101
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Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries. Proc Natl Acad Sci U S A 2015; 112:11999-2004. [PMID: 26371303 DOI: 10.1073/pnas.1507743112] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Traditional natural products discovery using a combination of live/dead screening followed by iterative bioassay-guided fractionation affords no information about compound structure or mode of action until late in the discovery process. This leads to high rates of rediscovery and low probabilities of finding compounds with unique biological and/or chemical properties. By integrating image-based phenotypic screening in HeLa cells with high-resolution untargeted metabolomics analysis, we have developed a new platform, termed Compound Activity Mapping, that is capable of directly predicting the identities and modes of action of bioactive constituents for any complex natural product extract library. This new tool can be used to rapidly identify novel bioactive constituents and provide predictions of compound modes of action directly from primary screening data. This approach inverts the natural products discovery process from the existing "grind and find" model to a targeted, hypothesis-driven discovery model where the chemical features and biological function of bioactive metabolites are known early in the screening workflow, and lead compounds can be rationally selected based on biological and/or chemical novelty. We demonstrate the utility of the Compound Activity Mapping platform by combining 10,977 mass spectral features and 58,032 biological measurements from a library of 234 natural products extracts and integrating these two datasets to identify 13 clusters of fractions containing 11 known compound families and four new compounds. Using Compound Activity Mapping we discovered the quinocinnolinomycins, a new family of natural products with a unique carbon skeleton that cause endoplasmic reticulum stress.
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102
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Sica V, Raja HA, El-Elimat T, Kertesz V, Van Berkel GJ, Pearce CJ, Oberlies NH. Dereplicating and Spatial Mapping of Secondary Metabolites from Fungal Cultures in Situ. JOURNAL OF NATURAL PRODUCTS 2015; 78:1926-36. [PMID: 26192135 PMCID: PMC4570219 DOI: 10.1021/acs.jnatprod.5b00268] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ambient ionization mass spectrometry techniques have recently become prevalent in natural product research due to their ability to examine secondary metabolites in situ. These techniques retain invaluable spatial and temporal details that are lost through traditional extraction processes. However, most ambient ionization techniques do not collect mutually supportive data, such as chromatographic retention times and/or UV/vis spectra, and this can limit the ability to identify certain metabolites, such as differentiating isomers. To overcome this, the droplet-liquid microjunction-surface sampling probe (droplet-LMJ-SSP) was coupled with UPLC-PDA-HRMS-MS/MS, thus providing separation, retention times, MS data, and UV/vis data used in traditional dereplication protocols. By capturing these mutually supportive data, the identity of secondary metabolites can be confidently and rapidly assigned in situ. Using the droplet-LMJ-SSP, a protocol was constructed to analyze the secondary metabolite profile of fungal cultures without any sample preparation. The results demonstrate that fungal cultures can be dereplicated from the Petri dish, thus identifying secondary metabolites, including isomers, and confirming them against reference standards. Furthermore, heat maps, similar to mass spectrometry imaging, can be used to ascertain the location and relative concentration of secondary metabolites directly on the surface and/or surroundings of a fungal culture.
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Affiliation(s)
- Vincent
P. Sica
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Huzefa A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Tamam El-Elimat
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Vilmos Kertesz
- Organic
and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Gary J. Van Berkel
- Organic
and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowlands
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
- Tel: 336-334-5474. E-mail:
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103
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass spectrometry tools and workflows for revealing microbial chemistry. Analyst 2015; 140:4949-66. [PMID: 25996313 PMCID: PMC5444374 DOI: 10.1039/c5an00171d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.
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104
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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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105
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Donner CD. Naphthopyranones--isolation, bioactivity, biosynthesis and synthesis. Nat Prod Rep 2015; 32:578-604. [PMID: 25531639 DOI: 10.1039/c4np00127c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 1H-naphtho[2,3-c]pyran-1-one (naphthopyranone) moiety forms the structural framework of a group of secondary metabolites that have been isolated from a range of organisms including fungi, bacteria, lichen and plants. This review documents the known naturally occurring naphthopyranones - their isolation, biosynthesis and biological activity. A survey of methods reported for the synthesis of naphthopyranone natural products is presented.
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106
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Mohamed A, Nguyen CH, Mamitsuka H. Current status and prospects of computational resources for natural product dereplication: a review. Brief Bioinform 2015; 17:309-21. [PMID: 26153512 DOI: 10.1093/bib/bbv042] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 01/08/2023] Open
Abstract
Research in natural products has always enhanced drug discovery by providing new and unique chemical compounds. However, recently, drug discovery from natural products is slowed down by the increasing chance of re-isolating known compounds. Rapid identification of previously isolated compounds in an automated manner, called dereplication, steers researchers toward novel findings, thereby reducing the time and effort for identifying new drug leads. Dereplication identifies compounds by comparing processed experimental data with those of known compounds, and so, diverse computational resources such as databases and tools to process and compare compound data are necessary. Automating the dereplication process through the integration of computational resources has always been an aspired goal of natural product researchers. To increase the utilization of current computational resources for natural products, we first provide an overview of the dereplication process, and then list useful resources, categorizing into databases, methods and software tools and further explaining them from a dereplication perspective. Finally, we discuss the current challenges to automating dereplication and proposed solutions.
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107
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Albright JC, Henke MT, Soukup AA, McClure RA, Thomson RJ, Keller NP, Kelleher NL. Large-scale metabolomics reveals a complex response of Aspergillus nidulans to epigenetic perturbation. ACS Chem Biol 2015; 10:1535-41. [PMID: 25815712 DOI: 10.1021/acschembio.5b00025] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The microbial world offers a rich source of bioactive compounds for those able to sift through it. Technologies capable of quantitatively detecting natural products while simultaneously identifying known compounds would expedite the search for new pharmaceutical leads. Prior efforts have targeted histone deacetylases in fungi to globally activate the production of new secondary metabolites, yet no study has directly assessed its effects with minimal bias at the metabolomic level. Using untargeted metabolomics, we monitored changes in >1000 small molecules secreted from the model fungus, Aspergillus nidulans, following genetic or chemical reductions in histone deacetylase activity (HDACi). Through quantitative, differential analyses, we found that nearly equal numbers of compounds were up- and down-regulated by >100 fold. We detected products from both known and unknown biosynthetic pathways and discovered that A. nidulans is capable of producing fellutamides, proteasome inhibitors whose expression was induced by ∼100 fold or greater upon HDACi. This work adds momentum to an "omics"-driven resurgence in natural products research, where direct detection replaces bioactivity as the primary screen for new pharmacophores.
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Affiliation(s)
- Jessica C. Albright
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Matthew T. Henke
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Alexandra A. Soukup
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ryan A. McClure
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Regan J. Thomson
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Nancy P. Keller
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Neil L. Kelleher
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
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108
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Chamoun R, Aliferis KA, Jabaji S. Identification of signatory secondary metabolites during mycoparasitism of Rhizoctonia solani by Stachybotrys elegans. Front Microbiol 2015; 6:353. [PMID: 25972848 PMCID: PMC4413796 DOI: 10.3389/fmicb.2015.00353] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/08/2015] [Indexed: 11/24/2022] Open
Abstract
Stachybotrys elegans is able to parasitize the fungal plant pathogen Rhizoctonia solani AG-3 following a complex and intimate interaction, which, among others, includes the production of cell wall-degrading enzymes, intracellular colonization, and expression of pathogenic process encoding genes. However, information on the metabolome level is non-existent during mycoparasitism. Here, we performed a direct-infusion mass spectrometry (DIMS) metabolomics analysis using an LTQ Orbitrap analyzer in order to detect changes in the profiles of induced secondary metabolites of both partners during this mycoparasitic interaction 4 and 5 days following its establishment. The diketopiperazine(s) (DKPs) cyclo(S-Pro-S-Leu)/cyclo(S-Pro-S-Ile), ethyl 2-phenylacetate, and 3-nitro-4-hydroxybenzoic acid were detected as the primary response of Rhizoctonia 4 days following dual-culturing with Stachybotrys, whereas only the latter metabolite was up-regulated 1 day later. On the other hand, trichothecenes and atranones were mycoparasite-derived metabolites identified during mycoparasitism 4 and 5 days following dual-culturing. All the above secondary metabolites are known to exhibit bioactivity, including fungitoxicity, and represent key elements that determine the outcome of the interaction being studied. Results could be further exploited in programs for the evaluation of the bioactivity of these metabolites per se or their chemical analogs, and/or genetic engineering programs to obtain more efficient mycoparasite strains with improved efficacy and toxicological profiles.
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Affiliation(s)
- Rony Chamoun
- Department of Plant Science, McGill University Sainte-Anne-de-Bellevue, QC, Canada
| | | | - Suha Jabaji
- Department of Plant Science, McGill University Sainte-Anne-de-Bellevue, QC, Canada
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109
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Dereplication of known nucleobase and nucleoside compounds in natural product extracts by capillary electrophoresis-high resolution mass spectrometry. Molecules 2015; 20:5423-37. [PMID: 25822081 PMCID: PMC6272742 DOI: 10.3390/molecules20045423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 12/15/2022] Open
Abstract
Nucleobase and nucleoside compounds exist widely in various organisms. An often occurring problem in the discovery of new bioactive compounds from natural products is reisolation of known nucleobase and nucleoside compounds. To resolve this problem, a capillary electrophoresis-high resolution mass spectrometry (CE-HR-MS) method providing both rapid separation and accurate mass full-scan MS data was developed for the first time to screen and dereplicate known nucleobase and nucleoside compounds in crude extracts of natural products. Instrumental parameters were optimized to obtain optimum conditions for CE separation and electrospray ionization-time-of-flight mass spectrometry (ESI-TOF/MS) detection. The proposed method was verified to be precise, reproducible, and sensitive. Using this method, known nucleobase and nucleoside compounds in different marine medicinal organisms including Syngnathus acus Linnaeus; Hippocampusjaponicus Kaup and Anthopleura lanthogrammica Berkly were successfully observed and identified. This work demonstrates that CE-HR-MS combined with an accurate mass database may be used as a powerful tool for dereplicating known nucleobase and nucleoside compounds in different types of natural products. Rapid dereplication of known nucleobase and nucleoside compounds allows researchers to focus on other leads with greater potential to yield new substances.
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110
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Bussey RO, Kaur A, Todd DA, Egan JM, El-Elimat T, Graf TN, Raja HA, Oberlies NH, Cech NB. Comparison of the chemistry and diversity of endophytes isolated from wild-harvested and greenhouse-cultivated yerba mansa ( Anemopsis californica). PHYTOCHEMISTRY LETTERS 2015; 11:202-208. [PMID: 25642298 PMCID: PMC4307022 DOI: 10.1016/j.phytol.2014.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With this study, we explored the identity and chemistry of fungal endophytes from the roots of yerba mansa [Anemopsis californica (Nutt.) Hook. & Arn. (Saururaceae)], a botanical traditionally used to treat infection. We compared the diversity of fungal endophytes isolated from a wild-harvested A. californica population, and those from plants cultivated for one year in a greenhouse environment. The wild-harvested population yielded thirteen fungal strains (eleven unique genotypes). Of the extracts prepared from these fungi, four inhibited growth of Staphylococcus aureus by >25% at 20 µg/mL, and three inhibited growth of Pseudomonas aeruginosa by ≥20% at 200 µg/mL. By comparison, A. californica roots after one year of cultivation in the greenhouse produced only two unique genotypes, neither of which displayed significant antimicrobial activity. The fungus Chaetomium cupreum isolated from wild-harvested A. californica yielded a new antimicrobial spirolactone, chaetocuprum (1). An additional fourteen known compounds were identified using LC-MS dereplication of the various fungal endophytes. This study provides new insights into the identity and chemistry of A. californica fungal endophytes, and demonstrates the importance of considering growing conditions when pursuing natural product drug discovery from endophytic fungi.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nadja B. Cech
- Corresponding Author. ; phone 336-324-5011; fax 336-324-5402
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111
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de Medeiros LS, Abreu LM, Nielsen A, Ingmer H, Larsen TO, Nielsen KF, Rodrigues-Filho E. Dereplication-guided isolation of depsides thielavins S-T and lecanorins D-F from the endophytic fungus Setophoma sp. PHYTOCHEMISTRY 2015; 111:154-162. [PMID: 25586883 DOI: 10.1016/j.phytochem.2014.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/13/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Dereplication methodology using UHPLC-DAD-QTOFMS was applied during the metabolic profiling investigation of the endophyte Setophoma sp., a fungus isolated from symptomless guava fruits. The approach performed allowed a fast analysis of the microbial secondary metabolites. From this fungus, seven highly C-alkylated depsides were isolated and identified as polyketides thielavins S, T, U and V and lecanorins D, E and F. Their structures were elucidated through spectroscopic methods including NMR, HRMS and especially with assistance of HRMS/MS experiments. The compounds were tested for quorum sensing regulation activity in the virulence gene expression of Staphylococcus aureus, but no inhibitory effect was detected. Nevertheless, moderate antibacterial activity was encountered in three of tested depsides, particularly with thielavin T, whose MIC was 6.25 μg/mL against S. aureus.
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Affiliation(s)
- Lívia S de Medeiros
- Department of Chemistry, Universidade Federal de São Carlos, LaBioMMi, Rod. Washington Luís, Km 265, 13565-905 São Carlos, SP, Brazil.
| | - Lucas M Abreu
- Department of Phytopathology, Universidade Federal de Lavras, 37200-000 Lavras, MG, Brazil
| | - Anita Nielsen
- Department of Veterinary Disease Biology, Food Safety and Zoonoses Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Food Safety and Zoonoses Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Copenhagen, Denmark
| | - Thomas O Larsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kgs. Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kgs. Lyngby, Denmark
| | - Edson Rodrigues-Filho
- Department of Chemistry, Universidade Federal de São Carlos, LaBioMMi, Rod. Washington Luís, Km 265, 13565-905 São Carlos, SP, Brazil
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112
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Nielsen KF, Larsen TO. The importance of mass spectrometric dereplication in fungal secondary metabolite analysis. Front Microbiol 2015; 6:71. [PMID: 25741325 PMCID: PMC4330896 DOI: 10.3389/fmicb.2015.00071] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/20/2015] [Indexed: 11/13/2022] Open
Abstract
Having entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids - which can all undergo extensive modifications by tailoring enzymes - thus potentially providing a large array of products from a single pathway. Elucidating the full chemical profile of a fungal species is a challenging exercise, even with elemental composition provided by high-resolution mass spectrometry (HRMS) used in combination with chemical databases (e.g., AntiBase) to dereplicate known compounds. This has led to a continuous effort to improve chromatographic separation in conjunction with improvement in HRMS detection. Major improvements have also occurred with 2D chromatography, ion-mobility, MS/MS and MS(3), stable isotope labeling feeding experiments, classic UV/Vis, and especially automated data-mining and metabolomics software approaches as the sheer amount of data generated is now the major challenge. This review will focus on the development and implementation of dereplication strategies and will highlight the importance of each stage of the process from sample preparation to chromatographic separation and finally toward both manual and more targeted methods for automated dereplication of fungal natural products using state-of-the art MS instrumentation.
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Affiliation(s)
- Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby Denmark
| | - Thomas O Larsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby Denmark
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113
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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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114
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Raja HA, Kaur A, El-Elimat T, Figueroa M, Kumar R, Deep G, Agarwal R, Faeth SH, Cech NB, Oberlies NH. Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle). Mycology 2015; 6:8-27. [PMID: 26000195 PMCID: PMC4409047 DOI: 10.1080/21501203.2015.1009186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/13/2015] [Indexed: 01/30/2023] Open
Abstract
Use of the herb milk thistle (Silybum marianum) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid-substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity.
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Affiliation(s)
- Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Amninder Kaur
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Tamam El-Elimat
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico, DF04510, Mexico
| | - Rahul Kumar
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO80045, USA
| | - Gagan Deep
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO80045, USA
| | - Rajesh Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO80045, USA
| | - Stanley H. Faeth
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Nadja B. Cech
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
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115
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El-Elimat T, Figueroa M, Raja HA, Graf TN, Swanson SM, Falkinham JO, Wani MC, Pearce CJ, Oberlies NH. Biosynthetically Distinct Cytotoxic Polyketides from Setophoma terrestris.. European J Org Chem 2015; 2015:109-121. [PMID: 25574154 PMCID: PMC4283843 DOI: 10.1002/ejoc.201402984] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Indexed: 11/09/2022]
Abstract
Sixteen polyketides belonging to diverse structural classes, including monomeric/dimeric tetrahydroxanthones and resorcylic acid lactones, were isolated from an organic extract of a fungal culture Setophoma terrestris (MSX45109) using bioactivity-directed fractionation as part of a search for anticancer leads from filamentous fungi. Of these, six were new: penicillixanthone B (5), blennolide H (6), 11-deoxy blennolide D (7), blennolide I (9), blennolide J (10), and pyrenomycin (16). The known compounds were: secalonic acid A (1), secalonic acid E (2), secalonic acid G (3), penicillixanthone A (4), paecilin B (8), aigialomycin A (11), hypothemycin (12), dihydrohypothemycin (13), pyrenochaetic acid C (14), and nidulalin B (15). The structures were elucidated using a set of spectroscopic and spectrometric techniques; the absolute configurations of compounds 1-10 were determined using ECD spectroscopy combined with time-dependent density functional theory (TDDFT) calculations, while a modified Mosher's ester method was used for compound 16. The cytotoxic activities of compounds (1-15) were evaluated using the MDA-MB-435 (melanoma) and SW-620 (colon) cancer cell lines. Compounds 1, 4, and 12 were the most potent with IC50 values ranging from 0.16 to 2.14 μM. When tested against a panel of bacteria and fungi, compounds 3 and 5 showed promising activity against the Gram-positive bacterium Micrococcus luteus with MIC values of 5 and 15 μg/mL, respectively.
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Affiliation(s)
- Tamam El-Elimat
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States, Homepage: http://www.uncg.edu/che/Group_Research_Page/NicholasOberlies
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México Mexico DF 04510, Mexico
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States, Homepage: http://www.uncg.edu/che/Group_Research_Page/NicholasOberlies
| | - Tyler N. Graf
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States, Homepage: http://www.uncg.edu/che/Group_Research_Page/NicholasOberlies
| | - Steven M. Swanson
- Department of Medicinal Chemistry and Pharmacognosy University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Joseph O. Falkinham
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Mansukh C. Wani
- Natural Products Laboratory, Research Triangle Institute, Research Triangle Park NC 27709 United States
| | | | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States, Homepage: http://www.uncg.edu/che/Group_Research_Page/NicholasOberlies
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116
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Hemalatha RG, Naik HR, Mariappa V, Pradeep T. Rapid detection of Fusarium wilt in basil (Ocimum sp.) leaves by desorption electrospray ionization mass spectrometry (DESI MS) imaging. RSC Adv 2015. [DOI: 10.1039/c4ra16706f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A rapid method to unravel the spatial distribution ofFusarium/other pathogen-contamination in asymptomatic leaves under ambient conditions.
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Affiliation(s)
- R. G. Hemalatha
- DST Unit on Nanoscience and Thematic Unit of Excellence
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai
- India
| | - Hemanta R. Naik
- DST Unit on Nanoscience and Thematic Unit of Excellence
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai
- India
| | - Vasundhara Mariappa
- Medicinal and Aromatic Section
- Department of Horticulture
- University of Agricultural Sciences
- Bangalore
- India
| | - T. Pradeep
- DST Unit on Nanoscience and Thematic Unit of Excellence
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai
- India
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117
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Andersen B, Nielsen KF, Fernández Pinto V, Patriarca A. Characterization of Alternaria strains from Argentinean blueberry, tomato, walnut and wheat. Int J Food Microbiol 2014; 196:1-10. [PMID: 25498470 DOI: 10.1016/j.ijfoodmicro.2014.11.029] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/12/2014] [Accepted: 11/27/2014] [Indexed: 01/31/2023]
Abstract
Alternaria species have the ability to produce a variety of secondary metabolite, which plays important roles in food safety. Argentina is the second largest exporter of fresh and processed food products to Europe, however, few studies on Alternaria mycotoxins and other bioactive secondary metabolites have been carried out on Argentinean cereals, fruit and vegetables. Knowing the full chemical potential and the distribution of Alternaria spp. on crops, it is necessary to establish a toxicological risk assessment for food products for human consumption. In the present study, 87 Alternaria strains from different substrates (tomato, wheat, blueberries and walnuts) were characterized according to morphology and metabolite production. Aggressive dereplication (accurate mass, isotopic patterns and lists of all described compounds from Alternaria) was used for high-throughput evaluation of the chemical potential. Four strains belonged to the Alternaria infectoria sp.-grp., 6 to the Alternaria arborescens sp.-grp., 6 showed a sporulation pattern similar to that of "M" according to Simmons, 1 to that of Alternaria vaccinii, and the remaining 70 constituted a diverse group belonging to morphological groups "G" and "H". The cluster analysis yielded 16 almost identical dendrograms and grouped the Alternaria strains into four clusters and 11 singletons and outlier groups. The chemical analysis showed that AOH and AME were the most common metabolites produced, followed by TEN, ALXs and TeA. The A. infectoria sp.-grp. had no metabolites in common with the rest of the strains. Several secondary metabolites isolated from large-spored Alternaria species or other fungal genera were detected, such as dehydrocurvularin, pyrenochaetic acid and alternarienonic acid. The strains isolated from tomato produced lower amounts of metabolites than strains from blueberries, walnut and wheat, although individual strains from tomato produced the highest amount of some metabolites. The A. infectoria sp.-grp. was unique to cereals, whereas strains classified as belonging to the A. arborescens sp.-grp or having sporulation pattern "M" were only isolated from tomatoes. Otherwise, no clear association between substrate and identity could be found. The analyses in the study show that at least 75% of the Argentinean strains are able to produce potential mycotoxins.
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Affiliation(s)
- Birgitte Andersen
- Department of Systems Biology, Søltofts Plads, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Systems Biology, Søltofts Plads, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Virginia Fernández Pinto
- Laboratorio de Microbiología de Alimentos, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, 3° Piso, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Andrea Patriarca
- Laboratorio de Microbiología de Alimentos, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, 3° Piso, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina.
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118
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Crevelin EJ, Crotti AEM, Zucchi TD, Melo IS, Moraes LAB. Dereplication of Streptomyces sp. AMC 23 polyether ionophore antibiotics by accurate-mass electrospray tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1117-1126. [PMID: 25395127 DOI: 10.1002/jms.3432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/09/2014] [Accepted: 07/03/2014] [Indexed: 06/04/2023]
Abstract
Actinomycetes, especially those belonging to the genus Streptomyces, are economically important from a biotechnological standpoint: they produce antibiotics, anticancer compounds and a variety of bioactive substances that are potentially applicable in the agrochemical and pharmaceutical industries. This paper combined accurate-mass electrospray tandem mass spectrometry in the full scan and product ion scan modes with compounds library data to identify the major compounds in the crude extract produced by Streptomyces sp. AMC 23; it also investigated how sodiated nonactin ([M + Na](+)) fragmented. Most product ions resulted from elimination of 184 mass units due to consecutive McLafferty-type rearrangements. The data allowed identification of four macrotetrolides homologous to nonactin (monactin, isodinactin, isotrinactin/trinactin and tetranactin) as well as three related linear dimer compounds (nonactyl nonactoate, nonactyl homononactoate and homononactyl homononactoate). The major product ions of the sodiated molecules of these compounds also originated from elimination of 184 and 198 mass units. UPLC-MS/MS in the neutral loss scan mode helped to identify these compounds on the basis of the elimination of 184 and 198 mass units. This method aided monitoring of the relative production of these compounds for 32 days and revealed that the biosynthetic process began with increased production of linear dimers as compared with macrotetrolides. These data could facilitate dereplication and identification of these compounds in other microbial crude extracts.
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Affiliation(s)
- Eduardo J Crevelin
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo-USP, Ribeirão Preto, SP, Brazil
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119
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Hoffmann T, Krug D, Hüttel S, Müller R. Improving natural products identification through targeted LC-MS/MS in an untargeted secondary metabolomics workflow. Anal Chem 2014; 86:10780-8. [PMID: 25280058 DOI: 10.1021/ac502805w] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tandem mass spectrometry is a widely applied and highly sensitive technique for the discovery and characterization of microbial natural products such as secondary metabolites from myxobacteria. Here, a data mining workflow based on MS/MS precursor lists targeting only signals related to bacterial metabolism is established using LC-MS data of crude extracts from shaking flask fermentations. The devised method is not biased toward specific compound classes or structural features and is capable of increasing the information content of LC-MS/MS analyses by directing fragmentation events to signals of interest. The approach is thus contrary to typical auto-MS(2) setups where precursor ions are usually selected according to signal intensity, which is regarded as a drawback for metabolite discovery applications when samples contain many overlapping signals and the most intense signals do not necessarily represent compounds of interest. In line with this, the method described here achieves improved MS/MS scan coverage for low-abundance precursor ions not captured by auto-MS(2) experiments and thereby facilitates the search for new secondary metabolites in complex biological samples. To underpin the effectiveness of the approach, the identification and structure elucidation of two new myxobacterial secondary metabolite classes is reported.
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Affiliation(s)
- Thomas Hoffmann
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University , Building C 2.3, D-66123 Saarbrücken, Germany
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120
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Sorbicillinoid analogs with cytotoxic and selective anti-Aspergillus activities from Scytalidium album. J Antibiot (Tokyo) 2014; 68:191-6. [PMID: 25248727 PMCID: PMC4372511 DOI: 10.1038/ja.2014.125] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/14/2014] [Accepted: 07/18/2014] [Indexed: 11/08/2022]
Abstract
As part of an ongoing project to explore filamentous fungi for anticancer and antibiotic leads, eleven compounds were isolated and identified from an organic extract of the fungus Scytalidium album (MSX51631) using bioactivity-directed fractionation against human cancer cell lines. Of these, eight were a series of sorbicillinoid analogues (1–8), of which four were new [scalbucillin A (2), scalbucillin B (3), scalbucillin C (6), and scalbucillin D (8)], two were phthalides (9–10), and one was naphthalenone (11). Compounds (1–11) were tested in the MDA-MB-435 (melanoma) and SW-620 (colon) cancer cell lines. Compound 1 was the most potent with IC50 values of 1.5 and 0.5 μM, respectively, followed by compound 5, with IC50 values of 2.3 and 2.5 μM at 72 h. Compound 1 showed a 48-h IC50 value of 3.1 μM when tested against the lymphocytic leukemia cell line OSU-CLL, while the nearly identical compound 5 had almost no activity in this assay. Compounds 1 and 5 showed selective and equipotent activity against Aspergillus niger with minimum inhibitory concentration values of 0.05 and 0.04 μg/ml (0.20 and 0.16 μM), respectively. The in vitro hemolytic activity against sheep erythrocytes of compounds 1 and 5 was investigated and were found to provoke 10% hemolysis at 52.5 and 45.0 μg/ml, respectively, indicative of a promising safety factor.
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121
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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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122
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Bouslimani A, Sanchez LM, Garg N, Dorrestein PC. Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 2014; 31:718-29. [PMID: 24801551 PMCID: PMC4161218 DOI: 10.1039/c4np00044g] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex biological systems. In this Highlight, we feature emerging mass spectrometric methods and tools used by the natural product community and give a perspective of future directions where the mass spectrometry field is migrating towards over the next decade.
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Affiliation(s)
- Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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123
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Bijttebier S, Zhani K, D'Hondt E, Noten B, Hermans N, Apers S, Voorspoels S. Generic characterization of apolar metabolites in red chili peppers (Capsicum frutescens L.) by orbitrap mass spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:4812-4831. [PMID: 24762165 DOI: 10.1021/jf500285g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The aim of the present study was to develop a generic analytical method for the identification and quantitation of apolar plant metabolites in biomass using liquid chromatography-photodiode array-accurate mass mass spectrometry (LC-PDA-amMS). During this study, a single generic sample preparation protocol was applied to extract apolar plant metabolites. Compound identification was performed using a single generic screening method for apolar compounds without the need for dedicated fractionation. Such a generic approach renders vast amounts of information and is virtually limited by only the solubility and detector response of the metabolites of interest. Method validation confirmed that this approach is applicable for quantitative purposes. Furthermore, an identification-quantitation strategy based on amMS and molar extinction coefficients was used for carotenoids, eliminating the need for reference standards for each carotenoid. To challenge the validated method, chili peppers (Capsicum frutescens L.) were analyzed to unravel their complex phytochemical composition (carotenoids, glycolipids, glycerolipids, capsaicinoids, lipid-soluble vitamins).
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Affiliation(s)
- Sebastiaan Bijttebier
- Business Unit Separation and Conversion Technology (SCT), Flemish Institute for Technological Research (VITO) , Boeretang 200, 2400 Mol, Belgium
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124
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Yang J, Liang Q, Wang M, Jeffries C, Smithson D, Tu Y, Boulos N, Jacob MR, Shelat AA, Wu Y, Ravu RR, Gilbertson R, Avery MA, Khan IA, Walker LA, Guy RK, Li XC. UPLC-MS-ELSD-PDA as a powerful dereplication tool to facilitate compound identification from small-molecule natural product libraries. JOURNAL OF NATURAL PRODUCTS 2014; 77:902-9. [PMID: 24617915 PMCID: PMC4784093 DOI: 10.1021/np4009706] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The generation of natural product libraries containing column fractions, each with only a few small molecules, using a high-throughput, automated fractionation system, has made it possible to implement an improved dereplication strategy for selection and prioritization of leads in a natural product discovery program. Analysis of databased UPLC-MS-ELSD-PDA information of three leads from a biological screen employing the ependymoma cell line EphB2-EPD generated details on the possible structures of active compounds present. The procedure allows the rapid identification of known compounds and guides the isolation of unknown compounds of interest. Three previously known flavanone-type compounds, homoeriodictyol (1), hesperetin (2), and sterubin (3), were identified in a selected fraction derived from the leaves of Eriodictyon angustifolium. The lignan compound deoxypodophyllotoxin (8) was confirmed to be an active constituent in two lead fractions derived from the bark and leaves of Thuja occidentalis. In addition, two new but inactive labdane-type diterpenoids with an uncommon triol side chain were also identified as coexisting with deoxypodophyllotoxin in a lead fraction from the bark of T. occidentalis. Both diterpenoids were isolated in acetylated form, and their structures were determined as 14S,15-diacetoxy-13R-hydroxylabd-8(17)-en-19-oic acid (9) and 14R,15-diacetoxy-13S-hydroxylabd-8(17)-en-19-oic acid (10), respectively, by spectroscopic data interpretation and X-ray crystallography. This work demonstrates that a UPLC-MS-ELSD-PDA database produced during fractionation may be used as a powerful dereplication tool to facilitate compound identification from chromatographically tractable small-molecule natural product libraries.
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Affiliation(s)
- Jin Yang
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
- School of Chemistry and Chemical Engineering, Beifang University of Nationalities, Yinchuan, Ningxia 750021, People’s Republic of China
| | - Qian Liang
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
| | - Mei Wang
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
| | - Cynthia Jeffries
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David Smithson
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ying Tu
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Nidal Boulos
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Melissa R. Jacob
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
| | - Anang A. Shelat
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yunshan Wu
- Department of Medicinal Chemistry, The University of Mississippi, University, MS 38677, USA
| | - Ranga Rao Ravu
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
| | - Richard Gilbertson
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mitchell A. Avery
- Department of Medicinal Chemistry, The University of Mississippi, University, MS 38677, USA
| | - Ikhlas A. Khan
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
- Department of Pharmacognosy, The University of Mississippi, University, MS 38677, USA
| | - Larry A. Walker
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
- Department of Pharmacology, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - R. Kiplin Guy
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Xing-Cong Li
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences
- Department of Pharmacognosy, The University of Mississippi, University, MS 38677, USA
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125
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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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126
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Smith KM, Gautschi JT, Freitag M. Decoding the cryptic genomes of fungi: the promise of novel antibiotics. Future Microbiol 2014; 9:265-8. [DOI: 10.2217/fmb.14.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Kristina M Smith
- Programs in Biology & Chemistry, Oregon State University-Cascades, 2600 Northwest College Way, Bend, OR 97701, USA
- Department of Biochemistry & Biophysics, 2011 ALS Bldg., Oregon State University, Corvallis, OR 97331, USA
| | - Jeffrey T Gautschi
- Programs in Biology & Chemistry, Oregon State University-Cascades, 2600 Northwest College Way, Bend, OR 97701, USA
- Department of Chemistry, Gilbert Hall, Oregon State University, Corvallis, OR 97331, USA
| | - Michael Freitag
- Department of Biochemistry & Biophysics, 2011 ALS Bldg., Oregon State University, Corvallis, OR 97331, USA
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127
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El-Elimat T, Raja HA, Graf TN, Faeth SH, Cech NB, Oberlies NH. Flavonolignans from Aspergillus iizukae, a fungal endophyte of milk thistle (Silybum marianum). JOURNAL OF NATURAL PRODUCTS 2014; 77:193-9. [PMID: 24456525 DOI: 10.1021/np400955q] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Silybin A (1), silybin B (2), and isosilybin A (3), three of the seven flavonolignans that constitute silymarin, an extract of the fruits of milk thistle (Silybum marianum), were detected for the first time from a fungal endophyte, Aspergillus iizukae, isolated from the surface-sterilized leaves of S. marianum. The flavonolignans were identified using a UPLC-PDA-HRMS-MS/MS method by matching retention times, HRMS, and MS/MS data with authentic reference compounds. Attenuation of flavonolignan production was observed following successive subculturing of the original flavonolignan-producing culture, as is often the case with endophytes that produce plant-based secondary metabolites. However, production of 1 and 2 resumed when attenuated spores were harvested from cultures grown on a medium to which autoclaved leaves of S. marianum were added. The cycle of attenuation followed by resumed biosynthesis of these flavonolignans was replicated in triplicate.
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Affiliation(s)
- Tamam El-Elimat
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro , Greensboro, North Carolina 27402, United States
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128
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Klitgaard A, Iversen A, Andersen MR, Larsen TO, Frisvad JC, Nielsen KF. Aggressive dereplication using UHPLC-DAD-QTOF: screening extracts for up to 3000 fungal secondary metabolites. Anal Bioanal Chem 2014; 406:1933-43. [PMID: 24442010 PMCID: PMC3955480 DOI: 10.1007/s00216-013-7582-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/03/2013] [Accepted: 12/14/2013] [Indexed: 11/30/2022]
Abstract
In natural-product drug discovery, finding new compounds is the main task, and thus fast dereplication of known compounds is essential. This is usually performed by manual liquid chromatography-ultraviolet (LC-UV) or visible light-mass spectroscopy (Vis-MS) interpretation of detected peaks, often assisted by automated identification of previously identified compounds. We used a 15 min high-performance liquid chromatography–diode array detection (UHPLC–DAD)–high-resolution MS method (electrospray ionization (ESI)+ or ESI−), followed by 10–60 s of automated data analysis for up to 3000 relevant elemental compositions. By overlaying automatically generated extracted-ion chromatograms from detected compounds on the base peak chromatogram, all major potentially novel peaks could be visualized. Peaks corresponding to compounds available as reference standards, previously identified compounds, and major contaminants from solvents, media, filters etc. were labeled to differentiate these from compounds only identified by elemental composition. This enabled fast manual evaluation of both known peaks and potential novel-compound peaks, by manual verification of: the adduct pattern, UV–Vis, retention time compared with log D, co-identified biosynthetic related compounds, and elution order. System performance, including adduct patterns, in-source fragmentation, and ion-cooler bias, was investigated on reference standards, and the overall method was used on extracts of Aspergillus carbonarius and Penicillium melanoconidium, revealing new nitrogen-containing biomarkers for both species.
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Affiliation(s)
- Andreas Klitgaard
- Department of Systems Biology, Søltofts Plads, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
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VanderMolen KM, Raja HA, El-Elimat T, Oberlies NH. Evaluation of culture media for the production of secondary metabolites in a natural products screening program. AMB Express 2013; 3:71. [PMID: 24342059 PMCID: PMC3917616 DOI: 10.1186/2191-0855-3-71] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
Variation in the growing environment can have significant impacts on the quantity and diversity of fungal secondary metabolites. In the industrial setting, optimization of growing conditions can lead to significantly increased production of a compound of interest. Such optimization becomes challenging in a drug-discovery screening situation, as the ideal conditions for one organism may induce poor metabolic diversity for a different organism. Here, the impact of different media types, including six liquid media and five solid media, on the secondary metabolite production of three fungal strains was examined in the context of the drug-discovery screening process. The relative production of marker compounds was used to evaluate the usefulness and reliability of each medium for the purpose of producing secondary metabolites.
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130
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Abida H, Ruchaud S, Rios L, Humeau A, Probert I, De Vargas C, Bach S, Bowler C. Bioprospecting marine plankton. Mar Drugs 2013; 11:4594-611. [PMID: 24240981 PMCID: PMC3853748 DOI: 10.3390/md11114594] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/06/2013] [Accepted: 10/09/2013] [Indexed: 12/18/2022] Open
Abstract
The ocean dominates the surface of our planet and plays a major role in regulating the biosphere. For example, the microscopic photosynthetic organisms living within provide 50% of the oxygen we breathe, and much of our food and mineral resources are extracted from the ocean. In a time of ecological crisis and major changes in our society, it is essential to turn our attention towards the sea to find additional solutions for a sustainable future. Remarkably, while we are overexploiting many marine resources, particularly the fisheries, the planktonic compartment composed of zooplankton, phytoplankton, bacteria and viruses, represents 95% of marine biomass and yet the extent of its diversity remains largely unknown and underexploited. Consequently, the potential of plankton as a bioresource for humanity is largely untapped. Due to their diverse evolutionary backgrounds, planktonic organisms offer immense opportunities: new resources for medicine, cosmetics and food, renewable energy, and long-term solutions to mitigate climate change. Research programs aiming to exploit culture collections of marine micro-organisms as well as to prospect the huge resources of marine planktonic biodiversity in the oceans are now underway, and several bioactive extracts and purified compounds have already been identified. This review will survey and assess the current state-of-the-art and will propose methodologies to better exploit the potential of marine plankton for drug discovery and for dermocosmetics.
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Affiliation(s)
- Heni Abida
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197 INSERM U1024, 46 rue d’Ulm, Paris CEDEX 05 75230, France; E-Mail:
| | - Sandrine Ruchaud
- Kinase Inhibitor Specialized Screening facility (KISSf), Station Biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS) USR 3151 (Protein Phosphorylation and Human Diseases), CS 90074, Roscoff CEDEX 29688, France; E-Mail:
| | - Laurent Rios
- Greentech France, Biopôle Clermont Limagne, Saint Beauzire 63360, France; E-Mail:
| | - Anne Humeau
- Soliance France, Centre de Biotechnologie Marine, Anse de Pors Gelin-Ile Grande, Plemeur-Bodou 22560, France; E-Mail:
| | - Ian Probert
- Roscoff Culture Collection, Station Biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS) USR 3151, Place Georges Teissier, CS 90074, Roscoff CEDEX 29688, France; E-Mail:
| | - Colomban De Vargas
- EPPO Laboratory, Station Biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS) USR 3151, Place Georges Teissier, CS 90074, Roscoff CEDEX 29688, France; E-Mail:
| | - Stéphane Bach
- Kinase Inhibitor Specialized Screening facility (KISSf), Station Biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS) USR 3151 (Protein Phosphorylation and Human Diseases), CS 90074, Roscoff CEDEX 29688, France; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (S.B.); (C.B.); Tel.: +33-2-98-29-23-91 (S.B.); Fax: +33-2-98-29-25-26 (S.B.); Tel.: +33-1-44-32-35-25 (C.B.); Fax: +33-1-44-32-39-35 (C.B.)
| | - Chris Bowler
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197 INSERM U1024, 46 rue d’Ulm, Paris CEDEX 05 75230, France; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (S.B.); (C.B.); Tel.: +33-2-98-29-23-91 (S.B.); Fax: +33-2-98-29-25-26 (S.B.); Tel.: +33-1-44-32-35-25 (C.B.); Fax: +33-1-44-32-39-35 (C.B.)
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2013. [DOI: 10.1039/c3np90036c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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