1
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Yang D, Chiang CH, Wititsuwannakul T, Brooks CL, Zimmerman PM, Narayan ARH. Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction. J Am Chem Soc 2024; 146:34352-34363. [PMID: 39642058 DOI: 10.1021/jacs.4c08420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2024]
Abstract
Non-heme iron (FeII), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of FeII/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features.
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Affiliation(s)
- Di Yang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chang-Hwa Chiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Enhanced Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Wang X, Yang L, Wang S, Wang J, Li K, Naowarojna N, Ju Y, Ye K, Han Y, Yan W, Liu X, Zhang L, Liu P. Characterizing Y224 conformational flexibility in FtmOx1-catalysis using 19F NMR spectroscopy. Catal Sci Technol 2024:d4cy01077a. [PMID: 39669701 PMCID: PMC11629144 DOI: 10.1039/d4cy01077a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Accepted: 10/30/2024] [Indexed: 12/14/2024]
Abstract
α-Ketoglutarate-dependent non-haem iron (αKG-NHFe) enzymes play a crucial role in natural product biosynthesis, and in some cases exhibiting multifunctional catalysis capability. This study focuses on αKG-NHFe enzyme FtmOx1, which catalyzes endoperoxidation, dealkylation, and alcohol oxidation reactions in verruculogen biosynthesis. We explore the hypothesis that the conformational dynamics of the active site Y224 confer the multifunctional activities of FtmOx1-catalysis. Utilizing Y224-to-3,5-difluorotyrosine-substituted FtmOx1, produced via the amber codon suppression method, we conducted 19F NMR characterization to investigate FtmOx1's structural flexibility. Subsequent biochemical and X-ray crystallographic analyses provided insights into how specific conformations of FtmOx1-substrate complexes influence their catalytic activities. These findings underscore the utility of 19F NMR as a powerful tool for elucidating the complex mechanisms of multifunctional enzymes, offering potential avenues for developing biocatalytic processes to produce novel therapeutic agents harnessing their unique catalytic properties.
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Affiliation(s)
- Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Lingyun Yang
- iHuman Institute, Shanghaitech University Shanghai 201210 China
| | - Shenlin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Jun Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Kelin Li
- Department of Chemistry, Boston University Boston Massachusetts 02215 USA
| | - Nathchar Naowarojna
- Program of Chemistry, Faculty of Science and Technology, Sakon Nakhon Rajabhat University Sakon Nakhon 47000 Thailand
| | - Yi Ju
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Ke Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Yuchen Han
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Wupeng Yan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Pinghua Liu
- Department of Chemistry, Boston University Boston Massachusetts 02215 USA
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3
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Quan Z, Awakawa T. Recent developments in the engineered biosynthesis of fungal meroterpenoids. Beilstein J Org Chem 2024; 20:578-588. [PMID: 38505236 PMCID: PMC10949012 DOI: 10.3762/bjoc.20.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Meroterpenoids are hybrid compounds that are partially derived from terpenoids. This group of natural products displays large structural diversity, and many members exhibit beneficial biological activities. This mini-review highlights recent advances in the engineered biosynthesis of meroterpenoid compounds with C15 and C20 terpenoid moieties, with the reconstruction of fungal meroterpenoid biosynthetic pathways in heterologous expression hosts and the mutagenesis of key enzymes, including terpene cyclases and α-ketoglutarate (αKG)-dependent dioxygenases, that contribute to the structural diversity. Notable progress in genome sequencing has led to the discovery of many novel genes encoding these enzymes, while continued efforts in X-ray crystallographic analyses of these enzymes and the invention of AlphaFold2 have facilitated access to their structures. Structure-based mutagenesis combined with applications of unnatural substrates has further diversified the catalytic repertoire of these enzymes. The information in this review provides useful knowledge for the design of biosynthetic machineries to produce a variety of bioactive meroterpenoids.
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Affiliation(s)
- Zhiyang Quan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takayoshi Awakawa
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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4
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Zhou L, Awakawa T, Ushimaru R, Kanaida M, Abe I. Characterization of Aziridine-Forming α-Ketoglutarate-Dependent Oxygenase in l-Isovaline Biosynthesis. Org Lett 2024; 26:724-727. [PMID: 38227980 DOI: 10.1021/acs.orglett.3c04185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
l-Isovaline biosynthesis by TqaLFM-ti from Tolypocladium inflatum was demonstrated in vitro. The biochemical analysis of the α-ketoglutarate-dependent oxygenase TqaL-ti revealed that it produces (2S,3S)-3-ethyl-3-methylaziridine-2-carboxylic acid from l-isoleucine, thus exhibiting a stereoselectivity different from those of the reported homologues. Remarkably, a single mutation on I295 in TqaL-ti completely exchanged its stereoselectivity to produce the C-3 stereoisomer. TqaFM-ti generates d-isovaline from (2S,3R)-aziridine-2-carboxylic acid, suggesting that the stereochemistry of the TqaL product defines that of isovaline.
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Affiliation(s)
- Lu Zhou
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masahiro Kanaida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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5
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Ushimaru R. Three-membered ring formation catalyzed by α-ketoglutarate-dependent nonheme iron enzymes. J Nat Med 2024; 78:21-32. [PMID: 37980694 PMCID: PMC10764440 DOI: 10.1007/s11418-023-01760-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/21/2023]
Abstract
Epoxides, aziridines, and cyclopropanes are found in various medicinal natural products, including polyketides, terpenes, peptides, and alkaloids. Many classes of biosynthetic enzymes are involved in constructing these ring structures during their biosynthesis. This review summarizes our current knowledge regarding how α-ketoglutarate-dependent nonheme iron enzymes catalyze the formation of epoxides, aziridines, and cyclopropanes in nature, with a focus on enzyme mechanisms.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
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6
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Tao H, Abe I. Oxidative modification of free-standing amino acids by Fe(II)/αKG-dependent oxygenases. ENGINEERING MICROBIOLOGY 2023; 3:100062. [PMID: 39628521 PMCID: PMC11611013 DOI: 10.1016/j.engmic.2022.100062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/06/2024]
Abstract
Fe(II)/α-ketoglutarate (αKG)-dependent oxygenases catalyze the oxidative modification of various molecules, from DNA, RNA, and proteins to primary and secondary metabolites. They also catalyze a variety of biochemical reactions, including hydroxylation, halogenation, desaturation, epoxidation, cyclization, peroxidation, epimerization, and rearrangement. Given the versatile catalytic capability of such oxygenases, numerous studies have been conducted to characterize their functions and elucidate their structure-function relationships over the past few decades. Amino acids, particularly nonproteinogenic amino acids, are considered as important building blocks for chemical synthesis and components for natural product biosynthesis. In addition, the Fe(II)/αKG-dependent oxygenase superfamily includes important enzymes for generating amino acid derivatives, as they efficiently modify various free-standing amino acids. The recent discovery of new Fe(II)/αKG-dependent oxygenases and the repurposing of known enzymes in this superfamily have promoted the generation of useful amino acid derivatives. Therefore, this study will focus on the recent progress achieved from 2019 to 2022 to provide a clear view of the mechanism by which these enzymes have expanded the repertoire of free amino acid oxidative modifications.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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7
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Awakawa T, Liu W, Bai T, Taniguchi T, Abe I. Orthoester formation in fungal meroterpenoid austalide F biosynthesis. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220037. [PMID: 36633279 PMCID: PMC9835590 DOI: 10.1098/rstb.2022.0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/03/2022] [Indexed: 01/13/2023] Open
Abstract
Fungal meroterpenoids are important bioactive natural products. Their biosynthetic machineries are highly diverse, and reconstitutions lead to the production of unnatural meroterpenoids. In this study, heterologous gene expression in Aspergillus oryzae and in vitro assays elucidated the biosynthetic pathway of the orthoester-containing fungal meroterpenoid austalide F. Remarkably, the α-ketoglutarate-dependent oxygenase AstB produces the hemiacetal intermediate, and the methyltransferase AstL transfers a methyl group on it to construct the orthoester functionality. This study presents the extraordinary orthoester biosynthetic machinery and provides valuable insights into the creation of unnatural novel bioactive meroterpenoids through engineered biosynthesis. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Wei Liu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tongxuan Bai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomo Taniguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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8
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Awakawa T, Mori T, Ushimaru R, Abe I. Structure-based engineering of α-ketoglutarate dependent oxygenases in fungal meroterpenoid biosynthesis. Nat Prod Rep 2023; 40:46-61. [PMID: 35642933 DOI: 10.1039/d2np00014h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-heme iron- and α-ketoglutarate-dependent oxygenases (αKG OXs) are key enzymes that play a major role in diversifying the structure of fungal meroterpenoids. They activate a specific C-H bond of the substrate to first generate radical species, which is usually followed by oxygen rebound to produce cannonical hydroxylated products. However, in some cases remarkable chemistry induces dramatic structural changes in the molecular scaffolds, depending on the stereoelectronic characters of the substrate/intermediates and the resulting conformational changes/movements of the active site of the enzyme. Their molecular bases have been extensively investigated by crystallographic structural analyses and structure-based mutagenesis, which revealed intimate structural details of the enzyme reactions. This information facilitates the manipulation of the enzyme reactions to create unnatural, novel molecules for drug discovery. This review summarizes recent progress in the structure-based engineering of αKG OX enzymes, involved in the biosynthesis of polyketide-derived fungal meroterpenoids. The literature published from 2016 through February 2022 is reviewed.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,ACT-X, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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9
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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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10
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Yan D, Matsuda Y. Biosynthetic Elucidation and Structural Revision of Brevione E: Characterization of the Key Dioxygenase for Pathway Branching from Setosusin Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202210938. [DOI: 10.1002/anie.202210938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dexiu Yan
- Department of Chemistry City University of Hong Kong Tat Chee Avenue Kowloon, Hong Kong SAR China
| | - Yudai Matsuda
- Department of Chemistry City University of Hong Kong Tat Chee Avenue Kowloon, Hong Kong SAR China
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11
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Hsiao YH, Huang SJ, Lin EC, Hsiao PY, Toh SI, Chen IH, Xu Z, Lin YP, Liu HJ, Chang CY. Crystal structure of the α-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer. Front Chem 2022; 10:1001311. [PMID: 36176888 PMCID: PMC9513391 DOI: 10.3389/fchem.2022.1001311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
CmnC is an α-ketoglutarate (α-KG)-dependent non-heme iron oxygenase involved in the formation of the l-capreomycidine (l-Cap) moiety in capreomycin (CMN) biosynthesis. CmnC and its homologues, VioC in viomycin (VIO) biosynthesis and OrfP in streptothricin (STT) biosynthesis, catalyze hydroxylation of l-Arg to form β-hydroxy l-Arg (CmnC and VioC) or β,γ-dihydroxy l-Arg (OrfP). In this study, a combination of biochemical characterization and structural determination was performed to understand the substrate binding environment and substrate specificity of CmnC. Interestingly, despite having a high conservation of the substrate binding environment among CmnC, VioC, and OrfP, only OrfP can hydroxylate the substrate enantiomer d-Arg. Superposition of the structures of CmnC, VioC, and OrfP revealed a similar folds and overall structures. The active site residues of CmnC, VioC, and OrfP are almost conserved; however Leu136, Ser138, and Asp249 around the substrate binding pocket in CmnC are replaced by Gln, Gly, and Tyr in OrfP, respectively. These residues may play important roles for the substrate binding. The mutagenesis analysis revealed that the triple mutant CmnCL136Q,S138G,D249Y switches the substrate stereoselectivity from l-Arg to d-Arg with ∼6% relative activity. The crystal structure of CmnCL136Q,S138G,D249Y in complex with d-Arg revealed that the substrate loses partial interactions and adopts a different orientation in the binding site. This study provides insights into the enzyme engineering to α-KG non-heme iron oxygenases for adjustment to the substrate stereoselectivity and development of biocatalysts.
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Affiliation(s)
- Yu-Hsuan Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Szu-Jo Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - En-Chi Lin
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Po-Yun Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Shu-Ing Toh
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - I-Hsuan Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing, China
| | - Yu-Pei Lin
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Hsueh-Ju Liu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- *Correspondence: Chin-Yuan Chang,
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12
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Zhu G, Yan W, Wang X, Cheng R, Naowarojna N, Wang K, Wang J, Song H, Wang Y, Liu H, Xia X, Costello CE, Liu X, Zhang L, Liu P. Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues. JACS AU 2022; 2:1686-1698. [PMID: 35911443 PMCID: PMC9326825 DOI: 10.1021/jacsau.2c00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•CoII•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•FeII•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.
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Affiliation(s)
- Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronghai Cheng
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Kun Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Heng Song
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei Province 430072, China
| | - Yuyang Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hairong Liu
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Xuekui Xia
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Catherine E. Costello
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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13
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Mori T, Nakashima Y, Chen H, Hoshino S, Mitsuhashi T, Abe I. Structure-based redesign of Fe(II)/2-oxoglutarate-dependent oxygenase AndA to catalyze spiro-ring formation. Chem Commun (Camb) 2022; 58:5510-5513. [PMID: 35420093 DOI: 10.1039/d2cc00736c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure- and mechanism-based redesign of the Fe(II)/2-oxoglutarate-dependent oxygenase AndA was performed. The function of AndA was expanded to catalyze a spiro-ring formation reaction from an isomerization reaction. The redesigned AndA variants produced two unnatural novel spiro-ring containing compounds through two and three consecutive oxidation reactions.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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14
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Li X, Xue S, Guo Y, Chang WC. Mechanism of Methyldehydrofosmidomycin Maturation: Use Olefination to Enable Chain Elongation. J Am Chem Soc 2022; 144:8257-8266. [PMID: 35482829 DOI: 10.1021/jacs.2c01924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Utilization of mononuclear iron- and 2-oxoglutarate-dependent (Fe/2OG) enzymes to enable C-H bond functionalization is a widely used strategy to diversify the structural complexity of natural products. Besides those well-studied reactions including hydroxylation, epoxidation, and halogenation, in the biosynthetic pathway of dehydrofosmidomycin, an Fe/2OG enzyme is reported to catalyze desaturation, alkyl chain elongation, along with demethylation in which trimethyl-2-aminoethylphosphonate is converted into methyldehydrofosmidomycin. How this transformation takes place is largely unknown. Herein, we characterized the reactive species, revealed the structure of the reaction intermediate, and used mechanistic probes to investigate the reaction pathway and mechanism. These results led to the elucidation of a two-step process in which the first reaction employs a long-lived Fe(IV)-oxo species to trigger C═C bond installation. During the second reaction, the olefin installed in situ enables C-C bond formation that is accompanied with a C-N bond cleavage and hydroxylation to furnish the alkyl chain elongation and demethylation. This work expands the reaction repertoire of Fe/2OG enzymes by introducing a new pathway to the known C-C bond formation mechanisms utilized by metalloenzymes.
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Affiliation(s)
- Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shan Xue
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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15
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Purdy TN, Moore BS, Lukowski AL. Harnessing ortho-Quinone Methides in Natural Product Biosynthesis and Biocatalysis. JOURNAL OF NATURAL PRODUCTS 2022; 85:688-701. [PMID: 35108487 PMCID: PMC9006567 DOI: 10.1021/acs.jnatprod.1c01026] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The implementation of ortho-quinone methide (o-QM) intermediates in complex molecule assembly represents a remarkably efficient strategy designed by Nature and utilized by synthetic chemists. o-QMs have been taken advantage of in biomimetic syntheses for decades, yet relatively few examples of o-QM-generating enzymes in natural product biosynthetic pathways have been reported. The biosynthetic enzymes that have been discovered thus far exhibit tremendous potential for biocatalytic applications, enabling the selective production of desirable compounds that are otherwise intractable or inherently difficult to achieve by traditional synthetic methods. Characterization of this biosynthetic machinery has the potential to shine a light on new enzymes capable of similar chemistry on diverse substrates, thus expanding our knowledge of Nature's catalytic repertoire. The presently known o-QM-generating enzymes include flavin-dependent oxidases, hetero-Diels-Alderases, S-adenosyl-l-methionine-dependent pericyclases, and α-ketoglutarate-dependent nonheme iron enzymes. In this review, we discuss their diverse enzymatic mechanisms and potential as biocatalysts in constructing natural product molecules such as cannabinoids.
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Affiliation(s)
- Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
| | - April L Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
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16
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Mori T, Yu Z, Tao H, Abe I. Rational Engineering of the Nonheme Iron- and 2-Oxoglutarate-Dependent Oxygenase SptF. Org Lett 2022; 24:1737-1741. [PMID: 35194997 DOI: 10.1021/acs.orglett.2c00409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Fe- and 2-oxoglutarate-dependent oxygenase SptF is a promising powerful biocatalys with unusual catalytic versatility and promiscuity. The site-specific random substitution of N150, I63, and N65, which are involved in substrate interactions, generated three compounds that were not produced by the SptF wild type. The substrate binding mode was dramatically altered by the introduction of only one or two substitutions. These results provide insights into the engineering of Fe- and 2-oxoglutarate-dependent oxygenases for chemoenzymatic syntheses of bioactive compounds.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Ziheng Yu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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17
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Tao H, Mori T, Chen H, Lyu S, Nonoyama A, Lee S, Abe I. Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/α-ketoglutarate-dependent oxygenase SptF. Nat Commun 2022; 13:95. [PMID: 35013177 PMCID: PMC8748661 DOI: 10.1038/s41467-021-27636-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Non-heme iron and α-ketoglutarate-dependent (Fe/αKG) oxygenases catalyze various oxidative biotransformations. Due to their catalytic flexibility and high efficiency, Fe/αKG oxygenases have attracted keen attention for their application as biocatalysts. Here, we report the biochemical and structural characterizations of the unusually promiscuous and catalytically versatile Fe/αKG oxygenase SptF, involved in the biosynthesis of fungal meroterpenoid emervaridones. The in vitro analysis revealed that SptF catalyzes several continuous oxidation reactions, including hydroxylation, desaturation, epoxidation, and skeletal rearrangement. SptF exhibits extremely broad substrate specificity toward various meroterpenoids, and efficiently produced unique cyclopropane-ring-fused 5/3/5/5/6/6 and 5/3/6/6/6 scaffolds from terretonins. Moreover, SptF also hydroxylates steroids, including androsterone, testosterone, and progesterone, with different regiospecificities. Crystallographic and structure-based mutagenesis studies of SptF revealed the molecular basis of the enzyme reactions, and suggested that the malleability of the loop region contributes to the remarkable substrate promiscuity. SptF exhibits great potential as a promising biocatalyst for oxidation reactions.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuang Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Shoukou Lee
- Sumitomo Dainippon Pharma Co., Ltd, Osaka, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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18
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Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase. Proc Natl Acad Sci U S A 2022; 119:2113770119. [PMID: 34969844 PMCID: PMC8740726 DOI: 10.1073/pnas.2113770119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 11/18/2022] Open
Abstract
The completion of the tetracyclic core of etoposide, classified by the World Health Organization as an essential medicine, by the Fe/2OG oxygenase deoxypodophyllotoxin synthase follows a hybrid radical-polar pathway not previously seen in other members of this enzyme class. The implication of a substrate-based benzylic carbocation in this mechanism will inform ongoing efforts to create analogs of this important drug with improved or emergent properties and represents a new route for resolution of the initial substrate radical that is common to members of the class. This study adds to our understanding on a growing number of biochemical transformations in which carbocation intermediates are likely to be crucial. Deoxypodophyllotoxin contains a core of four fused rings (A to D) with three consecutive chiral centers, the last being created by the attachment of a peripheral trimethoxyphenyl ring (E) to ring C. Previous studies have suggested that the iron(II)- and 2-oxoglutarate–dependent (Fe/2OG) oxygenase, deoxypodophyllotoxin synthase (DPS), catalyzes the oxidative coupling of ring B and ring E to form ring C and complete the tetracyclic core. Despite recent efforts to deploy DPS in the preparation of deoxypodophyllotoxin analogs, the mechanism underlying the regio- and stereoselectivity of this cyclization event has not been elucidated. Herein, we report 1) two structures of DPS in complex with 2OG and (±)-yatein, 2) in vitro analysis of enzymatic reactivity with substrate analogs, and 3) model reactions addressing DPS’s catalytic mechanism. The results disfavor a prior proposal of on-pathway benzylic hydroxylation. Rather, the DPS-catalyzed cyclization likely proceeds by hydrogen atom abstraction from C7', oxidation of the benzylic radical to a carbocation, Friedel–Crafts-like ring closure, and rearomatization of ring B by C6 deprotonation. This mechanism adds to the known pathways for transformation of the carbon-centered radical in Fe/2OG enzymes and suggests what types of substrate modification are likely tolerable in DPS-catalyzed production of deoxypodophyllotoxin analogs.
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19
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Tang J, Matsuda Y. Discovery of branching meroterpenoid biosynthetic pathways in Aspergillus insuetus: involvement of two terpene cyclases with distinct cyclization modes. Chem Sci 2022; 13:10361-10369. [PMID: 36277653 PMCID: PMC9473517 DOI: 10.1039/d2sc02994d] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022] Open
Abstract
Branching meroterpenoid biosynthetic pathways were discovered in the fungus Aspergillus insuetus CBS 107.25, in which two terpene cyclases, InsA7 and InsB2, accept the same substrate but generate distinctly cyclized products.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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20
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Li X, Awakawa T, Mori T, Ling M, Hu D, Wu B, Abe I. Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis. J Am Chem Soc 2021; 143:21425-21432. [PMID: 34881885 DOI: 10.1021/jacs.1c11548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Talaromyolides (1-6) are a group of unusual 6/6/6/6/6/6 hexacyclic meroterpenoids with (3R)-6-hydroxymellein and 4,5-seco-drimane substructures, isolated from the marine fungus Talaromyces purpureogenus. We have identified the biosynthetic gene cluster tlxA-J by heterologous expression in Aspergillus, in vitro enzyme assays, and CRISPR-Cas9-based gene inactivation. Remarkably, the heterodimer of non-heme iron (NHI) enzymes, TlxJ-TlxI, catalyzes three steps of oxidation including a key reaction, hydroxylation at C-5 and C-9 of 12, the intermediate with 3-ketohydroxydrimane scaffold, to facilitate a retro-aldol reaction, leading to the construction of the 4,5-secodrimane skeleton and characteristic ketal scaffold of 1-6. The products of TlxJ-TlxI, 1 and 4, were further hydroxylated at C-4'β by another NHI heterodimer, TlxA-TlxC, and acetylated by TlxB to yield the final products, 3 and 6. The X-ray structural analysis coupled with site-directed mutagenesis provided insights into the heterodimer TlxJ-TlxI formation and its catalysis. This is the first report to show that two NHI proteins form a heterodimer for catalysis and utilizes a novel methodology to create functional oxygenase structures in secondary metabolite biosynthesis.
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Affiliation(s)
- Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Meiqi Ling
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Bin Wu
- Ocean College, Zhejiang University, Hangzhou 310058, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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21
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Sogahata K, Ozaki T, Igarashi Y, Naganuma Y, Liu C, Minami A, Oikawa H. Biosynthetic Studies of Phomopsins Unveil Posttranslational Installation of Dehydroamino Acids by UstYa Family Proteins. Angew Chem Int Ed Engl 2021; 60:25729-25734. [PMID: 34608734 DOI: 10.1002/anie.202111076] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 12/29/2022]
Abstract
UstYa family proteins (DUF3328) are widely and specifically distributed in fungi. They are known to be involved in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs) and nonribosomal peptides, and possibly catalyze various reactions, including oxidative cyclization and chlorination. In this study, we focused on phomopsin A, a fungal RiPP consisting of unique nonproteinogenic amino acids. Gene knockout experiments demonstrated that three UstYa homologues, phomYc, phomYd, and phomYe, are essential for the desaturation of amino acid moieties, showing unprecedented function among UstYa family proteins. Sequence similarity network analysis indicated that their amino acid sequences are highly diverged and that most remain uncharacterized, paving the way for genome mining of fungal metabolites with unique modifications.
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Affiliation(s)
- Kaho Sogahata
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuya Igarashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuka Naganuma
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Chengwei Liu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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22
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Sogahata K, Ozaki T, Igarashi Y, Naganuma Y, Liu C, Minami A, Oikawa H. Biosynthetic Studies of Phomopsins Unveil Posttranslational Installation of Dehydroamino Acids by UstYa Family Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kaho Sogahata
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Taro Ozaki
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Yuya Igarashi
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Yuka Naganuma
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Chengwei Liu
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Atsushi Minami
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Hideaki Oikawa
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
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23
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Ren X, Fasan R. Engineered and Artificial Metalloenzymes for Selective C-H Functionalization. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 31:100494. [PMID: 34395950 PMCID: PMC8357270 DOI: 10.1016/j.cogsc.2021.100494] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The direct functionalization of C-H bonds constitutes a powerful strategy to construct and diversify organic molecules. However, controlling the chemo- and site-selectivity of this transformation in particularly complex molecular settings represents a significant challenge. Metalloenzymes are ideal platforms for achieving catalyst-controlled selective C-H bond functionalization as their reactivities can be tuned by protein engineering and/or redesign of their cofactor environment. In this review, we highlight recent progress in the development of engineered and artificial metalloenzymes for C-H functionalization, with a focus on biocatalytic strategies for selective C-H oxyfunctionalization and halogenation as well as C-H amination and C-H carbene insertion via abiological nitrene and carbene transfer chemistries. Engineered heme- and non-heme iron dependent enzymes have emerged as promising scaffolds for executing these transformations with high chemo-, regio- and stereocontrol as well as tunable selectivity. These emerging systems and methodologies have expanded the toolbox of sustainable strategies for organic synthesis and created new opportunities for the generation of chiral building blocks, the late-stage C-H functionalization of complex molecules, and the total synthesis of natural products.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
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24
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Mori T, Zhai R, Ushimaru R, Matsuda Y, Abe I. Molecular insights into the endoperoxide formation by Fe(II)/α-KG-dependent oxygenase NvfI. Nat Commun 2021; 12:4417. [PMID: 34285212 PMCID: PMC8292354 DOI: 10.1038/s41467-021-24685-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/30/2021] [Indexed: 11/08/2022] Open
Abstract
Endoperoxide-containing natural products are a group of compounds with structurally unique cyclized peroxide moieties. Although numerous endoperoxide-containing compounds have been isolated, the biosynthesis of the endoperoxides remains unclear. NvfI from Aspergillus novofumigatus IBT 16806 is an endoperoxidase that catalyzes the formation of fumigatonoid A in the biosynthesis of novofumigatonin. Here, we describe our structural and functional analyses of NvfI. The structural elucidation and mutagenesis studies indicate that NvfI does not utilize a tyrosyl radical in the reaction, in contrast to other characterized endoperoxidases. Further, the crystallographic analysis reveals significant conformational changes of two loops upon substrate binding, which suggests a dynamic movement of active site during the catalytic cycle. As a result, NvfI installs three oxygen atoms onto a substrate in a single enzyme turnover. Based on these results, we propose a mechanism for the NvfI-catalyzed, unique endoperoxide formation reaction to produce fumigatonoid A.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Rui Zhai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- ACT-X, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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25
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Bunno R, Awakawa T, Mori T, Abe I. Aziridine Formation by a Fe II /α-Ketoglutarate Dependent Oxygenase and 2-Aminoisobutyrate Biosynthesis in Fungi. Angew Chem Int Ed Engl 2021; 60:15827-15831. [PMID: 33973699 DOI: 10.1002/anie.202104644] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/03/2021] [Indexed: 11/08/2022]
Abstract
Aziridine is a characteristically reactive molecule with increased bioactivity due to its strained ring structure. Here, we investigated the biosynthesis of 2-aminoisobutyric acid (AIB) in Penicillium, and successfully reconstituted the three-step biosynthesis from L-Val to AIB in vitro. This previously unknown aziridine formation pathway proceeded with the non-heme iron and α-ketoglutarate-dependent (FeII /αKG) oxygenase TqaL, followed by aziridine ring opening by the haloalkanoic acid dehalogenase (HAD)-type hydrolase TqaF, and subsequent oxidative decarboxylation by the NovR/CloR-like non-heme iron oxygenase TqaM. Furthermore, the X-ray crystal structure of the C-N bond forming FeII /αKG oxygenase TqaL was solved at 2.0 Å resolution. This work presents the first molecular basis for aziridine biogenesis, thereby expanding the catalytic repertoire of the FeII /αKG oxygenases. We also report the unique aziridine ring opening by a HAD-type hydrolase and the remarkable oxidative decarboxylation by a non-heme iron oxygenase to produce AIB.
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Affiliation(s)
- Reito Bunno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- PRESTO (Japan) Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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26
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Bunno R, Awakawa T, Mori T, Abe I. Aziridine Formation by a Fe
II
/α‐Ketoglutarate Dependent Oxygenase and 2‐Aminoisobutyrate Biosynthesis in Fungi. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Reito Bunno
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
- PRESTO (Japan) Science and Technology Agency Kawaguchi Saitama 332-0012 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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27
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Awakawa T, Abe I. Reconstitution of Polyketide-Derived Meroterpenoid Biosynthetic Pathway in Aspergillus oryzae. J Fungi (Basel) 2021; 7:jof7060486. [PMID: 34208768 PMCID: PMC8235479 DOI: 10.3390/jof7060486] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 02/03/2023] Open
Abstract
The heterologous gene expression system with Aspergillus oryzae as the host is an effective method to investigate fungal secondary metabolite biosynthetic pathways for reconstruction to produce un-natural molecules due to its high productivity and genetic tractability. In this review, we focus on biosynthetic studies of fungal polyketide-derived meroterpenoids, a group of bioactive natural products, by means of the A. oryzae heterologous expression system. The heterologous expression methods and the biosynthetic reactions are described in detail for future prospects to create un-natural molecules via biosynthetic re-design.
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Affiliation(s)
- Takayoshi Awakawa
- Laboratory of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: (T.A.); (I.A.)
| | - Ikuro Abe
- Laboratory of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: (T.A.); (I.A.)
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28
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Chapman NC, Rutledge PJ. Isopenicillin N Synthase: Crystallographic Studies. Chembiochem 2021; 22:1687-1705. [PMID: 33415840 DOI: 10.1002/cbic.202000743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/01/2021] [Indexed: 02/02/2023]
Abstract
Isopenicillin N synthase (IPNS) is a non-heme iron oxidase (NHIO) that catalyses the cyclisation of tripeptide δ-(l-α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) to bicyclic isopenicillin N (IPN). Over the last 25 years, crystallography has shed considerable light on the mechanism of IPNS catalysis. The first crystal structure, for apo-IPNS with Mn bound in place of Fe at the active site, reported in 1995, was also the first structure for a member of the wider NHIO family. This was followed by the anaerobic enzyme-substrate complex IPNS-Fe-ACV (1997), this complex plus nitric oxide as a surrogate for co-substrate dioxygen (1997), and an enzyme product complex (1999). Since then, crystallography has been used to probe many aspects of the IPNS reaction mechanism, by crystallising the protein with a diversity of substrate analogues and triggering the oxidative reaction by using elevated oxygen pressures to force the gaseous co-substrate throughout protein crystals and maximise synchronicity of turnover in crystallo. In this way, X-ray structures have been elucidated for a range of complexes closely related to and/or directly derived from key intermediates in the catalytic cycle, thereby answering numerous mechanistic questions that had arisen from solution-phase experiments, and posing many new ones. The results of these crystallographic studies have, in turn, informed computational experiments that have brought further insight. These combined crystallographic and computational investigations augment and extend the results of earlier spectroscopic analyses and solution phase studies of IPNS turnover, to enrich our understanding of this important protein and the wider NHIO enzyme family.
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Affiliation(s)
- Nicole C Chapman
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia
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29
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Enzymology and biosynthesis of the orsellinic acid derived medicinal meroterpenoids. Curr Opin Biotechnol 2020; 69:52-59. [PMID: 33383296 DOI: 10.1016/j.copbio.2020.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/02/2020] [Accepted: 11/30/2020] [Indexed: 01/07/2023]
Abstract
The advent of synthetic biology has yielded fruitful studies on orsellinic acid-derived meroterpenoids, which reportedly possess important biological activities. Genomics and transcriptomics have significantly accelerated the discovery of the biosynthetic genes for orsellinic acid-derived fungal and plant meroterpenoids. Subsequently, a well-developed heterologous host provides a convenient platform to generate a supply of useful natural products. Furthermore, in vitro reconstitution and genome editing tools have been increasingly employed as efficient means to fully understand the enzyme reaction mechanisms. With the knowledge of the biosynthetic machinery, combinatorial and engineered biosyntheses have yielded novel molecules with improved bioactivities. These studies will lay the foundation for the production of meroterpenoids with novel medicinal properties.
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30
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Mitsuhashi T, Barra L, Powers Z, Kojasoy V, Cheng A, Yang F, Taniguchi Y, Kikuchi T, Fujita M, Tantillo DJ, Porco JA, Abe I. Exploiting the Potential of Meroterpenoid Cyclases to Expand the Chemical Space of Fungal Meroterpenoids. Angew Chem Int Ed Engl 2020; 59:23772-23781. [PMID: 32931152 PMCID: PMC8957209 DOI: 10.1002/anie.202011171] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Indexed: 12/20/2022]
Abstract
Fungal meroterpenoids are a diverse group of hybrid natural products with impressive structural complexity and high potential as drug candidates. In this work, we evaluate the promiscuity of the early structure diversity-generating step in fungal meroterpenoid biosynthetic pathways: the multibond-forming polyene cyclizations catalyzed by the yet poorly understood family of fungal meroterpenoid cyclases. In total, 12 unnatural meroterpenoids were accessed chemoenzymatically using synthetic substrates. Their complex structures were determined by 2D NMR studies as well as crystalline-sponge-based X-ray diffraction analyses. The results obtained revealed a high degree of enzyme promiscuity and experimental results which together with quantum chemical calculations provided a deeper insight into the catalytic activity of this new family of non-canonical, terpene cyclases. The knowledge obtained paves the way to design and engineer artificial pathways towards second generation meroterpenoids with valuable bioactivities based on combinatorial biosynthetic strategies.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Division of Advanced Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
| | - Lena Barra
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Zachary Powers
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Volga Kojasoy
- Department of Chemistry, University of California Davis 1 Shields Avenue, Davis, California 95616 (USA)
| | - Andrea Cheng
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Feng Yang
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies, Kirin Holdings Co. Ltd. 1-13-5, Fukuura Kana-zawa-ku, Yokohama-shi, Kanagawa, 236-0004 (Japan)
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo 196-8666 (Japan)
| | - Makoto Fujita
- Division of Advanced Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)
| | - Dean J. Tantillo
- Department of Chemistry, University of California Davis 1 Shields Avenue, Davis, California 95616 (USA)
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan)
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31
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Mitsuhashi T, Barra L, Powers Z, Kojasoy V, Cheng A, Yang F, Taniguchi Y, Kikuchi T, Fujita M, Tantillo DJ, Porco JA, Abe I. Exploiting the Potential of Meroterpenoid Cyclases to Expand the Chemical Space of Fungal Meroterpenoids. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011171] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Division of Advanced Molecular Science Institute for Molecular Science National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji Okazaki 444-8787 Japan
| | - Lena Barra
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Zachary Powers
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Volga Kojasoy
- Department of Chemistry University of California Davis 1 Shields Avenue Davis California 95616 USA
| | - Andrea Cheng
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Feng Yang
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies Kirin Holdings Co. Ltd. 1-13-5, Fukuura Kana-zawa-ku, Yokohama-shi Kanagawa 236-0004 Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8666 Japan
| | - Makoto Fujita
- Division of Advanced Molecular Science Institute for Molecular Science National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji Okazaki 444-8787 Japan
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Dean J. Tantillo
- Department of Chemistry University of California Davis 1 Shields Avenue Davis California 95616 USA
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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32
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Roy B, Rout N, Kuila P, Sarkar D. Synthesis and structural anomaly of
xyloketals‐unique
benzoxacycles: A review. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Barnali Roy
- Department of Chemistry NIT Rourkela Odisha India
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33
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Müller L, Hoof S, Keck M, Herwig C, Limberg C. Enhancing Tris(pyrazolyl)borate-Based Models of Cysteine/Cysteamine Dioxygenases through Steric Effects: Increased Reactivities, Full Product Characterization and Hints to Initial Superoxide Formation. Chemistry 2020; 26:11851-11861. [PMID: 32432367 PMCID: PMC7540079 DOI: 10.1002/chem.202001818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 02/03/2023]
Abstract
The design of biomimetic model complexes for the cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO) is reported, where the 3-His coordination of the iron ion is simulated by three pyrazole donors of a trispyrazolyl borate ligand (Tp) and protected cysteine and cysteamine represent substrate ligands. It is found that the replacement of phenyl groups-attached at the 3-positions of the pyrazole units in a previous model-by mesityl residues has massive consequences, as the latter arrange to a more spacious reaction pocket. Thus, the reaction with O2 proceeds much faster and afterwards the first structural characterization of an iron(II) η2 -O,O-sulfinate product became possible. If one of the three Tp-mesityl groups is placed in the 5-position, an even larger reaction pocket results, which leads to yet faster rates and accumulation of a reaction intermediate at low temperatures, as shown by UV/Vis and Mössbauer spectroscopy. After comparison with the results of investigations on the cobalt analogues this intermediate is tentatively assigned to an iron(III) superoxide species.
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Affiliation(s)
- Lars Müller
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Santina Hoof
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Matthias Keck
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Christian Herwig
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Christian Limberg
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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34
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Liu Y, Shi J, Liu Y. Mechanistic Insights into the Oxidative Ring Expansion from Penicillin N to Deacetoxycephalosporin C Catalyzed by a Nonheme Iron(II) and α-KG-Dependent Oxygenase. Inorg Chem 2020; 59:12218-12231. [PMID: 32822181 DOI: 10.1021/acs.inorgchem.0c01211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deacetoxycephalosporin C synthase (DAOCS) is a nonheme iron(II) and 2-oxoglutarate (α-KG)-dependent oxygenase that catalyzes the oxidative ring expansion of penicillin N (penN) to deacetoxycephalosporin C (DAOC). Earlier reported crystal structures of DAOCS indicated that the substrate penicillin binds at the same site of succinate, leading to the proposal of the unusual "ping-pong" mechanism. However, more recent data provided evidence of the formation of ternary DAOCS·α-KG·penN complex, and thus DAOCS should follow the usual consensus mechanism of α-KG-dependent nonheme iron(II) oxygenases. Nevertheless, how DAOCS catalyzes the ring expansion is unknown. In this paper, on the basis of the crystal structure, we constructed two reactant models and performed a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations to illuminate the catalysis of DAOCS. The binding mode of substrate was found to be crucial in determining which hydrogen atom in two methyl groups is first abstracted and whether the second H-abstraction to be abstracted in the final desaturation step locates in a suitable orientation. The highly reactive FeIV-oxo species prefers to abstract a hydrogen atom from one of two methyl groups in penN to trigger the ring arrangement. After the H-abstraction, the generated methylene radical intermediate can easily initiate the ring arrangement. First, the C-S bond cleaves to generate a thiyl radical, which is in concert with the formation of the terminal C═C double bond; the newly generated thiyl radical then rapidly shifts to the more stable tertiary C atom to complete ring expansion. In the final step, the FeIII-OH species abstracts the second hydrogen to give the desaturated DAOC product. During the catalysis, no active site residue is directly involved in the chemistry, which implies that the other pocket residues except the coordinate ones with iron play a role only in anchoring the substrate.
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Affiliation(s)
- Yaru Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Junyou Shi
- College of Chemistry and Environmental Science, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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35
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Abe I. Nonheme Iron- and 2-Oxoglutarate-Dependent Dioxygenases in Fungal Meroterpenoid Biosynthesis. Chem Pharm Bull (Tokyo) 2020; 68:823-831. [PMID: 32879222 DOI: 10.1248/cpb.c20-00360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review summarizes the recent progress in research on the non-heme Fe(II)- and 2-oxoglutarate-dependent dioxygenases, which are involved in the biosynthesis of pharmaceutically important fungal meroterpenoids. This enzyme class activates a selective C-H bond of the substrate and catalyzes a wide range of chemical reactions, from simple hydroxylation to dynamic carbon skeletal rearrangements, thereby significantly contributing to the structural diversification and complexification of the molecules. Structure-function studies of these enzymes provide an excellent platform for the development of useful biocatalysts for synthetic biology to create novel molecules for future drug discovery.
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Affiliation(s)
- Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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36
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Li H, Feng W, Li X, Kang X, Yan S, Chao M, Mo S, Sun W, Lu Y, Chen C, Wang J, Zhu H, Zhang Y. Terreuspyridine: An Unexpected Pyridine-Fused Meroterpenoid Alkaloid with a Tetracyclic 6/6/6/6 Skeleton from Aspergillus terreus. Org Lett 2020; 22:7041-7046. [PMID: 32841036 DOI: 10.1021/acs.orglett.0c02641] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Terreuspyridine (1), the first 3,5-demethylorsellinic acid (DMOA) derived meroterpenoid alkaloid, was isolated from the fungus Aspergillus terreus, which represents a new type of meroterpenoid possessing an unexpected tetracyclic 6/6/6/6 architecture. The structure of 1 with absolute configuration was determined by X-ray diffraction analysis. Biogenetically, it was proposed to be derived from the fusion of a DMOA-meroterpenoid and a glutamate. Terreuspyridine (1) exhibited moderate inhibitory activity against the BChE with an IC50 value of 16.4 μM.
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Affiliation(s)
- Huaqiang Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenya Feng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoxin Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Kang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shan Yan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Menghang Chao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuyuan Mo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuanyuan Lu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chunmei Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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37
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Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases. Nat Commun 2020; 11:2991. [PMID: 32532989 PMCID: PMC7293229 DOI: 10.1038/s41467-020-16729-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/15/2020] [Indexed: 12/05/2022] Open
Abstract
Biocatalysts that perform C–H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes. Rieske oxygenases are iron-dependent enzymes that catalyse C–H mono- and dihydroxylation reactions. Here, the authors characterise two cyanobacterial Rieske oxygenases, SxtT and GxtA that are involved in the biosynthesis of paralytic shellfish toxins and determine their substrate free and saxitoxin analog-bound crystal structures and by using mutagenesis experiments identify residues, which are important for substrate positioning and reaction selectivity.
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38
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Bai T, Matsuda Y, Tao H, Mori T, Zhang Y, Abe I. Structural Diversification of Andiconin-Derived Natural Products by α-Ketoglutarate-Dependent Dioxygenases. Org Lett 2020; 22:4311-4315. [DOI: 10.1021/acs.orglett.0c01358] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tongxuan Bai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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39
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Vila MA, Steck V, Rodriguez Giordano S, Carrera I, Fasan R. C-H Amination via Nitrene Transfer Catalyzed by Mononuclear Non-Heme Iron-Dependent Enzymes. Chembiochem 2020; 21:1981-1987. [PMID: 32189465 DOI: 10.1002/cbic.201900783] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/12/2020] [Indexed: 12/18/2022]
Abstract
Expanding the reaction scope of natural metalloenzymes can provide new opportunities for biocatalysis. Mononuclear non-heme iron-dependent enzymes represent a large class of biological catalysts involved in the biosynthesis of natural products and catabolism of xenobiotics, among other processes. Here, we report that several members of this enzyme family, including Rieske dioxygenases as well as α-ketoglutarate-dependent dioxygenases and halogenases, are able to catalyze the intramolecular C-H amination of a sulfonyl azide substrate, thereby exhibiting a promiscuous nitrene transfer reactivity. One of these enzymes, naphthalene dioxygenase (NDO), was further engineered resulting in several active site variants that function as C-H aminases. Furthermore, this enzyme could be applied to execute this non-native transformation on a gram scale in a bioreactor, thus demonstrating its potential for synthetic applications. These studies highlight the functional versatility of non-heme iron-dependent enzymes and pave the way to their further investigation and development as promising biocatalysts for non-native metal-catalyzed transformations.
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Affiliation(s)
- Maria Agustina Vila
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias. Facultad de Química, Universidad de la República, Av General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Viktoria Steck
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627, USA
| | - Sonia Rodriguez Giordano
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias. Facultad de Química, Universidad de la República, Av General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Ignacio Carrera
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias. Facultad de Química, Universidad de la República, Av General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627, USA
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40
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Shiina T, Ozaki T, Matsu Y, Nagamine S, Liu C, Hashimoto M, Minami A, Oikawa H. Oxidative Ring Contraction by a Multifunctional Dioxygenase Generates the Core Cycloocatadiene in the Biosynthesis of Fungal Dimeric Anhydride Zopfiellin. Org Lett 2020; 22:1997-2001. [DOI: 10.1021/acs.orglett.0c00340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tetsuya Shiina
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yusuke Matsu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shota Nagamine
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Chengwei Liu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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41
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Liu Y, You T, Wang HX, Tang Z, Zhou CY, Che CM. Iron- and cobalt-catalyzed C(sp3)–H bond functionalization reactions and their application in organic synthesis. Chem Soc Rev 2020; 49:5310-5358. [DOI: 10.1039/d0cs00340a] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review highlights the developments in iron and cobalt catalyzed C(sp3)–H bond functionalization reactions with emphasis on their applications in organic synthesis, i.e. natural products and pharmaceuticals synthesis and/or modification.
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Affiliation(s)
- Yungen Liu
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen
- P. R. China
| | - Tingjie You
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Hai-Xu Wang
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Zhou Tang
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Cong-Ying Zhou
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Chi-Ming Che
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen
- P. R. China
- Department of Chemistry
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42
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Doyon TJ, Perkins JC, Baker Dockrey SA, Romero EO, Skinner KC, Zimmerman PM, Narayan ARH. Chemoenzymatic o-Quinone Methide Formation. J Am Chem Soc 2019; 141:20269-20277. [PMID: 31840992 DOI: 10.1021/jacs.9b10474] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Generation of reactive intermediates and interception of these fleeting species under physiological conditions is a common strategy employed by Nature to build molecular complexity. However, selective formation of these species under mild conditions using classical synthetic techniques is an outstanding challenge. Here, we demonstrate the utility of biocatalysis in generating o-quinone methide intermediates with precise chemoselectivity under mild, aqueous conditions. Specifically, α-ketoglutarate-dependent non-heme iron enzymes, CitB and ClaD, are employed to selectively modify benzylic C-H bonds of o-cresol substrates. In this transformation, biocatalytic hydroxylation of a benzylic C-H bond affords a benzylic alcohol product which, under the aqueous reaction conditions, is in equilibrium with the corresponding o-quinone methide. o-Quinone methide interception by a nucleophile or a dienophile allows for one-pot conversion of benzylic C-H bonds into C-C, C-N, C-O, and C-S bonds in chemoenzymatic cascades on preparative scale. The chemoselectivity and mild nature of this platform is showcased here by the selective modification of peptides and chemoenzymatic synthesis of the chroman natural product (-)-xyloketal D.
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Fan J, Liao G, Ludwig-Radtke L, Yin WB, Li SM. Formation of Terrestric Acid in Penicillium crustosum Requires Redox-Assisted Decarboxylation and Stereoisomerization. Org Lett 2019; 22:88-92. [DOI: 10.1021/acs.orglett.9b04002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jie Fan
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Ge Liao
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Lena Ludwig-Radtke
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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45
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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46
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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Nakashima Y, Mitsuhashi T, Matsuda Y, Senda M, Sato H, Yamazaki M, Uchiyama M, Senda T, Abe I. Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis. J Am Chem Soc 2018; 140:9743-9750. [DOI: 10.1021/jacs.8b06084] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yudai Matsuda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies (Soken-dai), 1−1 Oho, Tsukuba, Ibaraki 305−0801, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Li H, Sun W, Deng M, Qi C, Chen C, Zhu H, Luo Z, Wang J, Xue Y, Zhang Y. Asperversins A and B, Two Novel Meroterpenoids with an Unusual 5/6/6/6 Ring from the Marine-Derived Fungus Aspergillus versicolor. Mar Drugs 2018; 16:md16060177. [PMID: 29882867 PMCID: PMC6025407 DOI: 10.3390/md16060177] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 11/16/2022] Open
Abstract
Asperversins A (1) and B (2), two novel meroterpenoids featuring an uncommon 5/6/6/6 ring system, along with five new analogues (3⁻7) and a known compound asperdemin (8), were obtained from the marine-derived fungus Aspergillus versicolor. Their structures and absolute configurations were confirmed by extensive spectroscopic analyses, single-crystal X-ray diffraction studies, and electronic circular dichroism (ECD) calculation. All new compounds were tested for their acetylcholinesterase enzyme (AChE) inhibitory activities and cytotoxic activities, of which compound 7 displayed moderate inhibitory activity against the AChE with an IC50 value of 13.6 μM.
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Affiliation(s)
- Huaqiang Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Mengyi Deng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Changxing Qi
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Chunmei Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zengwei Luo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yongbo Xue
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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