1
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Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
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Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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2
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Yang WQ, Lu QP, Chen CX, Zhu LP, Zhang X, Xu W, Hu LS, Chen J, Zhao ZX. Six undescribed 23-norursane triterpenoids from the biotransformation of ilexgenin a by endophytic fungi and their vascular protective activity. Fitoterapia 2024; 176:106053. [PMID: 38838828 DOI: 10.1016/j.fitote.2024.106053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024]
Abstract
Biotransformation of ursane-type triterpenoid ilexgenin A by endophytic fungi Lasiodiplodia sp. MQD-4 and Pestalotiopsis sp. ZZ-1, isolated from Ilex pubescences and Callicarpa kwangtungensis respectively, was investigated for the first time. Six previously undescribed metabolites (1-6) with 23-norursane triterpenoids skeleton were isolated and their structures were unambiguously established by the analysis of spectroscopic data and single-crystal X-ray crystallographic experiments. Decarboxylation, oxidation, and hydroxylation reactions were observed on the triterpenoid skeleton. Especially, the decarboxylation of C-23 provided definite evidence to understand the biogenetic process of 23-norursane triterpenoids. Moreover, the qualitative analysis of the extract of I. pubescences showed metabolites 1, 3, 4, and 6 could be detected in the originated plant, indicating biotransformation by endophytic fungi is a practical strategy for the isolation of novel natural products. Finally, all isolates were evaluated for the protective activities against H2O2-induced HUVECs dysfunction in vitro. Compound 5 could improve the viability of endothelial cells and decrease the level of intracellular ROS.
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Affiliation(s)
- Wei-Qun Yang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Qi-Ping Lu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Cai-Xin Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Li-Ping Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Wei Xu
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Le-Shi Hu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jie Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Zhong-Xiang Zhao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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3
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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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4
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Luo P, Huang JH, Lv JM, Wang GQ, Hu D, Gao H. Biosynthesis of fungal terpenoids. Nat Prod Rep 2024; 41:748-783. [PMID: 38265076 DOI: 10.1039/d3np00052d] [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: 01/25/2024]
Abstract
Covering: up to August 2023Terpenoids, which are widely distributed in animals, plants, and microorganisms, are a large group of natural products with diverse structures and various biological activities. They have made great contributions to human health as therapeutic agents, such as the anti-cancer drug paclitaxel and anti-malarial agent artemisinin. Accordingly, the biosynthesis of this important class of natural products has been extensively studied, which generally involves two major steps: hydrocarbon skeleton construction by terpenoid cyclases and skeleton modification by tailoring enzymes. Additionally, fungi (Ascomycota and Basidiomycota) serve as an important source for the discovery of terpenoids. With the rapid development of sequencing technology and bioinformatics approaches, genome mining has emerged as one of the most effective strategies to discover novel terpenoids from fungi. To date, numerous terpenoid cyclases, including typical class I and class II terpenoid cyclases as well as emerging UbiA-type terpenoid cyclases, have been identified, together with a variety of tailoring enzymes, including cytochrome P450 enzymes, flavin-dependent monooxygenases, and acyltransferases. In this review, our aim is to comprehensively present all fungal terpenoid cyclases identified up to August 2023, with a focus on newly discovered terpenoid cyclases, especially the emerging UbiA-type terpenoid cyclases, and their related tailoring enzymes from 2015 to August 2023.
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Affiliation(s)
- Pan Luo
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
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5
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Wang D, Wang Y, Zimudzi TJ, Chen LQ, Yang J. Harnessing the duality of bases toward controlled color and fluorescence. SCIENCE ADVANCES 2024; 10:eadn9692. [PMID: 38758781 PMCID: PMC11100562 DOI: 10.1126/sciadv.adn9692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
Bases can promote keto-enol tautomerism, a prevalent form of prototropic tautomerism, and facilitate the ring opening of anhydride ring structures. The intrinsic chemical distinctions between these processes provide an opportunity to modulate these seemingly parallel reactions. However, this potential remains largely unexplored. In this work, we report homophthalic anhydride, the first molecule exhibiting simultaneous halochromism, turn-on fluorescence (halofluorochromism), and subsequent self-destruction. Through comprehensive spectroscopic analysis and theoretical calculations, we unravel the mechanisms underlying these phenomena, revealing that the pivotal roles of the base's basicity and nucleophilicity specifically allow us to achieve controlled durations of color change and turn-on fluorescence. Capitalizing on these intriguing properties, we develop a highly dynamic CMY (cyan-magenta-yellow) palette ideal for entity encryption and anti-counterfeiting applications. Our work reshapes the understanding of the relationship between the basicity and nucleophilicity of bases, enriching the comprehension of keto-enol tautomerism and homophthalic anhydride chemistry, and unveils a spectrum of potential applications.
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Affiliation(s)
- Dingbowen Wang
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang 310030, China
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Wang
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tawanda J. Zimudzi
- Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Long-Qing Chen
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jian Yang
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang 310030, China
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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6
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Soler J, Gergel S, Hammer SC, Garcia-Borràs M. Molecular Basis for Chemoselectivity Control in Oxidations of Internal Aryl-Alkenes Catalyzed by Laboratory Evolved P450s. Chembiochem 2024; 25:e202400066. [PMID: 38567500 DOI: 10.1002/cbic.202400066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/04/2024]
Abstract
P450 enzymes naturally perform selective hydroxylations and epoxidations of unfunctionalized hydrocarbon substrates, among other reactions. The adaptation of P450 enzymes to a particular oxidative reaction involving alkenes is of great interest for the design of new synthetically useful biocatalysts. However, the mechanism that these enzymes utilize to precisely modulate the chemoselectivity and distinguishing between competing alkene double bond epoxidations and allylic C-H hydroxylations is sometimes not clear, which hampers the rational design of specific biocatalysts. In a previous work, a P450 from Labrenzia aggregata (P450LA1) was engineered in the laboratory using directed evolution to catalyze the direct oxidation of trans-β-methylstyrene to phenylacetone. The final variant, KS, was able to overcome the intrinsic preference for alkene epoxidation to directly generate a ketone product via the formation of a highly reactive carbocation intermediate. Here, additional library screening along this evolutionary lineage permitted to serendipitously detect a mutation that overcomes epoxidation and carbonyl formation by exhibiting a large selectivity of 94 % towards allylic C-H hydroxylation. A multiscalar computational methodology was applied to reveal the molecular basis towards this hydroxylation preference. Enzyme modelling suggests that introduction of a bulky substitution dramatically changes the accessible conformations of the substrate in the active site, thus modifying the enzymatic selectivity towards terminal hydroxylation and avoiding the competing epoxidation pathway, which is sterically hindered.
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Affiliation(s)
- Jordi Soler
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Sebastian Gergel
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
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7
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Jiang Y, Renata H. Modular chemoenzymatic synthesis of ten fusicoccane diterpenoids. Nat Chem 2024:10.1038/s41557-024-01533-w. [PMID: 38710830 DOI: 10.1038/s41557-024-01533-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
Fusicoccane diterpenoids display intriguing biological activities, including the ability to act as modulators of 14-3-3 protein-protein interactions. However, their innate structural complexity and diverse oxygenation patterns present enormous synthetic challenges. Here we develop a modular chemoenzymatic approach that combines de novo skeletal construction and late-stage hybrid C-H oxidations to achieve the synthesis of ten complex fusicoccanes in 8-13 steps each. A convergent fragment coupling strategy allowed rapid access to a key tricyclic intermediate, which was subjected to chemical and enzymatic C-H oxidations to modularly prepare five oxidized family members. We also conceived a complementary biomimetic skeletal remodelling strategy to synthetically access five rearranged fusicoccanes with unusual bridgehead double bonds. This work may facilitate future investigation into the biological activities of the fusicoccanes and also inspire the implementation of similar hybrid strategies to provide family-level synthetic solutions to other natural product scaffolds.
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Affiliation(s)
- Yanlong Jiang
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, USA
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, USA.
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8
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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9
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Song H, Zhang Z, Cao C, Tang Z, Gui J, Liu W. Biocatalytic Steroidal 9α-Hydroxylation and Fragmentation Enable the Concise Chemoenzymatic Synthesis of 9,10-Secosteroids. Angew Chem Int Ed Engl 2024; 63:e202319624. [PMID: 38376063 DOI: 10.1002/anie.202319624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
9,10-Secosteroids are an important group of marine steroids with diverse biological activities. Herein, we report a chemoenzymatic strategy for the concise, modular, and scalable synthesis of ten naturally occurring 9,10-secosteroids from readily available steroids in three to eight steps. The key feature lies in utilizing a Rieske oxygenase-like 3-ketosteroid 9α-hydroxylase (KSH) as the biocatalyst to achieve efficient C9-C10 bond cleavage and A-ring aromatization of tetracyclic steroids through 9α-hydroxylation and fragmentation. With synthesized 9,10-secosteroides, structure-activity relationship was evaluated based on bioassays in terms of previously unexplored anti-infective activity. This study provides experimental evidence to support the hypothesis that the biosynthetic pathway through which 9,10-secosteroids are formed in nature shares a similar 9α-hydroxylation and fragmentation cascade. In addition to the development of a biomimetic approach for 9,10-secosteroid synthesis, this study highlights the great potential of chemoenzymatic strategies in chemical synthesis.
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Affiliation(s)
- Hanxin Song
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zeliang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Chunyang Cao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zhijun Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jinghan Gui
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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10
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Cheung-Lee WL, Kolev JN, McIntosh JA, Gil AA, Pan W, Xiao L, Velásquez JE, Gangam R, Winston MS, Li S, Abe K, Alwedi E, Dance ZEX, Fan H, Hiraga K, Kim J, Kosjek B, Le DN, Marzijarani NS, Mattern K, McMullen JP, Narsimhan K, Vikram A, Wang W, Yan JX, Yang RS, Zhang V, Zhong W, DiRocco DA, Morris WJ, Murphy GS, Maloney KM. Engineering Hydroxylase Activity, Selectivity, and Stability for a Scalable Concise Synthesis of a Key Intermediate to Belzutifan. Angew Chem Int Ed Engl 2024; 63:e202316133. [PMID: 38279624 DOI: 10.1002/anie.202316133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Biocatalytic oxidations are an emerging technology for selective C-H bond activation. While promising for a range of selective oxidations, practical use of enzymes catalyzing aerobic hydroxylation is presently limited by their substrate scope and stability under industrially relevant conditions. Here, we report the engineering and practical application of a non-heme iron and α-ketoglutarate-dependent dioxygenase for the direct stereo- and regio-selective hydroxylation of a non-native fluoroindanone en route to the oncology treatment belzutifan, replacing a five-step chemical synthesis with a direct enantioselective hydroxylation. Mechanistic studies indicated that formation of the desired product was limited by enzyme stability and product overoxidation, with these properties subsequently improved by directed evolution, yielding a biocatalyst capable of >15,000 total turnovers. Highlighting the industrial utility of this biocatalyst, the high-yielding, green, and efficient oxidation was demonstrated at kilogram scale for the synthesis of belzutifan.
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Affiliation(s)
| | - Joshua N Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - John A McIntosh
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Agnieszka A Gil
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Weilan Pan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Li Xiao
- Modeling & Informatics, Discovery Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Juan E Velásquez
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rekha Gangam
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Matthew S Winston
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kotoe Abe
- Chemical Commercialization Technologies, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Embarek Alwedi
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Zachary E X Dance
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Haiyang Fan
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Kaori Hiraga
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jungchul Kim
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Birgit Kosjek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Diane N Le
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Keith Mattern
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Karthik Narsimhan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Ajit Vikram
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wei Wang
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Jia-Xuan Yan
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rong-Sheng Yang
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Victoria Zhang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wendy Zhong
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Daniel A DiRocco
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - William J Morris
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kevin M Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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11
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Frey M, Bathe U, Meink L, Balcke GU, Schmidt J, Frolov A, Soboleva A, Hassanin A, Davari MD, Frank O, Schlagbauer V, Dawid C, Tissier A. Combinatorial biosynthesis in yeast leads to over 200 diterpenoids. Metab Eng 2024; 82:193-200. [PMID: 38387676 DOI: 10.1016/j.ymben.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. The modular character of diterpene biosynthesis and the promiscuity of the enzymes involved make combinatorial biosynthesis a promising approach to generate libraries of diverse diterpenoids. Here, we report on the combinatorial assembly in yeast of ten diterpene synthases producing (+)-copalyl diphosphate-derived backbones and four cytochrome P450 oxygenases (CYPs) in diverse combinations. This resulted in the production of over 200 diterpenoids. Based on literature and chemical database searches, 162 of these compounds can be considered new-to-Nature. The CYPs accepted most substrates they were given but remained regioselective with few exceptions. Our results provide the basis for the systematic exploration of the diterpenoid chemical space in yeast using sequence databases.
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Affiliation(s)
- Maximilian Frey
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ulschan Bathe
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
| | - Luca Meink
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Gerd U Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Jürgen Schmidt
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Alena Soboleva
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ahmed Hassanin
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mehdi D Davari
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Oliver Frank
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Verena Schlagbauer
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Martin-Luther University Halle-Wittenberg, Institute of Pharmacy, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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12
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Monkcom EC, Gómez L, Lutz M, Ye S, Bill E, Costas M, Klein Gebbink RJM. Synthesis, Structure and Reactivity of a Mononuclear N,N,O-Bound Fe(II) α-Keto-Acid Complex. Chemistry 2024; 30:e202302710. [PMID: 37882223 DOI: 10.1002/chem.202302710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
A bulky, tridentate phenolate ligand (ImPh2 NNOtBu ) was used to synthesise the first example of a mononuclear, facial, N,N,O-bound iron(II) benzoylformate complex, [Fe(ImPh2 NNOtBu )(BF)] (2). The X-ray crystal structure of 2 reveals that the iron centre is pentacoordinate (τ=0.5), with a vacant site located cis to the bidentate BF ligand. The Mössbauer parameters of 2 are consistent with high-spin iron(II), and are very close to those reported for α-ketoglutarate-bound non-heme iron enzyme active sites. According to NMR and UV-vis spectroscopies, the structural integrity of 2 is retained in both coordinating and non-coordinating solvents. Cyclic voltammetry studies show that the iron centre has a very low oxidation potential and is more prone to electrochemical oxidation than the redox-active phenolate ligand. Complex 2 reacts with NO to form a S=3 /2 {FeNO}7 adduct in which NO binds directly to the iron centre, according to EPR, UV-vis, IR spectroscopies and DFT analysis. Upon O2 exposure, 2 undergoes oxidative decarboxylation to form a diiron(III) benzoate complex, [Fe2 (ImPh2 NNOtBu )2 (μ2 -OBz)(μ2 -OH)2 ]+ (3). A small amount of hydroxylated ligand was also observed by ESI-MS, hinting at the formation of a high-valent iron(IV)-oxo intermediate. Initial reactivity studies show that 2 is capable of oxygen atom transfer reactivity with O2 , converting methyl(p-tolyl)sulfide to sulfoxide.
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Affiliation(s)
- Emily C Monkcom
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Laura Gómez
- Serveis Tècnics de Recerca, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim an der Ruhr, Germany
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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13
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Zhang Z, Qian X, Gu Y, Gui J. Controllable skeletal reorganizations in natural product synthesis. Nat Prod Rep 2024; 41:251-272. [PMID: 38291905 DOI: 10.1039/d3np00066d] [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: 02/01/2024]
Abstract
Covering: 2016 to 2023The synthetic chemistry community is always in pursuit of efficient routes to natural products. Among the many available general strategies, skeletal reorganization, which involves the formation, cleavage, and migration of C-C and C-heteroatom bonds, stands out as a particularly useful approach for the efficient assembly of molecular skeletons. In addition, it allows for late-stage modification of natural products for quick access to other family members or unnatural derivatives. This review summarizes efficient syntheses of steroid, terpenoid, and alkaloid natural products that have been achieved by means of this strategy in the past eight years. Our goal is to illustrate the strategy's potency and reveal the spectacular human ingenuity demonstrated in its use and development.
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Affiliation(s)
- Zeliang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Xiao Qian
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Yucheng Gu
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Jinghan Gui
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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14
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Wang Y, Gui J. Bioinspired Skeletal Reorganization Approach for the Synthesis of Steroid Natural Products. Acc Chem Res 2024. [PMID: 38301249 DOI: 10.1021/acs.accounts.3c00716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
ConspectusSteroids, termed "keys to life" by Rupert Witzmann, have a wide variety of biological activities, including anti-inflammatory, antishock, immunosuppressive, stress-response-enhancing, and antifertility activities, and steroid research has made great contributions to drug discovery and development. According to a chart compiled by the Njardarson group at the University of Arizona, 15 of the top 200 small-molecule drugs (by retail sales in 2022) are steroid-related compounds. Therefore, synthetic and medicinal chemists have long pursued the chemical synthesis of steroid natural products (SNPs) with diverse architectures, and vital progress has been achieved, especially in the twentieth century. In fact, several chemists have been rewarded with a Nobel Prize for original contributions to the isolation of steroids, the elucidation of their structures and biosynthetic pathways, and their chemical synthesis. However, in contrast to classical steroids, which have a 6/6/6/5-tetracyclic framework, rearranged steroids (i.e., abeo-steroids and secosteroids), which are derived from classical steroids by reorganization of one or more C-C bonds of the tetracyclic skeleton, have started to gain attention from the synthetic community only in the last two decades. These unique rearranged steroids have complex frameworks with high oxidation states, are rich in stereogenic centers, and have attractive biological activities, rendering them popular yet formidable synthetic targets.Our group has a strong interest in the efficient synthesis of SNPs and, drawing inspiration from nature, we have found that bioinspired skeletal reorganization (BSR) is an efficient strategy for synthesizing challenging rearranged steroids. Using this strategy, we recently achieved concise syntheses of five different kinds of SNPs (cyclocitrinols, propindilactone G, bufospirostenin A, pinnigorgiol B, and sarocladione) with considerably rearranged skeletons; our work also enabled us to reassign the originally proposed structure of sarocladione. In this Account, we summarize the proposed biosyntheses of these SNPs and describe our BSR approach for the rapid construction of their core frameworks. In the work described herein, information gleaned from the proposed biosyntheses allowed us to develop routes for chemical synthesis. However, in several cases, the synthetic precursors that we used for our BSR approach differed substantially from the intermediates in the proposed biosyntheses, indicating the considerable challenges we encountered during this synthetic campaign. It is worth mentioning that during our pursuit of concise and scalable syntheses of these natural products, we developed two methods for accessing synthetically challenging targets: a method for rapid construction of bridged-ring molecules by means of point-to-planar chirality transfer and a method for efficient construction of macrocyclic molecules via a novel ruthenium-catalyzed endoperoxide fragmentation. Our syntheses vividly demonstrate that consideration of natural product biosynthesis can greatly facilitate chemical synthesis, and we expect that the BSR approach will find additional applications in the efficient syntheses of other structurally complex steroid and terpenoid natural products.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jinghan Gui
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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15
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Kries H, Trottmann F, Hertweck C. Novel Biocatalysts from Specialized Metabolism. Angew Chem Int Ed Engl 2024; 63:e202309284. [PMID: 37737720 DOI: 10.1002/anie.202309284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.
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Affiliation(s)
- Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440, Bayreuth, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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16
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Hopiavuori A, McKinnie SMK. Algal Kainoid Synthases Exhibit Substrate-Dependent Hydroxylation and Cyclization Activities. ACS Chem Biol 2023; 18:2457-2463. [PMID: 38047879 PMCID: PMC10728896 DOI: 10.1021/acschembio.3c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
FeII/α-ketoglutarate-dependent dioxygenases (Fe/αKG) make up a large enzyme family that functionalize C-H bonds on diverse organic substrates. Although Fe/αKG homologues catalyze an array of chemically useful reactions, hydroxylation typically predominates. Microalgal DabC uniquely forms a novel C-C bond to construct the bioactive pyrrolidine ring in domoic acid biosynthesis; however, we have identified that this kainoid synthase exclusively performs a stereospecific hydroxylation reaction on its cis substrate regioisomer. Mechanistic and kinetic analyses with native and alternative substrates identified a 20-fold rate increase in DabC radical cyclization over β-hydroxylation with no observable 1,5-hydrogen atom transfer. Moreover, this dual activity was conserved among macroalgal RadC1 and KabC homologues and provided insight into substrate recognition and reactivity trends. Investigation of this substrate-dependent chemistry improves our understanding of kainoid synthases and their biocatalytic application.
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Affiliation(s)
- Austin
R. Hopiavuori
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Shaun M. K. McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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17
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Bhargav P, Chaurasia S, Kumar A, Srivastava G, Pant Y, Chanotiya CS, Ghosh S. Unraveling the terpene synthase family and characterization of BsTPS2 contributing to (S)-( +)-linalool biosynthesis in Boswellia. PLANT MOLECULAR BIOLOGY 2023; 113:219-236. [PMID: 37898975 DOI: 10.1007/s11103-023-01384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023]
Abstract
Boswellia tree bark exudes oleo-gum resin in response to wounding, which is rich in terpene volatiles. But, the molecular and biochemical basis of wound-induced formation of resin volatiles remains poorly understood. Here, we combined RNA-sequencing (RNA-seq) and metabolite analysis to unravel the terpene synthase (TPS) family contributing to wound-induced biosynthesis of resin volatiles in B. serrata, an economically-important Boswellia species. The analysis of large-scale RNA-seq data of bark and leaf samples representing more than 600 million sequencing reads led to the identification of 32 TPSs, which were classified based on phylogenetic relationship into various TPSs families found in angiosperm species such as TPS-a, b, c, e/f, and g. Moreover, RNA-seq analysis of bark samples collected at 0-24 h post-wounding shortlisted 14 BsTPSs that showed wound-induced transcriptional upregulation in bark, suggesting their important role in wound-induced biosynthesis of resin volatiles. Biochemical characterization of a bark preferentially-expressed and wound-inducible TPS (BsTPS2) in vitro and in planta assays revealed its involvement in resin terpene biosynthesis. Bacterially-expressed recombinant BsTPS2 catalyzed the conversion of GPP and FPP into (S)-( +)-linalool and (E)-(-)-nerolidol, respectively, in vitro assays. However, BsTPS2 expression in Nicotiana benthamiana found that BsTPS2 is a plastidial linalool synthase. In contrast, cytosolic expression of BsTPS2 did not form any product. Overall, the present work unraveled a suite of TPSs that potentially contributed to the biosynthesis of resin volatiles in Boswellia and biochemically characterized BsTPS2, which is involved in wound-induced biosynthesis of (S)-( +)-linalool, a monoterpene resin volatile with a known role in plant defense.
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Affiliation(s)
- Pravesh Bhargav
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Seema Chaurasia
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Aashish Kumar
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Gaurav Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Yatish Pant
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Phytochemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Phytochemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sumit Ghosh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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18
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Dinday S, Ghosh S. Recent advances in triterpenoid pathway elucidation and engineering. Biotechnol Adv 2023; 68:108214. [PMID: 37478981 DOI: 10.1016/j.biotechadv.2023.108214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.
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Affiliation(s)
- Sandeep Dinday
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Sumit Ghosh
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India.
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19
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Bakanas I, Lusi RF, Wiesler S, Hayward Cooke J, Sarpong R. Strategic application of C-H oxidation in natural product total synthesis. Nat Rev Chem 2023; 7:783-799. [PMID: 37730908 DOI: 10.1038/s41570-023-00534-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/22/2023]
Abstract
The oxidation of unactivated C-H bonds has emerged as an effective tactic in natural product synthesis and has altered how chemists approach the synthesis of complex molecules. The use of C-H oxidation methods has simplified the process of synthesis planning by expanding the choice of starting materials, limiting functional group interconversion and protecting group manipulations, and enabling late-stage diversification. In this Review, we propose classifications for C-H oxidations on the basis of their strategic purpose: type 1, which installs functionality that is used to establish the carbon skeleton of the target; type 2, which is used to construct a heterocyclic ring; and type 3, which installs peripheral functional groups. The reactions are further divided based on whether they are directed or undirected. For each classification, examples from recent literature are analysed. Finally, we provide two case studies of syntheses from our laboratory that were streamlined by the judicious use of C-H oxidation reactions.
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Affiliation(s)
- Ian Bakanas
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Robert F Lusi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Stefan Wiesler
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Jack Hayward Cooke
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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20
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Stout CN, Renata H. Self-sufficient P450-reductase chimeras for biocatalysis. Methods Enzymol 2023; 693:51-71. [PMID: 37977738 DOI: 10.1016/bs.mie.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
In recent years, cytochromes P450 have emerged as powerful, versatile biocatalysts for the site-selective functionalization of small molecules. Catalyzing an impressive range of chemical transformations, these enzymes have been widely used to effect C-H oxidation, biaryl coupling, and carbon-heteroatom bond formation, among many other reactions. However, the majority of P450s are multi-protein systems that employ secondary redox partners in key steps of the catalytic cycle, which limits their broader applicability. In response, the discovery of self-sufficient P450s, such as P450BM3 and P450RhF, has provided a template for the construction of artificial, self-sufficient P450-reductase fusions. In this chapter, we describe a procedure for the design, assembly, and application of two engineered, self-sufficient P450s of Streptomyces origin via fusion with an exogenous reductase domain. In particular, we generated artificial chimeras of P450s PtmO5 and TleB by linking them covalently with the reductase domain of P450RhF. Upon verification of their activities, both enzymes were employed in preparative-scale biocatalytic reactions. This approach can feasibly be applied to any P450 of interest, thereby laying the groundwork for the production of self-sufficient P450s for diverse chemical applications.
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Affiliation(s)
- Carter N Stout
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, CA, United States
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, United States.
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21
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Yang J, Singh B, Cohen G, Ting CP. Chemoenzymatic Synthesis of 13-Oxoverruculogen. J Am Chem Soc 2023; 145:19189-19194. [PMID: 37625109 DOI: 10.1021/jacs.3c07078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Verruculogens are rare fumitremorgin alkaloids that contain a highly unusual eight-membered endoperoxide. In this paper, we report a concise chemoenzymatic synthesis of 13-oxoverruculogen using enzymatic C-H peroxidation and rhodium-catalyzed C-C bond activation reactions to install the eight-membered endoperoxide and the pentacyclic core of the natural product, respectively. Our strategy involves the use of 13-epi-fumitremorgin B as a substrate analog for endoperoxidation by verruculogen synthase, FtmOx1. The resulting product, 13-epi-verruculogen, is the first unnatural endoperoxide generated by FtmOx1 and is used in the first synthesis of 13-oxoverruculogen. This strategy enables a 10-step synthesis of this natural product from commercially available starting materials and illustrates a hybrid approach utilizing biocatalytic and transition-metal-catalyzed reactions to access challenging alkaloid architectures. Moreover, this work demonstrates the use of native enzyme promiscuity as a viable strategy for the chemoenzymatic synthesis of natural products.
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Affiliation(s)
- Jun Yang
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
| | - Brandon Singh
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
| | - Gabriel Cohen
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
| | - Chi P Ting
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
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22
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Romero EO, Saucedo AT, Hernández-Meléndez JR, Yang D, Chakrabarty S, Narayan ARH. Enabling Broader Adoption of Biocatalysis in Organic Chemistry. JACS AU 2023; 3:2073-2085. [PMID: 37654599 PMCID: PMC10466347 DOI: 10.1021/jacsau.3c00263] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 09/02/2023]
Abstract
Biocatalysis is becoming an increasingly impactful method in contemporary synthetic chemistry for target molecule synthesis. The selectivity imparted by enzymes has been leveraged to complete previously intractable chemical transformations and improve synthetic routes toward complex molecules. However, the implementation of biocatalysis in mainstream organic chemistry has been gradual to this point. This is partly due to a set of historical and technological barriers that have prevented chemists from using biocatalysis as a synthetic tool with utility that parallels alternative modes of catalysis. In this Perspective, we discuss these barriers and how they have hindered the adoption of enzyme catalysts into synthetic strategies. We also summarize tools and resources that already enable organic chemists to use biocatalysts. Furthermore, we discuss ways to further lower the barriers for the adoption of biocatalysis by the broader synthetic organic chemistry community through the dissemination of resources, demystifying biocatalytic reactions, and increasing collaboration across the field.
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Affiliation(s)
- Evan O. Romero
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anthony T. Saucedo
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - José R. Hernández-Meléndez
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Di Yang
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Suman Chakrabarty
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R. H. Narayan
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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24
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Stout CN, Wasfy NM, Chen F, Renata H. Charting the Evolution of Chemoenzymatic Strategies in the Syntheses of Complex Natural Products. J Am Chem Soc 2023; 145:18161-18181. [PMID: 37553092 PMCID: PMC11107883 DOI: 10.1021/jacs.3c03422] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Bolstered by recent advances in bioinformatics, genetics, and enzyme engineering, the field of chemoenzymatic synthesis has enjoyed a rapid increase in popularity and utility. This Perspective explores the integration of enzymes into multistep chemical syntheses, highlighting the unique potential of biocatalytic transformations to streamline the synthesis of complex natural products. In particular, we identify four primary conceptual approaches to chemoenzymatic synthesis and illustrate each with a number of landmark case studies. Future opportunities and challenges are also discussed.
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Affiliation(s)
- Carter N. Stout
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, CA 92037, USA
| | - Nour M. Wasfy
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, Texas, 77005, United States
| | - Fang Chen
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, Texas, 77005, United States
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, Texas, 77005, United States
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25
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Pérez Á, Quílez
del Moral JF, Galisteo A, Amaro JM, Barrero AF. Bioinspired Synthesis of Platensimycin from Natural ent-Kaurenoic Acids. Org Lett 2023; 25:5401-5405. [PMID: 37338151 PMCID: PMC10391625 DOI: 10.1021/acs.orglett.3c01470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Indexed: 06/21/2023]
Abstract
The biomimetic formal synthesis of the antibiotic platensimycin for the treatment of infection by multidrug-resistant bacteria was accomplished starting from either ent-kaurenoic acid or grandiflorenic acid, each of which is a natural compound available in multigram scale from its natural source. Apart from the natural origin of the selected precursors, the keys of the described approach are the long-distance functionalization of ent-kaurenoic acid at C11 and the efficient protocol for the A-ring degradation of the diterpene framework.
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Affiliation(s)
- Álvaro Pérez
- Department
of Organic Chemistry, Institute of Biotechnology, University of Granada, 18071 Granada, Spain
| | - José F. Quílez
del Moral
- Department
of Organic Chemistry, Institute of Biotechnology, University of Granada, 18071 Granada, Spain
| | - Alberto Galisteo
- Department
of Organic Chemistry, Institute of Biotechnology, University of Granada, 18071 Granada, Spain
| | - Juan M. Amaro
- Department
of Chemistry, Faculty of Sciences, University
of Los Andes, Merida 5101, Venezuela
| | - Alejandro F. Barrero
- Department
of Organic Chemistry, Institute of Biotechnology, University of Granada, 18071 Granada, Spain
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26
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Zheng CY, Yue JM. Allylic hydroxylation of enones useful for the functionalization of relevant drugs and natural products. Nat Commun 2023; 14:2399. [PMID: 37100800 PMCID: PMC10133259 DOI: 10.1038/s41467-023-38154-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Enones are privileged structural motifs in bioactive natural products and pharmaceuticals, but the γ-hydroxylation of enones is challenging. Here we show a mild and efficient method for the direct C(sp3)-H hydroxylation of enones via visible-light-induced hydrogen-atom transfer (HAT), which facilitates γ-hydroxylation of primary, secondary, and tertiary C-H bonds of different enones without involving metal and peroxide. The mechanism study shows that Na2-eosin Y serves as both the photocatalyst and the source of catalytic bromine radical species in the HAT-based catalytic cycle, and finally sacrifices itself completely by oxidative degradation to produce bromine radical and a major product phthalic anhydride in an environmentally friendly way. This scalable method was demonstrated by plenty of substrates (41 examples) including 10 clinical drugs and 15 natural products to be useful for the late-stage functionalization of enone-containing compounds, and, in particular, has potential application in industry for large-scale production.
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Affiliation(s)
- Cheng-Yu Zheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Jian-Min Yue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
- Research Units of Discovery of New Drug Lead Molecules, Chinese Academy of Medical Sciences, Shanghai, 201203, China.
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27
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Akter J, Stockdale TP, Child SA, Lee JHZ, De Voss JJ, Bell SG. Selective carbon-hydrogen bond hydroxylation using an engineered cytochrome P450 peroxygenase. J Inorg Biochem 2023; 244:112209. [PMID: 37080140 DOI: 10.1016/j.jinorgbio.2023.112209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The cytochrome P450 enzyme CYP102A1 (P450BM3) is a versatile monooxygenase enzyme which has been adapted and engineered for multiple applications in chemical synthesis. Mutation of threonine 268 to glutamate (Thr268Glu) converted the heme domain of this enzyme into a H2O2 utilizing peroxygenase. This variant displayed significantly increased peroxide driven hydroxylation activity towards the saturated linear fatty acids tested (undecanoic through to hexadecenoic acid) when compared to the wild-type heme domain. The product distributions arising from fatty acid oxidation using this peroxygenase variant were broadly similar to those obtained with the wild-type monooxygenase holoenzyme, with oxidation occurring predominantly at the ω-1 through to ω-3 positions. 10-Undecenoic acid was regioselectively hydroxylated at the allylic ω-2 carbon by the Thr268Glu peroxygenase. The effect of isotopic substitution were measured using [9,9,10,10-d4]-dodecanoic acid. The kinetic isotope effect for both the monooxygenase and peroxygenase systems ranged between 7.9 and 9.5, with that of the peroxygenase enzyme being marginally lower. This highlights that carbon‑hydrogen bond abstraction is important in the mechanism of both the monooxygenase and peroxygenase systems. This would infer that the ferryl-oxo radical cation intermediate, compound I, is the likely reactive intermediate in both systems. The peroxygenase variant offers the possibility of simpler cytochrome P450 systems for selective oxidations. To demonstrate this we used this system to oxidize tetradecanoic acid using light driven generation of H2O2 by a flavin.
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Affiliation(s)
- Jinia Akter
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia
| | - Tegan P Stockdale
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Stella A Child
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia
| | - Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia.
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia.
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28
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Kissman EN, Neugebauer ME, Sumida KH, Swenson CV, Sambold NA, Marchand JA, Millar DC, Chang MCY. Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases. Proc Natl Acad Sci U S A 2023; 120:e2214512120. [PMID: 36913566 PMCID: PMC10041140 DOI: 10.1073/pnas.2214512120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
Biocatalytic C-H activation has the potential to merge enzymatic and synthetic strategies for bond formation. FeII/αKG-dependent halogenases are particularly distinguished for their ability both to control selective C-H activation as well as to direct group transfer of a bound anion along a reaction axis separate from oxygen rebound, enabling the development of new transformations. In this context, we elucidate the basis for the selectivity of enzymes that perform selective halogenation to yield 4-Cl-lysine (BesD), 5-Cl-lysine (HalB), and 4-Cl-ornithine (HalD), allowing us to probe how site-selectivity and chain length selectivity are achieved. We now report the crystal structure of the HalB and HalD, revealing the key role of the substrate-binding lid in positioning the substrate for C4 vs C5 chlorination and recognition of lysine vs ornithine. Targeted engineering of the substrate-binding lid further demonstrates that these selectivities can be altered or switched, showcasing the potential to develop halogenases for biocatalytic applications.
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Affiliation(s)
- Elijah N. Kissman
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
| | - Kiera H. Sumida
- Department of Chemistry, University of California, Berkeley, CA94720
| | | | - Nicholas A. Sambold
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jorge A. Marchand
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
| | - Douglas C. Millar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, CA94720
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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29
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Zhang J, Maggiolo AO, Alfonzo E, Mao R, Porter NJ, Abney N, Arnold FH. Chemodivergent C(sp 3)-H and C(sp 2)-H Cyanomethylation Using Engineered Carbene Transferases. Nat Catal 2023; 6:152-160. [PMID: 36875868 PMCID: PMC9983643 DOI: 10.1038/s41929-022-00908-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/09/2022] [Indexed: 01/21/2023]
Abstract
The ubiquity of C-H bonds presents an attractive opportunity to elaborate and build complexity in organic molecules. Methods for selective functionalization, however, often must differentiate among multiple chemically similar and, in some cases indistinguishable, C-H bonds. An advantage of enzymes is that they can be finely tuned using directed evolution to achieve control over divergent C-H functionalization pathways. Here, we demonstrate engineered enzymes that effect a new-to-nature C-H alkylation with unparalleled selectivity: two complementary carbene C-H transferases derived from a cytochrome P450 from Bacillus megaterium deliver an α-cyanocarbene into the α-amino C(sp3)-H bonds or the ortho-arene C(sp2)-H bonds of N-substituted arenes. These two transformations proceed via different mechanisms, yet only minimal changes to the protein scaffold (nine mutations, less than 2% of the sequence) were needed to adjust the enzyme's control over the site-selectivity of cyanomethylation. The X-ray crystal structure of the selective C(sp3)-H alkylase, P411-PFA, reveals an unprecedented helical disruption which alters the shape and electrostatics in the enzyme active site. Overall, this work demonstrates the advantages of enzymes as C-H functionalization catalysts for divergent molecular derivatization.
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Affiliation(s)
- Juner Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Ailiena O. Maggiolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Edwin Alfonzo
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Runze Mao
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Nicholas J. Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Nayla Abney
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
- Present address: Department of Bioengineering, Stanford University; Stanford, California, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
- Division of Biology and Bioengineering, California Institute of Technology; Pasadena, California, United States
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30
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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31
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Abstract
The P450 superfamily comprises some of the most powerful and versatile enzymes for the site-selective oxidation of small molecules. One of the main drawbacks for the applications of the P450s in biotechnology is that the majority of these enzymes is multicomponent in nature and requires the presence of suitable redox partners to support their functions. Nevertheless, the discovery of several self-sufficient P450s, namely those from Classes VII and VIII, has served as an inspiration for fusion approaches to generate chimeric P450 systems that are self-sufficient. In this Perspective, we highlight the domain organizations of the Class VII and Class VIII P450 systems, summarize recent case studies in the engineering of catalytically self-sufficient P450s based on these systems, and outline outstanding challenges in the field, along with several emerging technologies as potential solutions.
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Affiliation(s)
- Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, 77005
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32
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Zhao XH, Meng LL, Liu XT, Shu PF, Yuan C, An XT, Jia TX, Yang QQ, Zhen X, Fan CA. Asymmetric Divergent Synthesis of ent-Kaurane-, ent-Atisane-, ent-Beyerane-, ent-Trachylobane-, and ent-Gibberellane-type Diterpenoids. J Am Chem Soc 2023; 145:311-321. [PMID: 36538760 DOI: 10.1021/jacs.2c09985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A unified strategy toward asymmetric divergent syntheses of nine C8-ethano-bridged diterpenoids A1-A9 (candol A, powerol, sicanadiol, epi-candol A, atisirene, ent-atisan-16α-ol, 4-decarboxy-4-methyl-GA12, trachinol, and ent-beyerane) has been developed based on late-stage transformations of common synthons having ent-kaurane and ent-trachylobane cores. The expeditious assembly of crucial advanced ent-kaurane- and ent-trachylobane-type building blocks is strategically explored through a regioselective and diastereoselective Fe-mediated hydrogen atom transfer (HAT) 6-exo-trig cyclization of the alkene/enone and 3-exo-trig cyclization of the alkene/ketone, showing the multi-reactivity of densely functionalized polycyclic substrates with πC═C and πC═O systems in HAT-initiated reactions. Following the rapid construction of five major structural skeletons (ent-kaurane-, ent-atisane-, ent-beyerane-, ent-trachylobane-, and ent-gibberellane-type), nine C8-ethano-bridged diterpenoids A1-A9 could be accessed in the longest linear 8 to 11 steps starting from readily available chiral γ-cyclogeraniol 1 and known chiral γ-substituted cyclohexenone 2, in which enantioselective total syntheses of candol A (A1, 8 steps), powerol (A2, 9 steps), sicanadiol (A3, 10 steps), epi-candol A (A4, 8 steps), ent-atisan-16α-ol (A6, 11 steps), and trachinol (A8, 10 steps) are achieved for the first time.
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Affiliation(s)
- Xian-He Zhao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Le-Le Meng
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xiao-Tao Liu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Peng-Fei Shu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Cheng Yuan
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xian-Tao An
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Tian-Xi Jia
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Qi-Qiong Yang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xiang Zhen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Chun-An Fan
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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33
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Merging enzymatic and synthetic chemistry with computational synthesis planning. Nat Commun 2022; 13:7747. [PMID: 36517480 PMCID: PMC9750992 DOI: 10.1038/s41467-022-35422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Synthesis planning programs trained on chemical reaction data can design efficient routes to new molecules of interest, but are limited in their ability to leverage rare chemical transformations. This challenge is acute for enzymatic reactions, which are valuable due to their selectivity and sustainability but are few in number. We report a retrosynthetic search algorithm using two neural network models for retrosynthesis-one covering 7984 enzymatic transformations and one 163,723 synthetic transformations-that balances the exploration of enzymatic and synthetic reactions to identify hybrid synthesis plans. This approach extends the space of retrosynthetic moves by thousands of uniquely enzymatic one-step transformations, discovers routes to molecules for which synthetic or enzymatic searches find none, and designs shorter routes for others. Application to (-)-Δ9 tetrahydrocannabinol (THC) (dronabinol) and R,R-formoterol (arformoterol) illustrates how our strategy facilitates the replacement of metal catalysis, high step counts, or costly enantiomeric resolution with more elegant hybrid proposals.
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34
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Hashimoto Y, Harada S, Kato R, Ikeda K, Nonnhoff J, Gröger H, Nemoto T. Merging Chemo- and Biocatalysis to Facilitate the Syntheses of Complex Natural Products: Enantioselective Construction of an N-Bridged [3.3.1] Ring System in Indole Terpenoids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshinori Hashimoto
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shingo Harada
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryosuke Kato
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kotaro Ikeda
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Jannis Nonnhoff
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Tetsuhiro Nemoto
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
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35
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Ouyang H, Yuan H, Huang J, Xian J, Wang W, Fu Z. CoN4-supported Co2N metal clusters for developing sensitive chemiluminescent immunochromatographic assays. Anal Chim Acta 2022; 1232:340478. [DOI: 10.1016/j.aca.2022.340478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 11/01/2022]
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36
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Sun Y, Chen Z, Wang G, Lv H, Mao Y, Ma K, Wang Y. De novo production of versatile oxidized kaurene diterpenes in Escherichia coli. Metab Eng 2022; 73:201-213. [DOI: 10.1016/j.ymben.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
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37
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Zhao Y, Zhang B, Sun ZQ, Zhang H, Wang W, Wang ZR, Guo ZK, Yu S, Tan RX, Ge HM. Biocatalytic C14-Hydroxylation on Androstenedione Enabled Modular Synthesis of Cardiotonic Steroids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zi Qian Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hao Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zi Ru Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Bio-technology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shouyun Yu
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
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38
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Chemo-enzymatic synthesis of natural products and their analogs. Curr Opin Biotechnol 2022; 77:102759. [PMID: 35908314 DOI: 10.1016/j.copbio.2022.102759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
Abstract
Enzymes continue to gain recognition as valuable tools in synthetic chemistry as they enable transformations, which elude conventional organochemical approaches. As such, the progressing expansion of the biocatalytic arsenal has introduced unprecedented opportunities for new synthetic strategies and retrosynthetic disconnections. As a result, enzymes have found a solid foothold in modern natural product synthesis for applications ranging from the generation of early chiral synthons to endgame transformations, convergent synthesis, and cascade reactions for the rapid construction of molecular complexity. As a primer to the state-of-the-art concerning strategic uses of enzymes in natural product synthesis and the underlying concepts, this review highlights selected recent literature examples, which make a strong case for the admission of enzymatic methodologies into the standard repertoire for complex small-molecule synthesis.
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Tao H, Abe I. Harnessing Fe(II)/α-ketoglutarate-dependent oxygenases for structural diversification of fungal meroterpenoids. Curr Opin Biotechnol 2022; 77:102763. [PMID: 35878474 DOI: 10.1016/j.copbio.2022.102763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Fungal meroterpenoids are structurally diverse natural products with important biological activities. During their biosynthesis, α-ketoglutarate-dependent oxygenases (αKG-DOs) catalyze a wide range of chemically challenging transformation reactions, including desaturation, epoxidation, oxidative rearrangement, and endoperoxide formation, by selective C-H bond activation, to produce molecules with more complex and divergent structures. Investigations on the structure-function relationships of αKG-DO enzymes have revealed the intimate molecular bases of their catalytic versatility and reaction mechanisms. Notably, the catalytic repertoire of αKG-DOs is further expanded by only subtle changes in their active site and lid-like loop-region architectures. Owing to their remarkable biocatalytic potential, αKG-DOs are ideal candidates for future chemoenzymatic synthesis and enzyme engineering for the generation of terpenoids with diverse structures and biological activities.
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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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40
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Santana VCS, Rocha ECS, Pavan JCS, Heleno VCG, de Lucca EC. Selective Oxidations in the Synthesis of Complex Natural ent-Kauranes and ent-Beyeranes. J Org Chem 2022; 87:10462-10466. [PMID: 35862248 DOI: 10.1021/acs.joc.2c01051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Syntheses of two natural products derived from the ent-kaurene kaurenoic acid are described for the first time using regio- and diastereoselective oxidations. Palladium- and manganese-mediated oxidations were used to accomplish the syntheses of two ent-beyerane metabolites. The use of the White-Gormisky-Zhao catalyst Mn(CF3-PDP) enabled the first application of a nondirected metal-catalyzed oxidation in an unactivated C-H bond in a total synthesis.
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Affiliation(s)
- Victor C S Santana
- Institute of Chemistry, University of Campinas, 13083-970 Campinas, SP, Brazil
| | - Eduardo C S Rocha
- Institute of Chemistry, University of Campinas, 13083-970 Campinas, SP, Brazil
| | - Julian C S Pavan
- Research Center in Exact and Technological Sciences, University of Franca, 14404-600 Franca, SP, Brazil
| | - Vladimir C G Heleno
- Research Center in Exact and Technological Sciences, University of Franca, 14404-600 Franca, SP, Brazil
| | - Emilio C de Lucca
- Institute of Chemistry, University of Campinas, 13083-970 Campinas, SP, Brazil
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41
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Li FR, Lin X, Yang Q, Tan NH, Dong LB. Efficient production of clerodane and ent-kaurane diterpenes through truncated artificial pathways in Escherichia coli. Beilstein J Org Chem 2022; 18:881-888. [PMID: 35957755 PMCID: PMC9344551 DOI: 10.3762/bjoc.18.89] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/15/2022] [Indexed: 11/23/2022] Open
Abstract
The clerodane and ent-kaurane diterpenoids are two typical categories of diterpenoid natural products with complicated polycyclic carbon skeletons and significant pharmacological activities. Despite exciting advances in organic chemistry, access to these skeletons is still highly challenging. Using synthetic biology to engineer microbes provides an innovative alternative to bypass synthetic challenges. In this study, we constructed two truncated artificial pathways to efficiently produce terpentetriene and ent-kaurene, two representative clerodane and ent-kaurane diterpenes, in Escherichia coli. Both pathways depend on the exogenous addition of isoprenoid alcohol to reinforce the supply of IPP and DMAPP via two sequential phosphorylation reactions. Optimization of these constructs provided terpentetriene and ent-kaurene titers of 66 ± 4 mg/L and 113 ± 7 mg/L, respectively, in shake-flask fermentation. The truncated pathways to overproduce clerodane and ent-kaurane skeletons outlined here may provide an attractive route to prepare other privileged diterpene scaffolds.
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Affiliation(s)
- Fang-Ru Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Xiaoxu Lin
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Qian Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Ning-Hua Tan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
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Li F, Deng H, Renata H. Remote B-Ring Oxidation of Sclareol with an Engineered P450 Facilitates Divergent Access to Complex Terpenoids. J Am Chem Soc 2022; 144:7616-7621. [PMID: 35452234 DOI: 10.1021/jacs.2c02958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Though chiral pool synthesis is widely accepted as a powerful strategy in complex molecule synthesis, the effectiveness of the approach is intimately linked to the range of available chiral building blocks and the functional groups they possess. To date, there is still a pressing need for new remote functionalization methods that would allow the installation of useful chemical handles on these building blocks to enable a broader spectrum of synthetic manipulations. Herein, we report the engineering of a P450BM3 variant for the regioselective C-H oxidation of sclareol at C6. The synthetic utility of the resulting product was demonstrated in a formal synthesis of ansellone B, the first total synthesis of the 2,3-seco-labdane excolide B, and a model study toward (+)-pallavicinin.
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Affiliation(s)
- Fuzhuo Li
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Heping Deng
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
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43
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Solans MM, Basistyi VS, Law JA, Bartfield NM, Frederich JH. Programmed Polyene Cyclization Enabled by Chromophore Disruption. J Am Chem Soc 2022; 144:6193-6199. [PMID: 35377634 PMCID: PMC10559755 DOI: 10.1021/jacs.2c02144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new polyene cyclization strategy exploiting β-ionyl derivatives was developed. Photoinduced deconjugation of the extended π-system within these chromophores unveils a contrathermodynamic polyene that engages in a Heck bicyclization to afford [4.4.1]-propellanes. This cascade improves upon the limited regioselectivity achieved using existing biomimetic tactics and tolerates both electron-rich and electron-deficient (hetero)aryl groups. The utility of this approach was demonstrated with the diverted total synthesis of taxodione and salviasperanol, two isomeric abietane diterpenes that were previously inaccessible along the same synthetic pathway.
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Affiliation(s)
- Megan M Solans
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Vitalii S Basistyi
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - James A Law
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Noah M Bartfield
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - James H Frederich
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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44
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Kumar Jha A, Deeksha, Inani H, Easwar S. An isatin Aldol Adduct as a precursor to α,α’-Difunctionalized Methyl Vinyl Ketones. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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45
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Pu Q, Huo M, Liang G, Bai L, Chen G, Li H, Xiang P, Zhou H, Zhou J. Divergent oxidative dearomatization coupling reactions to construct polycyclic cyclohexadienones. Chem Commun (Camb) 2022; 58:4348-4351. [PMID: 35293906 DOI: 10.1039/d2cc00183g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly selective divergent oxidative dearomatization coupling reactions, in which the chemoselectivity is controlled by catalysts and bases, are reported herein. Three different kinds of polycyclic cyclohexadienones are produced from the same reactants (41 examples, 85-99% yield). Our method marks a novel copper- and palladium-catalyzed C-H oxidative dearomatization of phenolic derivatives.
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Affiliation(s)
- Qian Pu
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Mingming Huo
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Guojuan Liang
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Lijuan Bai
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Genhui Chen
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Hongjiao Li
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Peng Xiang
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Hui Zhou
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Jing Zhou
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
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Roddan R, Carter EM, Thair B, Hailes HC. Chemoenzymatic approaches to plant natural product inspired compounds. Nat Prod Rep 2022; 39:1375-1382. [PMID: 35343542 PMCID: PMC9298680 DOI: 10.1039/d2np00008c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2003 up to the end of 2021Complex molecules produced by plants have provided us with a range of medicines, flavour and fragrance compounds and pesticides. However, there are challenges associated with accessing these in an economically viable manner, including low natural abundance and the requirement for complex multi-step synthetic strategies. Chemoenzymatic approaches provide a valuable alternative strategy by combining traditional synthetic methods with biocatalysis. This review highlights recent chemoenzymatic syntheses towards plant natural products and analogues, focusing on the advantages of incorporating biocatalysts into a synthetic strategy.
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Affiliation(s)
- Rebecca Roddan
- Department of Chemistry, University College London, Christopher Ingold Building, London WC1H 0AJ, UK.
| | - Eve M Carter
- Department of Chemistry, University College London, Christopher Ingold Building, London WC1H 0AJ, UK.
| | - Benjamin Thair
- Department of Chemistry, University College London, Christopher Ingold Building, London WC1H 0AJ, UK.
| | - Helen C Hailes
- Department of Chemistry, University College London, Christopher Ingold Building, London WC1H 0AJ, UK.
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Properties and Mechanisms of Flavin-Dependent Monooxygenases and Their Applications in Natural Product Synthesis. Int J Mol Sci 2022; 23:ijms23052622. [PMID: 35269764 PMCID: PMC8910399 DOI: 10.3390/ijms23052622] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products are usually highly complicated organic molecules with special scaffolds, and they are an important resource in medicine. Natural products with complicated structures are produced by enzymes, and this is still a challenging research field, its mechanisms requiring detailed methods for elucidation. Flavin adenine dinucleotide (FAD)-dependent monooxygenases (FMOs) catalyze many oxidation reactions with chemo-, regio-, and stereo-selectivity, and they are involved in the synthesis of many natural products. In this review, we introduce the mechanisms for different FMOs, with the classical FAD (C4a)-hydroperoxide as the major oxidant. We also summarize the difference between FMOs and cytochrome P450 (CYP450) monooxygenases emphasizing the advantages of FMOs and their specificity for substrates. Finally, we present examples of FMO-catalyzed synthesis of natural products. Based on these explanations, this review will expand our knowledge of FMOs as powerful enzymes, as well as implementation of the FMOs as effective tools for biosynthesis.
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48
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Abstract
Enzymes are renowned for their catalytic efficiency and selectivity. Despite the wealth of carbon-carbon bond forming transformations in traditional organic chemistry and nature, relatively few C-C bond forming enzymes have found their way into the biocatalysis toolbox. Here we show that the enzyme UstD performs a highly selective decarboxylative aldol addition with diverse aldehyde substrates to make non-standard, γ-hydroxy amino acids. We increased the activity of UstD through three rounds of classic directed evolution and an additional round of computationally-guided engineering. The enzyme that emerged, UstDv2.0, is efficient in a whole-cell biocatalysis format. The products are highly desirable, functionally rich bioactive γ-hydroxy amino acids that we demonstrate can be prepared stereoselectively on gram-scale. The X-ray crystal structure of UstDv2.0 at 2.25 Å reveals the active site and provides a foundation for probing the mechanism of UstD.
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49
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Chen Q, Yuan G, Yuan T, Zeng H, Zou ZR, Tu ZC, Gao J, Zou Y. Set of Cytochrome P450s Cooperatively Catalyzes the Synthesis of a Highly Oxidized and Rearranged Diterpene-Class Sordarinane Architecture. J Am Chem Soc 2022; 144:3580-3589. [PMID: 35170947 DOI: 10.1021/jacs.1c12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cytochrome P450s are one of the most versatile oxidases that catalyze significant and unique chemical transformations for the construction of complex structural frameworks during natural product biosynthesis. Here, we discovered a set of P450s, including SdnB, SdnH, SdnF, and SdnE, that cooperatively catalyzes the reshaping of the inert cycloaraneosene framework to form a highly oxidized and rearranged sordarinane architecture. Among them, SdnB is confirmed to be the first P450 (or oxidase) that cleaves the C-C bond of the epoxy residue to yield formyl groups in pairs. SdnF selectively oxidizes one generated formyl group to a carboxyl group and accelerates the final Diels-Alder cyclization to furnish the sordarinane architecture. Our work greatly enriches the enzyme functions of the P450 superfamily, supplies the missing skills of the P450 synthetic toolbox, and supports them as biocatalysts in further applications toward the synthesis of new chemical entities.
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Affiliation(s)
- Qibin Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Guanyin Yuan
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Tao Yuan
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Huiting Zeng
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Zheng-Rong Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Zong-Cai Tu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Jie Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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50
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Wein LA, Wurst K, Magauer T. Total Synthesis and Late-Stage C-H Oxidations of ent-Trachylobane Natural Products. Angew Chem Int Ed Engl 2022; 61:e202113829. [PMID: 34762359 PMCID: PMC7612322 DOI: 10.1002/anie.202113829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/23/2022]
Abstract
Herein, we present our studies to construct seven ent-trachylobane diterpenoids by employing a bioinspired two-phase synthetic strategy. The first phase provided enantioselective and scalable access to five ent-trachylobanes, of which methyl ent-trachyloban-19-oate was produced on a 300 mg scale. During the second phase, chemical C-H oxidation methods were employed to enable selective conversion to two naturally occurring higher functionalized ent-trachylobanes. The formation of regioisomeric analogs, which are currently inaccessible via enzymatic methods, reveals the potential as well as limitations of established chemical C-H oxidation protocols for complex molecule synthesis.
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Affiliation(s)
- Lukas Anton Wein
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens-University InnsbruckInnrain 80–826020InnsbruckAustria
| | - Klaus Wurst
- Institute of GeneralInorganic and Theoretical ChemistryLeopold-Franzens-University InnsbruckInnrain 80–826020InnsbruckAustria
| | - Thomas Magauer
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens-University InnsbruckInnrain 80–826020InnsbruckAustria
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