1
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Liu W, Zhai S, Zhang L, Chen Y, Liu Z, Ma W, Zhang T, Zhang W, Ma L, Zhang C, Zhang W. Expanding the Chemical Diversity of Grisechelins via Heterologous Expression. JOURNAL OF NATURAL PRODUCTS 2024; 87:371-380. [PMID: 38301035 DOI: 10.1021/acs.jnatprod.3c01132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Thiazole scaffold-based small molecules exhibit a range of biological activities and play important roles in drug discovery. Based on bioinformatics analysis, a putative biosynthetic gene cluster (BGC) for thiazole-containing compounds was identified from Streptomyces sp. SCSIO 40020. Heterologous expression of this BGC led to the production of eight new thiazole-containing compounds, grisechelins E, F, and I-N (1, 2, 5-10), and two quinoline derivatives, grisechelins G and H (3 and 4). The structures of 1-10, including their absolute configurations, were elucidated by HRESIMS, NMR spectroscopic data, ECD calculations, and single-crystal X-ray diffraction analysis. Grisechelin F (2) is a unique derivative, distinguished by the presence of a salicylic acid moiety. The biosynthetic pathway for 2 was proposed based on bioinformatics analysis and in vivo gene knockout experiments. Grisechelin E (1) displayed moderate antimycobacterial activity against Mycobacterium tuberculosis H37Ra (MIC of 8 μg mL-1).
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Affiliation(s)
- Wei Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- Department of Clinical Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 96 Dongchuan Road, Guangzhou 510080, People's Republic of China
| | - Shilan Zhai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 100 Central Xianlie Road, Guangzhou 510070, People's Republic of China
| | - Zhiyong Liu
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou 510530, People's Republic of China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangzhou National Laboratory, Guangzhou 510005, People's Republic of China
| | - Wanli Ma
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou 510530, People's Republic of China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
| | - Tianyu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangzhou National Laboratory, Guangzhou 510005, People's Republic of China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 100 Central Xianlie Road, Guangzhou 510070, People's Republic of China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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2
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Guo MX, Zhang MM, Sun K, Cui JJ, Liu YC, Gao K, Dong SH, Luo S. Genome Mining of Linaridins Provides Insights into the Widely Distributed LinC Oxidoreductases. JOURNAL OF NATURAL PRODUCTS 2023; 86:2333-2341. [PMID: 37819880 DOI: 10.1021/acs.jnatprod.3c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Linaridins are a family of underexplored ribosomally synthesized and post-translationally modified peptides despite the prevalence of their biosynthetic gene clusters (BGCs) in microbial genomes, as shown by bioinformatic studies. Our genome mining efforts reveal that 96 putative oxidoreductase genes, namely, LinC, are encoded in linaridin BGCs. We heterologously expressed two such LinC-containing linaridin BGCs, yan and ydn, from Streptomyces yunnanensis and obtained three new linaridins, named yunnanaridins A-C (1-3). Their structures are characterized by Z-configurations of the dehydrobutyrines and the presence of a variety of epimerized amino acid residues. Yunnanaridin A (1) is the sixth member of the family of type-B linaridins, whereas yunnanaridins B (2) and C (3) represent the first examples of expressed type-C linaridins. Interestingly, heterologous expression of the same BGCs with LinC in-frame knockouts produced the same compounds. This work expands the structural diversity of linaridins and provides evidence for the notion that the widespread LinCs may not be involved in linaridin biosynthesis.
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Affiliation(s)
- Meng-Xue Guo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Meng-Meng Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Ke Sun
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jiao-Jiao Cui
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yi-Cheng Liu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
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3
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Soualmia F, Guillot A, Sabat N, Brewee C, Kubiak X, Haumann M, Guinchard X, Benjdia A, Berteau O. Exploring the Biosynthetic Potential of TsrM, a B 12 -dependent Radical SAM Methyltransferase Catalyzing Non-radical Reactions. Chemistry 2022; 28:e202200627. [PMID: 35253932 DOI: 10.1002/chem.202200627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 12/20/2022]
Abstract
B12 -dependent radical SAM enzymes are an emerging enzyme family with approximately 200,000 proteins. These enzymes have been shown to catalyze chemically challenging reactions such as methyl transfer to sp2- and sp3-hybridized carbon atoms. However, to date we have little information regarding their complex mechanisms and their biosynthetic potential. Here we show, using X-ray absorption spectroscopy, mutagenesis and synthetic probes that the vitamin B12 -dependent radical SAM enzyme TsrM catalyzes not only C- but also N-methyl transfer reactions further expanding its synthetic versatility. We also demonstrate that TsrM has the unique ability to directly transfer a methyl group to the benzyl core of tryptophan, including the least reactive position C4. Collectively, our study supports that TsrM catalyzes non-radical reactions and establishes the usefulness of radical SAM enzymes for novel biosynthetic schemes including serial alkylation reactions at particularly inert C-H bonds.
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Affiliation(s)
- Feryel Soualmia
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Nazarii Sabat
- UPR 2301, Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, 91198, Gif-sur-Yvette, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Xavier Kubiak
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Xavier Guinchard
- UPR 2301, Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, 91198, Gif-sur-Yvette, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
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4
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Wu R, Ding W, Zhang Q. Consecutive Methylation catalyzed by
TsrM
, an atypical Class B radical
SAM
methylase. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Runze Wu
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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5
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Lin Z, Xue Y, Liang XW, Wang J, Lin S, Tao J, You SL, Liu W. Oxidative Indole Dearomatization for Asymmetric Furoindoline Synthesis by a Flavin-Dependent Monooxygenase Involved in the Biosynthesis of Bicyclic Thiopeptide Thiostrepton. Angew Chem Int Ed Engl 2021; 60:8401-8405. [PMID: 33496012 DOI: 10.1002/anie.202013174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/02/2021] [Indexed: 01/20/2023]
Abstract
The interest in indole dearomatization, which serves as a useful tool in the total synthesis of related alkaloid natural products, has recently been renewed with the intention of developing new methods efficient in both yield and stereoselective control. Here, we report an enzymatic approach for the oxidative dearomatization of indoles in the asymmetric synthesis of a variety of furoindolines with a vicinal quaternary carbon stereogenic center. This approach depends on the activity of a flavin-dependent monooxygenase, TsrE, which is involved in the biosynthesis of bicyclic thiopeptide antibiotic thiostrepton. TsrE catalyzes 2,3-epoxidation and subsequent epoxide opening in a highly enantioselective manner during the conversion of 2-methyl-indole-3-acetic acid or 2-methyl-tryptophol to furoindoline, with up to >99 % conversion and >99 % ee under mild reaction conditions. Complementing current chemical methods for oxidative indole dearomatization, the TsrE activity-based approach enriches the toolbox in the asymmetric synthesis of products possessing a furoindoline skeleton.
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Affiliation(s)
- Zhi Lin
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yufeng Xue
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Xiao-Wei Liang
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jian Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiang Tao
- Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Shu-Li You
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, 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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6
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Oxidative Indole Dearomatization for Asymmetric Furoindoline Synthesis by a Flavin‐Dependent Monooxygenase Involved in the Biosynthesis of Bicyclic Thiopeptide Thiostrepton. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Zdouc MM, Iorio M, Maffioli SI, Crüsemann M, Donadio S, Sosio M. Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus. JOURNAL OF NATURAL PRODUCTS 2021; 84:204-219. [PMID: 33496580 PMCID: PMC7922807 DOI: 10.1021/acs.jnatprod.0c00807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 06/12/2023]
Abstract
Despite an excellent track record, microbial drug discovery suffers from high rates of rediscovery. Better workflows for the rapid investigation of complex extracts are needed to increase throughput and to allow early prioritization of samples. In addition, systematic characterization of poorly explored strains is seldomly performed. Here, we report a metabolomic study of 72 isolates belonging to the rare actinomycete genus Planomonospora, using a workflow of commonly used open access tools to investigate its secondary metabolites. The results reveal a correlation of chemical diversity and strain phylogeny, with classes of metabolites exclusive to certain phylogroups. We were able to identify previously reported Planomonospora metabolites, including the ureylene-containing oligopeptide antipain, the thiopeptide siomycin including new congeners, and the ribosomally synthesized peptides sphaericin and lantibiotic 97518. In addition, we found that Planomonospora strains can produce the siderophore desferrioxamine or a salinichelin-like peptide. Analysis of the genomes of three newly sequenced strains led to the detection of 59 gene cluster families, of which three were connected to products found by LC-MS/MS profiling. This study demonstrates the value of metabolomic studies to investigate poorly explored taxa and provides a first picture of the biosynthetic capabilities of the genus Planomonospora.
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Affiliation(s)
- Mitja M. Zdouc
- Naicons
Srl., Viale Ortles 22/4, 20139 Milano, Italy
- Swammerdam
Institute for Life Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | | | | | - Max Crüsemann
- Institut
für Pharmazeutische Biologie, Rheinische
Friedrich-Wilhelms-Universität, Nußallee 6, 53115 Bonn, Germany
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8
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 408] [Impact Index Per Article: 136.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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9
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Chan DCK, Burrows LL. Thiopeptides: antibiotics with unique chemical structures and diverse biological activities. J Antibiot (Tokyo) 2020; 74:161-175. [PMID: 33349675 DOI: 10.1038/s41429-020-00387-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022]
Abstract
Thiopeptides are a class of natural product antibiotics with diverse structures and functions. Their complex structures and biosynthesis have intrigued researchers since their discovery in 1948, but not a single thiopeptide has been approved for human use. This is mainly due to their poor solubility, challenging synthesis, and low bioavailability. This review summarizes the current research on the biosynthesis and biological activity of thiopeptide antibiotics since 2015. The focus of research since 2015 has been on uncovering biosynthetic routes, developing methods for total synthesis, and understanding the biological activity of thiopeptides. Overall, there is still much to learn about this family of molecules.
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Affiliation(s)
- Derek C K Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada. .,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada.
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10
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Vinogradov AA, Suga H. Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem Biol 2020; 27:1032-1051. [PMID: 32698017 DOI: 10.1016/j.chembiol.2020.07.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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11
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Zhang E, Guo H, Chen D, Yang Q, Fan Y, Yin Y, Wang W, Chen D, Wang S, Liu W. Mutational biosynthesis to generate novel analogs of nosiheptide featuring a fluorinated indolic acid moiety. Org Biomol Chem 2020; 18:4051-4055. [PMID: 32412572 DOI: 10.1039/d0ob00084a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nosiheptide (NOS) is a member of bicyclic thiopeptides possessing a biologically important indolic acid (IA) moiety appended onto the family-characteristic core system. The IA formation relies primarily on NosL, a radical S-adenosylmethionine (SAM) protein that catalyzes a complex rearrangement of the carbon side chain of l-tryptophan, leading to the generation of 3-methyl-2-indolic acid (MIA). Here, we establish an efficient mutational biosynthesis strategy for the structural expansion of the side-ring system of NOS. The nosL-deficient mutant Streptomyces actuosus SL4005 complemented by chemically feeding 6-fluoro-MIA is capable of accumulating two new products. The target product 6'-fluoro-NOS contains an additional fluorine atom at C6 of the IA moiety, in contrast with an unexpected product 6'-fluoro-NOSint that features an open side ring and a bis-dehydroalanine (Dha) tail. The newly obtained 6'-fluoro-NOS displayed equivalent or slightly reduced activities against the tested drug-resistant pathogens compared with NOS, but dramatically decreased water solubility compared with NOS. Our results indicate that the modification of the IA moiety of NOS not only affects its biological activity but also affects its activity which will be key considerations for further modification.
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Affiliation(s)
- E Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, 336 West Road of Nan Xinzhuang, Jinan, 250022, China.
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12
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Yñigez-Gutierrez AE, Bachmann BO. Fixing the Unfixable: The Art of Optimizing Natural Products for Human Medicine. J Med Chem 2019; 62:8412-8428. [PMID: 31026161 DOI: 10.1021/acs.jmedchem.9b00246] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecules isolated from natural sources including bacteria, fungi, and plants are a long-standing source of therapeutics that continue to add to our medicinal arsenal today. Despite their potency and prominence in the clinic, complex natural products often exhibit a number of liabilities that hinder their development as therapeutics, which may be partially responsible for the current trend away from natural product discovery, research, and development. However, advances in synthetic biology and organic synthesis have inspired a new generation of natural product chemists to tackle powerful undeveloped scaffolds. In this Perspective, we will present case studies demonstrating the historical and current focus on making targeted, but significant, changes to natural product scaffolds via biosynthetic gene cluster manipulation, total synthesis, semisynthesis, or a combination of these methods, with a focus on increasing activity, decreasing toxicity, or improving chemical and pharmacological properties.
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Affiliation(s)
| | - Brian O Bachmann
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
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13
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Liu J, Lin Z, Li Y, Zheng Q, Chen D, Liu W. Insights into the thioamidation of thiopeptins to enhance the understanding of the biosynthetic logic of thioamide-containing thiopeptides. Org Biomol Chem 2019; 17:3727-3731. [DOI: 10.1039/c9ob00402e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In vivo experiments show that the thioamide moiety of thiopeptins is generated by a TfuA–YcaO pair, before the maturation of the bicyclic scaffold.
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Affiliation(s)
- Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Yuqing Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Dandan Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
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14
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Wang J, Lin Z, Bai X, Tao J, Liu W. Optimal design of thiostrepton-derived thiopeptide antibiotics and their potential application against oral pathogens. Org Chem Front 2019. [DOI: 10.1039/c9qo00219g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A new fluorinated thiostrepton-type thiopeptide antibiotic was designed and biosynthesized by using a biological approach with synthetic advantages. Related bioassays indicated that thiostrepton and its derivatives hold potential in oral pathogen treatment.
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Affiliation(s)
- Jian Wang
- Department of General Dentistry
- Ninth People's Hospital
- Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Stomatology
- Shanghai 200011
| | - Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Xuebing Bai
- Department of General Dentistry
- Ninth People's Hospital
- Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Stomatology
- Shanghai 200011
| | - Jiang Tao
- Department of General Dentistry
- Ninth People's Hospital
- Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Stomatology
- Shanghai 200011
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
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15
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Liu J, Lin Z, Chen H, Guo H, Tao J, Liu W. Biosynthesis of the Central Piperidine Nitrogen Heterocycle in SeriesaThiopeptides. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University 800 Dongchuan Road, Shanghai 200240 China
| | - Hua Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Heng Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Jiang Tao
- Department of General Dentistry, Ninth People's HospitalShanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai 200011 China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on 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, Zhejiang 313000 China
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16
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Ichikawa H, Bashiri G, Kelly WL. Biosynthesis of the Thiopeptins and Identification of an F 420H 2-Dependent Dehydropiperidine Reductase. J Am Chem Soc 2018; 140:10749-10756. [PMID: 30118217 PMCID: PMC6193465 DOI: 10.1021/jacs.8b04238] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thiopeptins are highly decorated thiopeptide antibiotics similar in structure to thiostrepton A and harbor two unusual features. All thiopeptins contain a thioamide, a rare moiety among natural products, and a subset of thiopeptins present with a piperidine in the core macrocycle rather than the more oxidated dehydropiperidine or pyridine rings typically observed in the thiopeptides. Here, we report the identification of the thiopeptin biosynthetic gene ( tpn) cluster in Streptomyces tateyamensis and the gene product, TpnL, which shows sequence similarity to (deaza)flavin-dependent oxidoreductases. Heterologous expression of TpnL in the thiostrepton A producer Streptomyces laurentii led to the production of a piperidine-containing analogue. Binding studies revealed that TpnL preferentially binds the deazaflavin cofactor coenzyme F420, and in vitro reconstitution of TpnL activity confirmed that this enzyme is an F420H2-dependent dehydropiperidine reductase. The identification of TpnL and its activity establishes the basis for the piperidine-containing series a thiopeptides, one of the five main structural groups of this diverse family of antibiotics.
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Affiliation(s)
- Hiro Ichikawa
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Wendy L. Kelly
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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17
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Zheng Q, Fang H, Liu W. Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 2018; 15:3376-3390. [PMID: 28358161 DOI: 10.1039/c7ob00466d] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins. Since the biosynthetic gene clusters of thiopeptides were first discovered in 2009, several research studies regarding the biochemistry and enzymology of thiopeptide biosyntheses have been reported, indicating that their characteristic framework is constructed via a cascade of common PTMs and that additional specific PTMs diversify the molecules. In this review, we primarily summarize recent advances in understanding the biosynthesis of thiopeptide antibiotics and propose some potential applications based on our insights into the biosynthetic logic and machinery.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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18
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Benjdia A, Balty C, Berteau O. Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Front Chem 2017; 5:87. [PMID: 29167789 PMCID: PMC5682303 DOI: 10.3389/fchem.2017.00087] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.
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Affiliation(s)
- Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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19
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Lin Z, Ji J, Zhou S, Zhang F, Wu J, Guo Y, Liu W. Processing 2-Methyl-l-Tryptophan through Tandem Transamination and Selective Oxygenation Initiates Indole Ring Expansion in the Biosynthesis of Thiostrepton. J Am Chem Soc 2017; 139:12105-12108. [DOI: 10.1021/jacs.7b05337] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Zhi Lin
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jia Ji
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Shuaixiang Zhou
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Fang Zhang
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jiequn Wu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, 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
| | - Yinlong Guo
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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20
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Lin Z, He Q, Liu W. Bio-inspired engineering of thiopeptide antibiotics advances the expansion of molecular diversity and utility. Curr Opin Biotechnol 2017; 48:210-219. [PMID: 28672170 DOI: 10.1016/j.copbio.2017.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 02/08/2023]
Abstract
Thiopeptide antibiotics, which are a class of sulfur-rich and highly modified peptide natural products, exhibit a wide variety of important biological properties. These antibiotics are ribosomally synthesized and arise from post-translational modifications, exemplifying a process through which nature develops the structural complexity from Ser/Thr and Cys-rich precursor peptides. Following a brief review of the knowledge gained from nature in terms of the formation of a common thiopeptide scaffold and its specialization to individual members, we highlight the significance of bio-inspired engineering, which has greatly expanded the molecular diversity and utility of thiopeptide antibiotics regarding the search for clinically useful agents, investigation into new mechanisms of action and access to typically 'inaccessible' biosynthetic processes over the past two years.
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Affiliation(s)
- Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qingli He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China.
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21
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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22
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Birnara C, Kessler VG, Papaefstathiou GS. Group III quinaldates: synthesis, structure and photoluminescence. J COORD CHEM 2017. [DOI: 10.1080/00958972.2017.1283416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Christiana Birnara
- Laboratory of Inorganic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece
| | - Vadim G. Kessler
- Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Giannis S. Papaefstathiou
- Laboratory of Inorganic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece
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23
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An α/β-hydrolase fold protein in the biosynthesis of thiostrepton exhibits a dual activity for endopeptidyl hydrolysis and epoxide ring opening/macrocyclization. Proc Natl Acad Sci U S A 2016; 113:14318-14323. [PMID: 27911800 DOI: 10.1073/pnas.1612607113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiostrepton (TSR), an archetypal bimacrocyclic thiopeptide antibiotic that arises from complex posttranslational modifications of a genetically encoded precursor peptide, possesses a quinaldic acid (QA) moiety within the side-ring system of a thiopeptide-characteristic framework. Focusing on selective engineering of the QA moiety, i.e., by fluorination or methylation, we have recently designed and biosynthesized biologically more active TSR analogs. Using these analogs as chemical probes, we uncovered an unusual indirect mechanism of TSR-type thiopeptides, which are able to act against intracellular pathogens through host autophagy induction in addition to direct targeting of bacterial ribosome. Herein, we report the accumulation of 6'-fluoro-7', 8'-epoxy-TSR, a key intermediate in the preparation of the analog 6'-fluoro-TSR. This unexpected finding led to unveiling of the TSR maturation process, which involves an unusual dual activity of TsrI, an α/β-hydrolase fold protein, for cascade C-N bond cleavage and formation during side-ring system construction. These two functions of TsrI rely on the same catalytic triad, Ser72-His200-Asp191, which first mediates endopeptidyl hydrolysis that occurs selectively between the residues Met-1 and Ile1 for removal of the leader peptide and then triggers epoxide ring opening for closure of the QA-containing side-ring system in a regio- and stereo-specific manner. The former reaction likely requires the formation of an acyl-Ser72 enzyme intermediate; in contrast, the latter is independent of Ser72. Consequently, C-6' fluorination of QA lowers the reactivity of the epoxide intermediate and, thereby, allows the dissection of the TsrI-associated enzymatic process that proceeds rapidly and typically is difficult to be realized during TSR biosynthesis.
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24
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Zheng Q, Wang S, Liao R, Liu W. Precursor-Directed Mutational Biosynthesis Facilitates the Functional Assignment of Two Cytochromes P450 in Thiostrepton Biosynthesis. ACS Chem Biol 2016; 11:2673-2678. [PMID: 27560135 DOI: 10.1021/acschembio.6b00419] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Side-ring-modified thiostrepton (TSR) derivatives that vary in their quinaldic acid (QA) substitution possess more potent biological activities and better pharmaceutical properties than the parent compound. In this work, we sought to introduce fluorine onto C-7' or C-8' of the TSR QA moiety via precursor-directed mutational biosynthesis to obtain new TSR variants. Unexpectedly, instead of the target product, the exogenous chemical feeding of 7-F-QA into the ΔtsrT mutant strain resulted in a unique TSR analog with an incomplete side-ring structure and an unoxidized QA moiety (1). Accordingly, two cytochrome P450 genes, tsrP and tsrR, were in-frame deleted to elucidate the candidate responsible for the monooxidation of the QA moiety in TSR. The unfluorinated analog of compound 1 that was thus isolated from ΔtsrP (2) and the abolishment of TSR production in ΔtsrR revealed not only the biosynthetic logic of the TSR side-ring but also the essential checkpoint in TSR maturation before macro-ring closure.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry,
Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Shoufeng Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry,
Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Rijing Liao
- State Key Laboratory of Bioorganic and Natural Products Chemistry,
Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry,
Shanghai Institute of Organic Chemistry, 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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25
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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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26
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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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27
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Ding W, Li Q, Jia Y, Ji X, Qianzhu H, Zhang Q. Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem 2016; 17:1191-7. [PMID: 27028019 DOI: 10.1002/cbic.201600107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 11/10/2022]
Abstract
Cobalamins comprise a group of cobalt-containing organometallic cofactors that play important roles in cellular metabolism. Although many cobalamin-dependent methyltransferases (e.g., methionine synthase MetH) have been extensively studied, a new group of methyltransferases that are cobalamin-dependent and utilize radical chemistry in catalysis is just beginning to be appreciated. In this Concept article, we summarize recent advances in the understanding of the radical-based and cobalamin-dependent methyltransferases and discuss the functional and mechanistic diversity of this emerging class of enzymes.
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Affiliation(s)
- Wei Ding
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qien Li
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Youli Jia
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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28
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Zhang F, Li C, Kelly WL. Thiostrepton Variants Containing a Contracted Quinaldic Acid Macrocycle Result from Mutagenesis of the Second Residue. ACS Chem Biol 2016; 11:415-24. [PMID: 26630475 DOI: 10.1021/acschembio.5b00731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiopeptides are a family of ribosomally synthesized and post-translationally modified peptide metabolites, and the vast majority of thiopeptides characterized to date possess one highly modified macrocycle. A few members, including thiostrepton A, harbor a second macrocycle that incorporates a quinaldic acid moiety and the four N-terminal residues of the peptide. The antibacterial properties of thiostrepton A are well established, and its recently discovered ability to inhibit the proteasome has additional implications for the development of antimalarial and anticancer therapeutics. We have conducted the saturation mutagenesis of Ala2 in the precursor peptide, TsrA, to examine which variants can be transformed into a mature thiostrepton analogue. Although the thiostrepton biosynthetic system is somewhat restrictive toward substitutions at the second residue, eight thiostrepton Ala2 analogues were isolated. The TsrA Ala2Ile and Ala2Val variants were largely channeled through an alternate processing pathway wherein the first residue of the core peptide, Ile1, is removed, and the resulting thiostrepton analogues bear quinaldic acid macrocycles abridged by one residue. This is the first report revealing that quinaldic acid loop size is amenable to alteration during the course of thiostrepton biosynthesis. Both the antibacterial and proteasome inhibitory properties of the thiostrepton Ala2 analogues were examined. While the identity of the residue at the second position of the core peptide influences thiostrepton biosynthesis, our report suggests it may not be crucial for antibacterial and proteasome inhibitory properties of the full-length variants. In contrast, the contracted quinaldic acid loop can, to differing degrees, affect both types of biological activity.
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Affiliation(s)
- Feifei Zhang
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Chaoxuan Li
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Wendy L. Kelly
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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29
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Duan P, Zheng Q, Lin Z, Wang S, Chen D, Liu W. Molecular engineering of thiostrepton via single “base”-based mutagenesis to generate side ring-derived variants. Org Chem Front 2016. [DOI: 10.1039/c6qo00320f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Six thiostrepton (TSR) analogs, siomycin (SIO) and SIO-Dha2Ser were produced in the engineered TSR-producing strain by using a single “base”-based mutagenesis strategy.
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Affiliation(s)
- Panpan Duan
- 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
| | - Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Shoufeng Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Dandan Chen
- Huzhou Center of Bio-Synthetic Innovation
- Huzhou 313000
- China
| | - 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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30
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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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31
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Zheng Q, Wang Q, Wang S, Wu J, Gao Q, Liu W. Thiopeptide Antibiotics Exhibit a Dual Mode of Action against Intracellular Pathogens by Affecting Both Host and Microbe. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.chembiol.2015.06.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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32
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Wang S, Zheng Q, Wang J, Zhao Z, Li Q, Yu Y, Wang R, Liu W. Target-oriented design and biosynthesis of thiostrepton-derived thiopeptide antibiotics with improved pharmaceutical properties. Org Chem Front 2015. [DOI: 10.1039/c4qo00288a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two QA moiety-modified thiostrepton derivatives were obtained via a mutagenesis strategy based on a rational design.
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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
| | - Zhixiong Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Qingye Li
- 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
| | - Renxiao Wang
- 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
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33
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Walsh CT. Biological matching of chemical reactivity: pairing indole nucleophilicity with electrophilic isoprenoids. ACS Chem Biol 2014; 9:2718-28. [PMID: 25303280 DOI: 10.1021/cb500695k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The indole side chain of tryptophan has latent nucleophilic reactivity at both N1 and all six (nonbridgehead) carbons, which is not generally manifested in post-translational reactions of proteins. On the other hand, all seven positions can be prenylated by the primary metabolite Δ(2)-isopentenyl diphosphate by dimethyallyl transferase (DMATs) family members as initial steps in biosynthetic pathways to bioactive fungal alkaloids including ergots and tremorgens. These are formulated as regioselective capture of isopentenyl allylic cationic transition states by the indole side chain as a nucleophile. The balance of regiospecificity and promiscuity among these indole prenyltransferases continues to raise questions about possible Cope and azaCope rearrangements of nascent products. In addition to these two electron reaction manifolds, there is evidence for one electron reaction manifolds in indole ring biosynthetic functionalization.
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Affiliation(s)
- Christopher T. Walsh
- ChEM-H Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
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34
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Zheng Q, Wang S, Liu W. Discovery and efficient synthesis of a biologically active alkaloid inspired by thiostrepton biosynthesis. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.076] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Just-Baringo X, Albericio F, Álvarez M. Engineering von Thiopeptiden: ein multidisziplinärer Weg zu neuen Wirkstoffen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Just-Baringo X, Albericio F, Álvarez M. Thiopeptide engineering: a multidisciplinary effort towards future drugs. Angew Chem Int Ed Engl 2014; 53:6602-16. [PMID: 24861213 DOI: 10.1002/anie.201307288] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Indexed: 11/12/2022]
Abstract
The recent development of thiopeptide analogues of antibiotics has allowed some of the limitations inherent to these naturally occurring substances to be overcome. Chemical synthesis, semisynthetic derivatization, and engineering of the biosynthetic pathway have independently led to complementary modifications of various thiopeptides. Some of the new substances have displayed improved profiles, not only as antibiotics, but also as antiplasmodial and anticancer drugs. The design of novel molecules based on the thiopeptide scaffold appears to be the only strategy to exploit the high potential they have shown in vitro. Herein we present the most relevant achievements in the production of thiopeptide analogues and also discuss the way the different approaches might be combined in a multidisciplinary strategy to produce more sophisticated structures.
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Affiliation(s)
- Xavier Just-Baringo
- Institute for Research in Biomedicine, Barcelona Science Park, University of Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain) http://www.pcb.ub.edu/fama/htm/home.htm; CIBER-BBN, Networking Centre on Bioengineering Biomaterials and Nanomedicine, 08028 Barcelona (Spain)
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37
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Xie P, Ma M, Rateb ME, Shaaban K, Yu Z, Huang SX, Zhao LX, Zhu X, Yan Y, Peterson R, Lohman JR, Yang D, Yin M, Rudolf JD, Jiang Y, Duan Y, Shen B. Biosynthetic potential-based strain prioritization for natural product discovery: a showcase for diterpenoid-producing actinomycetes. JOURNAL OF NATURAL PRODUCTS 2014; 77:377-87. [PMID: 24484381 PMCID: PMC3963700 DOI: 10.1021/np401063s] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 05/09/2023]
Abstract
Natural products remain the best sources of drugs and drug leads and serve as outstanding small-molecule probes to dissect fundamental biological processes. A great challenge for the natural product community is to discover novel natural products efficiently and cost effectively. Here we report the development of a practical method to survey biosynthetic potential in microorganisms, thereby identifying the most promising strains and prioritizing them for natural product discovery. Central to our approach is the innovative preparation, by a two-tiered PCR method, of a pool of pathway-specific probes, thereby allowing the survey of all variants of the biosynthetic machineries for the targeted class of natural products. The utility of the method was demonstrated by surveying 100 strains, randomly selected from our actinomycete collection, for their biosynthetic potential of four classes of natural products, aromatic polyketides, reduced polyketides, nonribosomal peptides, and diterpenoids, identifying 16 talented strains. One of the talented strains, Streptomyces griseus CB00830, was finally chosen to showcase the discovery of the targeted classes of natural products, resulting in the isolation of three diterpenoids, six nonribosomal peptides and related metabolites, and three polyketides. Variations of this method should be applicable to the discovery of other classes of natural products.
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Affiliation(s)
- Pengfei Xie
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ming Ma
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Mostafa E. Rateb
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Khaled
A. Shaaban
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Zhiguo Yu
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Sheng-Xiong Huang
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Li-Xing Zhao
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Xiangcheng Zhu
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Yijun Yan
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ryan
M. Peterson
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Division
of Pharmaceutical Sciences, University of
Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Jeremy R. Lohman
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Min Yin
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jeffrey D. Rudolf
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yi Jiang
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Yanwen Duan
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Ben Shen
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Division
of Pharmaceutical Sciences, University of
Wisconsin−Madison, Madison, Wisconsin 53705, United States
- Department
of Molecular Therapeutics, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
- Natural Products
Library Initiative, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
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38
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Thiopeptide antibiotics: retrospective and recent advances. Mar Drugs 2014; 12:317-51. [PMID: 24445304 PMCID: PMC3917276 DOI: 10.3390/md12010317] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/13/2013] [Accepted: 12/16/2013] [Indexed: 02/06/2023] Open
Abstract
Thiopeptides, or thiazolyl peptides, are a relatively new family of antibiotics that already counts with more than one hundred different entities. Although they are mainly isolated from soil bacteria, during the last decade, new members have been isolated from marine samples. Far from being limited to their innate antibacterial activity, thiopeptides have been found to possess a wide range of biological properties, including anticancer, antiplasmodial, immunosuppressive, etc. In spite of their ribosomal origin, these highly posttranslationally processed peptides have posed a fascinating synthetic challenge, prompting the development of various methodologies and strategies. Regardless of their limited solubility, intensive investigations are bringing thiopeptide derivatives closer to the clinic, where they are likely to show their veritable therapeutic potential.
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39
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Guo H, Wang J, Li Y, Yu Y, Zheng Q, Wu J, Liu W. Insight into bicyclic thiopeptide biosynthesis benefited from development of a uniform approach for molecular engineering and production improvement. Chem Sci 2014. [DOI: 10.1039/c3sc52015c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Wang S, Zhou S, Liu W. Opportunities and challenges from current investigations into the biosynthetic logic of nosiheptide-represented thiopeptide antibiotics. Curr Opin Chem Biol 2013; 17:626-34. [PMID: 23838388 DOI: 10.1016/j.cbpa.2013.06.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/04/2013] [Accepted: 06/17/2013] [Indexed: 11/16/2022]
Abstract
Nosiheptide is an archetypal thiopeptide antibiotic, possessing a characteristic macrocyclic core that contains a 6-membered heterocycle central to multiple azol(in)es and dehydroamino acids. The discovery of the ribosomal origin of thiopeptides revealed a unifying theme, showing that the structural complexity arises from post-translational modifications (PTMs) of precursor peptides. Thiopeptide framework formation proceeds via cyclodehydration/dehydrogenation (for azol(in)es), dehydration (for dehydroamino acids), and cycloaddition (for the central heterocycle domain). This common process has not been reproduced in vitro, partly due to the poorly understood logic of thiopeptide biosynthetic pathways. Utilizing nosiheptide biosynthesis as a model system, we herein consider how nature coordinates a number of highly interwined, common and specific PTMs to accomplish the complexity of ribosomally synthesized and post-translationally modified peptides.
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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, 345 Lingling Road, Shanghai 200032, China
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41
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Dunbar KL, Mitchell DA. Insights into the mechanism of peptide cyclodehydrations achieved through the chemoenzymatic generation of amide derivatives. J Am Chem Soc 2013; 135:8692-701. [PMID: 23721104 DOI: 10.1021/ja4029507] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Current strategies for generating peptides and proteins bearing amide carbonyl derivatives rely on solid-phase peptide synthesis for amide functionalization. Although such strategies have been successfully implemented, technical limitations restrict both the length and sequence of the synthetic fragments. Herein we report the repurposing of a thiazole/oxazole-modified microcin (TOMM) cyclodehydratase to site-specifically install amide backbone labels onto diverse peptide substrates, a method we refer to as azoline-mediated peptide backbone labeling (AMPL). This convenient chemoenzymatic strategy can generate both thioamides and amides with isotopically labeled oxygen atoms. Moreover, we demonstrate the first leader peptide-independent activity of a TOMM synthetase, circumventing the requirement that sequences of interest be fused to a leader peptide for modification. Through bioinformatics-guided site-directed mutagenesis, we also convert a strictly dehydrogenase-dependent TOMM azole synthetase into an azoline synthetase. This vastly expands the spectrum of substrates modifiable by AMPL by allowing any in vitro reconstituted TOMM synthetase to be employed. To demonstrate the utility of AMPL for mechanistic enzymology studies, an (18)O-labeled substrate was generated to provide direct evidence that cyclodehydrations in TOMMs occur through the phosphorylation of the carbonyl oxygen preceding the cyclized residue. Furthermore, we demonstrate that AMPL is a useful tool for establishing the location of azolines both on in vitro modified peptides and azoline-containing natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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42
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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43
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44
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Zhang Q, Liu W. Biosynthesis of thiopeptide antibiotics and their pathway engineering. Nat Prod Rep 2013; 30:218-26. [DOI: 10.1039/c2np20107k] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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45
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ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences. PLoS One 2012; 7:e45878. [PMID: 23029291 PMCID: PMC3454323 DOI: 10.1371/journal.pone.0045878] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022] Open
Abstract
Thiopeptides are a growing class of sulfur-rich, highly modified heterocyclic peptides that are mainly active against Gram-positive bacteria including various drug-resistant pathogens. Recent studies also reveal that many thiopeptides inhibit the proliferation of human cancer cells, further expanding their application potentials for clinical use. Thiopeptide biosynthesis shares a common paradigm, featuring a ribosomally synthesized precursor peptide and conserved posttranslational modifications, to afford a characteristic core system, but differs in tailoring to furnish individual members. Identification of new thiopeptide gene clusters, by taking advantage of increasing information of DNA sequences from bacteria, may facilitate new thiopeptide discovery and enrichment of the unique biosynthetic elements to produce novel drug leads by applying the principle of combinatorial biosynthesis. In this study, we have developed a web-based tool ThioFinder to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach. Fifty-four new putative thiopeptide biosynthetic gene clusters were found in the sequenced bacterial genomes of previously unknown producing microorganisms. ThioFinder is fully supported by an open-access database ThioBase, which contains the sufficient information of the 99 known thiopeptides regarding the chemical structure, biological activity, producing organism, and biosynthetic gene (cluster) along with the associated genome if available. The ThioFinder website offers researchers a unique resource and great flexibility for sequence analysis of thiopeptide biosynthetic gene clusters. ThioFinder is freely available at http://db-mml.sjtu.edu.cn/ThioFinder/.
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