1
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Song Y, Amaya JA, Murarka VC, Mendez H, Hogan M, Muldoon J, Evans P, Ortin Y, Kelly SL, Lamb DC, Poulos TL, Caffrey P. Biosynthesis of a new skyllamycin in Streptomyces nodosus: a cytochrome P450 forms an epoxide in the cinnamoyl chain. Org Biomol Chem 2024; 22:2835-2843. [PMID: 38511621 DOI: 10.1039/d4ob00178h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Activation of a silent gene cluster in Streptomyces nodosus leads to synthesis of a cinnamoyl-containing non-ribosomal peptide (CCNP) that is related to skyllamycins. This novel CCNP was isolated and its structure was interrogated using mass spectrometry and nuclear magnetic resonance spectroscopy. The isolated compound is an oxidised skyllamycin A in which an additional oxygen atom is incorporated in the cinnamoyl side-chain in the form of an epoxide. The gene for the epoxide-forming cytochrome P450 was identified by targeted disruption. The enzyme was overproduced in Escherichia coli and a 1.43 Å high-resolution crystal structure was determined. This is the first crystal structure for a P450 that forms an epoxide in a substituted cinnamoyl chain of a lipopeptide. These results confirm the proposed functions of P450s encoded by biosynthetic gene clusters for other epoxidized CCNPs and will assist investigation of how epoxide stereochemistry is determined in these natural products.
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Affiliation(s)
- Yuhao Song
- Centre for Synthesis and Chemical Biology and School of Biomolecular and Biomedical Science, University College Dublin, Ireland.
| | - Jose A Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences and Chemistry, University of California, Irvine, California, USA
| | - Vidhi C Murarka
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences and Chemistry, University of California, Irvine, California, USA
| | - Hugo Mendez
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences and Chemistry, University of California, Irvine, California, USA
| | - Mark Hogan
- Centre for Synthesis and Chemical Biology and School of Biomolecular and Biomedical Science, University College Dublin, Ireland.
| | - Jimmy Muldoon
- Centre for Synthesis and Chemical Biology and School of Chemistry, University College Dublin, Ireland
| | - Paul Evans
- Centre for Synthesis and Chemical Biology and School of Chemistry, University College Dublin, Ireland
| | - Yannick Ortin
- Centre for Synthesis and Chemical Biology and School of Chemistry, University College Dublin, Ireland
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Science, Institute of Life Science, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - David C Lamb
- Faculty of Medicine, Health and Life Science, Institute of Life Science, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences and Chemistry, University of California, Irvine, California, USA
| | - Patrick Caffrey
- Centre for Synthesis and Chemical Biology and School of Biomolecular and Biomedical Science, University College Dublin, Ireland.
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2
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Wang H, Qi H, Zhang H, Zhang SY, Zhang CH, Zhang LQ, Xiang WS, Wang JD. Anulamycins A-F, Cinnamoyl-Containing Peptides from a Lake Sediment Derived Streptomyces. JOURNAL OF NATURAL PRODUCTS 2023; 86:357-367. [PMID: 36753718 DOI: 10.1021/acs.jnatprod.2c00967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Bioinformatics analysis of a whole genome sequence coupled with HPLC-DAD analysis revealed that Streptomyces sp. Hu103 has the capacity to produce skyllamycin analogues. A subsequent chemical investigation of this strain yielded four new cinnamoyl-containing cyclopeptides, anulamycins A-D (1-4), two new cinnamoyl-containing linear peptides, anulamycins E and F (5 and 6), and two known cyclopeptides, skyllamycins A (7) and B (8). Their structures including absolute configurations were elucidated by detailed analysis of NMR and HRESIMS/MS spectroscopic data and the advanced Marfey's method. Compounds 1-4 exhibited antibacterial activity comparable to those of skyllamycins A and B.
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Affiliation(s)
- Han Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
- Life Science and Biotechnology Research Center, School of Life Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Huan Qi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
| | - Hui Zhang
- Life Science and Biotechnology Research Center, School of Life Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
- Institute of Natural Active Substances Research and Utilization, School of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou 318020, China
| | - Shao-Yong Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
| | - Cheng-Hong Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
| | - Li-Qin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
| | - Wen-Sheng Xiang
- Life Science and Biotechnology Research Center, School of Life Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Ji-Dong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
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3
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An JS, Kim MS, Han J, Jang SC, Im JH, Cui J, Lee Y, Nam SJ, Shin J, Lee SK, Yoon YJ, Oh DC. Nyuzenamide C, an Antiangiogenic Epoxy Cinnamic Acid-Containing Bicyclic Peptide from a Riverine Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:804-814. [PMID: 35294831 DOI: 10.1021/acs.jnatprod.1c00837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new nonribosomal peptide, nyuzenamide C (1), was discovered from riverine sediment-derived Streptomyces sp. DM14. Comprehensive analysis of the spectroscopic data of nyuzenamide C (1) revealed that 1 has a bicyclic backbone composed of six common amino acid residues (Asn, Leu, Pro, Gly, Val, and Thr) and four nonproteinogenic amino acid units, including hydroxyglycine, β-hydroxyphenylalanine, p-hydroxyphenylglycine, and 3,β-dihydroxytyrosine, along with 1,2-epoxypropyl cinnamic acid. The absolute configuration of 1 was proposed by J-based configuration analysis, the advanced Marfey's method, quantum mechanics-based DP4 calculations, and bioinformatic analysis of its nonribosomal peptide synthetase biosynthetic gene cluster. Nyuzenamide C (1) displayed antiangiogenic activity in human umbilical vein endothelial cells and induced quinone reductase in murine Hepa-1c1c7 cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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4
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Bracegirdle J, Hou P, Nowak VV, Ackerley DF, Keyzers RA, Owen JG. Skyllamycins D and E, Non-Ribosomal Cyclic Depsipeptides from Lichen-Sourced Streptomyces anulatus. JOURNAL OF NATURAL PRODUCTS 2021; 84:2536-2543. [PMID: 34490774 DOI: 10.1021/acs.jnatprod.1c00547] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The skyllamycins are a class of heavily modified, non-ribosomal peptides, first isolated from Streptomyces sp. KY11784. A Streptomyces strain with potent antibiotic activity against Bacillus subtilis was isolated from a sample of the New Zealand lichen Pseudocyphellaria dissimilis. Whole genome sequencing and biosynthetic gene cluster genetic analysis coupled with GNPS LCMS/MS molecular networking revealed that this strain had the capacity to produce skyllamycins, including previously undescribed congeners, and that these were likely the source of the observed biological activity. Guided by the results of the molecular networking, we isolated the previously reported skyllamycins A-C (1-3), along with two new congeners, skyllamycins D (4) and E (5). The structures of these compounds were elucidated using comprehensive 1D and 2D NMR analyses, along with HRESIMS fragmentation experiments. Antibacterial assays revealed that skyllamycin D possessed improved activity against B. subtilis E168 compared to previously reported congeners.
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5
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Yu J, Song J, Chi C, Liu T, Geng T, Cai Z, Dong W, Shi C, Ma X, Zhang Z, Ma X, Xing B, Jin H, Zhang L, Dong S, Yang D, Ma M. Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zonghui Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Cheng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhongyi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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6
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Pan C, Kuranaga T, Cao X, Suzuki T, Dohmae N, Shinzato N, Onaka H, Kakeya H. Amycolapeptins A and B, Cyclic Nonadepsipeptides Produced by Combined-culture of Amycolatopsis sp. and Tsukamurella pulmonis. J Org Chem 2021; 86:1843-1849. [PMID: 33410699 DOI: 10.1021/acs.joc.0c02660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two nonapeptide natural products, amycolapeptins A (1) and B (2) with a 22-membered cyclic depsipeptide skeleton, β-hydroxytyrosine, and a highly modified side chain, which were not produced in a monoculture of the rare actinomycete Amycolatopsis sp. 26-4, were discovered in broth of its combined-culture with Tsukamurella pulmonis TP-B0596. The planar structures were elucidated by spectroscopic analyses (extensive 2D-NMR and MALDI-TOF MS/MS). The absolute configurations of component amino acids were unambiguously determined by the highly sensitive advanced Marfey's method we recently developed. Additionally, the structures of unstable/unusual moieties were corroborated by chemical synthesis and CD analysis.
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Affiliation(s)
- Chengqian Pan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Xun Cao
- Ocean College, Zhejiang University, Hangzhou 310058, China
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Bioscience Building, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Bioscience Building, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoya Shinzato
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences & Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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7
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Bernhardt M, Berman S, Zechel D, Bechthold A. Role of Two Exceptional trans Adenylation Domains and MbtH-like Proteins in the Biosynthesis of the Nonribosomal Peptide WS9324A from Streptomyces calvus ATCC 13382. Chembiochem 2020; 21:2659-2666. [PMID: 32333627 PMCID: PMC7539972 DOI: 10.1002/cbic.202000142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/24/2020] [Indexed: 11/26/2022]
Abstract
Nonribosomal peptide synthetases (NRPS) are organized in a modular arrangement. Usually, the modular order corresponds to the assembly of the amino acids in the respective peptide, following the collinearity rule. The WS9326A biosynthetic gene cluster from Streptomyces calvus shows deviations from this rule. Most interesting is the presence of two trans adenylation domains that are located downstream of the modular NRPS arrangement. Adenylation domains are responsible for the activation of their respective amino acids. In this study, we confirmed the involvement of the trans adenylation domains in WS9326A biosynthesis by performing gene knockout experiments and by observing the selective adenylation of their predicted amino acid substrates in vitro. We conclude that the trans adenylation domains are essential for WS9326A biosynthesis. Moreover, both adenylation domains are observed to have MbtH‐like protein dependency. Overall, we conclude that the trans adenylation domains are essential for WS9326A biosynthesis.
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Affiliation(s)
- Mirjam Bernhardt
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strass 19, 79104, Freiburg im Breisgau, Germany
| | - Stefanie Berman
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strass 19, 79104, Freiburg im Breisgau, Germany
| | - David Zechel
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7 L 3 N6, Canada
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strass 19, 79104, Freiburg im Breisgau, Germany
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8
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Zhu J, Zhang S, Zechel DL, Paululat T, Bechthold A. Rational Design of Hybrid Natural Products by Utilizing the Promiscuity of an Amide Synthetase. ACS Chem Biol 2019; 14:1793-1801. [PMID: 31310500 DOI: 10.1021/acschembio.9b00351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
WS9326A and annimycin are produced by Streptomyces asterosporus DSM 41452. WS9326A is a nonribosomal peptide synthetase-(NRPS-) derived depsipeptide containing a cinnamoyl moiety, while annimycin is a linear polyketide bearing a 2-amino-3-hydroxycyclopent-2-enone (C5N) group. Both gene clusters have been sequenced and annotated. In this study, we show that the amide synthetase Ann1, responsible for attaching the C5N unit during annimycin biosynthesis, has the ability to catalyze fortuitous side reactions to polyenoic acids in addition to its main reaction. Novel compounds were generated by feeding experiments and in vitro studies. We also rationally designed a hybrid natural product consisting of the cinnamoyl moiety of WS9326A and the C5N moiety of annimycin by creating a mutant of S. asterosporus that retains genes encoding biosynthesis of the C5N unit of annimycin and the cinnamoyl group of WS9326A. The promiscuity of Ann1 also proved useful for trapping compounds that arise from acyl-ACP intermediates, which occur in the biosynthesis of the cinnamoyl moiety of WS9326A, by hydrolysis. In this pathway, we postulate that sas27 and sas28 genes are involved in the biosynthesis of the cinnamoyl moiety in WS9326A.
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Affiliation(s)
- Jing Zhu
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, Stefan-Meier-Str. 19, Freiburg, Germany
| | - Songya Zhang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, People’s Republic China
| | - David L. Zechel
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Thomas Paululat
- Department of Organic Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, Siegen, Germany
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, Stefan-Meier-Str. 19, Freiburg, Germany
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9
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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10
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Santa Maria KC, Chan AN, O'Neill EM, Li B. Targeted Rediscovery and Biosynthesis of the Farnesyl-Transferase Inhibitor Pepticinnamin E. Chembiochem 2019; 20:1387-1393. [PMID: 30694017 DOI: 10.1002/cbic.201900025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Indexed: 11/08/2022]
Abstract
The natural product pepticinnamin E potently inhibits protein farnesyl transferases and has potential applications in treating cancer and malaria. Pepticinnamin E contains a rare N-terminal cinnamoyl moiety as well as several nonproteinogenic amino acids, including the unusual 2-chloro-3-hydroxy-4-methoxy-N-methyl-L-phenylalanine. The biosynthesis of pepticinnamin E has remained uncharacterized because its original producing strain is no longer available. Here we identified a gene cluster (pcm) for this natural product in a new producer, Actinobacteria bacterium OK006, by means of a targeted rediscovery strategy. We demonstrated that the pcm cluster is responsible for the biosynthesis of pepticinnamin E, a nonribosomal peptide/polyketide hybrid. We also characterized a key O-methyltransferase that modifies 3,4-dihydroxy-l-phenylalanine. Our work has identified the gene cluster for pepticinnamins for the first time and sets the stage for elucidating the unique chemistry required for biosynthesis.
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Affiliation(s)
- Kevin C Santa Maria
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
| | - Andrew N Chan
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
| | - Erinn M O'Neill
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
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11
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Liu Q, Liu Z, Sun C, Shao M, Ma J, Wei X, Zhang T, Li W, Ju J. Discovery and Biosynthesis of Atrovimycin, an Antitubercular and Antifungal Cyclodepsipeptide Featuring Vicinal-dihydroxylated Cinnamic Acyl Chain. Org Lett 2019; 21:2634-2638. [PMID: 30958008 DOI: 10.1021/acs.orglett.9b00618] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Atrovimycin (1), a cyclodepsipeptide containing a unique vicinal-hydroxylated cinnamic acyl chain, was isolated and elucidated from Streptomyces atrovirens LQ13. The biosynthetic pathway of 1 was achieved, revealing cytochrome P450 (Avm43) and epoxide hydrolase (Avm29) enzymes constructing the vicinal-dihydroxy substitution, as well as a tailoring P450 (Avm28) enzyme catalyzing β-hydroxylation of the l-Phe moiety. Atrovimycin shows in vitro antifungal activity and antitubercular activity against Mycobacterium tuberculosis H37Rv both in vitro (with MIC of 2.5 μg/mL) and in vivo.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou 510301 , China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL) , Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou 510530 , China
| | - Changli Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou 510301 , China
| | - Mingwei Shao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou 510301 , China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou 510301 , China
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization , South China Botanical Garden, Chinese Academy of Sciences , Guangzhou 510650 , China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL) , Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou 510530 , China.,University of Chinese Academy of Sciences , Beijing 110039 , China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou 510301 , China.,University of Chinese Academy of Sciences , Beijing 110039 , China
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12
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Parmeggiani F, Rué Casamajo A, Walton CJW, Galman JL, Turner NJ, Chica RA. One-Pot Biocatalytic Synthesis of Substituted d-Tryptophans from Indoles Enabled by an Engineered Aminotransferase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00739] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Arnau Rué Casamajo
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Curtis J. W. Walton
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
| | - James L. Galman
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Roberto A. Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
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13
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Giltrap AM, Haeckl FPJ, Kurita KL, Linington RG, Payne RJ. Synthetic Studies Toward the Skyllamycins: Total Synthesis and Generation of Simplified Analogues. J Org Chem 2018; 83:7250-7270. [PMID: 29798664 DOI: 10.1021/acs.joc.8b00898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we report our synthetic studies toward the skyllamycins, a highly modified class of nonribosomal peptide natural products which contain a number of interesting structural features, including the extremely rare α-OH-glycine residue. Before embarking on the synthesis of the natural products, we prepared four structurally simpler analogues. Access to both the analogues and the natural products first required the synthesis of a number of nonproteinogenic amino acids, including three β-OH amino acids that were accessed from the convenient chiral precursor Garner's aldehyde. Following the preparation of the suitably protected nonproteinogenic amino acids, the skyllamycin analogues were assembled using a solid-phase synthetic route followed by a final stage solution-phase cyclization reaction. To access the natural products (skyllamycins A-C) the synthetic route used for the analogues was modified. Specifically, linear peptide precursors containing a C-terminal amide were synthesized via solid-phase peptide synthesis. After cleavage from the resin the N-terminal serine residue was oxidatively cleaved to a glyoxyamide moiety. The target natural products, skyllamycins A-C, were successfully prepared via a final step cyclization with concomitant formation of the unusual α-OH-glycine residue. Purification and spectroscopic comparison to the authentic isolated material confirmed the identity of the synthetic natural products.
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Affiliation(s)
- Andrew M Giltrap
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - F P Jake Haeckl
- Department of Chemistry , Simon Fraser University , Burnaby , British Columbia BC V5A 1S6 , Canada
| | - Kenji L Kurita
- Department of Chemistry , Simon Fraser University , Burnaby , British Columbia BC V5A 1S6 , Canada
| | - Roger G Linington
- Department of Chemistry , Simon Fraser University , Burnaby , British Columbia BC V5A 1S6 , Canada
| | - Richard J Payne
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
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14
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Zhang S, Zhu J, Zechel DL, Jessen-Trefzer C, Eastman RT, Paululat T, Bechthold A. New WS9326A Derivatives and One New Annimycin Derivative with Antimalarial Activity are Produced by Streptomyces asterosporus DSM 41452 and Its Mutant. Chembiochem 2017; 19:272-279. [PMID: 29148157 DOI: 10.1002/cbic.201700428] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 11/10/2022]
Abstract
In this study, we report that Streptomyces asterosporus DSM 41452 is a producer of new molecules related to the nonribosomal cyclodepsipeptide WS9326A and the polyketide annimycin. S. asterosporus DSM 41452 is shown to produce six cyclodepsipeptides and peptides, WS9326A to G. Notably, the compounds WS9326F and WS9326G have not been described before. The genome of S. asterosporus DSM 41452 was sequenced, and a putative WS9326A gene cluster was identified. Gene-deletion experiments confirmed that this cluster was responsible for the biosynthesis of WS9326A to G. Additionally, a gene-deletion experiment demonstrated that sas16 encoding a cytochrome P450 monooxygenase was involved in the synthesis of the novel (E)-2,3-dehydrotyrosine residue found in WS9326A and its derivatives. An insertion mutation within the putative annimycin gene cluster led to the production of a new annimycin derivative, annimycin B, which exhibited modest inhibitory activity against Plasmodium falciparum.
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Affiliation(s)
- Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Jing Zhu
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Richard T Eastman
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences/NIH, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Thomas Paululat
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068, Siegen, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
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15
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Giltrap AM, Haeckl FPJ, Kurita KL, Linington RG, Payne RJ. Total Synthesis of Skyllamycins A-C. Chemistry 2017; 23:15046-15049. [PMID: 28906041 DOI: 10.1002/chem.201704277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Indexed: 12/31/2022]
Abstract
The skyllamycins are a family of highly functionalized non-ribosomal cyclic depsipeptide natural products which contain the extremely rare α-OH-glycine functionality. Herein the first total synthesis of skyllamycins A-C is reported, together with the biofilm inhibitory activity of the natural products. Linear peptide precursors for each natural product were prepared through an efficient solid-phase route incorporating a number of synthetic modified amino acids. A novel macrocyclization step between a C-terminal amide and an N-terminal glyoxylamide moiety served as a key transformation to install the unique α-OH-glycine unit and generate the natural products in the final step of the synthesis.
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Affiliation(s)
- Andrew M Giltrap
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - F P Jake Haeckl
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Kenji L Kurita
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
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16
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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17
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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18
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Bae M, Kim H, Moon K, Nam SJ, Shin J, Oh KB, Oh DC. Mohangamides A and B, New Dilactone-Tethered Pseudo-Dimeric Peptides Inhibiting Candida albicans Isocitrate Lyase. Org Lett 2015; 17:712-5. [DOI: 10.1021/ol5037248] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Munhyung Bae
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Heegyu Kim
- Department of Agricultural Biotechnology, College of Agriculture & Life Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Kyuho Moon
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Sang-Jip Nam
- Department
of Chemistry and Nano Science, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, Republic of Korea
| | - Jongheon Shin
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea
| | - Dong-Chan Oh
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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19
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Van Arkel Professorship: R. D. Süssmuth / Nichols Medal: A. B. Smith III / ACS Catalysis Lectureship: S. Linic / FCI Dozentenpreis: G. H. Clever and F. Schoenebeck. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201406698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Van-Arkel-Professur: R. D. Süssmuth / Nichols-Medaille: A. B. Smith III / ACS-Katalysevorlesung: S. Linic / FCI-Dozentenpreis: G. H. Clever und F. Schoenebeck. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Haslinger K, Brieke C, Uhlmann S, Sieverling L, Süssmuth RD, Cryle MJ. The Structure of a Transient Complex of a Nonribosomal Peptide Synthetase and a Cytochrome P450 Monooxygenase. Angew Chem Int Ed Engl 2014; 53:8518-22. [DOI: 10.1002/anie.201404977] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Indexed: 11/11/2022]
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22
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Haslinger K, Brieke C, Uhlmann S, Sieverling L, Süssmuth RD, Cryle MJ. Die Struktur eines transienten Komplexes einer nicht-ribosomalen Peptidsynthetase mit einer P450-Monooxygenase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404977] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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