
- Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, China
- State Key Lab of New-Tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
- * E-mail: (XY); (WX)
| | - Xinsheng Yao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
- Shenyang Pharmaceutical University, Shenyang, China
- * E-mail: (XY); (WX)
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Liu WY, Wei ML, Wu CY, Zhu HY, Feng F, Xie N. Fingerprint of ethyl acetate extraction combined with qualitative and quantitative analysis onPatrinia scabraBunge: DistinguishP. scabraBunge from its confusable species. ACTA CHROMATOGR 2015. [DOI: 10.1556/achrom.27.2015.1.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Wolfender JL, Marti G, Thomas A, Bertrand S. Current approaches and challenges for the metabolite profiling of complex natural extracts. J Chromatogr A 2015; 1382:136-64. [DOI: 10.1016/j.chroma.2014.10.091] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/11/2022]
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26
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Hassan MH, Rateb ME, Hetta M, Abdelaziz TA, Sleim MA, Jaspars M, Mohammed R. Scalarane sesterterpenes from the Egyptian Red Sea sponge Phyllospongia lamellosa. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Bianco G, Buchicchio A, Lelario F, Cataldi TRI. Molecular formula analysis of fragment ions by isotope-selective collision-induced dissociation tandem mass spectrometry of pharmacologically active compounds. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1322-1329. [PMID: 25476951 DOI: 10.1002/jms.3468] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 08/15/2014] [Accepted: 08/15/2014] [Indexed: 06/04/2023]
Abstract
The purpose of this work is to explore the mass fragment characterization of commonly used drugs through a novel approach, which involves isotope-selective tandem mass spectrometry (MS/MS). Collision-induced dissociation (CID) was performed with a low-resolution linear ion trap mass spectrometer in positive electrospray ionization. Three pharmacologically active ingredients, i.e. omeprazole, meloxicam and brinzolamide, selected as model compounds in their own formulation, were investigated as a sodiated adduct [C17 H19 N3 O3 S + Na](+) (omeprazole) and as protonated adducts, [C14 H13 N3 O4 S2 + H](+) and [C12 H21 N3 O5 S3 + H](+) , meloxicam and brinzolamide, respectively. Selecting a narrow window of ±0.5 m/z units, precursor ion fragmentation by CID-MS/MS of isotopologues A + 0, A + 1 and A + 2 was found very useful to confirm the chemical formula of product ions, thus aiding the establishment of characteristic fragmentation pathways of all three examined compounds. The correctness of putative molecular formula of product ions was easily demonstrated by exploiting the isotope peak abundance ratios (i.e. IF+0 /IF+1 and IF+0 /IF+2 ) as simple constraints in low-resolution MS instrumentations.
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Affiliation(s)
- Giuliana Bianco
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano 10, 85100, Potenza, Italy
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28
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Kildgaard S, Mansson M, Dosen I, Klitgaard A, Frisvad JC, Larsen TO, Nielsen KF. Accurate dereplication of bioactive secondary metabolites from marine-derived fungi by UHPLC-DAD-QTOFMS and a MS/HRMS library. Mar Drugs 2014; 12:3681-705. [PMID: 24955556 PMCID: PMC4071597 DOI: 10.3390/md12063681] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 12/23/2022] Open
Abstract
In drug discovery, reliable and fast dereplication of known compounds is essential for identification of novel bioactive compounds. Here, we show an integrated approach using ultra-high performance liquid chromatography-diode array detection-quadrupole time of flight mass spectrometry (UHPLC-DAD-QTOFMS) providing both accurate mass full-scan mass spectrometry (MS) and tandem high resolution MS (MS/HRMS) data. The methodology was demonstrated on compounds from bioactive marine-derived strains of Aspergillus, Penicillium, and Emericellopsis, including small polyketides, non-ribosomal peptides, terpenes, and meroterpenoids. The MS/HRMS data were then searched against an in-house MS/HRMS library of ~1300 compounds for unambiguous identification. The full scan MS data was used for dereplication of compounds not in the MS/HRMS library, combined with ultraviolet/visual (UV/Vis) and MS/HRMS data for faster exclusion of database search results. This led to the identification of four novel isomers of the known anticancer compound, asperphenamate. Except for very low intensity peaks, no false negatives were found using the MS/HRMS approach, which proved to be robust against poor data quality caused by system overload or loss of lock-mass. Only for small polyketides, like patulin, were both retention time and UV/Vis spectra necessary for unambiguous identification. For the ophiobolin family with many structurally similar analogues partly co-eluting, the peaks could be assigned correctly by combining MS/HRMS data and m/z of the [M + Na]+ ions.
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Affiliation(s)
- Sara Kildgaard
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Maria Mansson
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Ina Dosen
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Jens C Frisvad
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Thomas O Larsen
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
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Zheng L, Cong H, Xue M, Xiang T, Yao Z, Wu B, Lin W. Characterization of chemical constituents and rats metabolites of Shuanghua Baihe tablets by HPLC-Q-TOF-MS/MS. Biomed Chromatogr 2014; 29:75-86. [DOI: 10.1002/bmc.3242] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/27/2014] [Accepted: 04/13/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Lu Zheng
- Yangtze River Pharmaceutical Group; Taizhou 225321 People's Republic of China
| | - Haijian Cong
- Shanghai Haini Pharmaceutical Co. Ltd.; Yangtze River Pharmaceutical Group; Shanghai 201318 People's Republic of China
| | - Ming Xue
- Yangtze River Pharmaceutical Group; Taizhou 225321 People's Republic of China
| | - Ting Xiang
- Yangtze River Pharmaceutical Group; Taizhou 225321 People's Republic of China
| | - Zhongqing Yao
- Yangtze River Pharmaceutical Group; Taizhou 225321 People's Republic of China
| | - Bin Wu
- Yangtze River Pharmaceutical Group; Taizhou 225321 People's Republic of China
| | - Wenhui Lin
- School of Chemical and Environmental Engineering; Shanghai Institute of Technology; Shanghai 201418 People's Republic of China
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Liu YR, Li WG, Chen LF, Xiao BK, Yang JY, Yang L, Zhang CG, Huang RQ, Dong JX. ABTS+ scavenging potency of selected flavonols from Hypericum perforatum L. by HPLC-ESI/MS QQQ: Reaction observation, adduct characterization and scavenging activity determination. Food Res Int 2014. [DOI: 10.1016/j.foodres.2014.01.051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL. Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 2014; 32:1180-204. [PMID: 24651031 DOI: 10.1016/j.biotechadv.2014.03.001] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 02/08/2023]
Abstract
Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Nadine Bohni
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Sylvain Schnee
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Olivier Schumpp
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Katia Gindro
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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32
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Xie P, Ma M, Rateb ME, Shaaban K, Yu Z, Huang SX, Zhao LX, Zhu X, Yan Y, Peterson R, Lohman JR, Yang D, Yin M, Rudolf JD, Jiang Y, Duan Y, Shen B. Biosynthetic potential-based strain prioritization for natural product discovery: a showcase for diterpenoid-producing actinomycetes. JOURNAL OF NATURAL PRODUCTS 2014; 77:377-87. [PMID: 24484381 PMCID: PMC3963700 DOI: 10.1021/np401063s] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 05/09/2023]
Abstract
Natural products remain the best sources of drugs and drug leads and serve as outstanding small-molecule probes to dissect fundamental biological processes. A great challenge for the natural product community is to discover novel natural products efficiently and cost effectively. Here we report the development of a practical method to survey biosynthetic potential in microorganisms, thereby identifying the most promising strains and prioritizing them for natural product discovery. Central to our approach is the innovative preparation, by a two-tiered PCR method, of a pool of pathway-specific probes, thereby allowing the survey of all variants of the biosynthetic machineries for the targeted class of natural products. The utility of the method was demonstrated by surveying 100 strains, randomly selected from our actinomycete collection, for their biosynthetic potential of four classes of natural products, aromatic polyketides, reduced polyketides, nonribosomal peptides, and diterpenoids, identifying 16 talented strains. One of the talented strains, Streptomyces griseus CB00830, was finally chosen to showcase the discovery of the targeted classes of natural products, resulting in the isolation of three diterpenoids, six nonribosomal peptides and related metabolites, and three polyketides. Variations of this method should be applicable to the discovery of other classes of natural products.
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Affiliation(s)
- Pengfei Xie
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ming Ma
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Mostafa E. Rateb
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Khaled
A. Shaaban
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Zhiguo Yu
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Sheng-Xiong Huang
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Li-Xing Zhao
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Xiangcheng Zhu
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Yijun Yan
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ryan
M. Peterson
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Division
of Pharmaceutical Sciences, University of
Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Jeremy R. Lohman
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Min Yin
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jeffrey D. Rudolf
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yi Jiang
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Yanwen Duan
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Ben Shen
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Division
of Pharmaceutical Sciences, University of
Wisconsin−Madison, Madison, Wisconsin 53705, United States
- Department
of Molecular Therapeutics, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
- Natural Products
Library Initiative, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
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33
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Ito T, Masubuchi M. Dereplication of microbial extracts and related analytical technologies. J Antibiot (Tokyo) 2014; 67:353-60. [PMID: 24569671 DOI: 10.1038/ja.2014.12] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/06/2014] [Accepted: 01/27/2014] [Indexed: 02/07/2023]
Abstract
Natural products still continue to have an important role as a resource of various biologically active substances. Dereplication is a key process in natural product screening that analyzes the extracts of microbial fermentation broths or plant samples. In this review article, we describe and discuss the analytical techniques of dereplication and related technologies in the following sections: 1. Direct detection from microbial colonies. 2. Ultra high performance liquid chromatography (UHPLC)-MS profiling for library construction. 3. Micro-fractionation to identify active peaks. 4. Quantification of small-amount compounds. 5. Structure identification from small amounts. Using these techniques, the desired compound in the mixture library can be rapidly identified.
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Affiliation(s)
- Tatsuya Ito
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Miyako Masubuchi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
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Wills RH, O'Connor PB. Structural characterization of actinomycin D using multiple ion isolation and electron induced dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:186-195. [PMID: 24297472 DOI: 10.1007/s13361-013-0774-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/13/2013] [Accepted: 10/06/2013] [Indexed: 06/02/2023]
Abstract
Non-ribosomal peptides are bio synthesized using a range of enzymes that allow much more structural variability compared with "normal" peptides. Deviations from the standard amino acid structures are common features of this diverse class of natural products, making sequencing a challenging process. FTICR mass spectrometry, specifically the complementary tandem mass spectrometry techniques collision activated dissociation (CAD) and electron induced dissociation (EID), have been used to reveal structural information on the non-ribosomal peptide actinomycin D. EID was also combined with a multiple ion isolation method in order to provide an accurate (sub-ppm) internal calibration for the product ions. EID has been found to produce more detailed, complementary data than CAD for actinomycin D, with additional information being provided through fragmentation of the sodium and lithium adducts. Furthermore, the use of isolation in the FTICR cell was found to increase product ion intensities relative to the precursor ion, enabling significantly more peaks to be detected than when using EID alone. The combination of multiple ion isolation with EID, therefore, enables an accurate internal calibration of the fragment ions to be made (average mass uncertainty of <0.3 ppm), as well as increasing the degree of fragmentation of the compound, resulting in detailed structural information.
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Affiliation(s)
- Rebecca H Wills
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Zhu F, Chen J, Wang J, Yin R, Li X, Jia X. Qualitative and Quantitative Analysis of the Constituents in Danmu Preparations by UPLC-PDA-TOF-MS. J Chromatogr Sci 2013; 52:862-71. [DOI: 10.1093/chromsci/bmt129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Johansen KT, Wubshet SG, Nyberg NT. HPLC-NMR revisited: using time-slice high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance with database-assisted dereplication. Anal Chem 2013; 85:3183-9. [PMID: 23432092 DOI: 10.1021/ac303455j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Time-based trapping of chromatographically separated compounds onto solid-phase extraction (SPE) cartridges and subsequent elution to NMR tubes was done to emulate the function of HPLC-NMR for dereplication purposes. Sufficient mass sensitivity was obtained by use of a state-of-the-art HPLC-SPE-NMR system with a cryogenically cooled probe head, designed for 1.7 mm NMR tubes. The resulting (1)H NMR spectra (600 MHz) were evaluated against a database of previously acquired and prepared spectra. The in-house-developed matching algorithm, based on partitioning of the spectra and allowing for changes in the chemical shifts, is described. Two mixtures of natural products were used to test the approach: an extract of Carthamus oxyacantha (wild safflower), containing an array of spiro compounds, and an extract of the endophytic fungus Penicillum namyslowski, containing griseofulvin and analogues. The database matching of the resulting spectra positively identified expected compounds, while the number of false positives was few and easily recognized.
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Affiliation(s)
- Kenneth T Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Scheubert K, Hufsky F, Böcker S. Computational mass spectrometry for small molecules. J Cheminform 2013; 5:12. [PMID: 23453222 PMCID: PMC3648359 DOI: 10.1186/1758-2946-5-12] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/01/2013] [Indexed: 12/29/2022] Open
Abstract
: The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline.
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Affiliation(s)
- Kerstin Scheubert
- Chair of Bioinformatics, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena, Germany.
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Wu ZJ, Huo JL, Chen JZ, Li N, Fang DM, Chen XZ, Zhang GL, Wang JH, Xu XY. Evaluation of relative isotopic abundance measurements in a quadrupole time-of-flight mass spectrometer for elemental composition determination of natural products in traditional Chinese medicine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:91-102. [PMID: 24261081 DOI: 10.1255/ejms.1219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The relative isotopic abundance (RIA) measurement errors of a quadrupole time-of-flight (Q-ToF) instrument incorporating analog-to-digital converter detectors were systemically evaluated by stochastically collecting about 200 data in positive ion mass spectrometry (MS) mode. Errors varied with peak intensities at definite spectral acquisition rates but were very close, even if peak intensities changed sharply at different spectral acquisition rates with the same concentration. Intensity thresholds were systematically defined at 1 Hz of spectral acquisition rates. RIA measurement errors were also evaluated using peak area. It seemed that peak area was better adapted for the high-intensity ions while peak intensity was suited for very low-intensity ions. Several known compounds were selected for RIA measurements for product ions in tandem mass spectropmetry (MS/MS) mode. An extract of a representative traditional Chinese medicinal, Paederia scandens was analyzed with high-performance liquid chromatography-electrospray ionization-QToF-MS/MS. The unique elemental compositions of some compounds could not be identified even with exact masses and MS/MS spectra of measured and reference compounds. RIA errors, especially of (M+2)M(-1), provided vital information for determining the elemental composition.
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Affiliation(s)
- Zhi-Jun Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
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39
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Wu H, Guo J, Chen S, Liu X, Zhou Y, Zhang X, Xu X. Recent developments in qualitative and quantitative analysis of phytochemical constituents and their metabolites using liquid chromatography–mass spectrometry. J Pharm Biomed Anal 2013; 72:267-91. [DOI: 10.1016/j.jpba.2012.09.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/30/2012] [Accepted: 09/02/2012] [Indexed: 12/14/2022]
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40
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Application of UPLC-Quadrupole-TOF-MS Coupled with Recycling Preparative HPLC in Isolation and Preparation of Coumarin Isomers with Similar Polarity from Peucedanum praeruptorum. Chromatographia 2012. [DOI: 10.1007/s10337-012-2368-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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41
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Kasper PT, Rojas-Chertó M, Mistrik R, Reijmers T, Hankemeier T, Vreeken RJ. Fragmentation trees for the structural characterisation of metabolites. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2275-86. [PMID: 22956319 PMCID: PMC3573646 DOI: 10.1002/rcm.6340] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 05/10/2023]
Abstract
Metabolite identification plays a crucial role in the interpretation of metabolomics research results. Due to its sensitivity and widespread implementation, a favourite analytical method used in metabolomics is electrospray mass spectrometry. In this paper, we demonstrate our results in attempting to incorporate the potentials of multistage mass spectrometry into the metabolite identification routine. New software tools were developed and implemented which facilitate the analysis of multistage mass spectra and allow for efficient removal of spectral artefacts. The pre-processed fragmentation patterns are saved as fragmentation trees. Fragmentation trees are characteristic of molecular structure. We demonstrate the reproducibility and robustness of the acquisition of such trees on a model compound. The specificity of fragmentation trees allows for distinguishing structural isomers, as shown on a pair of isomeric prostaglandins. This approach to the analysis of the multistage mass spectral characterisation of compounds is an important step towards formulating a generic metabolite identification method.
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Affiliation(s)
- Piotr T Kasper
- Netherlands Metabolomics CentreEinsteinweg 55, Leiden, The Netherlands
- Leiden/Amsterdam Centre for Drug Research (LACDR), Leiden UniversityEinsteinweg 55, Leiden, The Netherlands
| | - Miguel Rojas-Chertó
- Netherlands Metabolomics CentreEinsteinweg 55, Leiden, The Netherlands
- Leiden/Amsterdam Centre for Drug Research (LACDR), Leiden UniversityEinsteinweg 55, Leiden, The Netherlands
| | | | - Theo Reijmers
- Netherlands Metabolomics CentreEinsteinweg 55, Leiden, The Netherlands
- Leiden/Amsterdam Centre for Drug Research (LACDR), Leiden UniversityEinsteinweg 55, Leiden, The Netherlands
| | - Thomas Hankemeier
- Netherlands Metabolomics CentreEinsteinweg 55, Leiden, The Netherlands
- Leiden/Amsterdam Centre for Drug Research (LACDR), Leiden UniversityEinsteinweg 55, Leiden, The Netherlands
| | - Rob J Vreeken
- Netherlands Metabolomics CentreEinsteinweg 55, Leiden, The Netherlands
- Leiden/Amsterdam Centre for Drug Research (LACDR), Leiden UniversityEinsteinweg 55, Leiden, The Netherlands
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Exploring anti-TB leads from natural products library originated from marine microbes and medicinal plants. Antonie van Leeuwenhoek 2012; 102:447-61. [DOI: 10.1007/s10482-012-9777-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
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Funari CS, Eugster PJ, Martel S, Carrupt PA, Wolfender JL, Silva DHS. High resolution ultra high pressure liquid chromatography-time-of-flight mass spectrometry dereplication strategy for the metabolite profiling of Brazilian Lippia species. J Chromatogr A 2012; 1259:167-78. [PMID: 22520638 DOI: 10.1016/j.chroma.2012.03.069] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 01/15/2023]
Abstract
Plants belonging to the Lippia genus have been widely used in ethnobotany throughout South and Central America and in tropical Africa as foods, medicines, sweeteners and in beverage flavouring. Various taxonomic problems involving some genera from Verbenaceae, including Lippia, have been reported. In this study, the metabolite profiling of fifteen extracts of various organs of six Lippia species was performed and compared using UHPLC-PDA-TOF-MS. Fourteen phenolic compounds that were previously isolated from L. salviaefolia Cham. and L. lupulina Cham. were used as references. The annotation of the remaining LC peaks was based on concomitant online high mass accuracy measurements and subsequent molecular formula assignments following these different steps: (i) elimination of non-coherent putative molecular formulae by heuristic filtering, (ii) verification of the occurrence of remaining molecular formulae in databases, (iii) cross search with reported compounds in the Lippia genus, (iv) match with reported UV spectra, (v) estimation of the chromatographic retention behaviour based on the log P parameter of reference compounds. This strategy is generic and time-saving, avoids isolation/purification procedures, enables an efficient LC peak annotation of most of the studied compounds and is well adapted for plant chemotaxonomic studies. Within this study, the interconversion of four flavanone glucoside isomers was additionally highlighted by analytical HPLC isolation and immediate analysis using fast UHPLC gradients. Dereplication results and hierarchical data analysis demonstrated that L. salviaefolia, L. balansae, L. velutina and L. sidoides displayed significant chemical similarities, while the compositions of L. lasiocalicyna and L. lupulina differed substantially.
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Affiliation(s)
- Cristiano S Funari
- NuBBE - Nucleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais, Institute of Chemistry, São Paulo State University, Araraquara, SP, CP 355, CEP 14801-970, Brazil
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44
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Johansen KT, Wubshet SG, Nyberg NT, Jaroszewski JW. From retrospective assessment to prospective decisions in natural product isolation: HPLC-SPE-NMR analysis of Carthamus oxyacantha. JOURNAL OF NATURAL PRODUCTS 2011; 74:2454-2461. [PMID: 22060189 DOI: 10.1021/np200780m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
An extract of Carthamus oxyacantha (wild safflower) was investigated using two approaches: a traditional, nontarget fractionation by VLC and HPLC, and the hyphenated technique HPLC-PDA-HRMS-SPE-NMR followed by targeted isolation of selected constituents for inclusion in a screening library of pure natural products. While the nontarget fractionation involved considerable time spent on pursuing fractions containing well-known or undesired compounds, the hyphenated analysis was considerably faster and required less solvent and other consumables. The results were used to design and execute an optimized, HPLC-HRMS-guided, targeted isolation scheme aiming exclusively at a series of identified spiro compounds. Thus, HPLC-PDA-HRMS-SPE-NMR is a dereplication technique of choice, allowing economical acquisition of comprehensive data about compounds in crude extracts, which can be used for rational, prospective decisions about further isolation efforts. A total of 15 compounds were identified in the extract. Six spiro compounds, of which four have not previously been characterized, and tracheloside (a lignin glucoside) are presented with assigned 1H and 13C chemical shifts.
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Affiliation(s)
- Kenneth T Johansen
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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45
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Liu X, Bolla K, Ashforth EJ, Zhuo Y, Gao H, Huang P, Stanley SA, Hung DT, Zhang L. Systematics-guided bioprospecting for bioactive microbial natural products. Antonie van Leeuwenhoek 2011; 101:55-66. [PMID: 22086462 DOI: 10.1007/s10482-011-9671-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/27/2011] [Indexed: 01/26/2023]
Abstract
Advances in the taxonomic characterization of microorganisms have accelerated the rate at which new producers of natural products can be understood in relation to known organisms. Yet for many reasons, chemical efforts to characterize new compounds from new microbes have not kept pace with taxonomic advances. That there exists an ever-widening gap between the biological versus chemical characterization of new microorganisms creates tremendous opportunity for the discovery of novel natural products through the calculated selection and study of organisms from unique, untapped, ecological niches. A systematics-guided bioprospecting, including the construction of high quality libraries of marine microbes and their crude extracts, investigation of bioactive compounds, and increasing the active compounds by precision engineering, has become an efficient approach to drive drug leads discovery. This review outlines the recent advances in these issues and shares our experiences on anti-infectious drug discovery and improvement of avermectins production as well.
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Affiliation(s)
- Xueting Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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46
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Wang YF, Shi QW, Dong M, Kiyota H, Gu YC, Cong B. Natural Taxanes: Developments Since 1828. Chem Rev 2011; 111:7652-709. [DOI: 10.1021/cr100147u] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu-Fang Wang
- School of Pharmaceutical Sciences, Hebei Medical University, Shijiazhuang, Hebei Province, 050017, China
| | - Qing-Wen Shi
- School of Pharmaceutical Sciences, Hebei Medical University, Shijiazhuang, Hebei Province, 050017, China
| | - Mei Dong
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei Province, 050017, China
| | - Hiromasa Kiyota
- Department of Bioscience and Biotechnology for Future Bioindustry, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiya, Aoba-ku, Sendai 981-8555, Japan
| | - Yu-Cheng Gu
- School of Pharmaceutical Sciences, Hebei Medical University, Shijiazhuang, Hebei Province, 050017, China
- Syngenta Jealott’s Hill International Research Centre, Berkshire, RG42 6EY, U.K
| | - Bin Cong
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei Province, 050017, China
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47
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Rojas-Chertó M, Kasper PT, Willighagen EL, Vreeken RJ, Hankemeier T, Reijmers TH. Elemental composition determination based on MS(n). ACTA ACUST UNITED AC 2011; 27:2376-83. [PMID: 21757467 DOI: 10.1093/bioinformatics/btr409] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Identification of metabolites is essential for its use as biomarkers, for research in systems biology and for drug discovery. The first step before a structure can be elucidated is to determine its elemental composition. High-resolution mass spectrometry, which provides the exact mass, together with common constraint rules, for rejecting false proposed elemental compositions, cannot always provide one unique elemental composition solution. RESULTS The Multistage Elemental Formula (MEF) tool is presented in this article to enable the correct assignment of elemental composition to compounds, their fragment ions and neutral losses that originate from the molecular ion by using multistage mass spectrometry (MS(n)). The method provided by MEF reduces the list of predicted elemental compositions for each ion by analyzing the elemental compositions of its parent (precursor ion) and descendants (fragments). MS(n) data of several metabolites were processed using the MEF tool to assign the correct elemental composition and validate the efficacy of the method. Especially, the link between the mass accuracy needed to generate one unique elemental composition and the topology of the MS(n) tree (the width and the depth of the tree) was addressed. This method makes an important step toward semi-automatic de novo identification of metabolites using MS(n) data. AVAILABILITY Software available at: http://abs.lacdr.gorlaeus.net/people/rojas-cherto CONTACT m.rojas@lacdr.leidenuniv.nl; t.reijmers@lacdr.leidenuniv.nl SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Miguel Rojas-Chertó
- Netherlands Metabolomics Centre, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands.
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Kingston DGI. Modern natural products drug discovery and its relevance to biodiversity conservation. JOURNAL OF NATURAL PRODUCTS 2011; 74:496-511. [PMID: 21138324 PMCID: PMC3061248 DOI: 10.1021/np100550t] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Natural products continue to provide a diverse and unique source of bioactive lead compounds for drug discovery, but maintaining their continued eminence as source compounds is challenging in the face of the changing face of the pharmaceutical industry and the changing nature of biodiversity prospecting brought about by the Convention on Biological Diversity. This review provides an overview of some of these challenges and suggests ways in which they can be addressed so that natural products research can remain a viable and productive route to drug discovery. Results from International Cooperative Biodiversity Groups (ICBGs) working in Madagascar, Panama, and Suriname are used as examples of what can be achieved when biodiversity conservation is linked to drug discovery.
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Affiliation(s)
- David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States.
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Watchueng J, Kamnaing P, Gao JM, Kiyota T, Yeboah F, Konishi Y. Efficient purification of paclitaxel from yews using high-performance displacement chromatography technique. J Chromatogr A 2011; 1218:2929-35. [PMID: 21457989 DOI: 10.1016/j.chroma.2011.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 01/23/2023]
Abstract
Paclitaxel was purified using high-performance displacement chromatography (HPDC) technique, but not by the mechanism of HPDC. On small scale, paclitaxel was extracted with methanol from dry needles of Taxus canadensis and was enriched by extracting with chloroform after removing water-soluble hydrophilic components and hexane-soluble hydrophobic components. Then, 93-99% purity of paclitaxel was obtained using the HPDC technique. On large scale, taxanes were enriched by solvent partitioning between acetic acid/MeOH/H(2)O and hexane and extracted with CH(2)Cl(2). Taxanes except paclitaxel were further removed by extracting with methanol-water-trifluoroacetic acid (1.0:98.9:0.1, v/v/v). Applying HPDC technique to water-insoluble substances is problematic as this method requires a highly aqueous solvent system. In order to overcome this incompatibility, a system was set up where paclitaxel, although in low concentration, was extracted by methanol-water-trifluoroacetic acid (10.0:89.9:0.1, v/v/v). Recycling the extracting solvent to ensure minimal volume, the extracted paclitaxel was adsorbed on a C(18) trap column. A C(18) column of 4.6mm internal diameter was then connected to the trap column. The HPDC technique was thus carried out using an isocratic acetonitrile-water-trifluoroacetic acid (30.0:69.9:0.1, v/v/v) mobile phase consisting of a displacer cetylpyridinium trifluoroacetate (3mg/mL). Paclitaxel was co-eluted with the displacer and spontaneously crystallized. The crystal (114mg) showed 99.4% purity and only 10% of paclitaxel in the starting crude extract was lost during the enrichment/purification processes. This large scale purification method was successfully applied to purify paclitaxel from Chinese yew in small scale, suggesting general applicability of the method. This is the first report of purifying a water-insoluble natural product using HPDC technique.
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Affiliation(s)
- Jean Watchueng
- Chemical Biology Group, Biotechnology Research Institute, Montreal, Quebec, Canada
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Kind T, Fiehn O. Advances in structure elucidation of small molecules using mass spectrometry. BIOANALYTICAL REVIEWS 2010; 2:23-60. [PMID: 21289855 PMCID: PMC3015162 DOI: 10.1007/s12566-010-0015-9] [Citation(s) in RCA: 298] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 08/03/2010] [Indexed: 12/22/2022]
Abstract
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Kind
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
| | - Oliver Fiehn
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
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