101
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Horsman ME, Hari TPA, Boddy CN. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat Prod Rep 2016; 33:183-202. [DOI: 10.1039/c4np00148f] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioesterases (TEs) are product offloading enzymes from FAS, PKS, and NRPS complexes. We review the diversity, structure, and mechanism of PKS and NRPS TEs and analyze TE loading and release steps as possible logic gates with a view to predicting TE function in new pathways.
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Affiliation(s)
- Mark E. Horsman
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Taylor P. A. Hari
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Christopher N. Boddy
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
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102
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Hong H, Samborskyy M, Lindner F, Leadlay PF. An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone Antibiotics. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Hui Hong
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Markiyan Samborskyy
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Frederick Lindner
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
- Institut für Organische Chemie; Leibniz Universität Hannover; Schneiderberg 1 B 30167 Hannover Germany
| | - Peter F. Leadlay
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
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103
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Abstract
We report the identification of the biosynthetic gene cluster for the unusual antibiotic anthracimycin (atc) from the marine derived producer strain Streptomyces sp. T676 isolated off St. John's Island, Singapore. The 53 253 bps atc locus includes a trans-acyltransferase (trans-AT) polyketide synthase (PKS), and heterologous expression in Streptomyces coelicolor resulted in anthracimycin production. Analysis of the atc cluster revealed that anthracimycin is likely generated by four PKS gene products AtcC-AtcF without involvement of post-PKS tailoring enzymes, and a biosynthetic pathway is proposed. The availability of the atc cluster provides a basis for investigating the biosynthesis of anthracimycin and its subsequent bioengineering to provide novel analogues with improved pharmacological properties.
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Affiliation(s)
- Silke Alt
- Department
of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, United Kingdom
| | - Barrie Wilkinson
- Department
of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, United Kingdom
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104
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Jungmann K, Jansen R, Gerth K, Huch V, Krug D, Fenical W, Müller R. Two of a Kind--The Biosynthetic Pathways of Chlorotonil and Anthracimycin. ACS Chem Biol 2015; 10:2480-90. [PMID: 26348978 DOI: 10.1021/acschembio.5b00523] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chlorotonil A is a novel polyketide isolated from the myxobacterium Sorangium cellulosum So ce1525 that features a unique gem-dichloro-1,3-dione moiety. It exhibits potent bioactivity, most notably against the problematic malaria pathogen Plasmodium falciparum in the nanomolar range. In addition, strong antibacterial and moderate antifungal activity were determined. The outstanding biological activity of chlorotonil A as well as its unusual chemical structure triggered our interest in elucidating its biosynthesis, a prerequisite for alteration of the scaffold by synthetic biology approaches. This endeavor was facilitated by a recent report describing the strikingly similar structure of anthracimycin from a marine streptomycete, a compound of considerable interest due to its potent antibacterial activity. In this study, we report the identification and characterization of the chlorotonil A biosynthetic gene cluster from So ce1525 and compare it with that for anthracimycin biosynthesis. Access to both gene clusters allowed us to highlight commonalities between the two pathways and revealed striking differences, some of which can plausibly explain the structural differences observed between these intriguing natural products.
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Affiliation(s)
- Katrin Jungmann
- Department of Microbial
Natural Products, Helmholtz Institute for Pharmaceutical Research
Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken, Germany
| | - Rolf Jansen
- Helmholtz Centre for Infection Research, Department of Microbial Drugs, Braunschweig, Germany
| | - Klaus Gerth
- Helmholtz Centre for Infection Research, Department of Microbial Drugs, Braunschweig, Germany
| | - Volker Huch
- Department of Microbial
Natural Products, Helmholtz Institute for Pharmaceutical Research
Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken, Germany
| | - Daniel Krug
- Department of Microbial
Natural Products, Helmholtz Institute for Pharmaceutical Research
Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken, Germany
| | - William Fenical
- Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Rolf Müller
- Department of Microbial
Natural Products, Helmholtz Institute for Pharmaceutical Research
Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken, Germany
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105
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The structural biology of biosynthetic megaenzymes. Nat Chem Biol 2015; 11:660-70. [PMID: 26284673 DOI: 10.1038/nchembio.1883] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/02/2015] [Indexed: 01/27/2023]
Abstract
The modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) are among the largest and most complicated enzymes in nature. In these biosynthetic systems, independently folding protein domains, which are organized into units called 'modules', operate in assembly-line fashion to construct polymeric chains and tailor their functionalities. Products of PKSs and NRPSs include a number of blockbuster medicines, and this has motivated researchers to understand how they operate so that they can be modified by genetic engineering. Beginning in the 1990s, structural biology has provided a number of key insights. The emerging picture is one of remarkable dynamics and conformational programming in which the chemical states of individual catalytic domains are communicated to the others, configuring the modules for the next stage in the biosynthesis. This unexpected level of complexity most likely accounts for the low success rate of empirical genetic engineering experiments and suggests ways forward for productive megaenzyme synthetic biology.
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106
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Daduang R, Kitani S, Hashimoto J, Thamchaipenet A, Igarashi Y, Shin-ya K, Ikeda H, Nihira T. Characterization of the biosynthetic gene cluster for maklamicin, a spirotetronate-class antibiotic of the endophytic Micromonospora sp. NBRC 110955. Microbiol Res 2015; 180:30-9. [DOI: 10.1016/j.micres.2015.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/08/2015] [Accepted: 07/11/2015] [Indexed: 10/23/2022]
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107
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Schulze CJ, Donia MS, Siqueira-Neto JL, Ray D, Raskatov JA, Green RE, McKerrow JH, Fischbach MA, Linington RG. Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei. ACS Chem Biol 2015; 10:2373-81. [PMID: 26270237 DOI: 10.1021/acschembio.5b00308] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Marine natural products are an important source of lead compounds against many pathogenic targets. Herein, we report the discovery of lobosamides A-C from a marine actinobacterium, Micromonospora sp., representing three new members of a small but growing family of bacterially produced polyene macrolactams. The lobosamides display growth inhibitory activity against the protozoan parasite Trypanosoma brucei (lobosamide A IC50 = 0.8 μM), the causative agent of human African trypanosomiasis (HAT). The biosynthetic gene cluster of the lobosamides was sequenced and suggests a conserved cluster organization among the 26-membered macrolactams. While determination of the relative and absolute configurations of many members of this family is lacking, the absolute configurations of the lobosamides were deduced using a combination of chemical modification, detailed spectroscopic analysis, and bioinformatics. We implemented a "molecules-to-genes-to-molecules" approach to determine the prevalence of similar clusters in other bacteria, which led to the discovery of two additional macrolactams, mirilactams A and B from Actinosynnema mirum. These additional analogs have allowed us to identify specific structure-activity relationships that contribute to the antitrypanosomal activity of this class. This approach illustrates the power of combining chemical analysis and genomics in the discovery and characterization of natural products as new lead compounds for neglected disease targets.
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Affiliation(s)
- Christopher J. Schulze
- Department
of Chemistry and Biochemistry, University of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - Mohamed S. Donia
- Department
of Bioengineering and Therapeutic Sciences and the California Institute
for Quantitative Biosciences, University of California San Francisco, San
Francisco, California 94158, United States
| | - Jair L. Siqueira-Neto
- Skaggs
School of Pharmacy, University of California San Diego, San Diego, California 92093, United States
| | - Debalina Ray
- Department
of Pathology, University of California San Francisco, San Francisco, California 94158, United States
| | - Jevgenij A. Raskatov
- Department
of Chemistry and Biochemistry, University of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - Richard E. Green
- Department
of Biomolecular Engineering, University of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - James H. McKerrow
- Skaggs
School of Pharmacy, University of California San Diego, San Diego, California 92093, United States
| | - Michael A. Fischbach
- Department
of Bioengineering and Therapeutic Sciences and the California Institute
for Quantitative Biosciences, University of California San Francisco, San
Francisco, California 94158, United States
| | - Roger G. Linington
- Department
of Chemistry and Biochemistry, University of California Santa Cruz, Santa
Cruz, California 95064, United States
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108
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Derewacz DK, Covington BC, McLean JA, Bachmann BO. Mapping Microbial Response Metabolomes for Induced Natural Product Discovery. ACS Chem Biol 2015; 10:1998-2006. [PMID: 26039241 DOI: 10.1021/acschembio.5b00001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Intergeneric microbial interactions may originate a significant fraction of secondary metabolic gene regulation in nature. Herein, we expose a genomically characterized Nocardiopsis strain, with untapped polyketide biosynthetic potential, to intergeneric interactions via coculture with low inoculum exposure to Escherichia, Bacillus, Tsukamurella, and Rhodococcus. The challenge-induced responses of extracted metabolites were characterized via multivariate statistical and self-organizing map (SOM) analyses, revealing the magnitude and selectivity engendered by the limiting case of low inoculum exposure. The collected inventory of cocultures revealed substantial metabolomic expansion in comparison to monocultures with nearly 14% of metabolomic features in cocultures undetectable in monoculture conditions and many features unique to coculture genera. One set of SOM-identified responding features was isolated, structurally characterized by multidimensional NMR, and revealed to comprise previously unreported polyketides containing an unusual pyrrolidinol substructure and moderate and selective cytotoxicity. Designated ciromicin A and B, they are detected across mixed cultures with intergeneric preferences under coculture conditions. The structural novelty of ciromicin A is highlighted by its ability to undergo a diastereoselective photochemical 12-π electron rearrangement to ciromicin B at visible wavelengths. This study shows how organizing trends in metabolomic responses under coculture conditions can be harnessed to characterize multipartite cultures and identify previously silent secondary metabolism.
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Affiliation(s)
- Dagmara K. Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brett C. Covington
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O. Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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109
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Ueoka R, Uria AR, Reiter S, Mori T, Karbaum P, Peters EE, Helfrich EJN, Morinaka BI, Gugger M, Takeyama H, Matsunaga S, Piel J. Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms. Nat Chem Biol 2015; 11:705-12. [PMID: 26236936 DOI: 10.1038/nchembio.1870] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
Actin-targeting macrolides comprise a large, structurally diverse group of cytotoxins isolated from remarkably dissimilar micro- and macroorganisms. In spite of their disparate origins and structures, many of these compounds bind actin at the same site and exhibit structural relationships reminiscent of modular, combinatorial drug libraries. Here we investigate biosynthesis and evolution of three compound groups: misakinolides, scytophycin-type compounds and luminaolides. For misakinolides from the sponge Theonella swinhoei WA, our data suggest production by an uncultivated 'Entotheonella' symbiont, further supporting the relevance of these bacteria as sources of bioactive polyketides and peptides in sponges. Insights into misakinolide biosynthesis permitted targeted genome mining for other members, providing a cyanobacterial luminaolide producer as the first cultivated source for this dimeric compound family. The data indicate that this polyketide family is bacteria-derived and that the unusual macrolide diversity is the result of combinatorial pathway modularity for some compounds and of convergent evolution for others.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Agustinus R Uria
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Silke Reiter
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Tetsushi Mori
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| | - Petra Karbaum
- 1] Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] Kekulé Institute of Organic Chemistry and Biochemistry, Bonn, Germany
| | - Eike E Peters
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Eric J N Helfrich
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Brandon I Morinaka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Haruko Takeyama
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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110
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Jiang C, Qi Z, Kang Q, Liu J, Jiang M, Bai L. Formation of the Δ 18,19Double Bond and Bis(spiroacetal) in Salinomycin Is Atypically Catalyzed by SlnM, a Methyltransferase-like Enzyme. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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111
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Ding W, Li Y, Zhang Q. Substrate-Controlled Stereochemistry in Natural Product Biosynthesis. ACS Chem Biol 2015; 10:1590-8. [PMID: 25844528 DOI: 10.1021/acschembio.5b00104] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Enzymes are generally believed to be highly regio- and stereoselective catalysts that strictly control the reaction coordinates and dominate the final catalytic outcomes. However, recent studies have started to suggest that substrates sometimes play key roles in determining the product selectivity in enzyme catalysis. Here, we highlight several enzymatic reactions in which the stereoselectivity is, at least in large part, governed by the intrinsic properties of the substrate rather than by characteristics of the enzyme. These reactions are involved in the biosynthesis of different classes of natural products, including lanthipeptides, sactipeptides, and polyketides. Understanding the mechanism of substrate-controlled stereospecificity may not only expand our knowledge of enzyme catalysis and enzyme evolution but also guide bioengineering efforts to produce novel valuable products.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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112
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Fiers WD, Dodge GJ, Li Y, Smith JL, Fecik RA, Aldrich CC. Tylosin polyketide synthase module 3: stereospecificity, stereoselectivity and steady-state kinetic analysis of β-processing domains via diffusible, synthetic substrates. Chem Sci 2015; 6:5027-5033. [PMID: 26366283 PMCID: PMC4540058 DOI: 10.1039/c5sc01505g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/11/2015] [Indexed: 01/01/2023] Open
Abstract
Natural and modified substrates coupled with LC-MS/MS analysis of products revealed the stereospecificity and stereoselectivity of a polyketide didomain.
Polyketide synthase (PKS) β-processing domains are responsible for much of the stereochemical complexity of polyketide natural products. Although the importance of β-processing domains has been well noted and significantly explored, key stereochemical details pertaining to cryptic stereochemistry and the impact of remote stereogenic centers have yet to be fully discerned. To uncover the inner workings of ketoreductases (KR) and dehydratases (DH) from the tylosin pathway a didomain composed of TylDH3-KR3 was recombinantly expressed and interrogated with full-length tetraketide substrates to probe the impact of vicinal and distal stereochemistry. In vitro product isolation analysis revealed the products of the cryptic KR as d-alcohols and of the DH as trans-olefins. Steady-state kinetic analysis of the dehydration reaction demonstrated a strict stereochemical tolerance at the β-position as d-configured substrates were processed more than 100 times more efficiently than l-alcohols. Unexpectedly, the kcat/KM values were diminished 14- to 45-fold upon inversion of remote ε- and ζ-stereocenters. This stereochemical discrimination is predicted to be driven by a combination of allylic A1,3 strain that likely disfavors binding of the ε-epimer and a loss of electrostatic interactions with the ζ-epimer. Our results strongly suggest that dehydratases may play a role in refining the stereochemical outcomes of preceding modules through their substrate stereospecificity, honing the configurational purity of the final PKS product.
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Affiliation(s)
- William D Fiers
- Department of Medicinal Chemistry , College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , USA . ;
| | - Greg J Dodge
- Department of Biological Chemistry and Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , USA
| | - Yang Li
- Department of Medicinal Chemistry , College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , USA . ;
| | - Janet L Smith
- Department of Biological Chemistry and Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , USA
| | - Robert A Fecik
- Department of Medicinal Chemistry , College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , USA . ;
| | - Courtney C Aldrich
- Department of Medicinal Chemistry , College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , USA . ;
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113
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Jiang C, Qi Z, Kang Q, Liu J, Jiang M, Bai L. Formation of the Δ(18,19) Double Bond and Bis(spiroacetal) in Salinomycin Is Atypically Catalyzed by SlnM, a Methyltransferase-like Enzyme. Angew Chem Int Ed Engl 2015; 54:9097-100. [PMID: 26096919 PMCID: PMC4744726 DOI: 10.1002/anie.201503561] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Indexed: 11/30/2022]
Abstract
Salinomycin is a widely used polyether coccidiostat and was recently found to have antitumor activities. However, the mechanism of its biosynthesis remained largely speculative until now. Reported herein is the identification of an unprecedented function of SlnM, homologous to O‐methyltransferases, by correlating its activity with the formation of the Δ18,19 double bond and bis(spiroacetal). Detailed in vivo and in vitro investigations revealed that SlnM, using positively charged S‐adenosylmethionine (SAM) or sinefungin as the cofactor, catalyzed the spirocyclization‐coupled dehydration of C19 in a highly atypical fashion to yield salinomycin.
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Affiliation(s)
- Chunyan Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Shanghai 200240 (China)
| | - Zhen Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Shanghai 200240 (China)
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Shanghai 200240 (China)
| | - Jing Liu
- Institute of Health Sciences, School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601 (China)
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Shanghai 200240 (China)
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Shanghai 200240 (China).
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114
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Li Y, Dodge GJ, Fiers WD, Fecik RA, Smith JL, Aldrich CC. Functional Characterization of a Dehydratase Domain from the Pikromycin Polyketide Synthase. J Am Chem Soc 2015; 137:7003-6. [PMID: 26027428 DOI: 10.1021/jacs.5b02325] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolic engineering of polyketide synthase (PKS) pathways represents a promising approach to natural products discovery. The dehydratase (DH) domains of PKSs, which generate an α,β-unsaturated bond through a dehydration reaction, have been poorly studied compared with other domains, likely because of the simple nature of the chemical reaction they catalyze and the lack of a convenient assay to measure substrate turnover. Herein we report the first steady-state kinetic analysis of a PKS DH domain employing LC-MS/MS analysis for product quantitation. PikDH2 was selected as a model DH domain. Its substrate specificity and mechanism were interrogated with a systematic series of synthetic triketide substrates containing a nonhydrolyzable thioether linkage as well as by site-directed mutagenesis, evaluation of the pH dependence of the catalytic efficiency (V(max)/K(M)), and kinetic characterization of a mechanism-based inhibitor. These studies revealed that PikDH2 converts d-alcohol substrates to trans-olefin products. The reaction is reversible with equilibrium constants ranging from 1.2 to 2. Moreover, the enzyme activity is robust, and PikDH2 was used on a preparative scale for the chemoenzymatic synthesis of unsaturated triketide products. PikDH2 was shown to possess remarkably strict substrate specificity and is unable to turn over substrates that are epimeric at the β-, γ-, or δ-position. We also demonstrated that PikDH2 has a key ionizable group with a pK(a) of 7.0 and can be irreversibly inactivated through covalent modification by a mechanism-based inhibitor, which provides a foundation for future structural studies to elucidate substrate-protein interactions.
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Affiliation(s)
- Yang Li
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Greg J Dodge
- ‡Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - William D Fiers
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert A Fecik
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Janet L Smith
- ‡Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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115
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Cai W, Goswami A, Yang Z, Liu X, Green KD, Barnard-Britson S, Baba S, Funabashi M, Nonaka K, Sunkara M, Morris AJ, Spork AP, Ducho C, Garneau-Tsodikova S, Thorson JS, Van Lanen SG. The Biosynthesis of Capuramycin-type Antibiotics: IDENTIFICATION OF THE A-102395 BIOSYNTHETIC GENE CLUSTER, MECHANISM OF SELF-RESISTANCE, AND FORMATION OF URIDINE-5'-CARBOXAMIDE. J Biol Chem 2015; 290:13710-24. [PMID: 25855790 DOI: 10.1074/jbc.m115.646414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Indexed: 11/06/2022] Open
Abstract
A-500359s, A-503083s, and A-102395 are capuramycin-type nucleoside antibiotics that were discovered using a screen to identify inhibitors of bacterial translocase I, an essential enzyme in peptidoglycan cell wall biosynthesis. Like the parent capuramycin, A-500359s and A-503083s consist of three structural components: a uridine-5'-carboxamide (CarU), a rare unsaturated hexuronic acid, and an aminocaprolactam, the last of which is substituted by an unusual arylamine-containing polyamide in A-102395. The biosynthetic gene clusters for A-500359s and A-503083s have been reported, and two genes encoding a putative non-heme Fe(II)-dependent α-ketoglutarate:UMP dioxygenase and an l-Thr:uridine-5'-aldehyde transaldolase were uncovered, suggesting that C-C bond formation during assembly of the high carbon (C6) sugar backbone of CarU proceeds from the precursors UMP and l-Thr to form 5'-C-glycyluridine (C7) as a biosynthetic intermediate. Here, isotopic enrichment studies with the producer of A-503083s were used to indeed establish l-Thr as the direct source of the carboxamide of CarU. With this knowledge, the A-102395 gene cluster was subsequently cloned and characterized. A genetic system in the A-102395-producing strain was developed, permitting the inactivation of several genes, including those encoding the dioxygenase (cpr19) and transaldolase (cpr25), which abolished the production of A-102395, thus confirming their role in biosynthesis. Heterologous production of recombinant Cpr19 and CapK, the transaldolase homolog involved in A-503083 biosynthesis, confirmed their expected function. Finally, a phosphotransferase (Cpr17) conferring self-resistance was functionally characterized. The results provide the opportunity to use comparative genomics along with in vivo and in vitro approaches to probe the biosynthetic mechanism of these intriguing structures.
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Affiliation(s)
- Wenlong Cai
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Anwesha Goswami
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Zhaoyong Yang
- the Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China
| | - Xiaodong Liu
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Keith D Green
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Sandra Barnard-Britson
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Satoshi Baba
- the New Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Masanori Funabashi
- the Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co., Ltd., Tokyo, Japan
| | - Koichi Nonaka
- the Biologics Technology Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Manjula Sunkara
- the Division of Cardiovascular Medicine and Gill Heart Institute, College of Medicine, University of Kentucky, Lexington, Kentucky 40506, and
| | - Andrew J Morris
- the Division of Cardiovascular Medicine and Gill Heart Institute, College of Medicine, University of Kentucky, Lexington, Kentucky 40506, and
| | - Anatol P Spork
- the Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Christian Ducho
- the Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Sylvie Garneau-Tsodikova
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Jon S Thorson
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Steven G Van Lanen
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506,
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116
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Architecture of the polyketide synthase module: surprises from electron cryo-microscopy. Curr Opin Struct Biol 2015; 31:9-19. [PMID: 25791608 DOI: 10.1016/j.sbi.2015.02.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/18/2015] [Accepted: 02/23/2015] [Indexed: 01/16/2023]
Abstract
Modular polyketide synthases (PKS) produce a vast array of bioactive molecules that are the basis of many highly valued pharmaceuticals. The biosynthesis of these compounds is based on ordered assembly lines of multi-domain modules, each extending and modifying a specific chain-elongation intermediate before transfer to the next module for further processing. The first 3D structures of a full polyketide synthase module in different functional states were obtained recently by electron cryo-microscopy. The unexpected module architecture revealed a striking evolutionary divergence of the polyketide synthase compared to its metazoan fatty acid synthase homolog, as well as remarkable conformational rearrangements dependent on its biochemical state during the full catalytic cycle. The design and dynamics of the module are highly optimized for both catalysis and fidelity in the construction of complex, biologically active natural products.
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117
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Abstract
This review covers a breakthrough in the structural biology of the gigantic modular polyketide synthases (PKS): the structural characterization of intact modules by single-particle cryo-electron microscopy and small-angle X-ray scattering.
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Affiliation(s)
- Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- IMoPA
- UMR 7365
- Vandœuvre-lès-Nancy
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118
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Che Q, Li T, Liu X, Yao T, Li J, Gu Q, Li D, Li W, Zhu T. Genome scanning inspired isolation of reedsmycins A–F, polyene-polyol macrolides from Streptomyces sp. CHQ-64. RSC Adv 2015. [DOI: 10.1039/c4ra15415k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genome scanning of the reed rhizosphere soil-derived Streptomyces sp. CHQ-64 revealed a partial gene cluster, putatively encoding a polyene-polyol compound. Inspired by this, six new polyene-polyol macrolides, reedsmycins A–F (1–6), were obtained.
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Affiliation(s)
- Qian Che
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Tong Li
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Xiaofang Liu
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Tingting Yao
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Jing Li
- College of Marine Life Sciences
- Ocean University of China
- Qingdao 266003
- People's Republic of China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Dehai Li
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Wenli Li
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs
- Chinese Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
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119
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Li Y, Fiers WD, Bernard S, Smith JL, Aldrich CC, Fecik RA. Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains. ACS Chem Biol 2014; 9:2914-22. [PMID: 25299319 PMCID: PMC4273979 DOI: 10.1021/cb5006883] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/09/2014] [Indexed: 12/27/2022]
Abstract
Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases.
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Affiliation(s)
- Yang Li
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William D. Fiers
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steffen
M. Bernard
- Chemical Biology Program, Department of Biological
Chemistry,
and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Chemical Biology Program, Department of Biological
Chemistry,
and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Courtney C. Aldrich
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert A. Fecik
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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120
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Bruns N, Collisi W, Bernecker S, Stadler M, Richter C, Schwalbe H, Kalesse M. Spirangien Derivatives from the MyxobacteriumSorangium cellulosum: Isolation, Structure Elucidation, and Biological Activity. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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121
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Hari TPA, Labana P, Boileau M, Boddy CN. An evolutionary model encompassing substrate specificity and reactivity of type I polyketide synthase thioesterases. Chembiochem 2014; 15:2656-61. [PMID: 25354333 DOI: 10.1002/cbic.201402475] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/10/2022]
Abstract
Bacterial polyketides are a rich source of chemical diversity and pharmaceutical agents. Understanding the biochemical basis for their biosynthesis and the evolutionary driving force leading to this diversity is essential to take advantage of the enzymes as biocatalysts and to access new chemical diversity for drug discovery. Biochemical characterization of the thioesterase (TE) responsible for 6-deoxyerythronolide macrocyclization shows that a small, evolutionarily accessible change to the substrate can increase the chemical diversity of products, including macrodiolide formation. We propose an evolutionary model in which TEs are by nature non-selective for the type of chemistry they catalyze, producing a range of metabolites. As one metabolite becomes essential for improving fitness in a particular environment, the TE evolves to enrich for that corresponding reactivity. This hypothesis is supported by our phylogenetic analysis, showing convergent evolution of macrodiolide-forming TEs.
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Affiliation(s)
- Taylor P A Hari
- Departments of Chemistry and Biology, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5 (Canada)
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122
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Park H, Kevany BM, Dyer DH, Thomas MG, Forest KT. A polyketide synthase acyltransferase domain structure suggests a recognition mechanism for its hydroxymalonyl-acyl carrier protein substrate. PLoS One 2014; 9:e110965. [PMID: 25340352 PMCID: PMC4207774 DOI: 10.1371/journal.pone.0110965] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/27/2014] [Indexed: 11/20/2022] Open
Abstract
We have previously shown that the acyl transferase domain of ZmaA (ZmaA-AT) is involved in the biosynthesis of the aminopolyol polyketide/nonribosomal peptide hybrid molecule zwittermicin A from cereus UW85, and that it specifically recognizes the precursor hydroxymalonyl-acyl carrier protein (ACP) and transfers the hydroxymalonyl extender unit to a downstream second ACP via a transacylated AT domain intermediate. We now present the X-ray crystal structure of ZmaA-AT at a resolution of 1.7 Å. The structure shows a patch of solvent-exposed hydrophobic residues in the area where the AT is proposed to interact with the precursor ACP. We addressed the significance of the AT/ACP interaction in precursor specificity of the AT by testing whether malonyl- or methylmalonyl-ACP can be recognized by ZmaA-AT. We found that the ACP itself biases extender unit selection. Until now, structural information for ATs has been limited to ATs specific for the CoA-linked precursors malonyl-CoA and (2S)-methylmalonyl-CoA. This work contributes to polyketide synthase engineering efforts by expanding our knowledge of AT/substrate interactions with the structure of an AT domain that recognizes an ACP-linked substrate, the rare hydroxymalonate. Our structure suggests a model in which ACP interaction with a hydrophobic motif promotes secondary structure formation at the binding site, and opening of the adjacent substrate pocket lid to allow extender unit binding in the AT active site.
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Affiliation(s)
- Hyunjun Park
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian M. Kevany
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. Dyer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (MGT); (KTF)
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (MGT); (KTF)
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123
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Berkhan G, Hahn F. Eine Dehydratase-Domäne in der Ambruticin-Biosynthese zeigt zusätzliche Aktivität als Pyran-bildende Cyclase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407979] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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124
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Berkhan G, Hahn F. A Dehydratase Domain in Ambruticin Biosynthesis Displays Additional Activity as a Pyran-Forming Cyclase. Angew Chem Int Ed Engl 2014; 53:14240-4. [DOI: 10.1002/anie.201407979] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/04/2014] [Indexed: 01/11/2023]
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125
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He HY, Yuan H, Tang MC, Tang GL. An Unusual Dehydratase Acting on Glycerate and a Ketoreducatse Stereoselectively Reducing α-Ketone in Polyketide Starter Unit Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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126
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Surup F, Viehrig K, Mohr KI, Herrmann J, Jansen R, Müller R. Disciformycins A and B: 12-membered macrolide glycoside antibiotics from the myxobacterium Pyxidicoccus fallax active against multiresistant staphylococci. Angew Chem Int Ed Engl 2014; 53:13588-91. [PMID: 25294799 DOI: 10.1002/anie.201406973] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 02/01/2023]
Abstract
Two macrolide glycosides with a unique scaffold were isolated from cultures of the myxobacterium Pyxidicoccus fallax. Their structures, including absolute configurations, were elucidated by a combination of NMR, MS, degradation, and molecular modeling techniques. Analysis of the proposed biosynthetic gene cluster led to insights into the biosynthesis of the polyketide and confirmed the structure assignment. The more active compound, disciformycin B, potently inhibits methicillin- and vancomycin-resistant Staphylococcus aureus.
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Affiliation(s)
- Frank Surup
- Helmholtz Center for Infection Research (HZI), Department Microbial Drugs, Inhoffenstrasse 7, 38124 Braunschweig (Germany); German Center for Infection Research (DZIF), Location: Braunschweig (Germany)
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127
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Surup F, Viehrig K, Mohr KI, Herrmann J, Jansen R, Müller R. Disciformycine A und B: zwölfgliedrige Macrolid-Glycosid-Antibiotika aus dem MyxobakteriumPyxidicoccus fallaxmit Aktivität gegen multiresistente Staphylokokken. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406973] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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128
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Schieferdecker S, König S, Weigel C, Dahse HM, Werz O, Nett M. Structure and biosynthetic assembly of gulmirecins, macrolide antibiotics from the predatory bacterium Pyxidicoccus fallax. Chemistry 2014; 20:15933-40. [PMID: 25287056 DOI: 10.1002/chem.201404291] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 01/28/2023]
Abstract
The gulmirecins constitute a new class of glycosylated macrolides that were isolated from the predatory bacterium Pyxidicoccus fallax HKI 727. Their structures were solved by a combination of NMR spectroscopic experiments and chemical derivatization. Analysis of the annotated gulmirecin gene cluster complemented the configurational assignment and provided insights into the stereochemical course of the biosynthetic assembly. The gulmirecins exhibit strong activity against staphylococci, including methicillin-resistant Staphylococcus aureus, but no cytotoxic effects on human cells.
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Affiliation(s)
- Sebastian Schieferdecker
- Junior Research Group, "Secondary Metabolism of Predatory Bacteria", Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena (Germany), Fax: (+49) 3641-5320811
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129
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Piasecki SK, Zheng J, Axelrod AJ, Detelich M, Keatinge-Clay AT. Structural and functional studies of a trans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective α- and β-ketoreduction. Proteins 2014; 82:2067-77. [PMID: 24634061 PMCID: PMC4142079 DOI: 10.1002/prot.24561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/19/2014] [Accepted: 03/06/2014] [Indexed: 11/06/2022]
Abstract
While the cis-acyltransferase modular polyketide synthase assembly lines have largely been structurally dissected, enzymes from within the recently discovered trans-acyltransferase polyketide synthase assembly lines are just starting to be observed crystallographically. Here we examine the ketoreductase (KR) from the first polyketide synthase module of the bacillaene nonribosomal peptide synthetase/polyketide synthase at 2.35-Å resolution. This KR naturally reduces both α- and β-keto groups and is the only KR known to do so during the biosynthesis of a polyketide. The isolated KR not only reduced an N-acetylcysteamine-bound β-keto substrate to a D-β-hydroxy product, but also an N-acetylcysteamine-bound α-keto substrate to an L-α-hydroxy product. That the substrates must enter the active site from opposite directions to generate these stereochemistries suggests that the acyl-phosphopantetheine moiety is capable of accessing very different conformations despite being anchored to a serine residue of a docked acyl carrier protein. The features enabling stereocontrolled α-ketoreduction may not be extensive since a KR that naturally reduces a β-keto group within a cis-acyltransferase polyketide synthase was identified that performs a completely stereoselective reduction of the same α-keto substrate to generate the D-α-hydroxy product. A sequence analysis of trans-acyltransferase KRs reveals that a single residue, rather than a three-residue motif found in cis-acyltransferase KRs, is predictive of the orientation of the resulting β-hydroxyl group.
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Affiliation(s)
- Shawn K. Piasecki
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Jianting Zheng
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Abram J. Axelrod
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Madeline Detelich
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Adrian T. Keatinge-Clay
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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130
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He HY, Yuan H, Tang MC, Tang GL. An unusual dehydratase acting on glycerate and a ketoreducatse stereoselectively reducing α-ketone in polyketide starter unit biosynthesis. Angew Chem Int Ed Engl 2014; 53:11315-9. [PMID: 25160004 DOI: 10.1002/anie.201406602] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 11/06/2022]
Abstract
Polyketide synthases (PKSs) usually employ a ketoreductase (KR) to catalyze the reduction of a β-keto group, followed by a dehydratase (DH) that drives the dehydration to form a double bond between the α- and β-carbon atoms. Herein, a DH*-KR* involved in FR901464 biosynthesis was characterized: DH* acts on glyceryl-S-acyl carrier protein (ACP) to yield ACP-linked pyruvate; subsequently KR* reduces α-ketone that yields L-lactyl-S-ACP as starter unit for polyketide biosynthesis. Genetic and biochemical evidence was found to support a similar pathway that is involved in the biosynthesis of lankacidins. These results not only identified new PKS domains acting on different substrates, but also provided additional options for engineering the PKS starter pathway or biocatalysis.
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Affiliation(s)
- Hai-Yan He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032 (China)
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131
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Ge HM, Huang T, Rudolf JD, Lohman JR, Huang SX, Guo X, Shen B. Enediyne polyketide synthases stereoselectively reduce the β-ketoacyl intermediates to β-D-hydroxyacyl intermediates in enediyne core biosynthesis. Org Lett 2014; 16:3958-61. [PMID: 25019332 PMCID: PMC4144755 DOI: 10.1021/ol501767v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
PKSE
biosynthesizes an enediyne core precursor from decarboxylative
condensation of eight malonyl-CoAs. The KR domain of PKSE is responsible
for iterative β-ketoreduction in each round of polyketide chain
elongation. KRs from selected PKSEs were investigated in vitro with
β-ketoacyl-SNACs as substrate mimics. Each of the KRs reduced
the β-ketoacyl-SNACs stereoselectively, all affording the corresponding
β-d-hydroxyacyl-SNACs, and the catalytic efficiencies
(kcat/KM)
of the KRs increased significantly as the chain length of the β-ketoacyl-SNAC
substrate increases.
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Affiliation(s)
- Hui-Ming Ge
- Department of Chemistry, ‡Department of Molecular Therapeutics, and §Natural Products Library Initiatives, The Scripps Research Institute , Jupiter, Florida 33458, United States
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132
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Hartmann O, Kalesse M. The Structure Elucidation and Total Synthesis of β‐Lipomycin. Angew Chem Int Ed Engl 2014; 53:7335-8. [DOI: 10.1002/anie.201402259] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Olaf Hartmann
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover (Germany)
- Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig (Germany)
| | - Markus Kalesse
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover (Germany)
- Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig (Germany)
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133
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Structural rearrangements of a polyketide synthase module during its catalytic cycle. Nature 2014; 510:560-4. [PMID: 24965656 PMCID: PMC4074775 DOI: 10.1038/nature13409] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 04/28/2014] [Indexed: 12/12/2022]
Abstract
The polyketide synthase (PKS) mega-enzyme assembly line uses a modular architecture to synthesize diverse and bioactive natural products that often constitute the core structures or complete chemical entities for many clinically approved therapeutic agents. The architecture of a full-length PKS module from the pikromycin pathway of Streptomyces venezuelae creates a reaction chamber for the intramodule acyl carrier protein (ACP) domain that carries building blocks and intermediates between acyltransferase, ketosynthase and ketoreductase active sites (see accompanying paper). Here we determine electron cryo-microscopy structures of a full-length pikromycin PKS module in three key biochemical states of its catalytic cycle. Each biochemical state was confirmed by bottom-up liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry. The ACP domain is differentially and precisely positioned after polyketide chain substrate loading on the active site of the ketosynthase, after extension to the β-keto intermediate, and after β-hydroxy product generation. The structures reveal the ACP dynamics for sequential interactions with catalytic domains within the reaction chamber, and for transferring the elongated and processed polyketide substrate to the next module in the PKS pathway. During the enzymatic cycle the ketoreductase domain undergoes dramatic conformational rearrangements that enable optimal positioning for reductive processing of the ACP-bound polyketide chain elongation intermediate. These findings have crucial implications for the design of functional PKS modules, and for the engineering of pathways to generate pharmacologically relevant molecules.
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134
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Wang H, Zhang H, Zou Y, Mi Y, Lin S, Xie Z, Yan Y, Zhang H. Structural Insight into the Tetramerization of an Iterative Ketoreductase SiaM through Aromatic Residues in the Interfaces. PLoS One 2014; 9:e97996. [PMID: 24901639 PMCID: PMC4046962 DOI: 10.1371/journal.pone.0097996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/23/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Hua Wang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huaidong Zhang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Zou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanling Mi
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhixiong Xie
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Houjin Zhang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail:
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135
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Xu Z, Baunach M, Ding L, Peng H, Franke J, Hertweck C. Biosynthetic code for divergolide assembly in a bacterial mangrove endophyte. Chembiochem 2014; 15:1274-9. [PMID: 24867126 DOI: 10.1002/cbic.201402071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Indexed: 02/04/2023]
Abstract
Divergolides are structurally diverse ansamycins produced by a bacterial endophyte (Streptomyces sp.) of the mangrove tree Bruguiera gymnorrhiza. By genomic analyses a gene locus coding for the divergolide pathway was detected. The div gene cluster encodes genes for the biosynthesis of 3-amino-5-hydroxybenzoate and the rare extender units ethylmalonyl-CoA and isobutylmalonyl-CoA, polyketide assembly by a modular type I polyketide synthase (PKS), and enzymes involved in tailoring reactions, such as a Baeyer-Villiger oxygenase. A detailed PKS domain analysis confirmed the stereochemical integrity of the divergolides and provided valuable new insights into the formation of the diverse aromatic chromophores. The bioinformatic analyses and the isolation and full structural elucidation of four new divergolide congeners led to a revised biosynthetic model that illustrates the formation of four different types of ansamycin chromophores from a single polyketide precursor.
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Affiliation(s)
- Zhongli Xu
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena (Germany)
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136
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Hartmann O, Kalesse M. Die Strukturaufklärung und Totalsynthese von β‐Lipomycin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402259] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Olaf Hartmann
- Institut für Organische Chemie und Biomolekulares Wirkstoff‐ zentrum (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover (Deutschland)
- Helmholtz Zentrum für Infektionsforschung (HZI), Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
| | - Markus Kalesse
- Institut für Organische Chemie und Biomolekulares Wirkstoff‐ zentrum (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover (Deutschland)
- Helmholtz Zentrum für Infektionsforschung (HZI), Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
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137
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Khosla C, Herschlag D, Cane DE, Walsh CT. Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry 2014; 53:2875-83. [PMID: 24779441 PMCID: PMC4020578 DOI: 10.1021/bi500290t] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two hallmarks of assembly line polyketide synthases have motivated an interest in these unusual multienzyme systems, their stereospecificity and their capacity for directional biosynthesis. In this review, we summarize the state of knowledge regarding the mechanistic origins of these two remarkable features, using the 6-deoxyerythronolide B synthase as a prototype. Of the 10 stereocenters in 6-deoxyerythronolide B, the stereochemistry of nine carbon atoms is directly set by ketoreductase domains, which catalyze epimerization and/or diastereospecific reduction reactions. The 10th stereocenter is established by the sequential action of three enzymatic domains. Thus, the problem has been reduced to a challenge in mainstream enzymology, where fundamental gaps remain in our understanding of the structural basis for this exquisite stereochemical control by relatively well-defined active sites. In contrast, testable mechanistic hypotheses for the phenomenon of vectorial biosynthesis are only just beginning to emerge. Starting from an elegant theoretical framework for understanding coupled vectorial processes in biology [Jencks, W. P. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 75-106], we present a simple model that can explain assembly line polyketide biosynthesis as a coupled vectorial process. Our model, which highlights the important role of domain-domain interactions, not only is consistent with recent observations but also is amenable to further experimental verification and refinement. Ultimately, a definitive view of the coordinated motions within and between polyketide synthase modules will require a combination of structural, kinetic, spectroscopic, and computational tools and could be one of the most exciting frontiers in 21st Century enzymology.
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Affiliation(s)
- Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
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138
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Hahn F, Kandziora N, Friedrich S, Leadlay PF. Synthesis of complex intermediates for the study of a dehydratase from borrelidin biosynthesis. Beilstein J Org Chem 2014; 10:634-640. [PMID: 24778714 PMCID: PMC3999764 DOI: 10.3762/bjoc.10.55] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/30/2014] [Indexed: 01/14/2023] Open
Abstract
Herein, we describe the syntheses of a complex biosynthesis-intermediate analogue of the potent antitumor polyketide borrelidin and of reference molecules to determine the stereoselectivity of the dehydratase of borrelidin polyketide synthase module 3. The target molecules were obtained from a common precursor aldehyde in the form of N-acetylcysteamine (SNAc) thioesters and methyl esters in 13 to 15 steps. Key steps for the assembly of the polyketide backbone of the dehydratase substrate analogue were a Yamamoto asymmetric carbocyclisation and a Sakurai allylation as well as an anti-selective aldol reaction. Reference compounds representing the E- and Z-configured double bond isomers as potential products of the dehydratase reaction were obtained from a common precursor aldehyde by Wittig olefination and Still–Gennari olefination. The final deprotection of TBS ethers and methyl esters was performed under mildly acidic conditions followed by pig liver esterase-mediated chemoselective hydrolysis. These conditions are compatible with the presence of a coenzyme A or a SNAc thioester, suggesting that they are generally applicable to the synthesis of complex polyketide-derived thioesters suited for biosynthesis studies.
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Affiliation(s)
- Frank Hahn
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Nadine Kandziora
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Steffen Friedrich
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Peter Francis Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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139
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Bouhired SM, Crüsemann M, Almeida C, Weber T, Piel J, Schäberle TF, König GM. Biosynthesis of Phenylnannolone A, a Multidrug Resistance Reversal Agent from the Halotolerant MyxobacteriumNannocystis pusillaB150. Chembiochem 2014; 15:757-65. [DOI: 10.1002/cbic.201300676] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Indexed: 01/28/2023]
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140
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Boddy CN. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides. ACTA ACUST UNITED AC 2014; 41:443-50. [DOI: 10.1007/s10295-013-1368-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/14/2013] [Indexed: 12/12/2022]
Abstract
Abstract
Microbial natural products have played a key role in the development of clinical agents in nearly all therapeutic areas. Recent advances in genome sequencing have revealed that there is an incredible wealth of new polyketide and non-ribosomal peptide natural product diversity to be mined from genetic data. The diversity and complexity of polyketide and non-ribosomal peptide biosynthesis has required the development of unique bioinformatics tools to identify, annotate, and predict the structures of these natural products from their biosynthetic gene clusters. This review highlights and evaluates web-based bioinformatics tools currently available to the natural product community for genome mining to discover new polyketides and non-ribosomal peptides.
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Affiliation(s)
- Christopher N Boddy
- grid.28046.38 0000000121822255 Departments of Chemistry and Biology, Center for Advanced Research in Environmental Genomics University of Ottawa K1N 6N5 Ottawa ON Canada
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141
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Cummings M, Breitling R, Takano E. Steps towards the synthetic biology of polyketide biosynthesis. FEMS Microbiol Lett 2014; 351:116-25. [PMID: 24372666 PMCID: PMC4237116 DOI: 10.1111/1574-6968.12365] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Abstract
Nature is providing a bountiful pool of valuable secondary metabolites, many of which possess therapeutic properties. However, the discovery of new bioactive secondary metabolites is slowing down, at a time when the rise of multidrug-resistant pathogens and the realization of acute and long-term side effects of widely used drugs lead to an urgent need for new therapeutic agents. Approaches such as synthetic biology are promising to deliver a much-needed boost to secondary metabolite drug development through plug-and-play optimized hosts and refactoring novel or cryptic bacterial gene clusters. Here, we discuss this prospect focusing on one comprehensively studied class of clinically relevant bioactive molecules, the polyketides. Extensive efforts towards optimization and derivatization of compounds via combinatorial biosynthesis and classical engineering have elucidated the modularity, flexibility and promiscuity of polyketide biosynthetic enzymes. Hence, a synthetic biology approach can build upon a solid basis of guidelines and principles, while providing a new perspective towards the discovery and generation of novel and new-to-nature compounds. We discuss the lessons learned from the classical engineering of polyketide synthases and indicate their importance when attempting to engineer biosynthetic pathways using synthetic biology approaches for the introduction of novelty and overexpression of products in a controllable manner.
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Affiliation(s)
- Matthew Cummings
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Rainer Breitling
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Eriko Takano
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
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142
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Chany AC, Tresse C, Casarotto V, Blanchard N. History, biology and chemistry of Mycobacterium ulcerans infections (Buruli ulcer disease). Nat Prod Rep 2014; 30:1527-67. [PMID: 24178858 DOI: 10.1039/c3np70068b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mycobacterium ulcerans infections (Buruli ulcer disease) have a long history that can be traced back 150 years. The successive discoveries of the mycobacteria in 1948 and of mycolactone A/B in 1999, the toxin responsible for this dramatic necrotic skin disease, resulted in a paradigm shift concerning the disease itself and in a broader sense, delineated an entirely new role for bioactive polyketides as virulence factors. The fascinating history, biology and chemistry of M. ulcerans infections are discussed in this review.
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Affiliation(s)
- Anne-Caroline Chany
- Université de Haute Alsace, Laboratoire de Chimie Organique et Bioorganique, EA4566, Ecole Nationale Supérieure de Chimie de Mulhouse, 3 rue Alfred Werner, 68093 Mulhouse Cedex, France
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143
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Bonnett SA, Whicher JR, Papireddy K, Florova G, Smith JL, Reynolds KA. Structural and stereochemical analysis of a modular polyketide synthase ketoreductase domain required for the generation of a cis-alkene. ACTA ACUST UNITED AC 2014; 20:772-83. [PMID: 23790488 DOI: 10.1016/j.chembiol.2013.04.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
Abstract
The formation of an activated cis-3-cyclohexylpropenoic acid by Plm1, the first extension module of the phoslactomycin polyketide synthase, is proposed to occur through an L-3-hydroxyacyl-intermediate as a result of ketoreduction by an A-type ketoreductase (KR). Here, we demonstrate that the KR domain of Plm1 (PlmKR1) catalyzes the formation of an L-3-hydroxyacyl product. The crystal structure of PlmKR1 revealed a well-ordered active site with a nearby Trp residue characteristic of A-type KRs. Structural comparison of PlmKR1 with B-type KRs that produce D-3-hydroxyacyl intermediates revealed significant differences. The active site of cofactor-bound A-type KRs is in a catalysis-ready state, whereas cofactor-bound B-type KRs are in a precatalytic state. Furthermore, the closed lid loop in substrate-bound A-type KRs restricts active site access from all but one direction, which is proposed to control the stereochemistry of ketoreduction.
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Affiliation(s)
- Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, OR. 97201
| | - Jonathan R Whicher
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109
| | | | - Galina Florova
- Department of Chemistry, Portland State University, Portland, OR. 97201
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Kevin A Reynolds
- Department of Chemistry, Portland State University, Portland, OR. 97201
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144
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Kage H, Kreutzer MF, Wackler B, Hoffmeister D, Nett M. An iterative type I polyketide synthase initiates the biosynthesis of the antimycoplasma agent micacocidin. ACTA ACUST UNITED AC 2014; 20:764-71. [PMID: 23790487 DOI: 10.1016/j.chembiol.2013.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/17/2022]
Abstract
Micacocidin is a thiazoline-containing natural product from the bacterium Ralstonia solanacearum that shows significant activity against Mycoplasma pneumoniae. The presence of a pentylphenol moiety distinguishes micacocidin from the structurally related siderophore yersiniabactin, and this residue also contributes to the potent antimycoplasma effects. The biosynthesis of the pentylphenol moiety, as deduced from bioinformatic analysis and stable isotope feeding experiments, involves an iterative type I polyketide synthase (iPKS), which generates a linear tetraketide intermediate from acyl carrier protein-tethered hexanoic acid by three consecutive, decarboxylative Claisen condensations with malonyl-coenzyme A. The final conversion into 6-pentylsalicylic acid depends on a ketoreductase domain within the iPKS, as demonstrated by heterologous expression in E. coli and subsequent site-directed mutagenesis experiments. Our results unveil the early steps in micacocidin biosynthesis and illuminate a bacterial enzyme that functionally resembles fungal polyketide synthases.
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Affiliation(s)
- Hirokazu Kage
- Junior Research Group Secondary Metabolism of Predatory Bacteria, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
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145
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Gao H, Grüschow S, Barke J, Seipke RF, Hill LM, Orivel J, Yu DW, Hutchings M, Goss RJM. Filipins: the first antifungal “weed killers” identified from bacteria isolated from the trap-ant. RSC Adv 2014. [DOI: 10.1039/c4ra09875g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Allomerus ants cultivate fungus to fabricate their insect traps. Speculation is that the ants employ actinomycetes to help achieve fungal monoculture. From an associated actinomycete we identify the first antifungal compounds and encoding genes.
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Affiliation(s)
- Hong Gao
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Sabine Grüschow
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Jörg Barke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Ryan F. Seipke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | | | - Jérôme Orivel
- CNRS
- UMR Ecologie des Forêts de Guyane
- Campus Agronomique
- 97379 Kourou Cedex, France
| | - Douglas W. Yu
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
| | - Matthew Hutchings
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Rebecca J. M. Goss
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
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146
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Kandziora N, Andexer JN, Moss SJ, Wilkinson B, Leadlay PF, Hahn F. Uncovering the origin of Z-configured double bonds in polyketides: intermediate E-double bond formation during borrelidin biosynthesis. Chem Sci 2014. [DOI: 10.1039/c4sc00883a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The dehydratase domain BorDH3 is assayed with a synthetic surrogate of the predicted tetraketide substrate and shown to be E-selective. Detailed NMR spectroscopic analysis of pre-borrelidin assigns the timing of the E-5 Z-isomerization to the very final steps of borrelidin biosynthesis.
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Affiliation(s)
- Nadine Kandziora
- Institut für Organische Chemie
- Leibniz Universität Hannover
- 30167 Hannover, Germany
| | - Jennifer N. Andexer
- Department of Biochemistry
- University of Cambridge (UK)
- Cambridge CB2 1QW, UK
- Institut für Pharmazeutische Wissenschaften
- Albert-Ludwigs-Universität Freiburg
| | - Steven J. Moss
- Isomerase Therapeutics
- Chesterford Research Park
- Cambridge CB10 1XL, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology
- John Innes Centre Norwich NR4 7UH
- UK
| | - Peter F. Leadlay
- Department of Biochemistry
- University of Cambridge (UK)
- Cambridge CB2 1QW, UK
| | - Frank Hahn
- Institut für Organische Chemie
- Leibniz Universität Hannover
- 30167 Hannover, Germany
- Department of Biochemistry
- University of Cambridge (UK)
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147
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Young J, Stevens DC, Carmichael R, Tan J, Rachid S, Boddy CN, Müller R, Taylor RE. Elucidation of gephyronic acid biosynthetic pathway revealed unexpected SAM-dependent methylations. JOURNAL OF NATURAL PRODUCTS 2013; 76:2269-2276. [PMID: 24298873 DOI: 10.1021/np400629v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Gephyronic acid, a cytostatic polyketide produced by the myxobacterium Cystobacter violaceus Cb vi76, exhibits potent and selective eukaryotic protein synthesis inhibition. Next-generation sequencing of the C. violaceus genome revealed five type I polyketide synthases and post-PKS tailoring enzymes including an O-methyltransferase and a cytochrome P450 monooxygenase. Seven methyltransferase (MT) domains embedded within the PKS subunits were found to install the methyl branches throughout the gephyronic acid skeleton. A rare loading domain from the GNAT superfamily also contains an embedded MT domain that catalyzes the in situ production of an isobutyryl starter unit. Phylogenetic analysis identified new motifs that distinguish MT domains located in PKS pathways with in cis acyltransferase (AT) domains from MT domains located in PKS pathways with trans AT enzymes. The identification of the gene cluster sets the stage for the generation of a heterologous expression system, which will allow further investigation of selective eukaryotic protein synthesis inhibitors through the generation of gephyronic acid analogues.
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Affiliation(s)
- Jeanette Young
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana, United States
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148
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Gay D, You YO, Keatinge-Clay A, Cane DE. Structure and stereospecificity of the dehydratase domain from the terminal module of the rifamycin polyketide synthase. Biochemistry 2013; 52:8916-28. [PMID: 24274103 DOI: 10.1021/bi400988t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RifDH10, the dehydratase domain from the terminal module of the rifamycin polyketide synthase, catalyzes the stereospecific syn dehydration of the model substrate (2S,3S)-2-methyl-3-hydroxypentanoyl-RifACP10, resulting in the exclusive formation of (E)-2-methyl-2-pentenoyl-RifACP10. RifDH10 does not dehydrate any of the other three diastereomeric, RifACP10-bound, diketide thioester substrates. On the other hand, when EryACP6, from the sixth module of the erythromycin polyketide synthase, is substituted for RifACP10, RifDH10 stereospecifically dehydrates only (2R,3R)-2-methyl-3-hydroxypentanoyl-EryACP6 to give exclusively (E)-2-methyl-2-pentenoyl-EryACP6, with no detectable dehydration of any of the other three diastereomeric, EryACP6-bound, diketides. An identical alteration in substrate diastereospecificity was observed for the corresponding N-acetylcysteamine or pantetheine thioester analogues, regardless of acyl chain length or substitution pattern. Incubation of (2RS)-2-methyl-3-ketopentanoyl-RifACP10 with the didomain reductase-dehydratase RifKR10-RifDH10 yielded (E)-2-methyl-2-pentenoyl-RifACP10, the expected product of syn dehydration of (2S,3S)-2-methyl-3-hydroxypentanoyl-RifACP10, while incubation with the corresponding EryACP6-bound substrate, (2RS)-2-methyl-3-ketopentanoyl-EryACP6, gave only the reduction product (2S,3S)-2-methyl-3-hydroxypentanoyl-EryACP6 with no detectable dehydration. These results establish the intrinsic syn dehydration stereochemistry and substrate diastereoselectivity of RifDH10 and highlight the critical role of the natural RifACP10 domain in chaperoning the proper recognition and processing of the natural ACP-bound undecaketide substrate. The 1.82 Å resolution structure of RifDH10 reveals the atomic-resolution details of the active site and allows modeling of the syn dehydration of the (2S,3S)-2-methyl-3-hydroxyacyl-RifACP10 substrate. These results suggest that generation of the characteristic cis double bond of the rifamycins occurs after formation of the full-length RifACP10-bound acyclic trans-unsaturated undecaketide intermediate, most likely during the subsequent macrolactamization catalyzed by the amide synthase RifF.
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Affiliation(s)
- Darren Gay
- Department of Chemistry and Biochemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712-0165, United States
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149
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Lu HH, Raja A, Franke R, Landsberg D, Sasse F, Kalesse M. Die Synthese und biologische Evaluierung von Paläo-Soraphenen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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150
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Lu HH, Raja A, Franke R, Landsberg D, Sasse F, Kalesse M. Synthesis and Biological Evaluation of Paleo-Soraphens. Angew Chem Int Ed Engl 2013; 52:13549-52. [DOI: 10.1002/anie.201305331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/09/2013] [Indexed: 01/26/2023]
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