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Duangupama T, Pittayakhajonwut P, Intaraudom C, Suriyachadkun C, Tadtong S, Kuncharoen N, He YW, Tanasupawat S, Thawai C. Description of Streptomyces siderophoricus sp. nov., a promising nocardamine-producing species isolated from the rhizosphere soil of Mangifera indica. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00763-x. [PMID: 39054393 DOI: 10.1038/s41429-024-00763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/30/2024] [Accepted: 07/04/2024] [Indexed: 07/27/2024]
Abstract
An actinomycete, designated strain CH9-7T, was isolated from the rhizosphere soil of Mangifera indica. The morphological and chemotaxonomic properties, such as the production of spiral spore chains and the presence of LL-diaminopimelic acid in the peptidoglycan, showed that it belongs to the genus Streptomyces. Based on the 16S rRNA gene analysis, it was confirmed that strain CH9-7T was a member of the genus Streptomyces and revealed 99.9% 16S rRNA gene sequence similarity to its closest relative strains, Streptomyces lydicus NBRC 13058 T and Streptomyces chattanoogensis NBRC 12754 T. Although the strain showed high 16S rRNA gene sequence similarity values, however, genome relatedness indexes exhibited that the average nucleotide identity based on the MUMmer (ANIm) algorithm, the average amino acid identity (AAI), and the digital DNA-DNA hybridization values between strain CH9-7T and its closest phylogenomic relatives were below the threshold values for delineation of a novel species, (ANIm ranging from 87.5 to 88.6, AAI ranging from 80.6 to 84.6, and dDDH ranging from 28.4 to 31.7), respectively. A taxonomic position of strain CH9-7T in the phylogenomic tree showed that the closest relative strain was S. lydicus NBRC 13058 T. The comparative phenotypic studies between strain CH9-7T and its closest relatives revealed that strain CH9-7T could be classified as a novel species of the genus Streptomyces. Thus, the name Streptomyces siderophoricus sp. nov. is proposed for the strain. The type strain is CH9-7T ( = TBRC 17833 T = NBRC 116426 T). The chemical investigation led to the isolation of four known compounds (compounds 1-4). Among these compounds, compound 1 was identified to be nocardamine, a promising bioactive substance.
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Affiliation(s)
- Thitikorn Duangupama
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sarin Tadtong
- Department of Pharmacognosy, Faculty of Pharmacy, Srinakharinwirot University, Nakhon nayok, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chitti Thawai
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.
- Actinobacterial Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.
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Zdouc MM, Iorio M, Vind K, Simone M, Serina S, Brunati C, Monciardini P, Tocchetti A, Zarazúa GS, Crüsemann M, Maffioli SI, Sosio M, Donadio S. Effective approaches to discover new microbial metabolites in a large strain library. J Ind Microbiol Biotechnol 2021; 48:6144606. [PMID: 33599744 PMCID: PMC9113118 DOI: 10.1093/jimb/kuab017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/31/2020] [Indexed: 12/28/2022]
Abstract
Natural products have provided many molecules to treat and prevent illnesses in humans, animals and plants. While only a small fraction of the existing microbial diversity has been explored for bioactive metabolites, tens of thousands of molecules have been reported in the literature over the past 80 years. Thus, the main challenge in microbial metabolite screening is to avoid the re-discovery of known metabolites in a cost-effective manner. In this perspective, we report and discuss different approaches used in our laboratory over the past few years, ranging from bioactivity-based screening to looking for metabolic rarity in different datasets to deeply investigating a single Streptomyces strain. Our results show that it is possible to find novel chemistry through a limited screening effort, provided that appropriate selection criteria are in place.
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Affiliation(s)
- Mitja M Zdouc
- NAICONS Srl, 20139 Milan, Italy.,Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | | | - Kristiina Vind
- NAICONS Srl, 20139 Milan, Italy.,Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | | | | | | | | | | | - Guadalupe S Zarazúa
- Institut für Pharmazeutische Biologie, Rheinische Friedrich-Wilhelms-Universität, 53115 Bonn, Germany
| | - Max Crüsemann
- Institut für Pharmazeutische Biologie, Rheinische Friedrich-Wilhelms-Universität, 53115 Bonn, Germany
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Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain. Sci Rep 2021; 11:5827. [PMID: 33712632 PMCID: PMC7955054 DOI: 10.1038/s41598-021-84833-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
We report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type, on three newly constructed and seven previously reported mutant strains disabled in different genes required for pseudouridimycin biosynthesis. The results indicate that Streptomyces sp. ID38640 is able to produce, in addition to lydicamycins and deferroxiamines, as previously reported, also the lassopeptide ulleungdin, the non-ribosomal peptide antipain and the osmoprotectant ectoine. The corresponding biosynthetic gene clusters were readily identified in the strain genome. We also detected the known compound pyridindolol, for which we propose a previously unreported biosynthetic gene cluster, as well as three families of unknown metabolites. Remarkably, the levels of most metabolites varied strongly in the different mutant strains, an observation that enabled detection of metabolites unnoticed in the wild type. Systematic investigation of the accumulated metabolites in the ten different pum mutants identified shed further light on pseudouridimycin biosynthesis. We also show that several Streptomyces strains, able to produce pseudouridimycin, have distinct genetic relationship and metabolic profile with ID38640.
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Horne J, Beddingfield E, Knapp M, Mitchell S, Crawford L, Mills SB, Wrist A, Zhang S, Summers RM. Caffeine and Theophylline Inhibit β-Galactosidase Activity and Reduce Expression in Escherichia coli. ACS OMEGA 2020; 5:32250-32255. [PMID: 33376862 PMCID: PMC7758883 DOI: 10.1021/acsomega.0c03909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/03/2020] [Indexed: 05/04/2023]
Abstract
The β-galactosidase enzyme is a common reporter enzyme that has been used extensively in microbiological and synthetic biology research. Here, we demonstrate that caffeine and theophylline, common natural methylxanthine products found in many foods and pharmaceuticals, negatively impact both the expression and activity of β-galactosidase in Escherichia coli. The β-galactosidase activity in E. coli grown with increasing concentrations of caffeine and theophylline was reduced over sixfold in a dose-dependent manner. We also observed decreasing lacZ mRNA transcript levels with increasing methylxanthine concentrations in the growth media. Similarly, caffeine and theophylline inhibit the activity of the purified β-galactosidase enzyme, with an approximately 1.7-fold increase in K M toward o-nitrophenyl-β-galactoside and a concomitant decrease in v max. The authors recommend the use of alternative reporter systems when such methylxanthines are expected to be present.
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Affiliation(s)
| | - Elizabeth Beddingfield
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Madison Knapp
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Stephanie Mitchell
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Logan Crawford
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Shelby Brooks Mills
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Alexandra Wrist
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Shuyuan Zhang
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Moon K, Xu F, Zhang C, Seyedsayamdost MR. Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria. ACS Chem Biol 2019; 14:767-774. [PMID: 30830740 DOI: 10.1021/acschembio.9b00049] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria harbor an immense reservoir of potentially new and therapeutic small molecules in the form of "silent" biosynthetic gene clusters (BGCs). These BGCs can be identified bioinformatically but are sparingly expressed under normal laboratory growth conditions, or not at all, and therefore do not produce significant levels of the corresponding small molecule product. Several methods have been developed for activating silent BGCs. A major limitation for nearly all methods is that they require genetic procedures and/or do not report on the bioactivity of the cryptic metabolite. We herein report "Bioactivty-HiTES", an approach that links the bioactivity of cryptic metabolites to their induction while at the same time obviating the need for genetic manipulations. Using this method, we detected induction of cryptic antibiotics in three actinomycete strains that were tested. Follow-up studies in one case allowed us to structurally elucidate two cryptic metabolites, elicited by the β-blocker atenolol in Streptomyces hiroshimensis, with selective growth-inhibitory activity against Gram-negative bacteria, notably Escherichia coli and Acinetobacter baumannii. Atenolol turned out to be a global elicitor of secondary metabolism, and characterization of additional cryptic metabolites led to the discovery of a novel naphthoquinone epoxide. Bioactivity-HiTES is a general, widely applicable procedure that will be useful in identifying cryptic bioactive metabolites in the future.
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Affiliation(s)
- Kyuho Moon
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Fei Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chen Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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Hibino S. Synthetic Studies of Bioactive Heterocyclic Natural Products and Fused Heterocyclic Compounds Based on the Thermal Electrocyclic or Azaelectocyclic Reaction of 6π-Electron or Aza-6π-electron Systems. YAKUGAKU ZASSHI 2016; 136:607-48. [DOI: 10.1248/yakushi.15-00273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Satoshi Hibino
- Graduate School of Pharmacy and Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
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Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS. A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 2015; 44:7591-697. [PMID: 25735878 PMCID: PMC4560691 DOI: 10.1039/c4cs00426d] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.
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Affiliation(s)
- Sherif I Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Khaled A Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Madan K Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
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Nasr AZ, Mostafa MA. Utilization of Dipotassium Salt of Galactaric Acid Bis(Hydrazidocarbodithioic Acid) As a Synthone for Double-Headed 1,3,4-Thiadiazoline, 1,3,4-Oxadiazoline and 1,2,4-Triazoline Acyclo C-Nucleosides. PHOSPHORUS SULFUR 2006. [DOI: 10.1080/104265090888397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- A. Z. Nasr
- a Chemistry Department, Faculty of Science, Cairo University , Faiyoum, Egypt
| | - M. A. Mostafa
- b Chemistry Department, Faculty of Science, Alexandria University , Alexandria, Egypt
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Keller-Schierlein W, Müller A, Hagmann L, Schneider U, Zähner H. Stoffwechselprodukte von Mikroorganismen. 232. Mitteilung. (E)-3-(1H-Pyrrol-3-yl)-2-propensäure und (E)-3-(1H-Pyrrol-3-yl)-2-propensäureamid ausStreptomyces parvulus, Stamm Tü 2480. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19850680304] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hibino S, Kanekiyo N, Choshi T, Kuwada T, Sugino E. The First Total Synthesis of (R)-(-)-Pyridindolol K2 and Its Enantiomer. HETEROCYCLES 2000. [DOI: 10.3987/com-00-8975] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Shaban MA. The Chemistry of C-Nucleosides and Their Analogs II: C-Nucleosides of Condensed Heterocyclic Bases. ADVANCES IN HETEROCYCLIC CHEMISTRY 1997. [DOI: 10.1016/s0065-2725(08)60931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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Nash RJ, Watson AA, Asano N. Chapter Five Polyhydroxylated alkaloids that inhibit glycosidases. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0735-8210(96)80009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Aoyama T, Kojima F, Imada C, Muraoka Y, Naganawa H, Okami Y, Takeuchi T, Aoyagi T. Pyrostatins A and B, new inhibitors of N-acetyl-beta-D-glucosaminidase, produced by Streptomyces sp. SA-3501. JOURNAL OF ENZYME INHIBITION 1995; 8:223-32. [PMID: 7542319 DOI: 10.3109/14756369509020129] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pyrostatins A and B, new inhibitors of N-acetyl-beta-D-glucosaminidase (GlcNAc-ase), have been purified from the culture broth of Streptomyces sp. SA-3501 isolated from a marine environment. They were purified by chromatography on Dowex 50W, silica gel and Capcell Pak C18 (HPLC) followed treatment with active carbon and then isolated as white powders. The structures of pyrostatins A and B were determined by NMR studies to be 4-hydroxy-2-imino-1-methylpyrrolidine-5-carboxylic acid and 2-imino-1-methylpyrrolidine-5-carboxylic acid, respectively. They were competitive with the substrate, and the inhibition constants (Ki) of pyrostatins A and B were 1.7 x 10(-6) M and 2.0 x 10(-6) M respectively.
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Affiliation(s)
- T Aoyama
- Institute of Microbial Chemistry, Tokyo, Japan
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Walker JM, Winder JS, Kellam SJ. High-throughput microtiter plate-based chromogenic assays for glycosidase inhibitors. Appl Biochem Biotechnol 1993; 38:141-6. [PMID: 8346902 DOI: 10.1007/bf02916417] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rapid microtiter plate-based colorimetric assays have been developed that allow the screening of large numbers of samples for the presence of inhibitors of alpha-glucosidase, alpha-amylase, and beta-galactosidase. The assays are particularly useful for screening large numbers of microbial culture filtrates.
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Affiliation(s)
- J M Walker
- Division of Biosciences, University of Hertfordshire, Hatfield, Herts, England
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Glycosidase and Glycosyltransferase Inhibitors. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/b978-0-444-89558-5.50038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Chapter 12 Enzyme Inhibitors Produced by Microorganisms. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/s0301-4770(08)60403-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Deshpande B, Ambedkar S, Shewale J. Biologically active secondary metabolites from Streptomyces. Enzyme Microb Technol 1988. [DOI: 10.1016/0141-0229(88)90023-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nakatsuka SI, Feng BN, Goto T, Kihara K. Structures of flazin and YS, highly fluorescent compounds isolated from japanese soy sauce. Tetrahedron Lett 1986. [DOI: 10.1016/s0040-4039(00)84806-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Husson HP. Chapter 1 Simple Indole Alkaloids Including ß-Carbolines and Carbazoles. THE ALKALOIDS: CHEMISTRY AND PHARMACOLOGY 1985. [DOI: 10.1016/s0099-9598(08)60192-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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