1
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He Q, Zhang Q, Rolka AB, Suero MG. Alkoxy Diazomethylation of Alkenes by Photoredox-Catalyzed Oxidative Radical-Polar Crossover. J Am Chem Soc 2024; 146:12294-12299. [PMID: 38663863 PMCID: PMC11082901 DOI: 10.1021/jacs.4c00867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Herein, we present the discovery and development of the first photoredox-catalyzed alkoxy diazomethylation of alkenes with hypervalent iodine reagents and alcohols. This multicomponent process represents a new disconnection approach to diazo compounds and is featured by a broad scope, mild reaction conditions, and excellent selectivity. Key to the process was the generation of diazomethyl radicals, which engaged alkenes and alcohols in an inter- and intramolecular fashion by a photoredox-catalyzed oxidative radical-polar crossover leading to unexplored β-alkoxydiazo compounds. The synthetic utility of such diazo compounds was demonstrated with a series of transformations involving C-H, N-H, and O-H insertions as well as in the construction of complex sp3-rich heterocycles.
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Affiliation(s)
- Qiyuan He
- Institute
of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona
Institute of Science and Technology, Països Catalans 16, 43007 Tarragona, Spain
| | - Quan Zhang
- Institute
of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona
Institute of Science and Technology, Països Catalans 16, 43007 Tarragona, Spain
- Departament
de Química Analítica i Química Orgánica, Universitat Rovira i Virgili, Calle Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Alessa B. Rolka
- Institute
of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona
Institute of Science and Technology, Països Catalans 16, 43007 Tarragona, Spain
| | - Marcos G. Suero
- Institute
of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona
Institute of Science and Technology, Països Catalans 16, 43007 Tarragona, Spain
- ICREA,
Pg. Lluis Companys 23, 08010 Barcelona, Spain
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2
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Matsuda K, Wakimoto T. Bacterial Hydrazine Biosynthetic Pathways Featuring Cupin/Methionyl tRNA Synthetase-like Enzymes. Chembiochem 2024; 25:e202300874. [PMID: 38458972 DOI: 10.1002/cbic.202300874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Nitrogen-Nitrogen (N-N) bond-containing functional groups in natural products and synthetic drugs play significant roles in exerting biological activities. The mechanisms of N-N bond formation in natural organic molecules have garnered increasing attention over the decades. Recent advances have illuminated various enzymatic and nonenzymatic strategies, and our understanding of natural N-N bond construction is rapidly expanding. A group of didomain proteins with zinc-binding cupin/methionyl-tRNA synthetase (MetRS)-like domains, also known as hydrazine synthetases, generates amino acid-based hydrazines, which serve as key biosynthetic precursors of diverse N-N bond-containing functionalities such as hydrazone, diazo, triazene, pyrazole, and pyridazinone groups. In this review, we summarize the current knowledge on hydrazine synthetase mechanisms and the various pathways employing this unique bond-forming machinery.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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3
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Xuan W, Ma JA. Pinpointing Acidic Residues in Proteins. ChemMedChem 2024; 19:e202300623. [PMID: 38303683 DOI: 10.1002/cmdc.202300623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/18/2023] [Indexed: 02/03/2024]
Abstract
It is of great importance to pinpoint specific residues or sites of a protein in biological contexts to enable desired mechanism of action for small molecules or to precisely control protein function. In this regard, acidic residues including aspartic acid (Asp) and glutamic acid (Glu) hold great potential due to their great prevalence and unique function. To unlock the largely untapped potential, great efforts have been made recently by synthetic chemists, chemical biologists and pharmacologists. Herein, we would like to highlight the remarkable progress and particularly introduce the electrophiles that exhibit reactivity to carboxylic acids, the light-induced reactivities to carboxylic acids and the genetically encoded noncanonical amino acids that allow protein manipulations at acidic residues. We also comment on certain unresolved challenges, hoping to draw more attention to this rapidly developing area.
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Affiliation(s)
- Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jun-An Ma
- Department of Chemistry, Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, P. R. China
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4
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Luo W, Xu F, Wang Z, Pang J, Wang Z, Sun Z, Peng A, Cao X, Li L. Chemodivergent Staudinger Reactions of Secondary Phosphine Oxides and Application to the Total Synthesis of LL-D05139β Potassium Salt. Angew Chem Int Ed Engl 2023; 62:e202310118. [PMID: 37594845 DOI: 10.1002/anie.202310118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023]
Abstract
Unprecedented Staudinger reaction modes of secondary phosphine oxides (SPO) and organic azides are herein disclosed. By the application of various additives, selective nitrogen atom exclusion from the azide group has been achieved. Chlorotrimethylsilane mediates a stereoretentive Staudinger reaction with a 2-N exclusion which provides a valuable method for the synthesis of phosphinic amides and can be considered complementary to the stereoinvertive Atherton-Todd reaction. Alternatively, a 1-N exclusion pathway is promoted by acetic acid to provide the corresponding diazo compound. The effectiveness of this protocol has been further demonstrated by the total synthesis of the diazo-containing natural product LL-D05139β, which was prepared as a potassium salt for the first time in 6 steps and 26.5 % overall yield.
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Affiliation(s)
- Wenjun Luo
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
- PCFM Lab and GDHPRC Lab, Sun Yat-sen University, 510275, Guangzhou, P. R. China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of P. R. China, College of Pharmacy, Jinan University, 510632, Guangzhou, Guangdong, P. R. China
| | - Zhenguo Wang
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
- PCFM Lab and GDHPRC Lab, Sun Yat-sen University, 510275, Guangzhou, P. R. China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
| | - Zixu Wang
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
- PCFM Lab and GDHPRC Lab, Sun Yat-sen University, 510275, Guangzhou, P. R. China
| | - Zhixiu Sun
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
- PCFM Lab and GDHPRC Lab, Sun Yat-sen University, 510275, Guangzhou, P. R. China
| | - Aiyun Peng
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
| | - Xiaohui Cao
- School of Pharmacy, Guangdong Pharmaceutical University, 510006, Guangzhou, P. R. China
| | - Le Li
- School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, P. R. China
- PCFM Lab and GDHPRC Lab, Sun Yat-sen University, 510275, Guangzhou, P. R. China
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5
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Liu XY, Yang YL, Dang Y, Marek I, Zhang FG, Ma JA. Tetrazole Diversification of Amino Acids and Peptides via Silver-Catalyzed Intermolecular Cycloaddition with Aryldiazonium Salts. Angew Chem Int Ed Engl 2023; 62:e202304740. [PMID: 37212541 DOI: 10.1002/anie.202304740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/23/2023]
Abstract
Selective structural modification of amino acids and peptides is a central strategy in organic chemistry, chemical biology but also in pharmacology and material science. In this context, the formation of tetrazole rings, known to possess significant therapeutic properties, would expand the chemical space of unnatural amino acids but has received less attention. In this study, we demonstrated that the classic unimolecular Wolff rearrangement of α-amino acid-derived diazoketones could be replaced by a faster intermolecular cycloaddition reaction with aryldiazonium salts under identical practical conditions. This strategy provides an efficient synthetic platform that could transform proteinogenic α-amino acids into a plethora of unprecedented tetrazole-decorated amino acid derivatives with preservation of the stereocenters. Density functional theory studies shed some light on the reaction mechanism and provided information regarding the origins of the chemo- and regioselectivity. Furthermore, this diazo-cycloaddition protocol was applied to construct tetrazole-modified peptidomimetics and drug-like amino acid derivatives.
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Affiliation(s)
- Xuan-Yu Liu
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yi-Lin Yang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yanfeng Dang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Ilan Marek
- Schulich Faculty of Chemistry and the Resnick Sustainability Center for Catalysis, Technion-Israel Institute of Technology, Haifa, 3200009, Israel
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
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6
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Zhao Y, Liu X, Xiao Z, Zhou J, Song X, Wang X, Hu L, Wang Y, Sun P, Wang W, He X, Lin S, Deng Z, Pan L, Jiang M. O-methyltransferase-like enzyme catalyzed diazo installation in polyketide biosynthesis. Nat Commun 2023; 14:5372. [PMID: 37666836 PMCID: PMC10477347 DOI: 10.1038/s41467-023-41062-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Diazo compounds are rare natural products possessing various biological activities. Kinamycin and lomaiviticin, two diazo natural products featured by the diazobenzofluorene core, exhibit exceptional potency as chemotherapeutic agents. Despite the extensive studies on their biosynthetic gene clusters and the assembly of their polyketide scaffolds, the formation of the characteristic diazo group remains elusive. L-Glutamylhydrazine was recently shown to be the hydrazine donor in kinamycin biosynthesis, however, the mechanism for the installation of the hydrazine group onto the kinamycin scaffold is still unclear. Here we describe an O-methyltransferase-like protein, AlpH, which is responsible for the hydrazine incorporation in kinamycin biosynthesis. AlpH catalyses a unique SAM-independent coupling of L-glutamylhydrazine and polyketide intermediate via a rare Mannich reaction in polyketide biosynthesis. Our discovery expands the catalytic diversity of O-methyltransferase-like enzymes and lays a strong foundation for the discovery and development of novel diazo natural products through genome mining and synthetic biology.
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Affiliation(s)
- Yuchun Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Xiangyang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Zhihong Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Jie Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Xingyu Song
- Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, 200438, Shanghai, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Lijun Hu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Center for Bioactive Natural Molecules and Innovative Drugs Research, Jinan University, 510632, Guangzhou, P. R. China
| | - Ying Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Center for Bioactive Natural Molecules and Innovative Drugs Research, Jinan University, 510632, Guangzhou, P. R. China
| | - Peng Sun
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, 200433, Shanghai, P. R. China
| | - Wenning Wang
- Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, 200438, Shanghai, China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China.
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7
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Shikai Y, Kawai S, Katsuyama Y, Ohnishi Y. In vitro characterization of nonribosomal peptide synthetase-dependent O-(2-hydrazineylideneacetyl)serine synthesis indicates a stepwise oxidation strategy to generate the α-diazo ester moiety of azaserine. Chem Sci 2023; 14:8766-8776. [PMID: 37621439 PMCID: PMC10445470 DOI: 10.1039/d3sc01906c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/02/2023] [Indexed: 08/26/2023] Open
Abstract
Azaserine, a natural product containing a diazo group, exhibits anticancer activity. In this study, we investigated the biosynthetic pathway to azaserine. The putative azaserine biosynthetic gene (azs) cluster, which contains 21 genes, including those responsible for hydrazinoacetic acid (HAA) synthesis, was discovered using bioinformatics analysis of the Streptomyces fragilis genome. Azaserine was produced by the heterologous expression of the azs cluster in Streptomyces albus. In vitro enzyme assays using recombinant Azs proteins revealed the azaserine biosynthetic pathway as follows. AzsSPTF and carrier protein (CP) AzsQ are used to synthesize the 2-hydrazineylideneacetyl (HDA) moiety attached to AzsQ from HAA. AzsD transfers the HDA moiety to the C-terminal CP domain of AzsN. The heterocyclization (Cy) domain of the nonribosomal peptide synthetase AzsO synthesizes O-(2-hydrazineylideneacetyl)serine (HDA-Ser) attached to its CP domain from l-serine and HDA moiety-attached AzsN. The thioesterase AzsB hydrolyzes it to yield HDA-Ser, which appears to be converted to azaserine by oxidation. Bioinformatics analysis of the Cy domain of AzsO showed that it has a conserved DxxxxD motif; however, two conserved amino acid residues (Thr and Asp) important for heterocyclization are substituted for Asn. Site-directed mutagenesis of two Asp residues in the DxxxxD motif (D193 and D198) and two substituted Asn residues (N414 and N447) indicated that these four residues are important for ester bond synthesis. These results showed that the diazo ester of azasrine is synthesized by the stepwise oxidation of the HAA moiety and provided another strategy to biosynthesize the diazo group.
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Affiliation(s)
- Yusuke Shikai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
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8
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Kawai S, Yamada A, Du D, Sugai Y, Katsuyama Y, Ohnishi Y. Identification and Analysis of the Biosynthetic Gene Cluster for the Hydrazide-Containing Aryl Polyene Spinamycin. ACS Chem Biol 2023; 18:1821-1828. [PMID: 37498311 DOI: 10.1021/acschembio.3c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Natural products containing nitrogen-nitrogen (N-N) bonds have attracted much attention because of their bioactivities and chemical features. Several recent studies have revealed the nitrous acid-dependent N-N bond-forming machinery. However, the catalytic mechanisms of hydrazide synthesis using nitrous acid remain unknown. Herein, we focused on spinamycin, a hydrazide-containing aryl polyene produced by Streptomyces albospinus JCM3399. In the S. albospinus genome, we discovered a putative spinamycin biosynthetic gene (spi) cluster containing genes that encode a type II polyketide synthase and genes for the secondary metabolism-specific nitrous acid biosynthesis pathway. A gene inactivation experiment showed that this cluster was responsible for spinamycin biosynthesis. A feeding experiment using stable isotope-labeled sodium nitrite and analysis of nitrous acid-synthesizing enzymes in vitro strongly indicated that one of the nitrogen atoms of the hydrazide group was derived from nitrous acid. In vitro substrate specificity analysis of SpiA3, which is responsible for loading a starter substrate onto polyketide synthase, indicated that N-N bond formation occurs after starter substrate loading. In vitro analysis showed that the AMP-dependent ligase SpiA7 catalyzes the diazotization of an amino group on a benzene ring without a hydroxy group, resulting in a highly reactive diazo intermediate, which may be the key step in hydrazide group formation. Therefore, we propose the overall biosynthetic pathway of spinamycin. This study expands our knowledge of N-N bond formation in microbial secondary metabolism.
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Affiliation(s)
- Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akito Yamada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Danyao Du
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshinori Sugai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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9
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Van Cura D, Ng TL, Huang J, Hager H, Hartwig JF, Keasling JD, Balskus EP. Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α-Diazoester Production. Angew Chem Int Ed Engl 2023; 62:e202304646. [PMID: 37151182 PMCID: PMC10330308 DOI: 10.1002/anie.202304646] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/09/2023]
Abstract
Azaserine is a bacterial metabolite containing a biologically unusual and synthetically enabling α-diazoester functional group. Herein, we report the discovery of the azaserine (aza) biosynthetic gene cluster from Glycomyces harbinensis. Discovery of related gene clusters reveals previously unappreciated azaserine producers, and heterologous expression of the aza gene cluster confirms its role in azaserine assembly. Notably, this gene cluster encodes homologues of hydrazonoacetic acid (HYAA)-producing enzymes, implicating HYAA in α-diazoester biosynthesis. Isotope feeding and biochemical experiments support this hypothesis. These discoveries indicate that a 2-electron oxidation of a hydrazonoacetyl intermediate is required for α-diazoester formation, constituting a distinct logic for diazo biosynthesis. Uncovering this biological route for α-diazoester synthesis now enables the production of a highly versatile carbene precursor in cells, facilitating approaches for engineering complete carbene-mediated biosynthetic transformations in vivo.
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Affiliation(s)
- Devon Van Cura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Harry Hager
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institute for Advanced Technologies, Shenzhen, China
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
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10
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DiBello M, Healy AR, Nikolayevskiy H, Xu Z, Herzon SB. Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls. Acc Chem Res 2023; 56:1656-1668. [PMID: 37220079 PMCID: PMC10468810 DOI: 10.1021/acs.accounts.3c00183] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.
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Affiliation(s)
- Mikaela DiBello
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alan R Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Herman Nikolayevskiy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Zhi Xu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Departments of Pharmacology and Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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11
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Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD. Complete integration of carbene-transfer chemistry into biosynthesis. Nature 2023; 617:403-408. [PMID: 37138074 DOI: 10.1038/s41586-023-06027-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions1. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis2,3, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule-styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.
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Affiliation(s)
- Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Andrew Quest
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pablo Cruz-Morales
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kai Deng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Jose Henrique Pereira
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Devon Van Cura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ramu Kakumanu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Qingyun Dan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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12
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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13
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Ding S, Henkel JV, Hopmans EC, Bale NJ, Koenen M, Villanueva L, Sinninghe Damsté JS. Changes in the membrane lipid composition of a Sulfurimonas species depend on the electron acceptor used for sulfur oxidation. ISME COMMUNICATIONS 2022; 2:121. [PMID: 37938789 PMCID: PMC9789136 DOI: 10.1038/s43705-022-00207-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 11/09/2023]
Abstract
Sulfurimonas species are among the most abundant sulfur-oxidizing bacteria in the marine environment. They are capable of using different electron acceptors, this metabolic flexibility is favorable for their niche adaptation in redoxclines. When oxygen is depleted, most Sulfurimonas spp. (e.g., Sulfurimonas gotlandica) use nitrate ([Formula: see text]) as an electron acceptor to oxidize sulfur, including sulfide (HS-), S0 and thiosulfate, for energy production. Candidatus Sulfurimonas marisnigri SoZ1 and Candidatus Sulfurimonas baltica GD2, recently isolated from the redoxclines of the Black Sea and Baltic Sea respectively, have been shown to use manganese dioxide (MnO2) rather than [Formula: see text] for sulfur oxidation. The use of different electron acceptors is also dependent on differences in the electron transport chains embedded in the cellular membrane, therefore changes in the membrane, including its lipid composition, are expected but are so far unexplored. Here, we used untargeted lipidomic analysis to reveal changes in the composition of the lipidomes of three representative Sulfurimonas species grown using either [Formula: see text] and MnO2. We found that all Sulfurimonas spp. produce a series of novel phosphatidyldiazoalkyl-diacylglycerol lipids. Ca. Sulfurimonas baltica GD2 adapts its membrane lipid composition depending on the electron acceptors it utilizes for growth and survival. When carrying out MnO2-dependent sulfur oxidation, the novel phosphatidyldiazoalkyl-diacylglycerol headgroup comprises shorter alkyl moieties than when sulfur oxidation is [Formula: see text]-dependent. This is the first report of membrane lipid adaptation when an organism is grown with different electron acceptors. We suggest novel diazoalkyl lipids have the potential to be used as a biomarker for different conditions in redox-stratified systems.
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Affiliation(s)
- Su Ding
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands.
| | - Jan V Henkel
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Ellen C Hopmans
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Nicole J Bale
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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14
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Balakrishna B, Mossin S, Kramer S. Photo-induced metal-free dehydrogenative N-N homo-coupling. Chem Commun (Camb) 2022; 58:10977-10980. [PMID: 36093722 DOI: 10.1039/d2cc04204e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a photo-induced dehydrogenative N-N coupling of diarylimines, diarylamines, carbazoles, and anilines. These homo-coupling reactions require only the combination of readily available di-tert-butyl peroxide (DTBP) and light irradition. The operationally simple protocol works under catalyst- and metal-free conditions and exhibits a good substrate scope. Preliminary mechanistic studies indicate that the reaction proceeds via photo-induced homolytic cleavage of the peroxide followed by hydrogen atom transfer leading to the formation of N-centered radicals.
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Affiliation(s)
- Bugga Balakrishna
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| | - Susanne Mossin
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| | - Søren Kramer
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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15
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Xu Z, DiBello M, Wang Z, Rose JA, Chen L, Li X, Herzon SB. Stereocontrolled Synthesis of the Fully Glycosylated Monomeric Unit of Lomaiviticin A. J Am Chem Soc 2022; 144:16199-16205. [PMID: 35998350 DOI: 10.1021/jacs.2c07631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a stereocontrolled synthesis of 3, the fully glycosylated monomeric unit of the dimeric cytotoxic bacterial metabolite (-)-lomaiviticin A (2). A novel strategy involving convergent, site- and stereoselective coupling of the β,γ-unsaturated ketone 6 and the naphthyl bromide 7 (92%, 15:1 diastereomeric ratio (dr)), followed by radical-based annulation and silyl ether cleavage, provided the tetracycle 5 (57% overall), which contains the carbon skeleton of the aglycon of 3. The β-linked 2,4,6-trideoxy-4-aminoglycoside l-pyrrolosamine was installed in 73% yield and with 15:1 β:α selectivity using a modified Koenigs-Knorr glycosylation. The diazo substituent was introduced via direct diazo transfer to an electron-rich benzoindene (4 → 27). The α-linked 2,6-dideoxyglycoside l-oleandrose was introduced by gold-catalyzed activation of an o-alkynyl glycosylbenzoate (75%, >20:1 α:β selectivity). A carefully orchestrated endgame sequence then provided efficient access to 3. Cell viability studies indicated that monomer 3 is not cytotoxic at concentrations up to 1 μM, providing conclusive evidence that the dimeric structure of (-)-lomaiviticin A (2) is required for cytotoxic effects. The preparation of 3 provides a foundation to complete the synthesis of (-)-lomaiviticin A (2) itself.
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Affiliation(s)
- Zhi Xu
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States
| | - Mikaela DiBello
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States
| | - Zechun Wang
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States
| | - John A Rose
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States
| | - Lei Chen
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States
| | - Xin Li
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut06520, United States.,Departments of Pharmacology and Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut06520, United States
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16
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Nunez Avila AG, Deschênes-Simard B, Arnold JE, Morency M, Chartrand D, Maris T, Berger G, Day GM, Hanessian S, Wuest JD. Surprising Chemistry of 6-Azidotetrazolo[5,1- a]phthalazine: What a Purported Natural Product Reveals about the Polymorphism of Explosives. J Org Chem 2022; 87:6680-6694. [PMID: 35504046 DOI: 10.1021/acs.joc.2c00369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
6-Azidotetrazolo[5,1-a]phthalazine (ATPH) is a nitrogen-rich compound of surprisingly broad interest. It is purported to be a natural product, yet it is closely related to substances developed as explosives and is highly polymorphic despite having a nearly planar structure with little flexibility. Seven solid forms of ATPH have been characterized by single-crystal X-ray diffraction. The structures show diverse patterns of molecular organization, including both stacked sheets and herringbone packing. In all cases, N···N and C-H···N interactions play key roles in ensuring molecular cohesion. The high polymorphism of ATPH appears to arise in part from the ability of virtually every atom of nitrogen and hydrogen in the molecule to take part in close N···N and C-H···N contacts. As a result, adjacent molecules can adopt many different relative orientations that are energetically similar, thereby generating a polymorphic landscape with an unusually high density of potential structures. This landscape has been explored in detail by the computational prediction of crystal structures. Studying ATPH has provided insights into the field of energetic materials, where access to multiple polymorphs can be used to improve performance and clarify how it depends on molecular packing. In addition, our work with ATPH shows how valuable insights into molecular crystallization, often gleaned from statistical analyses of structural databases, can also come from in-depth empirical and theoretical studies of single compounds that show distinctive behavior.
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Affiliation(s)
| | | | - Joseph E Arnold
- School of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K
| | - Mathieu Morency
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Daniel Chartrand
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Thierry Maris
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Gilles Berger
- Microbiologie, Chimie bioorganique et macromoléculaire, Faculté de Pharmacie, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Bruxelles 1050, Belgium
| | - Graeme M Day
- School of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K
| | - Stephen Hanessian
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - James D Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
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17
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He HY, Niikura H, Du YL, Ryan KS. Synthetic and biosynthetic routes to nitrogen-nitrogen bonds. Chem Soc Rev 2022; 51:2991-3046. [PMID: 35311838 DOI: 10.1039/c7cs00458c] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nitrogen-nitrogen bond is a core feature of diverse functional groups like hydrazines, nitrosamines, diazos, and pyrazoles. Such functional groups are found in >300 known natural products. Such N-N bond-containing functional groups are also found in significant percentage of clinical drugs. Therefore, there is wide interest in synthetic and enzymatic methods to form nitrogen-nitrogen bonds. In this review, we summarize synthetic and biosynthetic approaches to diverse nitrogen-nitrogen-bond-containing functional groups, with a focus on biosynthetic pathways and enzymes.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada. .,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Haruka Niikura
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
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18
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Shafran YM, Hussein AA, Beliaev NA, Shevyrin VA, Shityakov S, Beryozkina TV, Bakulev VA. Selective Synthesis of Azoloyl NH-1,2,3-Triazoles and Azolyl Diazoketones: Experimental and Computational Insights. ACS OMEGA 2022; 7:5008-5031. [PMID: 35187318 PMCID: PMC8851643 DOI: 10.1021/acsomega.1c05898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Here, we report that the reaction of enaminones, from a class of azole series, with sulfonyl azides leads to a difficult-to-separate mixture of two pairs of compounds: (1) 4-azoloyl-NH-1,2,3-triazoles with sulfonamides and (2) azolyl diazoketones with N-sulfonamidines, as a result of the implementation of two competing reactions. On one hand, the electron-donating methyl or methoxy group in the aryl para-position of arylsulfonyl azides favors the production of NH-1,2,3-triazoles together with sulfonamides. On the other hand, the use of highly electrophilic 4-nitrophenylsulfonyl azide promotes the formation of diazoketones and sulfonamidines. It is shown that the direction of each reaction is not only controlled by the nature of the initial enaminones and sulfonyl azides but also depends on the tested solvent. The problem of removing sulfonamides and amidines from the desired products was solved for the first time using new water-soluble enaminones. Based on the experimental and computational studies, the factors contributing to the selective course of alternative reactions were identified, and methods for the synthesis of azoloyl-NH-1,2,3-triazoles and azolyl diazoketones were developed. Density functional theory (DFT) results have shown that the 1,3-dipolar cycloaddition is totally driven toward one single regioisomer with a high asynchronous bond formation, and the introduction of an electron-deficient group in sulfonyl azides induces faster cycloaddition. Additionally, DFT calculations were used to gain further mechanistic insights on the reaction studied here.
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Affiliation(s)
- Yuri M. Shafran
- Technology
for Organic Synthesis Department, Ural Federal
University, 19 Mira Street, Ekaterinburg 620002, Russia
| | - Aqeel A. Hussein
- Department
of Pharmacy, College of Medicine, Komar
University of Science and Technology, Sulaymaniyah 46002, Kurdistan Region, Iraq
| | - Nikolai A. Beliaev
- Technology
for Organic Synthesis Department, Ural Federal
University, 19 Mira Street, Ekaterinburg 620002, Russia
| | - Vadim A. Shevyrin
- Technology
for Organic Synthesis Department, Ural Federal
University, 19 Mira Street, Ekaterinburg 620002, Russia
| | - Sergey Shityakov
- Laboratory
of Chemoinformatics, Infochemistry Scientific Center, ITMO University, 9 Lomonosova Street, Saint-Petersburg 191002, Russia
| | - Tetyana V. Beryozkina
- Technology
for Organic Synthesis Department, Ural Federal
University, 19 Mira Street, Ekaterinburg 620002, Russia
| | - Vasiliy A. Bakulev
- Technology
for Organic Synthesis Department, Ural Federal
University, 19 Mira Street, Ekaterinburg 620002, Russia
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19
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Yahiaoui O, Murray LAM, Zhao F, Moore BS, Houk KN, Liu F, George JH. A Diazo-Hooker Reaction, Inspired by the Biosynthesis of Azamerone. Org Lett 2022; 24:490-495. [PMID: 34994200 PMCID: PMC9006554 DOI: 10.1021/acs.orglett.1c03810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Motivated by the biosynthesis of azamerone, we report the first example of a diazo-Hooker reaction, which involves the formation of a phthalazine ring system by the oxidative rearrangement of a diazoketone. Computational studies indicate that the diazo-Hooker reaction proceeds via an 8π-electrocyclization followed by ring contraction and aromatization. The biosynthetic origin of the diazoketone functional group was also chemically mimicked using a related natural product, naphterpin, as a model system.
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Affiliation(s)
- Oussama Yahiaoui
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lauren A M Murray
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Fengyue Zhao
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Fang Liu
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jonathan H George
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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20
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Martin ML, Boyer A. Controlling Selectivity in the Synthesis of
Z
‐α,β‐Unsaturated Amidines by Tuning the
N
‐Sulfonyl Group in a Rhodium(II) Catalyzed 1,2‐H Shift. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew L. Martin
- School of Chemistry University of Glasgow Joseph Black Building G12 8QQ Glasgow Scotland
| | - Alistair Boyer
- School of Chemistry University of Glasgow Joseph Black Building G12 8QQ Glasgow Scotland
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21
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Dong K, Gurung R, Xu X, Doyle MP. Enantioselective Catalytic Cyclopropanation-Rearrangement Approach to Chiral Spiroketals. Org Lett 2021; 23:3955-3959. [PMID: 33955755 DOI: 10.1021/acs.orglett.1c01113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A highly enantioselective synthesis of chiral heterobicyclic spiroketals is reported via a "one-pot" cyclopropanation-rearrangement (CP-RA) cascade reaction that is sequentially catalyzed by a chiral Rh(II) catalyst and tetrabutylammonium fluoride (TBAF). Exocyclic vinyl substrates form spirocyclopropanes with tert-butyldimethylsilyl-protected enoldiazoacetates in excellent yields and with excellent enantioselectivities when catalyzed by chiral dirhodium(II) carboxylates, and following desilylation with simultaneous rearrangement in the presence of TBAF, they give (S)-spiroketals in high yields with excellent chirality retention (>95% ee).
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Affiliation(s)
- Kuioyng Dong
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Raj Gurung
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Xinfang Xu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Michael P Doyle
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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22
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Kawai S, Sugaya Y, Hagihara R, Tomita H, Katsuyama Y, Ohnishi Y. Complete Biosynthetic Pathway of Alazopeptin, a Tripeptide Consisting of Two Molecules of 6-Diazo-5-oxo-l-norleucine and One Molecule of Alanine. Angew Chem Int Ed Engl 2021; 60:10319-10325. [PMID: 33624374 DOI: 10.1002/anie.202100462] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 11/06/2022]
Abstract
DON (6-diazo-5-oxo-l-norleucine), a diazo-containing amino acid, has been studied for more than 60 years as a potent antitumor agent, but its biosynthesis has not been elucidated. Here we reveal the complete biosynthetic pathway of alazopeptin, the tripeptide Ala-DON-DON, which has antitumor activity, by gene inactivation and in vitro analysis of recombinant enzymes. We also established heterologous production of N-acetyl-DON in Streptomyces albus. DON is synthesized from lysine by three enzymes and converted to alazopeptin by five enzymes and one carrier protein. Most interestingly, transmembrane protein AzpL was indicated to catalyze diazotization using 5-oxolysine and nitrous acid as substrates. Site-directed mutagenesis of AzpL indicated that the hydroxy group of Tyr-93 is important for the diazotization. These findings expand our knowledge of the enzymology of N-N bond formation.
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Affiliation(s)
- Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuko Sugaya
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryota Hagihara
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroya Tomita
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
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23
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Kawai S, Sugaya Y, Hagihara R, Tomita H, Katsuyama Y, Ohnishi Y. Complete Biosynthetic Pathway of Alazopeptin, a Tripeptide Consisting of Two Molecules of 6‐Diazo‐5‐oxo‐
l
‐norleucine and One Molecule of Alanine. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seiji Kawai
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yuko Sugaya
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Ryota Hagihara
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroya Tomita
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
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24
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Chen L, Deng Z, Zhao C. Nitrogen-Nitrogen Bond Formation Reactions Involved in Natural Product Biosynthesis. ACS Chem Biol 2021; 16:559-570. [PMID: 33721494 DOI: 10.1021/acschembio.1c00052] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Construction of nitrogen-nitrogen bonds involves sophisticated biosynthetic mechanisms to overcome the difficulties inherent to the nucleophilic nitrogen atom of amine. Over the past decade, a multitude of reactions responsible for nitrogen-nitrogen bond formation in natural product biosynthesis have been uncovered. On the basis of the intrinsic properties of these reactions, this Review classifies these reactions into three categories: comproportionation, rearrangement, and radical recombination reactions. To expound the metallobiochemistry underlying nitrogen-nitrogen bond formation reactions, we discuss the enzymatic mechanisms in comparison to well characterized canonical heme-dependent enzymes, mononuclear nonheme iron-dependent enzymes, and nonheme di-iron enzymes. We also illuminate the intermediary properties of nitrogen oxide species NO2-, NO+, and N2O3 in nitrogen-nitrogen bond formation reactions with clues derived from inorganic nitrogen metabolism driven by anammox bacteria and nitrifying bacteria. These multidimentional discussions will provide further insights into the mechanistic proposals of nitrogen-nitrogen bond formation in natural product biosynthesis.
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Affiliation(s)
- Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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25
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Jamshaid S, Devkota S, Lee YR. Catalyst- and Substituent-Controlled Regio- and Stereoselective Synthesis of Indolyl Acrylates by Lewis-Acid-Catalyzed Direct Functionalization of 3-Formylindoles with Diazo Esters. Org Lett 2021; 23:2140-2146. [PMID: 33650877 DOI: 10.1021/acs.orglett.1c00277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A facile and efficient In(OTf)3- and BF3·OEt2-catalyzed direct transformation of 3-formylindoles with diazo esters has been developed for synthesizing diverse and functionalized indolyl acrylates. This one-pot protocol furnishes various (Z)-α-hydroxy-β-indolyl acrylates, (E)-β-(2-alkoxy-2-oxoethoxy)-α-indolyl acrylates, and (Z)-3-hydroxy-2-indolyl acrylates by a catalyst- and substituent-controlled, regio- and stereoselective cascade reaction. The protocol has several advantages, including low loading of the catalyst, mild reaction conditions, broad scope, and high functional group tolerance. The synthesized compounds can be further converted into diversely functionalized materials.
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Affiliation(s)
- Sana Jamshaid
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Shreedhar Devkota
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Yong Rok Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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26
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Kaneko M, Li Z, Burk M, Colis L, Herzon SB. Synthesis and Biological Evaluation of (2 S,2' S)-Lomaiviticin A. J Am Chem Soc 2021; 143:1126-1132. [PMID: 33410680 PMCID: PMC8174553 DOI: 10.1021/jacs.0c11960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
(-)-Lomaiviticin A (1) is a genotoxic C2-symmetric metabolite that arises from the formal dimerization of two bis(glycosylated) diazotetrahydrobenzo[b]fluorenes. Here we present a synthesis of the monomer 17 and its coupling to form (2S,2'S)-lomaiviticin A (4), an unnatural diastereomer of 1. (2S,2'S)-Lomaiviticin A (4) is significantly less genotoxic, a result we attribute to changes in the orientation of the diazofluorene and carbohydrate residues, relative to 1. These data bring the importance of the configuration of the conjoining bond to light and place the total synthesis of 1 itself within reach.
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Affiliation(s)
- Miho Kaneko
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Zhenwu Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Matthew Burk
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Laureen Colis
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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27
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Synthesis and structure of dialkyl (Z)-3-amino-2-cyano-4-diazopent-2-enedioates. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02712-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Schuster CH, Dropinski JF, Shevlin M, Li H, Chen S. Ruthenium-Catalyzed Enantioselective Hydrogenation of Hydrazones. Org Lett 2020; 22:7562-7566. [PMID: 32946691 DOI: 10.1021/acs.orglett.0c02756] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prochiral hydrazones undergo efficient and highly selective hydrogenation in the presence of a chiral diphosphine ruthenium catalyst, yielding enantioenriched hydrazine products (up to 99% ee). The mild reaction conditions and broad functional group tolerance of this method allow access to versatile chiral hydrazine building blocks containing aryl bromide, heteroaryl, alkyl, cycloalkyl, and ester substituents. This method was also demonstrated on >150 g scale, providing a valuable hydrazine intermediate en route to an active pharmaceutical ingredient.
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Affiliation(s)
- Christopher H Schuster
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - James F Dropinski
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Michael Shevlin
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Hongming Li
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Song Chen
- Department of Synthetic Chemistry, Pharmaron Beijing Co., Ltd., No. 6, Tai-He Road, BDA, Beijing, 100176, P. R. China
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29
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Zeng Q, He C, Zhou S, Dong K, Qiu L, Xu X. Dirhodium(II)‐Catalyzed Cyclopropanation of Alkyne‐Containing α‐Diazoacetates for the Synthesis of Cycloalkynes. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qian Zeng
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 People's Republic of China
| | - Ciwang He
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 People's Republic of China
| | - Su Zhou
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat-sen University Guangzhou 510006 People's Republic of China
| | - Kuiyong Dong
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 People's Republic of China
| | - Lihua Qiu
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 People's Republic of China
| | - Xinfang Xu
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 People's Republic of China
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat-sen University Guangzhou 510006 People's Republic of China
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30
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Mügge C, Heine T, Baraibar AG, van Berkel WJH, Paul CE, Tischler D. Flavin-dependent N-hydroxylating enzymes: distribution and application. Appl Microbiol Biotechnol 2020; 104:6481-6499. [PMID: 32504128 PMCID: PMC7347517 DOI: 10.1007/s00253-020-10705-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 02/06/2023]
Abstract
Amino groups derived from naturally abundant amino acids or (di)amines can be used as "shuttles" in nature for oxygen transfer to provide intermediates or products comprising N-O functional groups such as N-hydroxy, oxazine, isoxazolidine, nitro, nitrone, oxime, C-, S-, or N-nitroso, and azoxy units. To this end, molecular oxygen is activated by flavin, heme, or metal cofactor-containing enzymes and transferred to initially obtain N-hydroxy compounds, which can be further functionalized. In this review, we focus on flavin-dependent N-hydroxylating enzymes, which play a major role in the production of secondary metabolites, such as siderophores or antimicrobial agents. Flavoprotein monooxygenases of higher organisms (among others, in humans) can interact with nitrogen-bearing secondary metabolites or are relevant with respect to detoxification metabolism and are thus of importance to understand potential medical applications. Many enzymes that catalyze N-hydroxylation reactions have specific substrate scopes and others are rather relaxed. The subsequent conversion towards various N-O or N-N comprising molecules is also described. Overall, flavin-dependent N-hydroxylating enzymes can accept amines, diamines, amino acids, amino sugars, and amino aromatic compounds and thus provide access to versatile families of compounds containing the N-O motif. Natural roles as well as synthetic applications are highlighted. Key points • N-O and N-N comprising natural and (semi)synthetic products are highlighted. • Flavin-based NMOs with respect to mechanism, structure, and phylogeny are reviewed. • Applications in natural product formation and synthetic approaches are provided. Graphical abstract .
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Affiliation(s)
- Carolin Mügge
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, Faculty of Chemistry and Physics, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Alvaro Gomez Baraibar
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
- Rottendorf Pharma GmbH, Ostenfelder Str. 51-61, 59320, Ennigerloh, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, HZ 2629, Delft, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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31
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Rose JA, Mahapatra S, Li X, Wang C, Chen L, Swick SM, Herzon SB. Synthesis of the bis(cyclohexenone) core of (-)-lomaiviticin A. Chem Sci 2020; 11:7462-7467. [PMID: 34123029 PMCID: PMC8159427 DOI: 10.1039/d0sc02770g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
(-)-Lomaiviticin A is a complex C 2-symmetric bacterial metabolite comprising two diazotetrahydrobenzo[b]fluorene (diazofluorene) residues and four 2,6-dideoxy glycosides, α-l-oleandrose and N,N-dimethyl-β-l-pyrrolosamine. The two halves of lomaiviticin A are linked by a single carbon-carbon bond oriented syn with respect to the oleandrose residues. While many advances toward the synthesis of lomaiviticin A have been reported, including synthesis of the aglycon, a route to the bis(cyclohexenone) core bearing any of the carbohydrate residues has not been disclosed. Here we describe a short route to a core structure of lomaiviticin A bearing two α-l-oleandrose residues. The synthetic route features a Stille coupling to form the conjoining carbon-carbon bond of the target and a double reductive transposition to establish the correct stereochemistry at this bond. Two synthetic routes were developed to elaborate the reductive transposition product to the bis(cyclohexenone) target. The more efficient pathway features an interrupted Barton vinyl iodide synthesis followed by oxidative elimination of iodide to efficiently establish the enone functionalities in the target. The bis(cyclohexenone) product may find use in a synthesis of lomaiviticin A itself.
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Affiliation(s)
- John A Rose
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA
| | - Subham Mahapatra
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA
| | - Xin Li
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA
| | - Chao Wang
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA
| | - Lei Chen
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA
| | - Steven M Swick
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA
| | - Seth B Herzon
- Department of Chemistry, Yale University New Haven Connecticut 06520 USA .,Department of Pharmacology, Yale School of Medicine New Haven Connecticut 06520 USA
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32
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Dong S, Fu X, Xu X. [3+2]‐Cycloaddition of Catalytically Generated Pyridinium Ylide: A General Access to Indolizine Derivatives. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000276] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shanliang Dong
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 China
| | - Xiang Fu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat-sen University Guangzhou 510006 China
| | - Xinfang Xu
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat-sen University Guangzhou 510006 China
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33
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Bernardim B, Dunsmore L, Li H, Hocking B, Nuñez-Franco R, Navo CD, Jiménez-Osés G, Burtoloso ACB, Bernardes GJL. Precise Installation of Diazo-Tagged Side-Chains on Proteins to Enable In Vitro and In-Cell Site-Specific Labeling. Bioconjug Chem 2020; 31:1604-1610. [DOI: 10.1021/acs.bioconjchem.0c00232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Barbara Bernardim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - He Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Brad Hocking
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Reyes Nuñez-Franco
- Computational Chemistry Lab, CIC bioGUNE-BRTA, Derio, Bizkaia, 48160, Spain
| | - Claudio D. Navo
- Computational Chemistry Lab, CIC bioGUNE-BRTA, Derio, Bizkaia, 48160, Spain
| | | | - Antonio C. B. Burtoloso
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Joao Dagnone, 1100, CEP 13563-120, São Carlos, São Paolo, Brazil
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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34
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Katsuyama Y. Mining novel biosynthetic machineries of secondary metabolites from actinobacteria. Biosci Biotechnol Biochem 2019; 83:1606-1615. [DOI: 10.1080/09168451.2019.1606700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ABSTRACT
Secondary metabolites produced by actinobacteria have diverse structures and important biological activities, making them a useful source of drug development. Diversity of the secondary metabolites indicates that the actinobacteria exploit various chemical reactions to construct a structural diversity. Thus, studying the biosynthetic machinery of these metabolites should result in discovery of various enzymes catalyzing interesting and useful reactions. This review summarizes our recent studies on the biosynthesis of secondary metabolites from actinobacteria, including the biosynthesis of nonproteinogenic amino acids used as building blocks of nonribosomal peptides, the type II polyketide synthase catalyzing polyene scaffold, the nitrous acid biosynthetic pathway involved in secondary metabolite biosynthesis and unique cytochrome P450 catalyzing nitrene transfer. These findings expand the knowledge of secondary metabolite biosynthesis machinery and provide useful tools for future bioengineering.
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Affiliation(s)
- Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Japan
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35
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Nagode SB, Kant R, Rastogi N. Hantzsch Ester-Mediated Benzannulation of Diazo Compounds under Visible Light Irradiation. Org Lett 2019; 21:6249-6254. [DOI: 10.1021/acs.orglett.9b02135] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Savita B. Nagode
- Academy of Scientific and Innovative Research, New Delhi 110001, India
| | | | - Namrata Rastogi
- Academy of Scientific and Innovative Research, New Delhi 110001, India
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36
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Dong K, Pei C, Zeng Q, Qiu L, Hu W, Qian Y, Xu X. Copper-catalyzed [4+1]-annulation of 2-alkenylindoles with diazoacetates: a facile access to dihydrocyclopenta[b]indoles. Chem Commun (Camb) 2019; 55:6393-6396. [DOI: 10.1039/c9cc02257k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A copper-catalyzed [4+1]-annulation of 2-vinylindoles with diazoacetates: a facile access to the dihydrocyclopenta[b]indoles bearing two contiguous all-carbon quaternary centers.
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Affiliation(s)
- Kuiyong Dong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- China
| | - Chao Pei
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Qian Zeng
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Lihua Qiu
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Wenhao Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- China
| | - Yu Qian
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- China
| | - Xinfang Xu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- China
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37
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Xie S, Yan Z, Li Y, Song Q, Ma M. Intrinsically Safe and Shelf-Stable Diazo-Transfer Reagent for Fast Synthesis of Diazo Compounds. J Org Chem 2018; 83:10916-10921. [PMID: 30122034 DOI: 10.1021/acs.joc.8b01587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a crystalline compound 2-azido-4,6-dimethoxy-1,3,5-triazine (ADT) as an intrinsically safe, highly efficient, and shelf-stable diazo-transfer reagent. Because the decomposition of ADT is an endothermal process (Δ H = 30.3 kJ mol-1), ADT is intrinsically nonexplosive, as proved by thermal, friction, and impact tests. The diazo-transfer reaction based on ADT gives diazo compounds in excellent yields within several minutes at room temperature. ADT is very stable upon >1 year storage under air at room temperature.
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Affiliation(s)
- Shibo Xie
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Innovation Center of Chemistry for Energy Materials), Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Ziqiang Yan
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Innovation Center of Chemistry for Energy Materials), Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Yuanheng Li
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Innovation Center of Chemistry for Energy Materials), Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Qun Song
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Innovation Center of Chemistry for Energy Materials), Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Mingming Ma
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Innovation Center of Chemistry for Energy Materials), Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
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38
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Hock KJ, Koenigs RM. The Generation of Diazo Compounds in Continuous-Flow. Chemistry 2018; 24:10571-10583. [PMID: 29575129 DOI: 10.1002/chem.201800136] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/13/2018] [Indexed: 01/19/2023]
Abstract
Toxic, cancerogenic and explosive-these attributes are typically associated with diazo compounds. Nonetheless, diazo compounds are nowadays a highly demanded class of reagents for organic synthesis, yet the concerns with regards to safe and scalable transformations of these compounds are still exceptionally high. Lately, the research area of the continuous-flow synthesis of diazo compounds attracted significant interest and a whole variety of protocols for their "on-demand" preparation have been realized to date. This concept article focuses on the recent developments using continuous-flow technologies to access diazo compounds; thus minimizing risks and hazards when working with this particular class of compounds. In this article we discuss these concepts and highlight different pre-requisites to access and to perform downstream functionalization reaction.
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Affiliation(s)
- Katharina J Hock
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Rene M Koenigs
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
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39
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Waldman AJ, Balskus EP. Discovery of a Diazo-Forming Enzyme in Cremeomycin Biosynthesis. J Org Chem 2018; 83:7539-7546. [PMID: 29771512 DOI: 10.1021/acs.joc.8b00367] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The molecular architectures and potent bioactivities of diazo-containing natural products have attracted the interest of synthetic and biological chemists. Despite this attention, the biosynthetic enzymes involved in diazo group construction have not been identified. Here, we show that the ATP-dependent enzyme CreM installs the diazo group in cremeomycin via late-stage N-N bond formation using nitrite. This finding should inspire efforts to use diazo-forming enzymes in biocatalysis and synthetic biology as well as enable genome-based discovery of new diazo-containing metabolites.
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Affiliation(s)
- Abraham J Waldman
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford St , Cambridge , Massachusetts 02138 , United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford St , Cambridge , Massachusetts 02138 , United States
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40
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Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C. Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environ Microbiol 2017; 19:4939-4952. [PMID: 29098760 PMCID: PMC5767755 DOI: 10.1111/1462-2920.13971] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/22/2017] [Indexed: 01/08/2023]
Abstract
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.
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Affiliation(s)
- Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Man-Young Jung
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 362-763, South Korea
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ping Han
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Inhoffenstr. 7B, Braunschweig 38124, Germany
| | - Luis A Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 362-763, South Korea
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, L'Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully CEDEX, France
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
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41
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Mehta G, Sengupta S. Progress in the total synthesis of epoxyquinone natural products: An update. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.09.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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Abstract
(-)-Lomaiviticin A (4) is a complex C2-symmetric bacterial metabolite that contains two diazofluorene functional groups. The diazofluorene consists of naphthoquinone, cyclopentadiene, and diazo substituents fused through a σ- and π-bonding network. Additionally, (-)-lomaiviticin A (4) is a potent cytotoxin, with half-maximal inhibitory potency (IC50) values in the low nanomolar range against many cancer cell lines. Because of limitations in supply, its mechanism of action had remained a "black box" since its isolation in the early 2000s. In this Account, I describe how studies directed toward the total synthesis of (-)-lomaiviticin A (4) provided a platform to elucidate the emergent properties of this metabolite and thereby connect chemical reactivity with cellular phenotype. We first developed a convergent strategy to prepare the diazofluorene (9 + 10 → 13). We then adapted this chemistry to the synthesis of lomaiviticin aglycon (21/22) and the natural monomeric diazofluorene (-)-kinamycin F (3). The key step in the lomaiviticin aglycon (21/22) synthesis involved the stereoselective oxidative coupling of two monomeric diazofluorenes (2 × 18 → 20) to establish the cojoining carbon-carbon bond of the target. As the absolute stereochemistry of the aglycon and carbohydrate residues of (-)-lomaiviticin A (4) were unknown, we developed a semisynthetic route to the metabolite that proceeds in one step and 42% yield by diazo transfer to the more abundant isolate (-)-lomaiviticin C (6). This allowed us to complete the stereochemical assignment of (-)-lomaiviticin A (4) and provided a renewable source of material. Using this material, we established that the remarkable cytotoxic effects of (-)-lomaiviticin A (4) derive from the induction of highly toxic double-strand breaks (DSBs) in DNA. At the molecular level, 1,7-nucleophilic additions to each electrophilic diazofluorene trigger homolytic decomposition pathways that produce sp2 radicals at the carbon atoms of each diazo group. These radicals abstract hydrogen atoms from the deoxyribose of DNA, a process known to initiate strand cleavage. NMR spectroscopy and molecular mechanics simulations were used to elucidate the mode of DNA binding. These studies showed that both diazofluorenes of (-)-lomaiviticin A (4) penetrate into the duplex. This mode of non-covalent binding places each diazo carbon atom in close proximity to each DNA strand. Throughout these studies, isolates containing one diazofluorene, such as (-)-lomaiviticin C (6) and (-)-kinamycin C (2), were used as controls. Consistent with our mechanistic model, these compounds do not induce DSBs in DNA and are several orders of magnitude less potent. Reactivity studies suggest that (-)-lomaiviticin A (4) is more electrophilic than simple monomeric diazofluorenes. We attribute this to through-space delocalization of the developing negative charge in the transition state for 1,7-addition. Consistent with this mechanism of action, (-)-lomaiviticin A (4) displays selective low-picomolar potencies toward DNA DSB repair-deficient cell types. The emergent properties of (-)-lomaiviticin A (4) derive from the specific arrangement of diazo, naphthoquinone, cyclopentadiene, and ketone functional groups. These functional groups work together to yield, essentially, a masked vinyl radical that can be exposed under biological conditions. Furthermore, the rotational symmetry of the metabolite, deriving from dimerization, allows it to interact with the antiparallel symmetry of DNA and affect cleavage of the duplex.
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Affiliation(s)
- Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States. Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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43
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Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017; 45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
| | - Stefanie Geigle
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
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44
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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45
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Dembitsky VM, Gloriozova TA, Poroikov VV. Pharmacological and Predicted Activities of Natural Azo Compounds. NATURAL PRODUCTS AND BIOPROSPECTING 2017; 7:151-169. [PMID: 28054247 PMCID: PMC5315673 DOI: 10.1007/s13659-016-0117-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/26/2016] [Indexed: 05/16/2023]
Abstract
This paper describes research on natural azo compounds isolated from fungi, plant, bacteria, and invertebrates. More than 120 biologically active diazene containing alkaloids demonstrate confirmed pharmacological activity, including antitumor, antimicrobial, and antibacterial effects. The structures, origin, and biological activities of azo compounds are reviewed. Utilizing the computer program PASS, some structure-activity relationship new activities are also predicted, pointing toward possible new applications of these compounds. This article emphasizes the role of natural azo compounds as an important source of drug prototypes and leads for drug discovery.
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Affiliation(s)
- Valery M Dembitsky
- National Scientific Center of Marine Biology, 17 Palchevsky Str., Vladivostok, Russia, 690041.
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46
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You M, Liu L, Zhang W. The covalently bound diazo group as an infrared probe for hydrogen bonding environments. Phys Chem Chem Phys 2017; 19:19420-19426. [DOI: 10.1039/c7cp01867c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bandwidth or position of diazo groups can probe the polarizability and HBA, or density of HBD groups.
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Affiliation(s)
- Min You
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
| | - Liyuan Liu
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
| | - Wenkai Zhang
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
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47
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Geigle SN, Wyss LA, Sturla SJ, Gillingham DG. Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction. Chem Sci 2017; 8:499-506. [PMID: 28451197 PMCID: PMC5341205 DOI: 10.1039/c6sc03502g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022] Open
Abstract
Cu(i) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted - other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(i)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage.
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Affiliation(s)
- Stefanie N Geigle
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , CH-4056 , Basel , Switzerland .
| | - Laura A Wyss
- Department of Health Sciences and Technology , ETH Zurich , Schmelzbergstrasse 9 , CH-8092 Zurich , Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology , ETH Zurich , Schmelzbergstrasse 9 , CH-8092 Zurich , Switzerland
| | - Dennis G Gillingham
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , CH-4056 , Basel , Switzerland .
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48
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Abstract
Diazo groups have broad and tunable reactivity. That and other attributes endow diazo compounds with the potential to be valuable reagents for chemical biologists. The presence of diazo groups in natural products underscores their metabolic stability and anticipates their utility in a biological context. The chemoselectivity of diazo groups, even in the presence of azido groups, presents many opportunities. Already, diazo compounds have served as chemical probes and elicited novel modifications of proteins and nucleic acids. Here, we review advances that have facilitated the chemical synthesis of diazo compounds, and we highlight applications of diazo compounds in the detection and modification of biomolecules.
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Affiliation(s)
- Kalie A. Mix
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Matthew R. Aronoff
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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49
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Yu B, Chen X, Cong H, Shu X, Peng Q. Photosensitive diazotized poly(ethylene glycol) covalent capillary coatings for analysis of proteins by capillary electrophoresis. Anal Bioanal Chem 2016; 408:6781-8. [PMID: 27475442 DOI: 10.1007/s00216-016-9804-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 07/09/2016] [Accepted: 07/18/2016] [Indexed: 11/30/2022]
Abstract
A new method for the fabrication of covalently cross-linked capillary coatings of poly(ethylene glycol) (PEG) is described using diazotized PEG (diazo-PEG) as a new photosensitive coating agent. The film of diazo-PEG depends on ionic bonding and was first prepared on the inner surface of capillary by self-assembly, and ionic bonding was converted into covalent bonding after reaction of ultraviolet light with diazo groups through unique photochemical reaction. The covalently bonded coating impedance adsorption of protein on the central surface of capillary and hence the four proteins ribonuclease A, cytochrome c, bovine serum albumin, and lysosome can be baseline separated by using capillary electrophoresis (CE). The covalently cross-linked diazo-PEG capillary column coatings not only improved the CE separation performance for proteins compared to non-covalently cross-linked coatings or bare capillary but also showed a remarkable chemical solidity and repeatability. Because photosensitive diazo-PEG took the place of the highly noxious and silane moisture-sensitive coating reagents in the fabrication of covalent coating, this technique shows the advantage of being environment-friendly and having a high efficiency for CE to make the covalently bonded capillaries.
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Affiliation(s)
- Bing Yu
- College of Materials Science and Engineering, Qingdao University, Qingdao, Shandong, 266071, China. .,Laboratory for New Fiber Materials and Modern Textile, Growing Base for State Key Laboratory, Qingdao, Shandong, 266071, China.
| | - Xin Chen
- College of Materials Science and Engineering, Qingdao University, Qingdao, Shandong, 266071, China
| | - Hailin Cong
- College of Materials Science and Engineering, Qingdao University, Qingdao, Shandong, 266071, China. .,Laboratory for New Fiber Materials and Modern Textile, Growing Base for State Key Laboratory, Qingdao, Shandong, 266071, China.
| | - Xi Shu
- College of Materials Science and Engineering, Qingdao University, Qingdao, Shandong, 266071, China
| | - Qiaohong Peng
- College of Materials Science and Engineering, Qingdao University, Qingdao, Shandong, 266071, China
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50
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Shi Y, Gao S. Recent advances of synthesis of fluorenone and fluorene containing natural products. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.02.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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