51
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Tetrodecamycin: An unusual and interesting tetronate antibiotic. Bioorg Med Chem 2016; 24:6269-6275. [DOI: 10.1016/j.bmc.2016.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/08/2016] [Accepted: 05/17/2016] [Indexed: 11/23/2022]
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52
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Dow GT, Thoden JB, Holden HM. Structural studies on KijD1, a sugar C-3'-methyltransferase. Protein Sci 2016; 25:2282-2289. [PMID: 27595766 DOI: 10.1002/pro.3034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/01/2016] [Accepted: 09/01/2016] [Indexed: 12/21/2022]
Abstract
Kijanimicin is an antitumor antibiotic isolated from Actinomadura kijaniata. It is composed of three distinct moieties: a pentacyclic core, a monosaccharide referred to as d-kijanose, and a tetrasaccharide chain composed of l-digitoxose units. d-Kijanose is a highly unusual nitro-containing tetradeoxysugar, which requires at least ten enzymes for its production. Here we describe a structural analysis of one of these enzymes, namely KijD1, which functions as a C-3'-methyltransferase using S-adenosylmethionine as its cofactor. For this investigation, two ternary complexes of KijD1, determined in the presence of S-adenosylhomocysteine (SAH) and dTDP or SAH and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-d-glucose, were solved to 1.7 or 1.6 Å resolution, respectively. Unexpectedly, these structures, as well as additional biochemical analyses, demonstrated that the quaternary structure of KijD1 is a dimer. Indeed, this is in sharp contrast to that previously observed for the sugar C-3'-methyltransferase isolated from Micromonospora chalcea. By the judicious use of site-directed mutagenesis, it was possible to convert the dimeric form of KijD1 into a monomeric version. The quaternary structure of KijD1 could not have been deduced based solely on bioinformatics approaches, and thus this investigation highlights the continuing need for experimental validation.
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Affiliation(s)
- Garrett T Dow
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706
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53
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Chen M, Liu J, Duan P, Li M, Liu W. Biosynthesis and molecular engineering of templated natural products. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Panpan Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mulin Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, Huzhou 313000, China
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54
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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55
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Zheng Q, Tian Z, Liu W. Recent advances in understanding the enzymatic reactions of [4+2] cycloaddition and spiroketalization. Curr Opin Chem Biol 2016; 31:95-102. [DOI: 10.1016/j.cbpa.2016.01.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 11/25/2022]
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56
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Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4. Cell Chem Biol 2016; 23:352-60. [DOI: 10.1016/j.chembiol.2016.01.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/13/2016] [Accepted: 01/17/2016] [Indexed: 11/23/2022]
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57
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Zaghouani M, Nay B. 3-Acylated tetramic and tetronic acids as natural metal binders: myth or reality? Nat Prod Rep 2016; 33:540-8. [PMID: 26879987 DOI: 10.1039/c5np00144g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 20153-Acylated tetramic and tetronic acids are characterized by a low pKa and are likely to be deprotonated under physiological conditions. In addition, their structure makes them excellent chelators of metallic cations. We will discuss the significance of these chemical properties with regard to the biological properties and mechanisms of action of these compounds, highlighting the importance of considering them as salts or chelates for biological purposes, rather than acids.
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Affiliation(s)
- Mehdi Zaghouani
- Muséum National d'Histoire Naturelle, CNRS, UMR 7245 Molécules de Communication et Adaptation des Micro-organismes, 57 rue Cuvier (CP 54), 75005 Paris, France.
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58
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Li Y, Li J, Tian Z, Xu Y, Zhang J, Liu W, Tan H. Coordinative Modulation of Chlorothricin Biosynthesis by Binding of the Glycosylated Intermediates and End Product to a Responsive Regulator ChlF1. J Biol Chem 2016; 291:5406-17. [PMID: 26750095 DOI: 10.1074/jbc.m115.695874] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/06/2022] Open
Abstract
Chlorothricin, isolated from Streptomyces antibioticus, is a parent member of spirotetronate family of antibiotics that have long been appreciated for their remarkable biological activities. ChlF1 plays bifunctional roles in chlorothricin biosynthesis by binding to its target genes (chlJ, chlF1, chlG, and chlK). The dissociation constants of ChlF1 to these genes are ∼ 102-140 nm. A consensus sequence, 5'-GTAANNATTTAC-3', was found in these binding sites. ChlF1 represses the transcription of chlF1, chlG, and chlK but activates chlJ, which encodes a key enzyme acyl-CoA carboxyl transferase involved in the chlorothricin biosynthesis. We demonstrate that the end product chlorothricin and likewise its biosynthetic intermediates (demethylsalicycloyl chlorothricin and deschloro-chlorothricin) can act as signaling molecules to modulate the binding of ChlF1 to its target genes. Intriguingly, a correlation between the antibacterial activity and binding ability of signaling molecules to the regulator ChlF1 is clearly observed. These features of the signaling molecules are associated with the glycosylation of spirotetronate macrolide aglycone. The findings provide new insights into the TetR family regulators responding to special structure of signaling molecules, and we reveal the regulatory mini-network mediated by ChlF1 in chlorothricin biosynthesis for the first time.
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Affiliation(s)
- Yue Li
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of Chinese Academy of Sciences, Beijing 100101, China, and
| | - Jingjing Li
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of Chinese Academy of Sciences, Beijing 100101, China, and
| | - Zhenhua Tian
- the State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Xu
- the State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jihui Zhang
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Liu
- the State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huarong Tan
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,
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59
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Perrin FG, Kiefer G, Jeanbourquin L, Racine S, Perrotta D, Waser J, Scopelliti R, Severin K. 1‐Alkynyltriazenes as Functional Analogues of Ynamides. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Florian G. Perrin
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Gregor Kiefer
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Loïc Jeanbourquin
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Sophie Racine
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Daniele Perrotta
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Jérôme Waser
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Kay Severin
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
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60
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Perrin FG, Kiefer G, Jeanbourquin L, Racine S, Perrotta D, Waser J, Scopelliti R, Severin K. 1-Alkynyltriazenes as Functional Analogues of Ynamides. Angew Chem Int Ed Engl 2015; 54:13393-6. [PMID: 26374083 DOI: 10.1002/anie.201507033] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 01/25/2023]
Abstract
The chemical reactivity of 1-alkynyltriazenes has been investigated and is found to parallel the reactivity of ynamides. The similarity in reactivity of these two classes of compounds is demonstrated by addition reactions with acids, by cycloaddition reactions with ketenes, tetracyanoethene, and cyclopropanes, as well as by intramolecular cyclization reactions. The presence of reactive triazene groups in the products enables subsequent transformations. Overall, our results suggest that 1-alkynyltriazenes should become valuable reagents in synthetic organic chemistry.
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Affiliation(s)
- Florian G Perrin
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Gregor Kiefer
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Loïc Jeanbourquin
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Sophie Racine
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Daniele Perrotta
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Jérôme Waser
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland)
| | - Kay Severin
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, (Switzerland).
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61
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Chopin N, Yanai H, Iikawa S, Pilet G, Bouillon JP, Médebielle M. A Rapid Entry to Diverse γ-Ylidenetetronate Derivatives through Regioselective Bromination of Tetronic Acid Derived γ-Lactones and Metal-Catalyzed Postfunctionalization. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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62
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Lacoske MH, Xu J, Mansour N, Gao C, Theodorakis EA. Synthetic Strategies Toward the Decalin Motif of Maklamicin and Related Spirotetronates. Org Chem Front 2015; 2:388-393. [PMID: 26257916 PMCID: PMC4527581 DOI: 10.1039/c4qo00332b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a scalable approach to the decalin moiety of maklamicin. Key to the synthesis is an intramolecular Diels-Alder (IMDA) reaction that proceeds via an endo-axial transition state to generate the desired stereochemistry. We explored the diastereoselectivity of the IMDA reaction as a function of both chiral catalysis and acyclic precursor stereochemistry.
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Affiliation(s)
- Michelle H. Lacoske
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jing Xu
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Noel Mansour
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Chao Gao
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Emmanuel A. Theodorakis
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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63
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Chernykh AV, Radchenko DS, Grygorenko OO, Daniliuc CG, Volochnyuk DM, Komarov IV. Synthesis and Structural Analysis of Angular Monoprotected Diamines Based on Spiro[3.3]heptane Scaffold. J Org Chem 2015; 80:3974-81. [DOI: 10.1021/acs.joc.5b00323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anton V. Chernykh
- Institute
of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska 5, Kyiv 02660, Ukraine
- Enamine Ltd., Alexandra Matrosova
Street 23, Kyiv 01103, Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd., Alexandra Matrosova
Street 23, Kyiv 01103, Ukraine
- Institute
of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska
60, Kyiv 01601, Ukraine
| | - Oleksandr O. Grygorenko
- Department
of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska
64, Kyiv 01601, Ukraine
| | - Constantin G. Daniliuc
- Westfalische Wilhelms-Universitat Munster, Institute
of Organic Chemistry, Corrensstrasse 40, Munster 48149, Germany
| | - Dmitriy M. Volochnyuk
- Institute
of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska 5, Kyiv 02660, Ukraine
| | - Igor V. Komarov
- Enamine Ltd., Alexandra Matrosova
Street 23, Kyiv 01103, Ukraine
- Institute
of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska
60, Kyiv 01601, Ukraine
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