1
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Xiang C, Yao S, Wang R, Zhang L. Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain. Beilstein J Org Chem 2024; 20:1476-1485. [PMID: 38978744 PMCID: PMC11228615 DOI: 10.3762/bjoc.20.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Polyketides are a major class of natural products, including bioactive medicines such as erythromycin and rapamycin. They are often rich in stereocenters biosynthesized by the ketoreductase (KR) domain within the polyketide synthase (PKS) assembly line. Previous studies have identified conserved motifs in KR sequences that enable the bioinformatic prediction of product stereochemistry. However, the reliability and applicability of these prediction methods have not been thoroughly assessed. In this study, we conducted a comprehensive bioinformatic analysis of 1,762 KR sequences from cis-AT PKSs to reevaluate the residues involved in conferring stereoselectivity. Our findings indicate that the previously identified fingerprint motifs remain valid for KRs in β-modules from actinobacteria, but their reliability diminishes for KRs from other module types or taxonomic origins. Additionally, we have identified several new motifs that exhibit a strong correlation with the stereochemical outcomes of KRs. These updated fingerprint motifs for stereochemical prediction not only enhance our understanding of the enzymatic mechanisms governing stereocontrol but also facilitate accurate stereochemical prediction and genome mining of polyketides derived from modular cis-AT PKSs.
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Affiliation(s)
- Changjun Xiang
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Shunyu Yao
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Ruoyu Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
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2
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Yin Z, Dickschat JS. Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis. Beilstein J Org Chem 2024; 20:734-740. [PMID: 38590531 PMCID: PMC10999986 DOI: 10.3762/bjoc.20.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
An isotopic labelling method was developed to investigate substrate binding by ketosynthases, exemplified by the second ketosynthase of the polyketide synthase BaeJ involved in bacillaene biosynthesis (BaeJ-KS2). For this purpose, both enantiomers of a 13C-labelled N-acetylcysteamine thioester (SNAC ester) surrogate of the proposed natural intermediate of BaeJ-KS2 were synthesised, including an enzymatic step with glutamate decarboxylase, and incubated with BaeJ-KS2. Substrate binding was demonstrated through 13C NMR analysis of the products against the background of various control experiments.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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3
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Kimishima A, Tsuruoka I, Tsutsumi H, Honsho M, Honma S, Matsui H, Sugamata M, Wasuwanich P, Inahashi Y, Hanaki H, Asami Y. A new tetronomycin analog, broad-spectrum and potent antibiotic against drug-resistant Gram-positive bacteria. Chem Biodivers 2024; 21:e202301834. [PMID: 38179845 DOI: 10.1002/cbdv.202301834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/06/2024]
Abstract
We discovered a new tetronomycin analog, C-32-OH tetronomycin (2) from the Streptomyces sp. K20-0247 strain, which produces tetronomycin (1). After NMR analysis of 2, we determined the planar structure. Futhermore, the absolute stereochemistry of 2 was deduced based on the biosynthetic pathway of 1 in the K20-0247 strain and a comparison of experimental electronic circular dichroism (ECD) results of 1 with 2. While 2 exihibits potent antibacterial activity aganist Gram-positive baceria including vancomycin-intermediate Staphylococcus aureus (VISA) strains and vancomycin-resistant Enterococci (VRE), the antibacterial activity of 2 shows 16-32-folds weaker than that of 1 suggesting that the C-34 methyl group in 1 is one of the very important functinal group. Moreover, we evaluated the ionophore activity of 1 and 2 and neither compound shows ionophore activity at reasonable concetrations. Our research suggests that 1 and 2 would have different target(s) from an ionophore mechanism in the antibacterial activity and tetronomycins are promising natural products for broad-spectrum antibiotics.
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Affiliation(s)
- Aoi Kimishima
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Iori Tsuruoka
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Hayama Tsutsumi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Masako Honsho
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Sota Honma
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Hidehito Matsui
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Miho Sugamata
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Paul Wasuwanich
- University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Hideaki Hanaki
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
| | - Yukihiro Asami
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane Minato-ku, 108-8641, Tokyo, Japan
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4
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Ogonkov A, Dieterich CL, Meoded RA, Piel J, Fraley AE, Sasso S. Characterization of an Unusual α-Oxoamine Synthase Off-Loading Domain from a Cyanobacterial Type I Fatty Acid Synthase. Chembiochem 2023; 24:e202300209. [PMID: 37144248 DOI: 10.1002/cbic.202300209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/06/2023]
Abstract
Type I fatty acid synthases (FASs) are known from higher eukaryotes and fungi. We report the discovery of FasT, a rare type I FAS from the cyanobacterium Chlorogloea sp. CCALA695. FasT possesses an unusual off-loading domain, which was heterologously expressed in E. coli and found to act as an α-oxoamine synthase (AOS) in vitro. Similar to serine palmitoyltransferases from sphingolipid biosynthesis, the AOS off-loading domain catalyzes a decarboxylative Claisen condensation between l-serine and a fatty acyl thioester. While the AOS domain was strictly specific for l-serine, thioesters with saturated fatty acyl chains of six carbon atoms and longer were tolerated, with the highest activity observed for stearoyl-coenzyme A (C18 ). Our findings suggest a novel route to α-amino ketones via the direct condensation of iteratively produced long-chain fatty acids with l-serine by a FAS with a cis-acting AOS off-loading domain.
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Affiliation(s)
- Andrei Ogonkov
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
- Institute of Biology, Leipzig University, Johannisallee 23, 04107, Leipzig, Germany
| | - Cora L Dieterich
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Roy A Meoded
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jörn Piel
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Amy E Fraley
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Severin Sasso
- Institute of Biology, Leipzig University, Johannisallee 23, 04107, Leipzig, Germany
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5
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Yang M, Li W, Zhou L, Lin X, Zhang W, Shen Y, Deng H, Lin HW, Zhou Y. Biosynthesis of trialkyl-substituted aromatic polyketide NFAT-133 involves unusual P450 monooxygenase-mediating aromatization and a putative metallo-beta-lactamase fold hydrolase. Synth Syst Biotechnol 2023; 8:349-356. [PMID: 37325182 PMCID: PMC10265476 DOI: 10.1016/j.synbio.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
The bacterial trialkyl-substituted aromatic polyketides are structurally featured with the unusual aromatic core in the middle of polyketide chain such as TM-123 (1), veramycin A (2), NFAT-133 (3) and benwamycin I (4), which were discovered from Streptomyces species and demonstrated with antidiabetic and immunosuppressant activities. Though the biosynthetic pathway of 1-3 was reported as a type I polyketide synthase (PKS), the PKS assembly line was interpreted inconsistently, and it remains a mystery how the compound 3 was generated. Herein, the PKS assembly logic of 1-4 was revised by site-mutagenetic analysis of the PKS dehydratase domains. Based on gene deletion and complementation, the putative P450 monooxygenase nftE1 and metallo-beta-lactamase (MBL) fold hydrolase nftF1 were verified as essential genes for the biosynthesis of 1-4. The absence of nftE1 led to abolishment of 1-4 and accumulation of new products (5-8). Structural elucidation reveals 5-8 as the non-aromatic analogs of 1, suggesting the NftE1-catalyzed aromatic core formation. Deletion of nftF1 resulted in disappearance of 3 and 4 with the compounds 1 and 2 unaffected. As a rare MBL-fold hydrolase from type I PKSs, NftF1 potentially generates the compound 3 through two strategies: catalyze premature chain-offloading as a trans-acting thioesterase or hydrolyze the lactone-bond of compound 1 as an esterase.
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Affiliation(s)
- Ming Yang
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Wanlu Li
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lin Zhou
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiao Lin
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, 530200, PR China
| | - Wenyu Zhang
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yaoyao Shen
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Hou-wen Lin
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yongjun Zhou
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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6
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Tan B, Zhang Q, Li J, Zhu Y, Zhang L, Zhang W, Zhang H, Chen Y, Zhang C. Totopotensamide Congeners from a Halogenase-Inactivated Mutant. JOURNAL OF NATURAL PRODUCTS 2023; 86:76-84. [PMID: 36606742 DOI: 10.1021/acs.jnatprod.2c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The installation of halogen atoms into aromatic and less activated polyketide substrates by halogenases is a powerful strategy to tune the bioactivity, bioavailability, and reactivity of compounds. In the biosynthetic pathway of totopotensamide A (1), the halogenase TotH was confirmed in vivo to catalyze the C-4 chlorination to form the nonproteinogenic amino acid ClMeDPG. Herein, we report the isolation, structure elucidation, and bioactivity evaluation of six new deschloro totopotensamide (TPM) congeners TPMs H2-H7 (5-10) from the totH-inactivated strain and the proposed absolute configuration of the polyketide chain in TPMs using 4 as a model compound by a combination of the JBCA and bioinformatic analysis. Compounds 5, 6, 8, and 9 displayed cytotoxicity against the A549, PANC-1, Calu3, and BXPC3 cell lines with IC50 values ranging from 2.3 to 9.7 μM.
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Affiliation(s)
- Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Jieyi Li
- School of Pharmaceutical, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yang Chen
- School of Pharmaceutical, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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7
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Wagner L, Stang J, Derra S, Hollmann T, Hahn F. Towards understanding oxygen heterocycle-forming biocatalysts: a selectivity study of the pyran synthase PedPS7. Org Biomol Chem 2022; 20:9645-9649. [PMID: 36412217 DOI: 10.1039/d2ob02064e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Intramolecular oxa-Michael addition-catalysing cyclases are widespread in polyketide biosynthetic pathways. Although they have significant potential in biotechnology and chemoenzymatic synthesis of chiral heterocycles, they have only scarcely been studied. Here, we present detailed investigations on the selectivity profile of the pyran synthase PedPS7 showing that it combines broad substrate tolerance with high selectivity for the formation of up to two new stereocentres and relaxed precursor stereoisomer discrimination. Two of the four possible tetrahydropyran stereoisomers are reliably accessible by this enzyme. The results indicate fundamental differences between the individual subtypes of intramolecular oxa-Michael addition-catalysing cyclases.
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Affiliation(s)
- Lisa Wagner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Jörg Stang
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Sebastian Derra
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Tim Hollmann
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
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8
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Dickschat JS. Enzymes in biosynthesis. Beilstein J Org Chem 2022; 18:1131-1132. [PMID: 36105723 PMCID: PMC9443342 DOI: 10.3762/bjoc.18.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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9
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Schröder M, Roß T, Hemmerling F, Hahn F. Studying a Bottleneck of Multimodular Polyketide Synthase Processing: the Polyketide Structure-Dependent Performance of Ketoreductase Domains. ACS Chem Biol 2022; 17:1030-1037. [PMID: 35412301 DOI: 10.1021/acschembio.2c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ketoreductases (KRs) are canonical domains of type I polyketide synthases (PKSs). They stereoselectively reduce ACP-bound β-ketothioester intermediates and are responsible for a large part of the stereocenters in reduced polyketides. Albeit essential for the understanding and engineering of PKS, the specific effects of altering the polyketide part of KR precursors on their performance has rarely been studied. We present investigations on the substrate-dependent performance of six isolated KR domains using a library of structurally diverse surrogates for PKS thioester intermediates. A pronounced correlation between the polyketide structure and the KR performance was observed with activity and stereoselectivity diminishing with growing deviation from the natural KR precursor structure. The extent of this decrease and the profile of arising side products was characteristic for the individual KRs. Our results reinforce the importance of structure-KR performance relationships and suggest extended studies with isolated domains and whole PKS modules.
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Affiliation(s)
- Marius Schröder
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Theresa Roß
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
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10
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Caffrey P, Hogan M, Song Y. New Glycosylated Polyene Macrolides: Refining the Ore from Genome Mining. Antibiotics (Basel) 2022; 11:334. [PMID: 35326797 PMCID: PMC8944477 DOI: 10.3390/antibiotics11030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 01/26/2023] Open
Abstract
Glycosylated polyene macrolides include effective antifungal agents, such as pimaricin, nystatin, candicidin, and amphotericin B. For the treatment of systemic mycoses, amphotericin B has been described as a gold-standard antibiotic because of its potent activity against a broad spectrum of fungal pathogens, which do not readily become resistant. However, amphotericin B has severe toxic side effects, and the development of safer alternatives remains an important objective. One approach towards obtaining such compounds is to discover new related natural products. Advances in next-generation sequencing have delivered a wealth of microbial genome sequences containing polyene biosynthetic gene clusters. These typically encode a modular polyketide synthase that catalyzes the assembly of the aglycone core, a cytochrome P450 that oxidizes a methyl branch to a carboxyl group, and additional enzymes for synthesis and attachment of a single mycosamine sugar residue. In some cases, further P450s catalyze epoxide formation or hydroxylation within the macrolactone. Bioinformatic analyses have identified over 250 of these clusters. Some are predicted to encode potentially valuable new polyenes that have not been uncovered by traditional screening methods. Recent experimental studies have characterized polyenes with new polyketide backbones, previously unknown late oxygenations, and additional sugar residues that increase water-solubility and reduce hemolytic activity. Here we review these studies and assess how this new knowledge can help to prioritize silent polyene clusters for further investigation. This approach should improve the chances of discovering better antifungal antibiotics.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland; (M.H.); (Y.S.)
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11
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Yin Z, Liebhart E, Stegmann E, Brötz-Oesterhelt H, Dickschat JS. An isotopic probe to follow the stereochemical course of dehydratase reactions in polyketide and fatty acid biosynthesis. Org Chem Front 2022. [DOI: 10.1039/d2qo00272h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four stereoisomeric and isotopically labelled probes that are suitable to easily follow the stereochemical course of dehydratases have been synthesised.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Elisa Liebhart
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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12
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Heinrich S, Grote M, Sievers S, Kushnir S, Schulz F. Polyether Cyclization Cascade Alterations in Response to Monensin Polyketide Synthase Mutations. Chembiochem 2021; 23:e202100584. [PMID: 34729883 DOI: 10.1002/cbic.202100584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Indexed: 11/11/2022]
Abstract
The targeted manipulation of polyketide synthases has in recent years led to numerous new-to-nature polyketides. For type I polyketide synthases the response of post-polyketide synthases (PKS) processing enzymes onto the most frequently polyketide backbone manipulations is so far insufficiently studied. In particular, complex processes such as the polyether cyclisation in the biosynthesis of ionophores such as monensin pose interesting objects of research. We present here a study of the substrate promiscuity of the polyether cyclisation cascade enzymes in monensin biosynthesis in the conversion of redox derivatives of the nascent polyketide chain. LC-HRMS/MS2 -based studies revealed a remarkable flexibility of the post-PKS enzymes. They acted on derivatized polyketide backbones based on the three possible polyketide redox states within two different modules and gave rise to an altered polyether structure. One of these monensin derivatives was isolated and characterized by 2D-NMR spectroscopy, crystallography, and bioactivity studies.
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Affiliation(s)
- Sascha Heinrich
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Marius Grote
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Sonja Sievers
- Max PIanck Institute for molecular Physiology, COMAS - Compound Management and Screening Center, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Susanna Kushnir
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Frank Schulz
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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13
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Fujiyama K, Kato N, Re S, Kinugasa K, Watanabe K, Takita R, Nogawa T, Hino T, Osada H, Sugita Y, Takahashi S, Nagano S. Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Keisuke Fujiyama
- Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Current address: Dormancy and Adaptation Research Unit RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro, Tsurumi Yokohama Kanagawa 230-0045 Japan
| | - Naoki Kato
- Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Faculty of Agriculture Setsunan University 45-1 Nagaotoge-cho, Hirakata Osaka 573-0101 Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation RIKEN Center for Biosystems Dynamics Research 2-2-3 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
- Artificial Intelligence Center for Health and Biomedical Research National Institutes of Biomedical Innovation, Health, and Nutrition 7-6-8, Saito-Asagi, Ibaraki Osaka 567-0085 Japan
| | - Kiyomi Kinugasa
- Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kohei Watanabe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ryo Takita
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshihiko Nogawa
- Chemical Biology Research Group RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Tomoya Hino
- Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation RIKEN Center for Biosystems Dynamics Research 2-2-3 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
- Theoretical Molecular Science Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Computational Biophysics Research Team RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi Chuo-ku Kobe, Hyogo 650-0047 Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
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14
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Fujiyama K, Kato N, Re S, Kinugasa K, Watanabe K, Takita R, Nogawa T, Hino T, Osada H, Sugita Y, Takahashi S, Nagano S. Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*. Angew Chem Int Ed Engl 2021; 60:22401-22410. [PMID: 34121297 PMCID: PMC8518865 DOI: 10.1002/anie.202106186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Indexed: 12/02/2022]
Abstract
Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.
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Affiliation(s)
- Keisuke Fujiyama
- Department of Chemistry and BiotechnologyGraduate School of EngineeringTottori University4-101 Koyama-choMinamiTottori680-8552Japan
- Current address: Dormancy and Adaptation Research UnitRIKEN Center for Sustainable Resource Science1-7-22 Suehiro, TsurumiYokohamaKanagawa230-0045Japan
| | - Naoki Kato
- Natural Product Biosynthesis Research UnitRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
- Faculty of AgricultureSetsunan University45-1 Nagaotoge-cho, HirakataOsaka573-0101Japan
| | - Suyong Re
- Laboratory for Biomolecular Function SimulationRIKEN Center for Biosystems Dynamics Research2-2-3 Minatojima-minami-machi, Chuo-kuKobeHyogo650-0047Japan
- Artificial Intelligence Center for Health and Biomedical ResearchNational Institutes of Biomedical Innovation, Health, and Nutrition7-6-8, Saito-Asagi, IbarakiOsaka567-0085Japan
| | - Kiyomi Kinugasa
- Natural Product Biosynthesis Research UnitRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Kohei Watanabe
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7-3-1 Hongo, Bunkyo-kuTokyo113-0033Japan
| | - Ryo Takita
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7-3-1 Hongo, Bunkyo-kuTokyo113-0033Japan
| | - Toshihiko Nogawa
- Chemical Biology Research GroupRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Tomoya Hino
- Department of Chemistry and BiotechnologyGraduate School of EngineeringTottori University4-101 Koyama-choMinamiTottori680-8552Japan
- Center for Research on Green Sustainable ChemistryTottori University4-101 Koyama-choMinamiTottori680-8552Japan
| | - Hiroyuki Osada
- Chemical Biology Research GroupRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function SimulationRIKEN Center for Biosystems Dynamics Research2-2-3 Minatojima-minami-machi, Chuo-kuKobeHyogo650-0047Japan
- Theoretical Molecular Science LaboratoryRIKEN Cluster for Pioneering Research2-1 HirosawaWakoSaitama351-0198Japan
- Computational Biophysics Research TeamRIKEN Center for Computational Science7-1-26 Minatojima-minami-machiChuo-kuKobe, Hyogo650-0047Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research UnitRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Shingo Nagano
- Department of Chemistry and BiotechnologyGraduate School of EngineeringTottori University4-101 Koyama-choMinamiTottori680-8552Japan
- Center for Research on Green Sustainable ChemistryTottori University4-101 Koyama-choMinamiTottori680-8552Japan
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15
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Luo M, Xu H, Dong Y, Shen K, Lu J, Yin Z, Qi M, Sun G, Tang L, Xiang J, Deng Z, Dickschat JS, Sun Y. Der Mechanismus von dehydatisierenden Bimodulen in der
trans
‐Acyltransferase‐Polketidbiosynthese: Eine Modellstudie am hepatoprotektiven Hangtaimycin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Houchao Xu
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Yulu Dong
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Kun Shen
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Junlei Lu
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Zhiyong Yin
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Miaomiao Qi
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Lingjie Tang
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Jin Xiang
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
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16
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Luo M, Xu H, Dong Y, Shen K, Lu J, Yin Z, Qi M, Sun G, Tang L, Xiang J, Deng Z, Dickschat JS, Sun Y. The Mechanism of Dehydrating Bimodules in trans-Acyltransferase Polyketide Biosynthesis: A Showcase Study on Hepatoprotective Hangtaimycin. Angew Chem Int Ed Engl 2021; 60:19139-19143. [PMID: 34219345 PMCID: PMC8456789 DOI: 10.1002/anie.202106250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/30/2021] [Indexed: 11/29/2022]
Abstract
A bioassay‐guided fractionation led to the isolation of hangtaimycin (HTM) from Streptomyces spectabilis CCTCC M2017417 and the discovery of its hepatoprotective properties. Structure elucidation by NMR suggested the need for a structural revision. A putative HTM degradation product was also isolated and its structure was confirmed by total synthesis. The biosynthetic gene cluster was identified and resembles a hybrid trans‐AT PKS/NRPS biosynthetic machinery whose first PKS enzyme contains an internal dehydrating bimodule, which is usually found split in other trans‐AT PKSs. The mechanisms of such dehydrating bimodules have often been proposed, but have never been deeply investigated. Here we present in vivo mutations and in vitro enzymatic experiments that give first and detailed mechanistic insights into catalysis by dehydrating bimodules.
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Affiliation(s)
- Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Yulu Dong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Kun Shen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Junlei Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Miaomiao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Lingjie Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Jin Xiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
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17
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Yin Z, Dickschat JS. Cis double bond formation in polyketide biosynthesis. Nat Prod Rep 2021; 38:1445-1468. [PMID: 33475122 DOI: 10.1039/d0np00091d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2020Polyketides form a large group of bioactive secondary metabolites that usually contain one or more double bonds. Although most of the double bonds found in polyketides are trans or E-configured, several cases are known in which cis or Z-configurations are observed. Double bond formation by polyketide synthases (PKSs) is widely recognised to be catalysed by ketoreduction and subsequent dehydration of the acyl carrier protein (ACP)-tethered 3-ketoacyl intermediate in the PKS biosynthetic assembly line with a specific stereochemical course in which the ketoreduction step determines the usual trans or more rare cis double bond configuration. Occasionally, other mechanisms for the installation of cis double bonds such as double bond formation during chain release or post-PKS modifications including, amongst others, isomerisations or double bond installations by oxidation are observed. This review discusses the peculiar mechanisms of cis double bond formation in polyketide biosynthesis.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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18
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Andler O, Kazmaier U. A Straightforward Synthesis of Polyketides via Ester Dienolate Matteson Homologation. Chemistry 2021; 27:949-953. [PMID: 33089903 PMCID: PMC7839490 DOI: 10.1002/chem.202004650] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 12/22/2022]
Abstract
Application of ester dienolates as nucleophiles in Matteson homologations allows for the stereoselective synthesis of highly substituted α,β-unsaturated δ-hydroxy carboxyl acids, structural motifs widespread found in polyketide natural products. The protocol is rather flexible and permits the introduction of substituents and functionalities also at those positions which are not accessible by the commonly used aldol reaction. Therefore, this ester dienolate Matteson approach is an interesting alternative to the "classical" polyketide syntheses.
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Affiliation(s)
- Oliver Andler
- Institut für Organische ChemieUniversität des SaarlandesCampus C4.266123SaarbrückenGermany
| | - Uli Kazmaier
- Institut für Organische ChemieUniversität des SaarlandesCampus C4.266123SaarbrückenGermany
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19
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Walker PD, Weir ANM, Willis CL, Crump MP. Polyketide β-branching: diversity, mechanism and selectivity. Nat Prod Rep 2021; 38:723-756. [PMID: 33057534 DOI: 10.1039/d0np00045k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.
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Affiliation(s)
- P D Walker
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - A N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - C L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - M P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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20
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Drufva EE, Spengler NR, Hix EG, Bailey CB. Site-Directed Mutagenesis of Modular Polyketide Synthase Ketoreductase Domains for Altered Stereochemical Control. Chembiochem 2020; 22:1122-1150. [PMID: 33185924 DOI: 10.1002/cbic.202000613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Indexed: 12/18/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a high degree of stereochemical control. Due to their colinear properties, they have been considerable targets for rational biosynthetic pathway engineering. Among the domains harbored within these complex assembly lines, ketoreductase (KR) domains have been extensively studied with the goal of altering their stereoselectivity by site-directed mutagenesis, as they confer much of the stereochemical complexity present in pharmaceutically active reduced polyketide scaffolds. Here we review all efforts to date to perform site-directed mutagenesis on PKS KRs, most of which have been done in the context of excised KR domains on model diffusible substrates such as β-keto N-acetyl cysteamine thioesters. We also discuss the challenges around translating the findings of these studies to alter stereocontrol in the context of a complex multidomain enzymatic assembly line.
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Affiliation(s)
- Erin E Drufva
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Nolan R Spengler
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Elijah G Hix
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
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21
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Hou SY, Zhang MY, Wang HD, Zhang YX. Biosynthesis Gene Cluster and Oxazole Ring Formation Enzyme for Inthomycins in Streptomyces sp. Strain SYP-A7193. Appl Environ Microbiol 2020; 86:e01388-20. [PMID: 32801183 PMCID: PMC7531957 DOI: 10.1128/aem.01388-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022] Open
Abstract
Inthomycins belong to a growing family of oxazole-containing polyketides and exhibit a broad spectrum of anti-oomycete and herbicidal activities. In this study, we purified inthomycins A and B from the metabolites of Streptomyces sp. strain SYP-A7193 and determined their chemical structures. Genome sequencing, comparative genomic analysis, and gene disruption of Streptomyces sp. SYP-A7193 showed that the inthomycin biosynthetic gene cluster (itm) belonged to the hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) system. Functional domain comparison and disruption/complementation experiments of itm12 resulted in the complete loss of inthomycins A and B and the subsequent restoration of their production, confirming that itm12 encodes a discrete acyltransferase (AT), and hence, itm was considered to belong to the trans-AT type I PKS system. Moreover, the disruption/complementation experiments of itm15 also resulted in the loss and restoration of inthomycin A and B formation. Further gene cloning, expression, purification, and activity verification of itm15 revealed that Itm15 is a cyclodehydratase that catalyzes a straight-chain dehydration reaction to form an oxazole ring for the biosynthesis of inthomycins A and B. Thus, we discovered a novel enzyme that catalyzes oxazole ring formation and elucidated the complete biosynthetic pathway of inthomycins.IMPORTANCEStreptomyces species produce numerous secondary metabolites with diverse structures and pharmacological activities that are beneficial for human health and have several applications in agriculture. In this study, hybrid nonribosomal peptide synthetase/polyketide synthase metabolites inthomycins A and B were isolated from after fermenting Streptomyces sp. SYP-A7193. Genome sequencing, gene disruption, gene complementation, heterologous expression, and activity assay revealed that the biosynthesis gene assembly line of inthomycins A and B was a 95.3-kb trans-AT type I PKS system in the strain SYP-A7193. More importantly, Itm15, a cyclodehydratase, was identified to be an oxazole ring formation enzyme required for the biosynthesis of inthomycins A and B; it is significant to discover this catalyzation reaction in the PKS/NRPS system in the field of microbiology. Our findings could provide further insights into the diversity of trans-AT type I PKS systems and the mechanism of oxazole cyclization involved in the biosynthesis of natural products.
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Affiliation(s)
- Shao-Yang Hou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Hong-Da Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
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22
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Wunderlich J, Roß T, Schröder M, Hahn F. Step-Economic Synthesis of Biomimetic β-Ketopolyene Thioesters and Demonstration of Their Usefulness in Enzymatic Biosynthesis Studies. Org Lett 2020; 22:4955-4959. [PMID: 32610930 DOI: 10.1021/acs.orglett.0c01348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies on the biosynthetic processing of polyene thioester intermediates are complicated by limited access to appropriate substrate surrogates. We present a step-economic synthetic access to biomimetic β-ketopolyene thioesters that is based on an Ir-catalyzed reductive Horner-Wadsworth-Emmons olefination. New β-ketotriene and pentaenethioates of pantetheine and N-acetylcysteamine were exemplarily synthesized via short and concise routes. The usefulness of these compounds was demonstrated in an in vitro assay with the ketoreductase domain MycKRB from mycolactone biosynthesis.
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Affiliation(s)
- Johannes Wunderlich
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Theresa Roß
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Marius Schröder
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Frank Hahn
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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23
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Liu LL, Chen ZF, Liu Y, Tang D, Gao HH, Zhang Q, Gao JM. Molecular networking-based for the target discovery of potent antiproliferative polycyclic macrolactam ansamycins from Streptomyces cacaoi subsp. asoensis. Org Chem Front 2020. [DOI: 10.1039/d0qo00557f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular networking-based for the target discovery of potent antiproliferative polycyclic macrolactam ansamycins.
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Affiliation(s)
- Ling-Li Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Zhi-Fan Chen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Yao Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Dan Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Hua-Hua Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
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24
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Kornfuehrer T, Eustáquio AS. Diversification of polyketide structures via synthase engineering. MEDCHEMCOMM 2019; 10:1256-1272. [PMID: 32180918 PMCID: PMC7053703 DOI: 10.1039/c9md00141g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
| | - Alessandra S Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
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25
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Häckh M, Lucas X, Marolt M, Leadlay PF, Müller M, Günther S, Lüdeke S. Hidden Specificities in Enzyme Catalysis: Structural Basis of Substrate Structure‐Selectivity Relationship of a Ketoreductase. Chembiochem 2019; 20:1150-1154. [DOI: 10.1002/cbic.201800799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Matthias Häckh
- Institute of Pharmaceutical SciencesUniversity of Freiburg Albertstrasse 25 79104 Freiburg Germany
| | - Xavier Lucas
- Institute of Pharmaceutical SciencesUniversity of Freiburg Albertstrasse 25 79104 Freiburg Germany
- Present addressRoche Pharma Research and Early DevelopmentRoche Innovation Center 4070 Basel Switzerland
| | - Marija Marolt
- Institute of Pharmaceutical SciencesUniversity of Freiburg Albertstrasse 25 79104 Freiburg Germany
| | - Peter F. Leadlay
- Department of BiochemistryUniversity of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Michael Müller
- Institute of Pharmaceutical SciencesUniversity of Freiburg Albertstrasse 25 79104 Freiburg Germany
| | - Stefan Günther
- Institute of Pharmaceutical SciencesUniversity of Freiburg Albertstrasse 25 79104 Freiburg Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical SciencesUniversity of Freiburg Albertstrasse 25 79104 Freiburg Germany
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26
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Adamek M, Alanjary M, Ziemert N. Applied evolution: phylogeny-based approaches in natural products research. Nat Prod Rep 2019; 36:1295-1312. [DOI: 10.1039/c9np00027e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we highlight how phylogenetic analyses can be used to facilitate natural product discovery and structure elucidation.
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Affiliation(s)
- Martina Adamek
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| | | | - Nadine Ziemert
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
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27
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Kim MC, Machado H, Jang KH, Trzoss L, Jensen PR, Fenical W. Integration of Genomic Data with NMR Analysis Enables Assignment of the Full Stereostructure of Neaumycin B, a Potent Inhibitor of Glioblastoma from a Marine-Derived Micromonospora. J Am Chem Soc 2018; 140:10775-10784. [PMID: 30085661 DOI: 10.1021/jacs.8b04848] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, derivatization, X-ray diffraction analysis, synthesis, or other time-consuming approaches to assign the complete stereostructure. As an alternative approach, we sequenced the genome of the producing strain and identified the neaumycin gene cluster ( neu). By integrating the known stereospecificities of biosynthetic enzymes with comprehensive NMR analysis, the full stereostructure of neaumycin B was confidently assigned. This approach exemplifies how mining gene cluster information while integrating NMR-based structure data can achieve rapid, efficient, and accurate stereostructural assignments for complex macrolides.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Kyoung Hwa Jang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Lynnie Trzoss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Center for Microbiome Innovation , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Moores Comprehensive Cancer Center , University of California, San Diego , La Jolla , California 92093-0204 , United States
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28
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Zhang L, Ji J, Yuan M, Feng Y, Wang L, Deng Z, Bai L, Zheng J. Stereospecificity of Enoylreductase Domains from Modular Polyketide Synthases. ACS Chem Biol 2018; 13:871-875. [PMID: 29437374 DOI: 10.1021/acschembio.7b00982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An enoylreductase (ER) domain of a polyketide synthase module recruiting a methylmalonate extender unit sets the C2 methyl branch to either the S or R configuration during processing of a polyketide intermediate carried by an acyl carrier protein (ACP) domain. In the present study, pantetheine- and ACP-bound trans-2-methylcrotonyl substrate surrogates were used to scrutinize the stereospecificity of the ER domains. The pantetheine-bound thioester was reduced to mixtures of both 2 R and 2 S products, whereas the expected 2 S epimer was almost exclusively generated when the cognate ACP-bound substrate surrogate was utilized. The analogous incubation of an ER with the substrate surrogate carried by a noncognate ACP significantly increased the generation of the unexpected 2 R epimer, highlighting the dependence of stereospecificity on proper protein-protein interactions between ER and ACP domains. The ER mutant assays revealed the involvement of the conserved tyrosine and lysine in stereocontrol. Taken together, these results expand the current understanding of the ER stereochemistry and help in the engineering of modular PKSs.
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Affiliation(s)
- Luyun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junjie Ji
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, People’s Republic of China
| | - Meijuan Yuan
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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29
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Xie X, Garg A, Khosla C, Cane DE. Elucidation of the Cryptic Methyl Group Epimerase Activity of Dehydratase Domains from Modular Polyketide Synthases Using a Tandem Modules Epimerase Assay. J Am Chem Soc 2017; 139:9507-9510. [PMID: 28682630 DOI: 10.1021/jacs.7b05502] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dehydratase (DH) domains of cryptic function are often found in polyketide synthase (PKS) modules that produce epimerized (2S)-2-methyl-3-ketoacyl-ACP (acyl carrier protein) intermediates. A combination of tandem equilibrium isotope exchange (EIX) and a newly developed Tandem Modules Epimerase assay revealed the intrinsic epimerase activity of NanDH1 and NanDH5, from modules 1 and 5, respectively, of the nanchangmycin (1) PKS as well of NigDH1, from module 1 of the nigericin (3) PKS. Unexpectedly, all three epimerase-active DH domains were also found to possess intrinsic dehydratase activity, whereas the conventional DH domains, EryDH4, from module 4 of the erythromycin synthase, and NanDH2 from module 2 of the nanchangmycin synthase, were shown to have cryptic epimerase activity.
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Ashish Garg
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
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