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Bartholomé A, Janso JE, Reilly U, O'Hagan D. Fluorometabolite biosynthesis: isotopically labelled glycerol incorporations into the antibiotic nucleocidin in Streptomyces calvus. Org Biomol Chem 2018; 15:61-64. [PMID: 27845468 DOI: 10.1039/c6ob02291j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deuterium and carbon-13 labelled glycerols have been fed to Streptomyces calvus fermentations and isotope incorporation into the fluorine containing antibiotic nucleocidin have been evaluated by 19F-NMR. A single deuterium atom was incorporated from [2H5]- and (R)-[2H2]-glycerol into C-5' of the antibiotic, suggesting that an oxidation occurs at this carbon after ribose ring assembly from glycerol (pentose phosphate pathway), during nucleocidin biosynthesis.
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Affiliation(s)
- Axel Bartholomé
- University of St Andrews, School of Chemistry and Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | - Jeffrey E Janso
- Worldwide Research and Development, Medicinal Sciences, Pfizer, 445 Eastern Point Rd, Groton, CT 06340, USA
| | - Usa Reilly
- Worldwide Research and Development, Medicinal Sciences, Pfizer, 445 Eastern Point Rd, Groton, CT 06340, USA
| | - David O'Hagan
- University of St Andrews, School of Chemistry and Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife KY16 9ST, UK.
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Mahmoudi F, Baradaran B, Dehnad A, Shanehbandi D, Mohamed Khosroshahi L, Aghapour M. The immunomodulatory activity of secondary metabolites isolated fromStreptomyces calvuson human peripheral blood mononuclear cells. Br J Biomed Sci 2016; 73:97-103. [DOI: 10.1080/09674845.2016.1188476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL. Biosynthesis of the Fluorinated Natural Product Nucleocidin inStreptomyces calvusIs Dependent on thebldA-Specified Leu-tRNAUUAMolecule. Chembiochem 2015; 16:2498-506. [DOI: 10.1002/cbic.201500402] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Xi Ming Zhu
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stefanie Hackl
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Maulik N. Thaker
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Lindsay Kalan
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Claudia Weber
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Dagmar S. Urgast
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Eva M. Krupp
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Alyssa Brewer
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stephanie Vanner
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Anjuli Szawiola
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Grace Yim
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Jörg Feldmann
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - David L. Zechel
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
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Mujumdar P, Poulsen SA. Natural Product Primary Sulfonamides and Primary Sulfamates. JOURNAL OF NATURAL PRODUCTS 2015; 78:1470-1477. [PMID: 26035239 DOI: 10.1021/np501015m] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Primary sulfonamide and primary sulfamate functional groups feature prominently in the structures of U.S. FDA-approved drugs. However, the natural product chemical space contains few examples of these well-known zinc-binding chemotypes, with just two primary sulfonamide and five primary sulfamate natural products isolated and characterized to date. One of these natural products was isolated from a marine sponge, with the remainder isolated from Streptomyces species. In this review are outlined for the first time the discovery, isolation, striking breadth of bioactivity, and total synthesis (where available) for this rare group of natural products.
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Affiliation(s)
- Prashant Mujumdar
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
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Walker MC, Chang MCY. Natural and engineered biosynthesis of fluorinated natural products. Chem Soc Rev 2015; 43:6527-36. [PMID: 24776946 DOI: 10.1039/c4cs00027g] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both natural products and synthetic organofluorines play important roles in the discovery and design of pharmaceuticals. The combination of these two classes of molecules has the potential to be useful in the ongoing search for new bioactive compounds but our ability to produce site-selectively fluorinated natural products remains limited by challenges in compatibility between their high structural complexity and current methods for fluorination. Living systems provide an alternative route to chemical fluorination and could enable the production of organofluorine natural products through synthetic biology approaches. While the identification of biogenic organofluorines has been limited, the study of the native organisms and enzymes that utilize these compounds can help to guide efforts to engineer the incorporation of this unusual element into complex pharmacologically active natural products. This review covers recent advances in understanding both natural and engineered production of organofluorine natural products.
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Affiliation(s)
- Mark C Walker
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, 125 Lewis, Berkeley, CA 94720-1460, USA.
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Kalan L, Gessner A, Thaker MN, Waglechner N, Zhu X, Szawiola A, Bechthold A, Wright GD, Zechel DL. A cryptic polyene biosynthetic gene cluster in Streptomyces calvus is expressed upon complementation with a functional bldA gene. ACTA ACUST UNITED AC 2013; 20:1214-24. [PMID: 24120331 DOI: 10.1016/j.chembiol.2013.09.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 11/29/2022]
Abstract
Streptomyces calvus is best known as the producer of the fluorinated natural product nucleocidin. This strain of Streptomycetes is also unusual for displaying a "bald" phenotype that is deficient in the formation of aerial mycelium and spores. Genome sequencing of this organism revealed a point mutation in the bldA gene that is predicted to encode a misfolded Leu-tRNA(UUA) molecule. Complementation of S. calvus with a correct copy of bldA restored sporulation and additionally promoted production of a polyeneoic acid amide, 4-Z-annimycin, and a minor amount of the isomer, 4-E-annimycin. Bioassays reveal that these compounds inhibit morphological differentiation in other Actinobacteria. The annimycin gene cluster encoding a type 1 polyketide synthase was identified and verified through disruption studies. This study underscores the importance of the bldA gene in regulating the expression of cryptic biosynthetic genes.
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Affiliation(s)
- Lindsay Kalan
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
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Walker MC, Wen M, Weeks AM, Chang MCY. Temporal and fluoride control of secondary metabolism regulates cellular organofluorine biosynthesis. ACS Chem Biol 2012; 7:1576-85. [PMID: 22769062 DOI: 10.1021/cb3002057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating mechanisms of natural organofluorine biosynthesis is essential for a basic understanding of fluorine biochemistry in living systems as well as for expanding biological methods for fluorine incorporation into small molecules of interest. To meet this goal we have combined massively parallel sequencing technologies, genetic knockout, and in vitro biochemical approaches to investigate the fluoride response of the only known genetic host of an organofluorine-producing pathway, Streptomyces cattleya. Interestingly, we have discovered that the major mode of S. cattleya's resistance to the fluorinated toxin it produces, fluoroacetate, may be due to temporal control of production rather than the ability of the host's metabolic machinery to discriminate between fluorinated and non-fluorinated molecules. Indeed, neither the acetate kinase/phosphotransacetylase acetate assimilation pathway nor the TCA cycle enzymes (citrate synthase and aconitase) exclude fluorinated substrates based on in vitro biochemical characterization. Furthermore, disruption of the fluoroacetate resistance gene encoding a fluoroacetyl-CoA thioesterase (FlK) does not appear to lead to an observable growth defect related to organofluorine production. By showing that a switch in central metabolism can mediate and control molecular fluorine incorporation, our findings reveal a new potential strategy toward diversifying simple fluorinated building blocks into more complex products.
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Affiliation(s)
- Mark C. Walker
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
| | - Miao Wen
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
| | - Amy M. Weeks
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
| | - Michelle C. Y. Chang
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
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Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MCY. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry 2010; 49:9269-79. [PMID: 20836570 PMCID: PMC3461317 DOI: 10.1021/bi101102u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-CoA (k(cat)/K(M) = 5 × 10⁷ M⁻¹ s⁻¹) and acetyl-CoA (k(cat)/K(M) = 30 M⁻¹ s⁻¹) based on a single fluorine substitution that originates from differences in both substrate reactivity and binding. We show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that influence substrate selectivity. We propose that FlK minimizes interaction with the thioester carbonyl, leading to selection against acetyl-CoA binding that can be recovered in part by new C═O interactions in the T42S and T42C mutants. We hypothesize that the loss of these interactions is compensated by the entropic driving force for fluorinated substrate binding in a hydrophobic binding pocket created by a lid structure, containing Val 23, Leu 26, Phe 33, and Phe 36, that is not found in other structurally characterized members of this superfamily. We further suggest that water plays a critical role in fluorine specificity based on biochemical and structural studies focused on the unique Phe 36 "gate" residue, which functions to exclude water from the active site. Taken together, the findings from these studies offer molecular insights into organofluorine recognition and design of fluorine-specific enzymes.
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Affiliation(s)
- Amy M. Weeks
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
| | - Scott M. Coyle
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Martin Jinek
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
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