1
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Zhao H. Recent advances in enzymatic carbon-carbon bond formation. RSC Adv 2024; 14:25932-25974. [PMID: 39161440 PMCID: PMC11331486 DOI: 10.1039/d4ra03885a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Enzymatic carbon-carbon (C-C) bond formation reactions have become an effective and invaluable tool for designing new biological and medicinal molecules, often with asymmetric features. This review provides a systematic overview of key C-C bond formation reactions and enzymes, with the focus of reaction mechanisms and recent advances. These reactions include the aldol reaction, Henry reaction, Knoevenagel condensation, Michael addition, Friedel-Crafts alkylation and acylation, Mannich reaction, Morita-Baylis-Hillman (MBH) reaction, Diels-Alder reaction, acyloin condensations via Thiamine Diphosphate (ThDP)-dependent enzymes, oxidative and reductive C-C bond formation, C-C bond formation through C1 resource utilization, radical enzymes for C-C bond formation, and other C-C bond formation reactions.
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Affiliation(s)
- Hua Zhao
- Department of Bioproducts and Biosystems Engineering, University of Minnesota St. Paul MN 55108 USA
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2
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Su Y, Lai W. Unraveling the Mechanism of the Oxidative C-C Bond Coupling Reaction Catalyzed by Deoxypodophyllotoxin Synthase. Inorg Chem 2024; 63:13948-13958. [PMID: 39008659 DOI: 10.1021/acs.inorgchem.4c01263] [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: 07/17/2024]
Abstract
Deoxypodophyllotoxin synthase (DPS), a nonheme Fe(II)/2-oxoglutarate (2OG)-dependent oxygenase, is a key enzyme that is involved in the construction of the fused-ring system in (-)-podophyllotoxin biosynthesis by catalyzing the C-C coupling reaction. However, the mechanistic details of DPS-catalyzed ring formation remain unclear. Herein, our quantum mechanics/molecular mechanics (QM/MM) calculations reveal a novel mechanism that involves the recycling of CO2 (a product of decarboxylation of 2OG) to prevent the formation of hydroxylated byproducts. Our results show that CO2 can react with the FeIII-OH species to generate an unusual FeIII-bicarbonate species. In this way, hydroxylation is avoided by consuming the OH group. Then, the C-C coupling followed by desaturation yields the final product, deoxypodophyllotoxin. This work highlights the crucial role of the CO2 molecule, generated in the crevice between the iron active site and the substrate, in controlling the reaction selectivity.
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Affiliation(s)
- Yanzhuang Su
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Wenzhen Lai
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
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3
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Ushimaru R. Functions and mechanisms of enzymes assembling lignans and norlignans. Curr Opin Chem Biol 2024; 80:102462. [PMID: 38692182 DOI: 10.1016/j.cbpa.2024.102462] [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: 02/24/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Lignans and norlignans are distributed throughout the plant kingdom and exhibit diverse chemical structures and biological properties that offer potential for therapeutic use. Originating from the phenylpropanoid biosynthesis pathway, their characteristic carbon architectures are formed through unique enzyme catalysis, featuring regio- and stereoselective C-C bond forming processes. Despite extensive research on these plant natural products, their biosynthetic pathways, and enzyme mechanisms remain enigmatic. This review highlights recent advancements in elucidating the functions and mechanisms of the biosynthetic enzymes responsible for constructing the distinct carbon frameworks of lignans and norlignans.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
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4
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Hardy FG, Wong HPH, de Visser SP. Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin. Chemistry 2024; 30:e202400019. [PMID: 38323740 DOI: 10.1002/chem.202400019] [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: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.
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Affiliation(s)
- Fintan G Hardy
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Henrik P H Wong
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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5
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Verma S, Paliwal S. Recent Developments and Applications of Biocatalytic and Chemoenzymatic Synthesis for the Generation of Diverse Classes of Drugs. Curr Pharm Biotechnol 2024; 25:448-467. [PMID: 37885105 DOI: 10.2174/0113892010238984231019085154] [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: 12/15/2022] [Revised: 08/26/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023]
Abstract
Biocatalytic and chemoenzymatic biosynthesis are powerful methods of organic chemistry that use enzymes to execute selective reactions and allow the efficient production of organic compounds. The advantages of these approaches include high selectivity, mild reaction conditions, and the ability to work with complex substrates. The utilization of chemoenzymatic techniques for the synthesis of complicated compounds has lately increased dramatically in the area of organic chemistry. Biocatalytic technologies and modern synthetic methods are utilized synergistically in a multi-step approach to a target molecule under this paradigm. Chemoenzymatic techniques are promising for simplifying access to essential bioactive compounds because of the remarkable regio- and stereoselectivity of enzymatic transformations and the reaction diversity of modern organic chemistry. Enzyme kits may include ready-to-use, reproducible biocatalysts. Its use opens up new avenues for the synthesis of active therapeutic compounds and aids in drug development by synthesizing active components to construct scaffolds in a targeted and preparative manner. This study summarizes current breakthroughs as well as notable instances of biocatalytic and chemoenzymatic synthesis. To assist organic chemists in the use of enzymes for synthetic applications, it also provides some basic guidelines for selecting the most appropriate enzyme for a targeted reaction while keeping aspects like cofactor requirement, solvent tolerance, use of whole cell or isolated enzymes, and commercial availability in mind.
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Affiliation(s)
- Swati Verma
- Department of Pharmacy, ITS College of Pharmacy, Muradnagar, Ghaziabad, India
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
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6
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Kobayashi K, Yamamura M, Mikami B, Shiraishi A, Kumatani M, Satake H, Ono E, Umezawa T. Anthriscus sylvestris Deoxypodophyllotoxin Synthase Involved in the Podophyllotoxin Biosynthesis. PLANT & CELL PHYSIOLOGY 2023; 64:1436-1448. [PMID: 37948767 DOI: 10.1093/pcp/pcad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023]
Abstract
Tetrahydrofuran ring formation from dibenzylbutyrolactone lignans is a key step in the biosynthesis of aryltetralin lignans including deoxypodophyllotoxin and podophyllotoxin. Previously, Fe(II)- and 2-oxoglutarate-dependent dioxygenase (2-ODD) from Podophyllum hexandrum (Himalayan mayapple, Berberidaceae) was found to catalyze the cyclization of a dibenzylbutyrolactone lignan, yatein, to give deoxypodophyllotoxin and designated as deoxypodophyllotoxin synthase (DPS). Recently, we reported that the biosynthesis of deoxypodophyllotoxin and podophyllotoxin evolved in a lineage-specific manner in phylogenetically unrelated plant species such as P. hexandrum and Anthriscus sylvestris (cow parsley, Apiaceae). Therefore, a comprehensive understanding of the characteristics of DPSs that catalyze the cyclization of yatein to deoxypodophyllotoxin in various plant species is important. However, for plant species other than P. hexandrum, the isolation of the DPS enzyme gene and the type of the enzyme, e.g. whether it is 2-ODD or another type of enzyme such as cytochrome P-450, have not been reported. In this study, we report the identification and characterization of A. sylvestris DPS (AsDPS). Phylogenetic analysis showed that AsDPS belonged to the 2-ODD superfamily and shared moderate amino acid sequence identity (40.8%) with P. hexandrum deoxypodophyllotoxin synthase (PhDPS). Recombinant protein assay indicated that AsDPS and PhDPS differ in terms of the selectivity of substrate enantiomers. Protein modeling using AlphaFold2 and site-directed mutagenesis indicated that the Tyr305 residue of AsDPS probably contributes to substrate recognition. This study advances our understanding of the podophyllotoxin biosynthetic pathway in A. sylvestris and provides new insight into 2-ODD involved in plant secondary (specialized) metabolism.
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Affiliation(s)
- Keisuke Kobayashi
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, 2-1, Minami-josanjima-cho, Tokushima, 770-8502 Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284 Japan
| | - Masato Kumatani
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284 Japan
| | - Eiichiro Ono
- Research Institute, Suntory Global Innovation Center Ltd., 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284 Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
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7
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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: 3] [Impact Index Per Article: 3.0] [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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8
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Xiang C, Fu Y, Hao T, Wei L, Liu Y, Fan ZC, Guo N, Yu P, Teng YO. Podophyllotoxin-loaded PEGylated E-selectin peptide conjugate targeted cancer site to enhance tumor inhibition and reduce side effect. Eur J Med Chem 2023; 260:115780. [PMID: 37666045 DOI: 10.1016/j.ejmech.2023.115780] [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: 08/04/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
E-selectin, which is highly expressed in vascular endothelial cells near tumor and get involved in the all tumor growth steps: occurrence, proliferation and metastasis, is considered as a promise targeted protein for antitumor drug discovery. Herein, we would like to report the design, preparation and the anticancer evaluation of the peptide-PEG-podophyllotoxin conjugate(PEG-Pep-PODO), in which the short peptide (CIELLQAR) was used as the E-selectin ligand for the targeting purpose and the PEG portion the molecule got the conjugate self-assembled to form a water soluble nanoparticle. In vitro release study showed that the conjugated and entrapped PODO could be released simultaneously in the presence of GSH (highly expressed in tumor environmental conditions) and the GSH would catalyze the break of the disufur bond which linked of the PODO and the peptide-PEG portion of the conjugate. Cell adhesion test of the PEG-Pep-PODO indicated that E-selectin ligand peptide CIELLQAR could get specifically and efficiently binding to the E-selectin expressing human umbilical vein endothelial cells (HUVEC). In vitro cytotoxicity assay further revealed that PEG-Pep-PODO significantly improved the selectivity of PEG-Pep-PODO for killing the tumor cells and normal cells compared with PODO solution formulation. More importantly, the in vivo experiment demonstrated that the conjugate would accumulate of the PODO payload in tumor through targeting endothelial cells in the tumor microenvironment, which resulted in the much improved in vivo inhibition of tumor growth, intratumoral microvessel density, and decreased systemic toxicity of this nanoparticle over the free PODO. Furthermore, this water soluble conjugate greatly improved the pharmacokinetic properties of the mother molecule.
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Affiliation(s)
- Cen Xiang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China; College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Ying Fu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Tiantian Hao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China; Medicinal Chemistry Department, Shouyao Holdings (Beijing) Co., Ltd., Beijing, China
| | - Linlin Wei
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yuning Liu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhen-Chuan Fan
- College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Na Guo
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Peng Yu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yu-Ou Teng
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China.
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9
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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10
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Zhang HQ, Yan CX, Xiao J, Wang YW, Peng Y. Recent advances in the total synthesis of 2,7'-cyclolignans. Org Biomol Chem 2022; 20:1623-1636. [PMID: 35129186 DOI: 10.1039/d1ob02457d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthetic progress of bioactive 2,7'-cyclolignans is reviewed. After a short introduction to biosynthesis and chemoenzymatic synthesis, the chemical synthesis of various aryltetralin, dihydronaphthalene and 7'-arylnaphthalene-types of these lignans is demonstrated. Notably, newly developed methods, such as Pd-catalyzed C-H arylation, organocatalysis and photocatalysis under visible-light, are discussed during the construction of their skeleton. These efforts will stimulate further development of novel synthetic strategies for this kind of natural product with important biological activities.
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Affiliation(s)
- Han-Qiu Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, People's Republic of China.
| | - Chu-Xuan Yan
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, People's Republic of China.
| | - Jian Xiao
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, People's Republic of China.
| | - Ya-Wen Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, People's Republic of China.
| | - Yu Peng
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, People's Republic of China.
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11
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Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase. Proc Natl Acad Sci U S A 2022; 119:2113770119. [PMID: 34969844 PMCID: PMC8740726 DOI: 10.1073/pnas.2113770119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 11/18/2022] Open
Abstract
The completion of the tetracyclic core of etoposide, classified by the World Health Organization as an essential medicine, by the Fe/2OG oxygenase deoxypodophyllotoxin synthase follows a hybrid radical-polar pathway not previously seen in other members of this enzyme class. The implication of a substrate-based benzylic carbocation in this mechanism will inform ongoing efforts to create analogs of this important drug with improved or emergent properties and represents a new route for resolution of the initial substrate radical that is common to members of the class. This study adds to our understanding on a growing number of biochemical transformations in which carbocation intermediates are likely to be crucial. Deoxypodophyllotoxin contains a core of four fused rings (A to D) with three consecutive chiral centers, the last being created by the attachment of a peripheral trimethoxyphenyl ring (E) to ring C. Previous studies have suggested that the iron(II)- and 2-oxoglutarate–dependent (Fe/2OG) oxygenase, deoxypodophyllotoxin synthase (DPS), catalyzes the oxidative coupling of ring B and ring E to form ring C and complete the tetracyclic core. Despite recent efforts to deploy DPS in the preparation of deoxypodophyllotoxin analogs, the mechanism underlying the regio- and stereoselectivity of this cyclization event has not been elucidated. Herein, we report 1) two structures of DPS in complex with 2OG and (±)-yatein, 2) in vitro analysis of enzymatic reactivity with substrate analogs, and 3) model reactions addressing DPS’s catalytic mechanism. The results disfavor a prior proposal of on-pathway benzylic hydroxylation. Rather, the DPS-catalyzed cyclization likely proceeds by hydrogen atom abstraction from C7', oxidation of the benzylic radical to a carbocation, Friedel–Crafts-like ring closure, and rearomatization of ring B by C6 deprotonation. This mechanism adds to the known pathways for transformation of the carbon-centered radical in Fe/2OG enzymes and suggests what types of substrate modification are likely tolerable in DPS-catalyzed production of deoxypodophyllotoxin analogs.
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12
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Decembrino D, Raffaele A, Knöfel R, Girhard M, Urlacher VB. Synthesis of (-)-deoxypodophyllotoxin and (-)-epipodophyllotoxin via a multi-enzyme cascade in E. coli. Microb Cell Fact 2021; 20:183. [PMID: 34544406 PMCID: PMC8454061 DOI: 10.1186/s12934-021-01673-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/07/2021] [Indexed: 01/30/2023] Open
Abstract
Background The aryltetralin lignan (−)−podophyllotoxin is a potent antiviral and anti-neoplastic compound that is mainly found in Podophyllum plant species. Over the years, the commercial demand for this compound rose notably because of the high clinical importance of its semi-synthetic chemotherapeutic derivatives etoposide and teniposide. To satisfy this demand, (−)−podophyllotoxin is conventionally isolated from the roots and rhizomes of Sinopodophyllum hexandrum, which can only grow in few regions and is now endangered by overexploitation and environmental damage. For these reasons, targeting the biosynthesis of (−)−podophyllotoxin precursors or analogues is fundamental for the development of novel, more sustainable supply routes. Results We recently established a four-step multi-enzyme cascade to convert (+)−pinoresinol into (−)−matairesinol in E. coli. Herein, a five-step multi-enzyme biotransformation of (−)−matairesinol to (−)−deoxypodophyllotoxin was proven effective with 98 % yield at a concentration of 78 mg/L. Furthermore, the extension of this cascade to a sixth step leading to (−)−epipodophyllotoxin was evaluated. To this end, seven enzymes were combined in the reconstituted pathway involving inter alia three plant cytochrome P450 monooxygenases, with two of them being functionally expressed in E. coli for the first time. Conclusions Both, (−)−deoxypodophyllotoxin and (−)−epipodophyllotoxin, are direct precursors to etoposide and teniposide. Thus, the reconstitution of biosynthetic reactions of Sinopodophyllum hexandrum as an effective multi-enzyme cascade in E. coli represents a solid step forward towards a more sustainable production of these essential pharmaceuticals. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01673-5.
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Affiliation(s)
- Davide Decembrino
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Alessandra Raffaele
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ronja Knöfel
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Marco Girhard
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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13
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Pyser J, Chakrabarty S, Romero EO, Narayan ARH. State-of-the-Art Biocatalysis. ACS CENTRAL SCIENCE 2021; 7:1105-1116. [PMID: 34345663 PMCID: PMC8323117 DOI: 10.1021/acscentsci.1c00273] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Indexed: 05/03/2023]
Abstract
The use of enzyme-mediated reactions has transcended ancient food production to the laboratory synthesis of complex molecules. This evolution has been accelerated by developments in sequencing and DNA synthesis technology, bioinformatic and protein engineering tools, and the increasingly interdisciplinary nature of scientific research. Biocatalysis has become an indispensable tool applied in academic and industrial spheres, enabling synthetic strategies that leverage the exquisite selectivity of enzymes to access target molecules. In this Outlook, we outline the technological advances that have led to the field's current state. Integration of biocatalysis into mainstream synthetic chemistry hinges on increased access to well-characterized enzymes and the permeation of biocatalysis into retrosynthetic logic. Ultimately, we anticipate that biocatalysis is poised to enable the synthesis of increasingly complex molecules at new levels of efficiency and throughput.
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Affiliation(s)
- Joshua
B. Pyser
- Department
of Chemistry, Life Sciences Institute, and Program in Chemical Biology, University of Michigan, , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United
States
| | - Suman Chakrabarty
- Department
of Chemistry, Life Sciences Institute, and Program in Chemical Biology, University of Michigan, , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United
States
| | - Evan O. Romero
- Department
of Chemistry, Life Sciences Institute, and Program in Chemical Biology, University of Michigan, , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United
States
| | - Alison R. H. Narayan
- Department
of Chemistry, Life Sciences Institute, and Program in Chemical Biology, University of Michigan, , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United
States
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14
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Harwood LA, Wong LL, Robertson J. Enzymatic Kinetic Resolution by Addition of Oxygen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lucy A. Harwood
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Luet L. Wong
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
| | - Jeremy Robertson
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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15
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Harwood LA, Wong LL, Robertson J. Enzymatic Kinetic Resolution by Addition of Oxygen. Angew Chem Int Ed Engl 2021; 60:4434-4447. [PMID: 33037837 PMCID: PMC7986699 DOI: 10.1002/anie.202011468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 12/25/2022]
Abstract
Kinetic resolution using biocatalysis has proven to be an excellent complementary technique to traditional asymmetric catalysis for the production of enantioenriched compounds. Resolution using oxidative enzymes produces valuable oxygenated structures for use in synthetic route development. This Minireview focuses on enzymes which catalyse the insertion of an oxygen atom into the substrate and, in so doing, can achieve oxidative kinetic resolution. The Baeyer-Villiger rearrangement, epoxidation, and hydroxylation are included, and biological advancements in enzyme development, and applications of these key enantioenriched intermediates in natural product synthesis are discussed.
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Affiliation(s)
- Lucy A. Harwood
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RoadOxfordOX1 3QRUK
- Oxford Suzhou Centre for Advanced ResearchRuo Shui Road, Suzhou Industrial ParkJiangsu215123P. R. China
| | - Jeremy Robertson
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Oxford Suzhou Centre for Advanced ResearchRuo Shui Road, Suzhou Industrial ParkJiangsu215123P. R. China
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16
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Wojdyla Z, Borowski T. Enzyme Multifunctionality by Control of Substrate Positioning Within the Catalytic Cycle—A QM/MM Study of Clavaminic Acid Synthase. Chemistry 2020; 27:2196-2211. [DOI: 10.1002/chem.202004426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8 30239 Krakow Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8 30239 Krakow Poland
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17
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Dunham NP, Arnold FH. Nature's Machinery, Repurposed: Expanding the Repertoire of Iron-Dependent Oxygenases. ACS Catal 2020; 10:12239-12255. [PMID: 33282461 PMCID: PMC7710332 DOI: 10.1021/acscatal.0c03606] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron is an especially important redox-active cofactor in biology because of its ability to mediate reactions with atmospheric O2. Iron-dependent oxygenases exploit this earth-abundant transition metal for the insertion of oxygen atoms into organic compounds. Throughout the astounding diversity of transformations catalyzed by these enzymes, the protein framework directs reactive intermediates toward the precise formation of products, which, in many cases, necessitates the cleavage of strong C-H bonds. In recent years, members of several iron-dependent oxygenase families have been engineered for new-to-nature transformations that offer advantages over conventional synthetic methods. In this Perspective, we first explore what is known about the reactivity of heme-dependent cytochrome P450 oxygenases and nonheme iron-dependent oxygenases bearing the 2-His-1-carboxylate facial triad by reviewing mechanistic studies with an emphasis on how the protein scaffold maximizes the catalytic potential of the iron-heme and iron cofactors. We then review how these cofactors have been repurposed for abiological transformations by engineering the protein frameworks of these enzymes. Finally, we discuss contemporary challenges associated with engineering these platforms and comment on their roles in biocatalysis moving forward.
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Affiliation(s)
- Noah P. Dunham
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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18
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Li J, Zhang X, Renata H. Biocatalytic Oxidative Cyclization with 2-ODD-PH. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2020.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Zwick CR, Renata H. Harnessing the biocatalytic potential of iron- and α-ketoglutarate-dependent dioxygenases in natural product total synthesis. Nat Prod Rep 2020; 37:1065-1079. [PMID: 32055818 PMCID: PMC7426249 DOI: 10.1039/c9np00075e] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to the end of 2019Iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGs) represent a versatile and intriguing enzyme family by virtue of their ability to directly functionalize unactivated C-H bonds at the cost of αKG and O2. Fe/αKGs play an important role in the biosynthesis of natural products, valuable biologically active secondary metabolites frequently pursued as drug leads. The field of natural product total synthesis seeks to contruct these molecules as effeciently as possible, although natural products continue to challenge chemists due to their intricate structural complexity. Chemoenzymatic approaches seek to remedy the shortcomings of traditional synthetic methodology by combining Nature's biosynthetic machinery with traditional chemical methods to efficiently construct natural products. Although other oxygenase families have been widely employed for this purpose, Fe/αKGs remain underutilized. The following review will cover recent chemoenzymatic total syntheses involving Fe/αKG enzymes. Additionally, related information involving natural product biosynthesis, methods development, and non-chemoenzymatic total syntheses will be discussed to inform retrosynthetic logic and synthetic design.
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Affiliation(s)
- Christian R Zwick
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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20
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Lu J, Wang B, Shaik S, Lai W. QM/MM Calculations Reveal the Important Role of α-Heteroatom Substituents in Controlling Selectivity of Mononuclear Nonheme HppE-Catalyzed Reactions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiarui Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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21
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Zetzsche LE, Narayan ARH. Broadening the scope of biocatalytic C-C bond formation. Nat Rev Chem 2020; 4:334-346. [PMID: 34430708 PMCID: PMC8382263 DOI: 10.1038/s41570-020-0191-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 12/18/2022]
Abstract
The impeccable control over chemo-, site-, and stereoselectivity possible in enzymatic reactions has led to a surge in the development of new biocatalytic methods. Despite carbon-carbon (C-C) bonds providing the central framework for organic molecules, development of biocatalytic methods for their formation has been largely confined to the use of a select few lyases over the last several decades, limiting the types of C-C bond-forming transformations possible through biocatalytic methods. This Review provides an update on the suite of enzymes available for highly selective biocatalytic C-C bond formation. Examples will be discussed in reference to the (1) native activity of enzymes, (2) alteration of activity through protein or substrate engineering for broader applicability, and (3) utility of the biocatalyst for abiotic synthesis.
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Affiliation(s)
- Lara E. Zetzsche
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison R. H. Narayan
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Li J, Amatuni A, Renata H. Recent advances in the chemoenzymatic synthesis of bioactive natural products. Curr Opin Chem Biol 2020; 55:111-118. [PMID: 32086167 PMCID: PMC7237303 DOI: 10.1016/j.cbpa.2020.01.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 01/18/2023]
Abstract
The field of organic chemistry has recently witnessed a rapid rise in the use of chemoenzymatic strategies for the synthesis of complex molecules. Under this paradigm, biocatalytic methods and contemporary synthetic methods are used synergistically in a multistep approach toward a target molecule. In light of the unparalleled regioselectivity and stereoselectivity of enzymatic transformations and the reaction diversity of contemporary organic chemistry, chemoenzymatic strategies hold enormous potential for streamlining access to important bioactive molecules. This review covers recent demonstrations of chemoenzymatic approaches in chemical synthesis, with special emphasis on the preparation of medicinally relevant natural products.
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Affiliation(s)
- Jian Li
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Alexander Amatuni
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.
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23
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Maldonado-Domínguez M, Srnec M. Understanding and Predicting Post H-Atom Abstraction Selectivity through Reactive Mode Composition Factor Analysis. J Am Chem Soc 2020; 142:3947-3958. [PMID: 32000494 DOI: 10.1021/jacs.9b12800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The selective functionalization of C-H bonds is one of the Grails of synthetic chemistry. In this work, we demonstrate that the selectivity toward fast hydroxylation or radical diffusion (known as the OH-rebound and dissociation mechanisms) following H-atom abstraction (HAA) from a substrate C-H bond by high-valent iron-oxo oxidants is already encoded in the HAA step when the post-HAA barriers are much lower than the preceding one. By applying the reactive mode composition factor (RMCF) analysis, which quantifies the kinetic energy distribution (KED) at the reactive mode (RM) of transition states, we show that reactions following the OH-rebound coordinate concentrate the RM kinetic energy on the motion of the reacting oxygen atom and the nascent substrate radical, whereas reactions following the dissociation channel localize most of their kinetic energy in H-atom motion. These motion signatures serve to predict the post-HAA selectivity, and since KED is affected by the free energy of reaction and asynchronicity (factor η) of HAA, we show that bimolecular HAA reactions in solution that are electron transfer-driven and highly exergonic have the lowest fraction of KED on the transferred H-atom and the highest chance to follow rebound hydroxylation. Finally, the RMCF analysis predicts that the H/D primary kinetic isotope effect can serve as a probe for these mechanisms, as confirmed in virtually all reported examples in the literature.
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Affiliation(s)
- Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
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24
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Wan Y, Peng H, Yang Q, Liu W, Deng G. Selective Synthesis of 2-(4-Aminoaryl)-2-(4-pyranonyl)acetates and 2,2-Bis(4-aminoaryl)-2-(4-pyranonyl)acetates from 2-Diazo-3,5-dioxo-6-ynoates (ynones) and Aromatic Amines. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yinbo Wan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China); Hunan Normal University; 410081 Changsha China
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province; Hunan Normal University; 410081 Changsha China
| | - Haiyun Peng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China); Hunan Normal University; 410081 Changsha China
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province; Hunan Normal University; 410081 Changsha China
| | - Qin Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China); Hunan Normal University; 410081 Changsha China
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province; Hunan Normal University; 410081 Changsha China
| | - Weishun Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China); Hunan Normal University; 410081 Changsha China
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province; Hunan Normal University; 410081 Changsha China
| | - Guisheng Deng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China); Hunan Normal University; 410081 Changsha China
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province; Hunan Normal University; 410081 Changsha China
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25
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Pan J, Wenger ES, Matthews ML, Pollock CJ, Bhardwaj M, Kim AJ, Allen BD, Grossman RB, Krebs C, Bollinger JM. Evidence for Modulation of Oxygen Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases. J Am Chem Soc 2019; 141:15153-15165. [PMID: 31475820 DOI: 10.1021/jacs.9b06689] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases generate iron(IV)-oxo (ferryl) intermediates that can abstract hydrogen from aliphatic carbons (R-H). Hydroxylation proceeds by coupling of the resultant substrate radical (R•) and oxygen of the Fe(III)-OH complex ("oxygen rebound"). Nonhydroxylation outcomes result from different fates of the Fe(III)-OH/R• state; for example, halogenation results from R• coupling to a halogen ligand cis to the hydroxide. We previously suggested that halogenases control substrate-cofactor disposition to disfavor oxygen rebound and permit halogen coupling to prevail. Here, we explored the general implication that, when a ferryl intermediate can ambiguously target two substrate carbons for different outcomes, rebound to the site capable of the alternative outcome should be slower than to the adjacent, solely hydroxylated site. We evaluated this prediction for (i) the halogenase SyrB2, which exclusively hydroxylates C5 of norvaline appended to its carrier protein but can either chlorinate or hydroxylate C4 and (ii) two bifunctional enzymes that normally hydroxylate one carbon before coupling that oxygen to a second carbon (producing an oxacycle) but can, upon encountering deuterium at the first site, hydroxylate the second site instead. In all three cases, substrate hydroxylation incorporates a greater fraction of solvent-derived oxygen at the site that can also undergo the alternative outcome than at the other site, most likely reflecting an increased exchange of the initially O2-derived oxygen ligand in the longer-lived Fe(III)-OH/R• states. Suppression of rebound may thus be generally important for nonhydroxylation outcomes by these enzymes.
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Affiliation(s)
| | | | | | | | - Minakshi Bhardwaj
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40546-0312 , United States
| | | | | | - Robert B Grossman
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40546-0312 , United States
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26
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Li J, Zhang X, Renata H. Asymmetric Chemoenzymatic Synthesis of (-)-Podophyllotoxin and Related Aryltetralin Lignans. Angew Chem Int Ed Engl 2019; 58:11657-11660. [PMID: 31241812 DOI: 10.1002/anie.201904102] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Indexed: 11/06/2022]
Abstract
(-)-Podophyllotoxin is one of the most potent microtubule depolymerizing agents and has served as an important lead compound in antineoplastic drug discovery. Reported here is a short chemoenzymatic total synthesis of (-)-podophyllotoxin and related aryltetralin lignans. Vital to this approach is the use of an enzymatic oxidative C-C coupling reaction to construct the tetracyclic core of the natural product in a diastereoselective fashion. This strategy allows gram-scale access to (-)-deoxypodophyllotoxin and is readily adaptable to the preparation of related aryltetralin lignans.
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Affiliation(s)
- Jian Li
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Xiao Zhang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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27
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Li J, Zhang X, Renata H. Asymmetric Chemoenzymatic Synthesis of (−)‐Podophyllotoxin and Related Aryltetralin Lignans. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian Li
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Xiao Zhang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Hans Renata
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
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28
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Dunham NP, Del Río Pantoja JM, Zhang B, Rajakovich LJ, Allen BD, Krebs C, Boal AK, Bollinger JM. Hydrogen Donation but not Abstraction by a Tyrosine (Y68) during Endoperoxide Installation by Verruculogen Synthase (FtmOx1). J Am Chem Soc 2019; 141:9964-9979. [PMID: 31117657 PMCID: PMC6901024 DOI: 10.1021/jacs.9b03567] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hydrogen-atom transfer (HAT) from a substrate carbon to an iron(IV)-oxo (ferryl) intermediate initiates a diverse array of enzymatic transformations. For outcomes other than hydroxylation, coupling of the resultant carbon radical and hydroxo ligand (oxygen rebound) must generally be averted. A recent study of FtmOx1, a fungal iron(II)- and 2-(oxo)glutarate-dependent oxygenase that installs the endoperoxide of verruculogen by adding O2 between carbons 21 and 27 of fumitremorgin B, posited that tyrosine (Tyr or Y) 224 serves as HAT intermediary to separate the C21 radical (C21•) and Fe(III)-OH HAT products and prevent rebound. Our reinvestigation of the FtmOx1 mechanism revealed, instead, direct HAT from C21 to the ferryl complex and surprisingly competitive rebound. The C21-hydroxylated (rebound) product, which undergoes deprenylation, predominates when low [O2] slows C21•-O2 coupling in the next step of the endoperoxidation pathway. This pathway culminates with addition of the C21-O-O• peroxyl adduct to olefinic C27 followed by HAT to the C26• from a Tyr. The last step results in sequential accumulation of Tyr radicals, which are suppressed without detriment to turnover by inclusion of the reductant, ascorbate. Replacement of each of four candidates for the proximal C26 H• donor (including Y224) with phenylalanine (F) revealed that only the Y68F variant (i) fails to accumulate the first Tyr• and (ii) makes an altered major product, identifying Y68 as the donor. The implied proximities of C21 to the iron cofactor and C26 to Y68 support a new docking model of the enzyme-substrate complex that is consistent with all available data.
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Affiliation(s)
- Noah P. Dunham
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, PA 16802
- Present Address: Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, CA 91125
| | - José M. Del Río Pantoja
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, PA 16802
- Present Address: Department of Chemistry and Chemical
Biology, Harvard University, Cambridge, MA 02138
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
- Present Address: Renewable Energy Group, Inc., 600 Gateway
Blvd, South San Francisco, CA 94080
| | - Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, PA 16802
- Present Address: Department of Chemistry and Chemical
Biology, Harvard University, Cambridge, MA 02138
| | - Benjamin D. Allen
- The Huck Institutes for Life Sciences, The Pennsylvania
State University, University Park, PA 16802
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
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29
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Lazzarotto M, Hammerer L, Hetmann M, Borg A, Schmermund L, Steiner L, Hartmann P, Belaj F, Kroutil W, Gruber K, Fuchs M. Chemoenzymatische Totalsynthese von Deoxy‐,
epi
‐ und Podophyllotoxin sowie biokatalytische kinetische Racematspaltung von Dibenzylbutyrolactonen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900926] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mattia Lazzarotto
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
| | - Lucas Hammerer
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology c/o Karl-Franzens-Universität Graz Graz Österreich
| | - Michael Hetmann
- Institut für Molekulare Biowissenschaften Karl-Franzens-Universität Graz Humboldtstraße 50/III 8010 Graz Österreich
| | - Annika Borg
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
| | - Luca Schmermund
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
| | - Lorenz Steiner
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
| | - Peter Hartmann
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
| | - Ferdinand Belaj
- Institut für Chemie Anorganische Chemie Karl-Franzens-Universität Graz Schubertstraße 1/III 8010 Graz Österreich
| | - Wolfgang Kroutil
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften Karl-Franzens-Universität Graz Humboldtstraße 50/III 8010 Graz Österreich
| | - Michael Fuchs
- Institut für Chemie Organische und Bioorganische Chemie Karl-Franzens-Universität Graz Heinrichstrasse 28/II 8010 Graz Österreich
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30
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Lazzarotto M, Hammerer L, Hetmann M, Borg A, Schmermund L, Steiner L, Hartmann P, Belaj F, Kroutil W, Gruber K, Fuchs M. Chemoenzymatic Total Synthesis of Deoxy-, epi-, and Podophyllotoxin and a Biocatalytic Kinetic Resolution of Dibenzylbutyrolactones. Angew Chem Int Ed Engl 2019; 58:8226-8230. [PMID: 30920120 PMCID: PMC6563474 DOI: 10.1002/anie.201900926] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/06/2023]
Abstract
Podophyllotoxin is probably the most prominent representative of lignan natural products. Deoxy‐, epi‐, and podophyllotoxin, which are all precursors to frequently used chemotherapeutic agents, were prepared by a stereodivergent biotransformation and a biocatalytic kinetic resolution of the corresponding dibenzylbutyrolactones with the same 2‐oxoglutarate‐dependent dioxygenase. The reaction can be conducted on 2 g scale, and the enzyme allows tailoring of the initial, “natural” structure and thus transforms various non‐natural derivatives. Depending on the substitution pattern, the enzyme performs an oxidative C−C bond formation by C−H activation or hydroxylation at the benzylic position prone to ring closure.
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Affiliation(s)
- Mattia Lazzarotto
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
| | - Lucas Hammerer
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, c/o University of Graz, Graz, Austria
| | - Michael Hetmann
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/III, 8010, Graz, Austria
| | - Annika Borg
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
| | - Luca Schmermund
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
| | - Lorenz Steiner
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
| | - Peter Hartmann
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
| | - Ferdinand Belaj
- Institute of Chemistry, Inorganic Chemistry, University of Graz, Schubertstraße 1/III, 8010, Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/III, 8010, Graz, Austria
| | - Michael Fuchs
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/II, 8010, Graz, Austria
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