1
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Hu Z, Gu D, Skyrud W, Du Y, Zhai R, Wang J, Zhang W. Engineered Biosynthesis and Anticancer Studies of Ring-Expanded Antimycin-Type Depsipeptides. ACS Synth Biol 2024; 13:1562-1571. [PMID: 38679882 PMCID: PMC11483242 DOI: 10.1021/acssynbio.4c00193] [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] [Indexed: 05/01/2024]
Abstract
Respirantins are 18-membered antimycin-type depsipeptides produced by Streptomyces sp. and Kitasatospora sp. These compounds have shown extraordinary anticancer activities against a panel of cancer cell lines with nanomolar levels of IC50 values. However, further investigation has been impeded by the low titers of the natural producers and the challenging chemical synthesis due to their structural complexity. The biosynthetic gene cluster (BGC) of respirantin was previously proposed based on a bioinformatic comparison of the four members of antimycin-type depsipeptides. In this study, we report the first successful reconstitution of respirantin in Streptomyces albus using a synthetic BGC. This heterologous system serves as an accessible platform for the production and diversification of respirantins. Through polyketide synthase pathway engineering, biocatalysis, and chemical derivatization, we generated nine respirantin compounds, including six new derivatives. Cytotoxicity screening against human MCF-7 and Hela cancer cell lines revealed a unique biphasic dose-response profile of respirantin. Furthermore, a structure-activity relationship study has elucidated the essential functional groups that contribute to its remarkable cytotoxicity. This work paves the way for respirantin-based anticancer drug discovery and development.
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Affiliation(s)
- Zhijuan Hu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou 310024, China
| | - Di Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Will Skyrud
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Juan Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
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2
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Wu Z, Xia Z, Tang Z, Li J, Liu W. Mutasynthesis generates nine new pyrroindomycins. Org Biomol Chem 2024; 22:2813-2818. [PMID: 38511276 DOI: 10.1039/d4ob00239c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Pyrroindomycins (PYRs) represent the only spirotetramate natural products discovered in nature, and possess potent activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Their unique structure and impressive biological activities make them attractive targets for synthesis and biosynthesis; however, the discovery and generation of new PYRs remains challenging. To date, only the initial components A and B have been reported. Herein, we report a mutasynthesis approach for the generation of nine new PYRs with varying acyl modifications on their deoxy-trisaccharide moieties. This was achieved by blocking the formation of the acyl group 1,8-dihydropyrrolo[2,3-b]indole (DHPI) via gene pyrK1 inactivation and supplying chemical acyl precursors. The gene pyrK1 encodes a DUF1864 family protein that probably catalyzes the oxidative transformation of L-tryptophan to DHPI, and its deletion results in the abolishment of DHPI-containing PYRs and the accumulation of three new PYRs either without acyl modification or with DHPI replaced by benzoic acid and pyrrole-2-carboxylic acid. Capitalizing on the capacity of the ΔpyrK1 mutant to produce new PYRs, we have successfully developed a mutasynthesis strategy for the generation of six novel PYR analogs with various aromatic acid modifications on their deoxy-trisaccharide moieties, showcasing the potential for generating structurally diverse PYRs. Overall, this research contributes significantly to understanding the biosynthesis of PYRs and offers valuable perspectives on their structural diversity.
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Affiliation(s)
- Zhuhua Wu
- National key Laboratory of Lead druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Copernicus Road, Shanghai 201203, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Zhengxiang Xia
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Pharmacy, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, 399 Middle Yan Chang Road, Shanghai, 200072, China
| | - Zhijun Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Ji'an Li
- National key Laboratory of Lead druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Copernicus Road, Shanghai 201203, China.
| | - Wen Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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3
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Tian W, Chen X, Zhang J, Zheng M, Wei G, Deng Z, Qu X. Biosynthesis of Tetronates by a Nonribosomal Peptide Synthetase-Polyketide Synthase System. Org Lett 2023; 25:1628-1632. [PMID: 36876998 DOI: 10.1021/acs.orglett.3c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
A cryptic tetronate biosynthetic pathway was identified in Kitasatospora niigatensis DSM 44781 via heterologous expression. Distinct from the currently known biosynthetic pathways, this system utilizes a partially functional nonribosomal peptide synthetase and a broadly selective polyketide synthase to direct the assembly and lactonization of the tetronate scaffold. By employing a permissive crotonyl-CoA reductase/carboxylase to provide different extender units, seven new tetronates (kitaniitetronins A-G) were obtained via precursor-directed biosynthesis.
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Affiliation(s)
- Wenya Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinru Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xudong Qu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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4
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Guo S, Sang Y, Zheng C, Xue XS, Tang Z, Liu W. Enzymatic α-Ketothioester Decarbonylation Occurs in the Assembly Line of Barbamide for Skeleton Editing. J Am Chem Soc 2023; 145:5017-5028. [PMID: 36821526 DOI: 10.1021/jacs.2c10277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The decarbonylation reaction has been developed significantly in organic chemistry as an effective approach to various synthetic applications, but enzymatic precedents for this reaction are rare. Based on investigations into the hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line of barbamide, we report an on-line α-ketothioester decarbonylation reaction that leads to one-carbon truncation of the elongating skeleton. This enzymatic editing reaction occurs in the first round of lipopeptide extension and modification involving the multienzymes BarE and BarF, which successively house an NRPS module to initiate the biosynthesis and a PKS module to catalyze the first round of chain extension. Starting with processing a leucine-derived α-ketoacyl starter, the ketosynthase domain in BarE displays an unusual dual activity that results in net one-carbon chain elongation. It extrudes carbon monoxide from α-keto-isocaproyl thioester and then mediates decarboxylative condenses of the resultant isovaleryl thioester with malonyl thioester to form a diketide intermediate, followed by BarF-based O-methylation to stabilize the enol form of the β-carbonyl and afford an unusual E-double bond. Biochemical characterization, chemical synthesis, computational analysis, and the experimental outcome of site-directed mutagenesis illustrate the extraordinary catalytic capability of this ketosynthase domain. This work furthers the appreciation of assembly line chemistry and opens the door to new approaches for skeleton editing/engineering of related molecules using synthetic biology approaches.
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Affiliation(s)
- Shengjie Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yueqian Sang
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Song Xue
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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5
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Zheng M, Zhang J, Zhang W, Yang L, Yan X, Tian W, Liu Z, Lin Z, Deng Z, Qu X. An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold. Angew Chem Int Ed Engl 2022; 61:e202208734. [DOI: 10.1002/anie.202208734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Lu Yang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xiaoli Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zhihao Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
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6
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Zheng M, Zhang J, Zhang W, Yang L, Yan X, Tian W, Liu Z, Lin Z, Deng Z, Qu X. An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mengmeng Zheng
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Jun Zhang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Wan Zhang
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Lu Yang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xiaoli Yan
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Wenya Tian
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zhihao Liu
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhi Lin
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zixin Deng
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xudong Qu
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology 800 Dongchuan Rd. 200240 Shanghai CHINA
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7
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Gu D, Zhang W. Engineered biosynthesis of alkyne-tagged polyketides. Methods Enzymol 2022; 665:347-373. [PMID: 35379442 PMCID: PMC9829517 DOI: 10.1016/bs.mie.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polyketides have demonstrated their significance as therapeutics, industrial products, pesticides, and biological probes following intense study over the past decades. Tagging polyketides with a bioorthogonal functionality enables various applications such as diversification, quantification, visualization and mode-of-action elucidation. The terminal alkyne moiety, as a small, stable and highly selective clickable functionality, is widely adopted in tagging natural products. De novo biosynthesis of alkyne-tagged polyketides offers the unique advantage of reducing the background from feeding the biorthogonal moiety itself, leading to the accomplishment of in situ generation of a clickable functionality for bioorthogonal reactions. Here, we introduce several engineering strategies to apply terminal alkyne biosynthetic machinery, represented by JamABC, which produces a short terminal alkyne-bearing fatty acyl chain on a carrier protein, to functions with different downstream polyketide synthases (PKSs). Successful results in engineering type III and type I PKSs provide engineering guidelines and strategies that are applicable to additional PKSs to produce targeted alkyne-tagged metabolites for chemical and biological applications.
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Affiliation(s)
- Di Gu
- Department of Chemistry, University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States,Chan Zuckerberg Biohub, San Francisco, CA, United States,Corresponding author:
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8
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Popov KK, Campbell JLP, Kysilka O, Hošek J, Davies CD, Pour M, Kočovský P. Reductive Amination Revisited: Reduction of Aldimines with Trichlorosilane Catalyzed by Dimethylformamide─Functional Group Tolerance, Scope, and Limitations. J Org Chem 2021; 87:920-943. [PMID: 34841878 DOI: 10.1021/acs.joc.1c01561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aldimines, generated in situ from aliphatic, aromatic, and heteroaromatic aldehydes and aliphatic, aromatic, and heteroaromatic primary or secondary amines, can be reduced with trichlorosilane in the presence of dimethylformamide (DMF) as an organocatalyst (≤10 mol %) in toluene or CH2Cl2 at room temperature. The reduction tolerates ketone carbonyls, esters, amides, nitriles, sulfones, sulfonamides, NO2, SF5, and CF3 groups, boronic esters, azides, phosphine oxides, C═C and C≡C bonds, and ferrocenyl nucleus, but sulfoxides and N-oxides are reduced. α,β-Unsaturated aldimines undergo 1,2-reduction only, leaving the C═C bond intact. N-Monoalkylation of primary amines is attained with a 1:1 aldehyde to amine ratio, whereas excess of the aldehyde (≥2:1) allows second alkylation, giving rise to tertiary amines. Reductive N-alkylation of α-amino acids proceeds without racemization; the resulting products, containing a C≡C bond or N3 group, are suitable for click chemistry. This reaction thus offers advantages over the traditional methods (borohydride reduction or catalytic hydrogenation) in terms of efficiency and chemoselectivity. Solubility of some of the reacting partners appears to be the only limitation. The byproducts generated by the workup with aqueous NaHCO3 (i.e., NaCl and silica) are environmentally benign. As a greener alternative, DMA can be employed as a catalyst instead of DMF.
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Affiliation(s)
- Kirill K Popov
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43 Prague 2, Czech Republic
| | - Joanna L P Campbell
- Syngenta, Grangemouth Manufacturing Centre, Earl's Road, Grangemouth FK3 8XG, U.K
| | - Ondřej Kysilka
- Trelleborg Bohemia, Akademika Bedrny 531/8a, Věkoše, 500 03 Hradec Králové Czech Republic
| | - Jan Hošek
- Farmak, Na vlčinci 16/3, Klášterní Hradisko, 77900 Olomouc, Czech Republic
| | | | - Milan Pour
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Pavel Kočovský
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43 Prague 2, Czech Republic.,Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic
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9
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Zhang J, Zheng M, Yan J, Deng Z, Zhu D, Qu X. A Permissive Medium Chain Acyl-CoA Carboxylase Enables the Efficient Biosynthesis of Extender Units for Engineering Polyketide Carbon Scaffolds. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jun Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayan Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
| | - Dongqing Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Li X, Lv JM, Hu D, Abe I. Biosynthesis of alkyne-containing natural products. RSC Chem Biol 2021; 2:166-180. [PMID: 34458779 PMCID: PMC8341276 DOI: 10.1039/d0cb00190b] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Alkyne-containing natural products are important molecules that are widely distributed in microbes and plants. Inspired by the advantages of acetylenic products used in the fields of medicinal chemistry, organic synthesis and material science, great efforts have focused on discovering the biosynthetic enzymes and pathways for alkyne formation. Here, we summarize the biosyntheses of alkyne-containing natural products and introduce de novo biosynthetic strategies for alkyne-tagged compound production.
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Affiliation(s)
- Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
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11
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Baldassari LL, Mantovani AC, Jardim M, Maryasin B, Lüdtke DS. Meyer–Schuster-type rearrangement for the synthesis of α-selanyl-α,β-unsaturated thioesters. Chem Commun (Camb) 2021; 57:117-120. [DOI: 10.1039/d0cc07019j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A new approach to prepare α-selanyl-α,β-unsaturated thioesters from propargylthioalkynes and an electrophilic selenium species is reported.
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Affiliation(s)
- Lucas L. Baldassari
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- UFRGS
- Porto Alegre
- Brazil
| | - Anderson C. Mantovani
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- UFRGS
- Porto Alegre
- Brazil
| | - Micaela Jardim
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- UFRGS
- Porto Alegre
- Brazil
| | - Boris Maryasin
- Institute of Organic Chemistry
- University of Vienna
- 1090 Vienna
- Austria
- Institute of Theoretical Chemistry
| | - Diogo S. Lüdtke
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- UFRGS
- Porto Alegre
- Brazil
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12
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Lv J, Gao Y, Zhao H, Awakawa T, Liu L, Chen G, Yao X, Hu D, Abe I, Gao H. Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian‐Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan University Guangzhou 510632 P. R. China
| | - Yao‐Hui Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Huan Zhao
- College of Traditional Chinese Medicine Jinan University Guangzhou 510632 P. R. China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ling Liu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 P. R. China
| | - Guo‐Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Xin‐Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
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13
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Lv J, Gao Y, Zhao H, Awakawa T, Liu L, Chen G, Yao X, Hu D, Abe I, Gao H. Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation. Angew Chem Int Ed Engl 2020; 59:13531-13536. [DOI: 10.1002/anie.202004364] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Jian‐Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan University Guangzhou 510632 P. R. China
| | - Yao‐Hui Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Huan Zhao
- College of Traditional Chinese Medicine Jinan University Guangzhou 510632 P. R. China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ling Liu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 P. R. China
| | - Guo‐Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Xin‐Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
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14
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Porterfield WB, Poenateetai N, Zhang W. Engineered Biosynthesis of Alkyne-Tagged Polyketides by Type I PKSs. iScience 2020; 23:100938. [PMID: 32146323 PMCID: PMC7063234 DOI: 10.1016/j.isci.2020.100938] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 01/20/2023] Open
Abstract
Polyketides produced by modular polyketide synthases (PKSs) are important small molecules widely used as drugs, pesticides, and biological probes. Tagging these polyketides with a clickable functionality enables the visualization, diversification, and mode of action study through bio-orthogonal chemistry. We report the de novo biosynthesis of alkyne-tagged polyketides by modular type I PKSs through starter unit engineering. Specifically, we use JamABC, a terminal alkyne biosynthetic machinery from the jamaicamide B biosynthetic pathway, in combination with representative modular PKSs. We demonstrate that JamABC works as a trans loading system for engineered type I PKSs to produce alkyne-tagged polyketides. In addition, the production efficiency can be improved by enhancing the interactions between the carrier protein (JamC) and PKSs using docking domains and site-directed mutagenesis of JamC. This work thus provides engineering guidelines and strategies that are applicable to additional modular type I PKSs to produce targeted alkyne-tagged metabolites for chemical and biological applications. Alkyne-tagged polyketides are de novo biosynthesized using type I PKSs Docking domains and ACP mutagenesis improve alkyne starter unit translocation Docking domains, but not ACP mutagenesis, perturb alkyne biosynthetic machinery
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Affiliation(s)
- William B Porterfield
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA
| | - Nannalin Poenateetai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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15
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Martínez-Bailén M, Galbis E, Carmona AT, de-Paz MV, Robina I. Preparation of water-soluble glycopolymers derived from five-membered iminosugars. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Seidel J, Miao Y, Porterfield W, Cai W, Zhu X, Kim SJ, Hu F, Bhattarai-Kline S, Min W, Zhang W. Structure-activity-distribution relationship study of anti-cancer antimycin-type depsipeptides. Chem Commun (Camb) 2019; 55:9379-9382. [PMID: 31317975 PMCID: PMC6675640 DOI: 10.1039/c9cc03051d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Small-molecule natural products have been an essential source of pharmaceuticals to treat human diseases, but very little is known about their behavior inside dynamic, live human cells. Here, we demonstrate the first structure-activity-distribution relationship (SADR) study of complex natural products, the anti-cancer antimycin-type depsipeptides, using the emerging bioorthogonal Stimulated Raman Scattering (SRS) Microscopy. Our results show that the intracellular enrichment and distribution of these compounds are driven by their potency and specific protein targets, as well as the lipophilic nature of compounds.
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Affiliation(s)
- Jeremy Seidel
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Yupeng Miao
- Department of Chemistry, Columbia University, NY 10025, USA
| | - William Porterfield
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Xuejun Zhu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Seong-Jong Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Fanghao Hu
- Department of Chemistry, Columbia University, NY 10025, USA
| | - Santi Bhattarai-Kline
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Wei Min
- Department of Chemistry, Columbia University, NY 10025, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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17
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Mo J, Wang S, Zhang W, Li C, Deng Z, Zhang L, Qu X. Efficient editing DNA regions with high sequence identity in actinomycetal genomes by a CRISPR-Cas9 system. Synth Syst Biotechnol 2019; 4:86-91. [PMID: 30891508 PMCID: PMC6403111 DOI: 10.1016/j.synbio.2019.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 11/28/2022] Open
Abstract
Actinobacteria able to produce varieties of bioactive natural products have been long appreciated by the field of drug discovery and development. Recently, a few of CRISPR/Cas9 systems bearing different types of replicons (pSG5 and pIJ101) were developed to efficiently edit their genomes. Despite wide application in gene editing, their utility in editing challenging DNA regions e.g. high sequence identity has not been compared. In this study, we confirmed that the widely used temperature-sensitive pSG5 replicon is indeed not suitable for editing modular polyketide synthase (PKS) genes due to causing unpredicted gene recombination. This problem can be addressed by replacing the pSG5 with the segregationally unstable pIJ101 replicon. By introducing a counter-selection marker CodA, convenient cloning sites in the single guide RNAs (sgRNAs) and homologous template scaffolds, we developed a new CRISPR-Cas9 system pMWCas9. This system was successfully used to delete/replace erythromycin PKS and other biosynthetic genes in Saccharopolyspora erythraea and Streptomyces sp. AL2110. By swapping the promoters of antB and antC with ermE and kasOp, we achieved a deacyl-antimycin hyper producer which produces a 9-fold higher yield than the original Streptomyces sp. AL2110 strain. Our results provide a robust and useful Cas9 tool for genetic studies in Actinobacteria.
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Affiliation(s)
- Jingjun Mo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Chunyu Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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18
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Albumycin, a new isoindolequinone from Streptomyces albus J1074 harboring the fluostatin biosynthetic gene cluster. J Antibiot (Tokyo) 2019; 72:311-315. [DOI: 10.1038/s41429-019-0161-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 01/20/2023]
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19
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Zhang D, Zhang F, Liu W. A KAS-III Heterodimer in Lipstatin Biosynthesis Nondecarboxylatively Condenses C 8 and C 14 Fatty Acyl-CoA Substrates by a Variable Mechanism during the Establishment of a C 22 Aliphatic Skeleton. J Am Chem Soc 2019; 141:3993-4001. [PMID: 30763089 DOI: 10.1021/jacs.8b12843] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Ketoacyl-acyl carrier protein synthase-III (KAS-III) and its homologues are thiolase-fold proteins that typically behave as homodimers functioning in diverse thioester-based reactions for C-C, C-O, or C-N bond formation. Here, we report an exception observed in the biosynthesis of lipstatin. During the establishment of the C22 aliphatic skeleton of this β-lactone lipase inhibitor, LstA and LstB, which both are KAS-III homologues but phylogenetically distinct from each other, function together by forming an unusual heterodimer to catalyze a nondecarboxylating Claisen condensation of C8 and C14 fatty acyl-CoA substrates. The resulting C22 α-alkyl β-ketoacid, which is unstable and tends to be spontaneously decarboxylated to a shunt C21 hydrocarbon product, is transformed by the stereoselective β-ketoreductase LstD into a relatively stable C22 α-alkyl β-hydroxyacid for further transformation. LstAB activity tolerates changes in the stereochemistry, saturation degree, and thioester form of both long-chain fatty acyl-CoA substrates. This flexibility, along with the characterization of catalytic residues, benefits our investigations into the individual roles of the two KAS-III homologues in the heterodimer-catalyzed reactions. The large subunit LstA contains a characteristic Cys-His-Asn triad and likely reacts with C8 acyl-CoA to form an acyl-Cys enzyme intermediate. In contrast, the small subunit LstB lacks this triad but possesses a catalytic Glu residue, which can act on the C8 acyl-Cys enzyme intermediate in a substrate-dependent manner, either as a base for Cα deprotonation or as a nucleophile for a Michael-type addition-initiated cascade reaction, to produce an enolate anion for head-to-head assembly with C14 acyl-CoA through a unidirectional nucleophilic substitution. Uncovering LstAB catalysis draws attention to thiolase-fold proteins that are noncanonical in both active form and catalytic reaction/mechanism. LstAB homologues are widespread in bacteria and remain to be functionally assigned, generating great interest in their corresponding products and associated biological functions.
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Affiliation(s)
- Daozhong Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , University of Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Fang Zhang
- Innovation Research Institute of Traditional Chinese Medicine , Shanghai University of Traditional Chinese Medicine , 1200 Cailun Road , Shanghai 201203 , China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , University of Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China.,Huzhou Center of Bio-Synthetic Innovation , 1366 Hongfeng Road , Huzhou 313000 , China
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20
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Hamada C, Usuki Y, Takeuchi D, Ogawa H, Abe R, Satoh T. Total Syntheses and Configuration Assignments of JBIR-06 and Related Depsipeptides. Org Lett 2019; 21:965-968. [DOI: 10.1021/acs.orglett.8b03944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chie Hamada
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Yoshinosuke Usuki
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Daiki Takeuchi
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Hikaru Ogawa
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Ryota Abe
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Tetsuya Satoh
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
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21
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Yan Y, Liu Q, Jacobsen SE, Tang Y. The impact and prospect of natural product discovery in agriculture: New technologies to explore the diversity of secondary metabolites in plants and microorganisms for applications in agriculture. EMBO Rep 2018; 19:embr.201846824. [PMID: 30361392 DOI: 10.15252/embr.201846824] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Qikun Liu
- Department of Molecular, Cell, and Developmental Biology, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
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22
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Jiang G, Zuo R, Zhang Y, Powell MM, Zhang P, Hylton SM, Loria R, Ding Y. One-Pot Biocombinatorial Synthesis of Herbicidal Thaxtomins. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Magan M. Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Peilan Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Sarah M. Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
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23
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Reprogramming of the antimycin NRPS-PKS assembly lines inspired by gene evolution. Nat Commun 2018; 9:3534. [PMID: 30166552 PMCID: PMC6117356 DOI: 10.1038/s41467-018-05877-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/01/2018] [Indexed: 11/09/2022] Open
Abstract
Reprogramming of the NRPS/PKS assembly line is an attractive method for the production of new bioactive molecules. However, it is usually hampered by the loss of intimate domain/module interactions required for the precise control of chain transfer and elongation reactions. In this study, we first establish heterologous expression systems of the unique antimycin-type cyclic depsipeptides: JBIR-06 (tri-lactone) and neoantimycin (tetra-lactone), and engineer their biosyntheses by taking advantage of bioinformatic analyses and evolutionary insights. As a result, we successfully accomplish three manipulations: (i) ring contraction of neoantimycin (from tetra-lactone to tri-lactone), (ii) ring expansion of JBIR-06 (from tri-lactone to tetra-lactone), and (iii) alkyl chain diversification of JBIR-06 by the incorporation of various alkylmalonyl-CoA extender units, to generate a set of unnatural derivatives in practical yields. This study presents a useful strategy for engineering NRPS-PKS module enzymes, based on nature’s diversification of the domain and module organizations. Modifying the non-ribosomal peptide synthase (NRPS)/polyketide synthase (PKS) pathway to generate novel non-ribosomal peptides often results in a loss of productivity. Here the authors use evolutionary alignments of NRPS/PKS gene clusters to guide rational design of complexes that can produce novel lactones.
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24
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Zhou Y, Lin X, Williams SR, Liu L, Shen Y, Wang SP, Sun F, Xu S, Deng H, Leadlay PF, Lin HW. Directed Accumulation of Anticancer Depsipeptides by Characterization of Neoantimycins Biosynthetic Pathway and an NADPH-Dependent Reductase. ACS Chem Biol 2018; 13:2153-2160. [PMID: 29979567 DOI: 10.1021/acschembio.8b00325] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neoantimycins (NATs) are members of antimycin-types of depsipeptides with outstanding anticancer activities. We isolated NAT-A (1) and -F (2) from the fermentation extract of Streptomyces conglobatus. The NAT biosynthetic gene cluster ( nat BGC) was identified by genome sequencing and bioinformatics analysis. nat BGC includes two nonribosomal peptide synthetase (NRPS) and one polyketide synthase (PKS) gene, and a gene cassette (10 genes), of which the encoded enzymes share high homology to the ones responsible for 3-formamidosalicylate (3-FAS) biosynthesis in the antimycin biosynthetic pathway. Heterologous expression of the partial nat BGC without the 3-FAS gene cassette in the antimycin producer, Streptomyces albus J1074, results in the production of 1 and 2, suggesting that the nat BGC indeed directs NATs biosynthesis. Targeted in-frame deletion of the reductase gene ( natE) abolished the production of 1 and 2 but accumulated two NAT derivatives, the known NAT-H (3) and a new NAT-I (4). Biochemical verification demonstrated that the recombinant NatE indeed catalyzes an NADPH-dependent reaction of 3 or 4 to 1 or 2, respectively. Compound 3 presented significantly stronger activities against eight cancer cell lines than the ones using cisplatin, the clinical chemotherapy medicine. In particular, 3 displayed 559- and 57-fold higher activity toward human melanoma and cervix epidermoid carcinoma cells, respectively, compared with cisplatin. The new derivative, 4, was 1.5- to 10.9-fold more active than cisplatin toward five cancer cell lines. The evaluation of NATs biosynthesis depicted here will pave the way to generate new NAT derivatives through rational pathway engineering.
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Affiliation(s)
- Yongjun Zhou
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao Lin
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Simon R. Williams
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Liyun Liu
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yaoyao Shen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shu-Ping Wang
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Sun
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shihai Xu
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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25
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Pramanik S, Rej S, Kando S, Tsurugi H, Mashima K. Organosilicon Reducing Reagents for Stereoselective Formations of Silyl Enol Ethers from α-Halo Carbonyl Compounds. J Org Chem 2018; 83:2409-2417. [DOI: 10.1021/acs.joc.7b03005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman Pramanik
- Department of Chemistry,
Graduate School
of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Supriya Rej
- Department of Chemistry,
Graduate School
of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Shun Kando
- Department of Chemistry,
Graduate School
of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Hayato Tsurugi
- Department of Chemistry,
Graduate School
of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Kazushi Mashima
- Department of Chemistry,
Graduate School
of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
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26
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Li G, Lou HX. Strategies to diversify natural products for drug discovery. Med Res Rev 2017; 38:1255-1294. [PMID: 29064108 DOI: 10.1002/med.21474] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/18/2017] [Accepted: 09/28/2017] [Indexed: 12/11/2022]
Abstract
Natural product libraries contain specialized metabolites derived from plants, animals, and microorganisms that play a pivotal role in drug discovery due to their immense structural diversity and wide variety of biological activities. The strategies to greatly extend natural product scaffolds through available biological and chemical approaches offer unique opportunities to access a new series of natural product analogues, enabling the construction of diverse natural product-like libraries. The affordability of these structurally diverse molecules has been a crucial step in accelerating drug discovery. This review provides an overview of various approaches to exploit the diversity of compounds for natural product-based drug development, drawing upon a series of examples to illustrate each strategy.
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Affiliation(s)
- Gang Li
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China
| | - Hong-Xiang Lou
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China.,Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
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27
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Dhakal D, Sohng JK. Coalition of Biology and Chemistry for Ameliorating Antimicrobial Drug Discovery. Front Microbiol 2017; 8:734. [PMID: 28522993 PMCID: PMC5415603 DOI: 10.3389/fmicb.2017.00734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon UniversityAsan-si, South Korea
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28
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 554] [Impact Index Per Article: 79.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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29
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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30
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Zhang MM, Qiao Y, Ang EL, Zhao H. Using natural products for drug discovery: the impact of the genomics era. Expert Opin Drug Discov 2017; 12:475-487. [PMID: 28277838 DOI: 10.1080/17460441.2017.1303478] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Evolutionarily selected over billions of years for their interactions with biomolecules, natural products have been and continue to be a major source of pharmaceuticals. In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging isolation, and low production titers. Propelled by advances in DNA sequencing and synthetic biology technologies, insights into microbial secondary metabolism provided have inspired a number of strategies to address these challenges. Areas covered: This review highlights the importance of genomics and metagenomics in natural product discovery, and provides an overview of the technical and conceptual advances that offer unprecedented access to molecules encoded by biosynthetic gene clusters. Expert opinion: Genomics and metagenomics revealed nature's remarkable biosynthetic potential and her vast chemical inventory that we can now prioritize and systematically mine for novel chemical scaffolds with desirable bioactivities. Coupled with synthetic biology and genome engineering technologies, significant progress has been made in identifying and predicting the chemical output of biosynthetic gene clusters, as well as in optimizing cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.
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Affiliation(s)
- Mingzi M Zhang
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Yuan Qiao
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Ee Lui Ang
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Huimin Zhao
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore.,b Department of Chemical and Biomolecular Engineering , University of Illinois at Urbana-Champaign , Urbana , IL , USA
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31
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Zhang W, Che Q, Tan H, Qi X, Li J, Li D, Gu Q, Zhu T, Liu M. Marine Streptomyces sp. derived antimycin analogues suppress HeLa cells via depletion HPV E6/E7 mediated by ROS-dependent ubiquitin-proteasome system. Sci Rep 2017; 7:42180. [PMID: 28176847 PMCID: PMC5296914 DOI: 10.1038/srep42180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/06/2017] [Indexed: 12/26/2022] Open
Abstract
Four new antimycin alkaloids (1–4) and six related known analogs (5–10) were isolated from the culture of a marine derived Streptomyces sp. THS-55, and their structures were elucidated by extensive spectroscopic analysis. All of the compounds exhibited potent cytotoxicity in vitro against HPV-transformed HeLa cell line. Among them, compounds 6–7 were derived as natural products for the first time, and compound 5 (NADA) showed the highest potency. NADA inhibited the proliferation, arrested cell cycle distribution, and triggered apoptosis in HeLa cancer cells. Our molecular mechanic studies revealed NADA degraded the levels of E6/E7 oncoproteins through ROS-mediated ubiquitin-dependent proteasome system activation. This is the first report that demonstrates antimycin alkaloids analogue induces the degradation of high-risk HPV E6/E7 oncoproteins and finally induces apoptosis in cervical cancer cells. The present work suggested that these analogues could serve as lead compounds for the development of HPV-infected cervical cancer therapeutic agents, as well as research tools for the study of E6/E7 functions.
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Affiliation(s)
- Weiyi Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China
| | - Hongsheng Tan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Xin Qi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, 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, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China
| | - Ming Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China
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32
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Ray L, Valentic TR, Miyazawa T, Withall DM, Song L, Milligan JC, Osada H, Takahashi S, Tsai SC, Challis GL. A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. Nat Commun 2016; 7:13609. [PMID: 28000660 PMCID: PMC5187497 DOI: 10.1038/ncomms13609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters. X-ray crystal structures of the unusual β-subunit of the acyl-CoA carboxylase (YCC) responsible for this reaction, alone and in complex with hexanoyl-CoA, reveal the molecular basis for substrate recognition, inspiring the development of methodology for polyketide bio-orthogonal tagging via incorporation of 6-azidohexanoic acid and 8-nonynoic acid into novel stambomycin analogues.
Polyketides are typically assembled from a starter unit and malonyl- and/or methylmalonyl-CoA-derived extender units, but the macrolide antibiotics stambomycins incorporate non-standard alkylmalonyl-CoA extender units. Here, the authors describe the biosynthetic pathway responsible for this unusual synthesis.
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Affiliation(s)
- Lauren Ray
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy R Valentic
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - David M Withall
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jacob C Milligan
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Shiou-Chuan Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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33
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Coordinate Regulation of Antimycin and Candicidin Biosynthesis. mSphere 2016; 1:mSphere00305-16. [PMID: 27981234 PMCID: PMC5143413 DOI: 10.1128/msphere.00305-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/11/2016] [Indexed: 12/14/2022] Open
Abstract
Natural products produced by members of the phylum Actinobacteria underpin many industrially and medically important compounds; however, the majority of the ~30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. Understanding the diversity of regulatory strategies controlling the expression of these pathways is therefore critical if their biosynthetic potential is to be explored for new drug leads. Our findings reveal that the candicidin cluster-situated regulator FscRI coordinately controls the biosynthesis of both candicidin and antimycin, which is the first observation of cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products. We anticipate that this will emerge as a major strategy by which members of the phylum Actinobacteria coordinately produce natural products, which will advance our understanding of how the expression of secondary metabolism is controlled and will aid the pursuit of “silent” biosynthetic pathway activation. Streptomyces species produce an incredible array of high-value specialty chemicals and medicinal therapeutics. A single species typically harbors ~30 biosynthetic pathways, but only a few them are expressed in the laboratory; thus, poor understanding of how natural-product biosynthesis is regulated is a major bottleneck in drug discovery. Antimycins are a large family of anticancer compounds widely produced by Streptomyces species, and their regulation is atypical compared to that of most other natural products. Here we demonstrate that antimycin production by Streptomyces albus S4 is regulated by FscRI, a PAS-LuxR family cluster-situated regulator of the polyene antifungal agent candicidin. We report that heterologous production of antimycins by Streptomyces coelicolor is dependent on FscRI and show that FscRI activates the transcription of key biosynthetic genes. We also demonstrate through chromatin immunoprecipitation sequencing that FscRI regulation is direct, and we provide evidence that this regulation strategy is conserved and unique to short-form antimycin gene clusters. Our study provides direct in vivo evidence of the cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products and expands the paradigmatic understanding of the regulation of secondary metabolism. IMPORTANCE Natural products produced by members of the phylum Actinobacteria underpin many industrially and medically important compounds; however, the majority of the ~30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. Understanding the diversity of regulatory strategies controlling the expression of these pathways is therefore critical if their biosynthetic potential is to be explored for new drug leads. Our findings reveal that the candicidin cluster-situated regulator FscRI coordinately controls the biosynthesis of both candicidin and antimycin, which is the first observation of cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products. We anticipate that this will emerge as a major strategy by which members of the phylum Actinobacteria coordinately produce natural products, which will advance our understanding of how the expression of secondary metabolism is controlled and will aid the pursuit of “silent” biosynthetic pathway activation.
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34
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Zhu X, Shieh P, Su M, Bertozzi CR, Zhang W. A fluorogenic screening platform enables directed evolution of an alkyne biosynthetic tool. Chem Commun (Camb) 2016; 52:11239-42. [PMID: 27561030 DOI: 10.1039/c6cc05990b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Directed evolution was used to improve the activity of JamB, a membrane-bound bifunctional desaturase/acetylenase. To quickly assess the protein engineering outcomes, we developed a new platform for quantifying extracellular alkyne-tagged metabolites through a fluorogenic click reaction. Random mutagenesis yielded the best JamB variant with ∼20-fold increased activity in E. coli.
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Affiliation(s)
- Xuejun Zhu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94704, USA
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35
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Chen M, Liu J, Duan P, Li M, Liu W. Biosynthesis and molecular engineering of templated natural products. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Panpan Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mulin Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, Huzhou 313000, China
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36
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Lin Z, Chen D, Liu W. Biosynthesis-based artificial evolution of microbial natural products. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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37
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King JR, Edgar S, Qiao K, Stephanopoulos G. Accessing Nature's diversity through metabolic engineering and synthetic biology. F1000Res 2016; 5. [PMID: 27081481 PMCID: PMC4813638 DOI: 10.12688/f1000research.7311.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.
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Affiliation(s)
- Jason R King
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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38
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Yang Y, Zhou H, Du G, Feng K, Feng T, Fu X, Liu J, Zeng Y. A Monooxygenase from
Boreostereum vibrans
Catalyzes Oxidative Decarboxylation in a Divergent Vibralactone Biosynthesis Pathway. Angew Chem Int Ed Engl 2016; 55:5463-6. [PMID: 27007916 DOI: 10.1002/anie.201510928] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/09/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Yan‐Long Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Gang Du
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke‐Na Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Tao Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Xiao‐Li Fu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
| | - Ji‐Kai Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
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39
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Yang Y, Zhou H, Du G, Feng K, Feng T, Fu X, Liu J, Zeng Y. A Monooxygenase from
Boreostereum vibrans
Catalyzes Oxidative Decarboxylation in a Divergent Vibralactone Biosynthesis Pathway. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510928] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yan‐Long Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Gang Du
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke‐Na Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Tao Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Xiao‐Li Fu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
| | - Ji‐Kai Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
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40
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Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
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Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
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41
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Kundert J, Gulder TAM. Erweiterung der Strukturvielfalt von Polyketiden durch Einsatz modifizierter Carboxylase/Reduktase-Enzyme. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jana Kundert
- Biosystems Chemistry; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Tobias A. M. Gulder
- Biosystems Chemistry; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
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42
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Han M, Yin H, Zou Y, Brock NL, Huang T, Deng Z, Chu Y, Lin S. An Acyl Transfer Reaction Catalyzed by an Epimerase MarH. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mo Han
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Haixing Yin
- Sichuan
Industrial Institute of Antibiotics, Chengdu University, 168 Huaguan
Road, Chengdu 610052, China
| | - Yi Zou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Nelson L. Brock
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiwen Chu
- Sichuan
Industrial Institute of Antibiotics, Chengdu University, 168 Huaguan
Road, Chengdu 610052, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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43
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Liu J, Zhu X, Kim SJ, Zhang W. Antimycin-type depsipeptides: discovery, biosynthesis, chemical synthesis, and bioactivities. Nat Prod Rep 2016; 33:1146-65. [DOI: 10.1039/c6np00004e] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review discusses the isolation, structural variation, biosynthesis, chemical synthesis, and biological activities of antimycin-type depsipeptides.
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Affiliation(s)
- Joyce Liu
- Department of Bioengineering
- University of California
- Berkeley
- USA
| | - Xuejun Zhu
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
| | - Seong Jong Kim
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
- Physical Biosciences Division
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44
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Wang S, Zheng Q, Wang J, Chen D, Yu Y, Liu W. Concurrent modifications of the C-terminus and side ring of thiostrepton and their synergistic effects with respect to improving antibacterial activities. Org Chem Front 2016. [DOI: 10.1039/c5qo00433k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Five new C-terminally methylated TSR derivatives that varied in side-ring structure were obtained via the chemical feeding of quinaldic acid analogs to a double-mutant strain ΔtsrB/T.
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Affiliation(s)
- Shoufeng Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Jianfeng Wang
- Department of Infectious Diseases
- Sir Run Run Shaw Hospital
- College of Medicine
- Zhejiang University
- Hangzhou
| | - Dandan Chen
- Huzhou Center of Bio-Synthetic Innovation
- Huzhou 313000
- China
| | - Yunsong Yu
- Department of Infectious Diseases
- Sir Run Run Shaw Hospital
- College of Medicine
- Zhejiang University
- Hangzhou
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
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45
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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46
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Kundert J, Gulder TAM. Extending Polyketide Structural Diversity by Using Engineered Carboxylase/Reductase Enzymes. Angew Chem Int Ed Engl 2015; 55:858-60. [DOI: 10.1002/anie.201510402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Jana Kundert
- Biosystems Chemistry, Center for Integrated Protein Science Munich (CIPSM) at the; Department of Chemistry; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
| | - Tobias A. M. Gulder
- Biosystems Chemistry, Center for Integrated Protein Science Munich (CIPSM) at the; Department of Chemistry; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
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47
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Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 2015; 11:649-59. [PMID: 26284672 DOI: 10.1038/nchembio.1893] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022]
Abstract
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
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48
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Zhang L, Mori T, Zheng Q, Awakawa T, Yan Y, Liu W, Abe I. Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13462-5. [DOI: 10.1002/anie.201506899] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Qingfei Zheng
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yan Yan
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Wen Liu
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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49
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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50
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Zhang L, Mori T, Zheng Q, Awakawa T, Yan Y, Liu W, Abe I. Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Qingfei Zheng
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yan Yan
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Wen Liu
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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