1
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Duez Q, van de Wiel J, van Sluijs B, Ghosh S, Baltussen MG, Derks MTGM, Roithová J, Huck WTS. Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry. J Am Chem Soc 2024; 146:20778-20787. [PMID: 39013149 PMCID: PMC11295183 DOI: 10.1021/jacs.4c04218] [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: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer. Feeding uniformly 13C-labeled inputs to the enzymatic network generates all isotopically labeled reaction intermediates and products, which are individually detected by ion mobility-mass spectrometry (IMS-MS) based on their mass-to-charge ratios and inverse ion mobilities. The metabolic flux can be continuously and quantitatively monitored by diluting the ERN output with nonlabeled standards of known concentrations. The real-time quantitative data obtained by IMS-MS are then harnessed to train a model of network kinetics, which proves sufficiently predictive to control the ERN output after a single optimally designed experiment. The high resolution of the time-course data provided by this approach is an important stepping stone to design and control sizable and intricate ERNs.
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Affiliation(s)
| | | | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Souvik Ghosh
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Max T. G. M. Derks
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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2
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Zhang Q, Chen Q, Shaik S, Wang B. Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angew Chem Int Ed Engl 2024; 63:e202318629. [PMID: 38299700 DOI: 10.1002/anie.202318629] [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: 12/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Flavoenzymes can mediate a large variety of oxidation reactions through the activation of oxygen. However, the O2 activation chemistry of flavin enzymes is not yet fully exploited. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, Flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that Flavin-N5OOH acts as a powerful nucleophile that promotes C-N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that Flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplish generally selective general base catalysis and C-X (X=N, S, Cl, O) cleavage reactions that are otherwise challenging with solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes.
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Affiliation(s)
- Qiaoyu Zhang
- 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, 361005, P. R. China
| | - Qianqian Chen
- 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, 361005, 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
| | - 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, 361005, P. R. China
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3
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Tiwari G, Khanna A, Mishra VK, Sagar R. Recent developments on microwave-assisted organic synthesis of nitrogen- and oxygen-containing preferred heterocyclic scaffolds. RSC Adv 2023; 13:32858-32892. [PMID: 37942237 PMCID: PMC10628940 DOI: 10.1039/d3ra05986c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
In recent decades, the utilization of microwave energy has experienced an extraordinary surge, leading to the introduction of innovative and revolutionary applications across various fields of chemistry such as medicinal chemistry, materials science, organic synthesis and heterocyclic chemistry. Herein, we provide a comprehensive literature review on the microwave-assisted organic synthesis of selected heterocycles. We highlight the use of microwave irradiation as an effective method for constructing a diverse range of molecules with high yield and selectivity. We also emphasize the impact of microwave irradiation on the efficient synthesis of N- and O-containing heterocycles that possess bioactive properties, such as anti-cancer, anti-proliferative, and anti-tumor activities. Specific attention is given to the efficient synthesis of pyrazolopyrimidines-, coumarin-, quinoline-, and isatin-based scaffolds, which have been extensively studied for their potential in drug discovery. The article provides valuable insights into the recent synthetic protocols and trends for the development of new drugs using heterocyclic molecules.
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Affiliation(s)
- Ghanshyam Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University Varanasi 221005 India
| | - Ashish Khanna
- Department of Chemistry, Institute of Science, Banaras Hindu University Varanasi 221005 India
| | - Vinay Kumar Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University Varanasi 221005 India
| | - Ram Sagar
- Department of Chemistry, Institute of Science, Banaras Hindu University Varanasi 221005 India
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University New Delhi 110067 India
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4
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Koser L, Bach T. Total Synthesis of (-)-5-Deoxyenterocin and Attempted Late-Stage Functionalization Reactions. Chemistry 2023; 29:e202301996. [PMID: 37452638 DOI: 10.1002/chem.202301996] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
The first total synthesis of (-)-5-deoxyenterocin has been accomplished starting from pentane-1,3,5-triol (16 steps in the longest linear sequence, 0.2 % overall yield). (-)-Menthone served as the source of chirality to distinguish the enantiotopic hydroxymethyl groups of the substrate. Key steps of the synthesis include two aldol reactions to either end of the C5 -skeleton, a diastereoselective hydroxylation reaction and a biomimetic twofold intramolecular aldol reaction as the final step. Although this step suffered from geometrical constraints and was low yielding (10 %), enough synthetic material could be secured to substantiate the relative and absolute configuration of the natural product. Additional experiments were directed toward a C-H functionalization at carbon atom C5. Despite the fact that several protocols could be successfully applied to (3aR)-(+)-sclareolide as model substrate, (-)-5-deoxyenterocin withstood any selective functionalization.
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Affiliation(s)
- Lilla Koser
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
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5
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Feng KN, Zhang Y, Zhang M, Yang YL, Liu JK, Pan L, Zeng Y. A flavin-monooxygenase catalyzing oxepinone formation and the complete biosynthesis of vibralactone. Nat Commun 2023; 14:3436. [PMID: 37301868 PMCID: PMC10257657 DOI: 10.1038/s41467-023-39108-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Oxepinone rings represent one of structurally unusual motifs of natural products and the biosynthesis of oxepinones is not fully understood. 1,5-Seco-vibralactone (3) features an oxepinone motif and is a stable metabolite isolated from mycelial cultures of the mushroom Boreostereum vibrans. Cyclization of 3 forms vibralactone (1) whose β-lactone-fused bicyclic core originates from 4-hydroxybenzoate, yet it remains elusive how 4-hydroxybenzoate is converted to 3 especially for the oxepinone ring construction in the biosynthesis of 1. In this work, using activity-guided fractionation together with proteomic analyses, we identify an NADPH/FAD-dependent monooxygenase VibO as the key enzyme performing a crucial ring-expansive oxygenation on the phenol ring to generate the oxepin-2-one structure of 3. The crystal structure of VibO reveals that it forms a dimeric phenol hydroxylase-like architecture featured with a unique substrate-binding pocket adjacent to the bound FAD. Computational modeling and solution studies provide insight into the likely VibO active site geometry, and suggest possible involvement of a flavin-C4a-OO(H) intermediate.
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Affiliation(s)
- Ke-Na Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingfang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan-Long Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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6
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Xiang L, Shi J, Zhu A, Xu ZF, Liu SH, Wang YS, Guo ZK, Jiao RH, Tan RX, Ge HM. Total Biosynthesis of Mutaxanthene Unveils a Flavoprotein Monooxygenase Catalyzing Xanthene Ring Formation. Angew Chem Int Ed Engl 2023; 62:e202218660. [PMID: 36727486 DOI: 10.1002/anie.202218660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/03/2023]
Abstract
Flavoprotein monooxygenases (FPMOs) play important roles in generating structural complexity and diversity in natural products biosynthesized by type II polyketide synthases (PKSs). In this study, we used genome mining to discover novel mutaxanthene analogues and investigated the biosynthesis of these aromatic polyketides and their unusual xanthene framework. We determined the complete biosynthetic pathway of mutaxathene through in vivo gene deletion and in vitro biochemical experiments. We show that a multifunctional FPMO, MtxO4, catalyzes ring rearrangement and generates the required xanthene ring through a multistep transformation. In addition, we successfully obtained all necessary enzymes for in vitro reconstitution and completed the total biosynthesis of mutaxanthene in a stepwise manner. Our results revealed the formation of a rare xanthene ring in type II polyketide biosynthesis, and demonstrate the potential of using total biosynthesis for the discovery of natural products synthesized by type II PKSs.
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Affiliation(s)
- Lang Xiang
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ao Zhu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zi Fei Xu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shuang He Liu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yi Shuang Wang
- State Key Laboratory of Ph armaceutical 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 Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Rui Hua Jiao
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Ph armaceutical 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 Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
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7
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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8
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [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: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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9
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Zhang H, Liao G, Luo X, Tang X. Harnessing nature's biosynthetic capacity to facilitate total synthesis. Natl Sci Rev 2022; 9:nwac178. [PMID: 36425752 PMCID: PMC9681125 DOI: 10.1093/nsr/nwac178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/07/2022] [Accepted: 08/23/2022] [Indexed: 07/25/2024] Open
Affiliation(s)
- Haili Zhang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, China
| | - Ge Liao
- Institute of Chemical Biology, Shenzhen Bay Laboratory, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, China
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10
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Bouthillette LM, Aniebok V, Colosimo DA, Brumley D, MacMillan JB. Nonenzymatic Reactions in Natural Product Formation. Chem Rev 2022; 122:14815-14841. [PMID: 36006409 DOI: 10.1021/acs.chemrev.2c00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosynthetic mechanisms of natural products primarily depend on systems of protein catalysts. However, within the field of biosynthesis, there are cases in which the inherent chemical reactivity of metabolic intermediates and substrates evades the involvement of enzymes. These reactions are difficult to characterize based on their reactivity and occlusion within the milieu of the cellular environment. As we continue to build a strong foundation for how microbes and higher organisms produce natural products, therein lies a need for understanding how protein independent or nonenzymatic biosynthetic steps can occur. We have classified such reactions into four categories: intramolecular, multicomponent, tailoring, and light-induced reactions. Intramolecular reactions is one of the most well studied in the context of biomimetic synthesis, consisting of cyclizations and cycloadditions due to the innate reactivity of the intermediates. There are two subclasses that make up multicomponent reactions, one being homologous multicomponent reactions which results in dimeric and pseudodimeric natural products, and the other being heterologous multicomponent reactions, where two or more precursors from independent biosynthetic pathways undergo a variety of reactions to produce the mature natural product. The third type of reaction discussed are tailoring reactions, where postmodifications occur on the natural products after the biosynthetic machinery is completed. The last category consists of light-induced reactions involving ecologically relevant UV light rather than high intensity UV irradiation that is traditionally used in synthetic chemistry. This review will cover recent nonenzymatic biosynthetic mechanisms and include sources for those reviewed previously.
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Affiliation(s)
- Leah M Bouthillette
- Deparment of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Victor Aniebok
- Deparment of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Dominic A Colosimo
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 United States
| | - David Brumley
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 United States
| | - John B MacMillan
- Deparment of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 United States
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11
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Wu C, Yin Y, Zhu L, Zhang Y, Li YZ. Metagenomic sequencing-driven multidisciplinary approaches to shed light on the untapped microbial natural products. Drug Discov Today 2021; 27:730-742. [PMID: 34775105 DOI: 10.1016/j.drudis.2021.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/07/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022]
Abstract
The advantage of metagenomics over the culture-based natural product (NP) discovery pipeline is the ability to access the biosynthetic potential of uncultivable microbes. Advances in DNA sequencing are revolutionizing conventional metagenomics approaches for microbial NP discovery. The genomes of (in)cultivable bugs can be resolved straightforwardly from environmental samples, enabling in situ prediction of biosynthetic gene clusters (BGCs). The predicted chemical diversities could be realized not only by heterologous expression of gene clusters originating from DNA synthesis or direct cloning, but also potentially by bioinformatic-directed organic synthesis or chemoenzymatic total synthesis. In this review, we suggest that metagenomic sequencing in tandem with multidisciplinary approaches will form a versatile platform to shed light on a plethora of microbial 'dark matter'.
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Affiliation(s)
- Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lele Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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12
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Koser L, Lechner VM, Bach T. Biomimetic Total Synthesis of Enterocin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lilla Koser
- Technische Universität München School of Natural Sciences Department of Chemistry and Catalysis Research Center Lichtenbergstrasse 4 85747 Garching Germany
| | - Vivian Miles Lechner
- Technische Universität München School of Natural Sciences Department of Chemistry and Catalysis Research Center Lichtenbergstrasse 4 85747 Garching Germany
| | - Thorsten Bach
- Technische Universität München School of Natural Sciences Department of Chemistry and Catalysis Research Center Lichtenbergstrasse 4 85747 Garching Germany
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13
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Koser L, Lechner VM, Bach T. Biomimetic Total Synthesis of Enterocin. Angew Chem Int Ed Engl 2021; 60:20269-20273. [PMID: 34278701 PMCID: PMC8457242 DOI: 10.1002/anie.202108157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Indexed: 02/06/2023]
Abstract
The first chemical total synthesis of the highly oxygenated polyketide enterocin has been accomplished. The key step of the synthesis was a late‐stage biomimetic reaction cascade involving two intramolecular aldol reactions in which each step proceeded in 52 % yield (averaged) and which established four of the seven stereogenic centers. The pivotal precursor for the cascade reaction was assembled from three readily available building blocks. A chiral dithioacetal with two stereogenic centers originating from L‐arabinose represented the core fragment to both ends of which the other building blocks were attached by aldol reactions. The remaining stereogenic center was installed by Davis oxygenation immediately prior to the key step.
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Affiliation(s)
- Lilla Koser
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Vivian Miles Lechner
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Thorsten Bach
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstrasse 4, 85747, Garching, Germany
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14
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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15
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Moore SJ, Lai HE, Chee SM, Toh M, Coode S, Chengan K, Capel P, Corre C, de los Santos ELC, Freemont PS. A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology. ACS Synth Biol 2021; 10:402-411. [PMID: 33497199 PMCID: PMC7901020 DOI: 10.1021/acssynbio.0c00581] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Prokaryotic
cell-free coupled transcription–translation
(TX-TL) systems are emerging as a powerful tool to examine natural
product biosynthetic pathways in a test tube. The key advantages of
this approach are the reduced experimental time scales and controlled
reaction conditions. To realize this potential, it is essential to
develop specialized cell-free systems in organisms enriched for biosynthetic
gene clusters. This requires strong protein production and well-characterized
synthetic biology tools. The Streptomyces genus is
a major source of natural products. To study enzymes and pathways
from Streptomyces, we originally developed a homologous Streptomyces cell-free system to provide a native protein
folding environment, a high G+C (%) tRNA pool, and an active background
metabolism. However, our initial yields were low (36 μg/mL)
and showed a high level of batch-to-batch variation. Here, we present
an updated high-yield and robust Streptomyces TX-TL
protocol, reaching up to yields of 266 μg/mL of expressed recombinant
protein. To complement this, we rapidly characterize a range of DNA
parts with different reporters, express high G+C (%) biosynthetic
genes, and demonstrate an initial proof of concept for combined transcription,
translation, and biosynthesis of Streptomyces metabolic
pathways in a single “one-pot” reaction.
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Affiliation(s)
- Simon J. Moore
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Hung-En Lai
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Soo-Mei Chee
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Ming Toh
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Seth Coode
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Kameshwari Chengan
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Patrick Capel
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Christophe Corre
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Emmanuel LC de los Santos
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Paul S. Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0N, U.K
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16
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 550] [Impact Index Per Article: 183.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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17
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Cowled MS, Lacey E, Karuso P, Piggott AM. Rechoreographing Enterocin’s Ballet of Isomers: Structure Revision of Enterocins C, D, and F. Org Lett 2020; 22:9688-9692. [DOI: 10.1021/acs.orglett.0c03745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michael S. Cowled
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ernest Lacey
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew M. Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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18
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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19
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Wohlgemuth R. Biocatalysis - Key enabling tools from biocatalytic one-step and multi-step reactions to biocatalytic total synthesis. N Biotechnol 2020; 60:113-123. [PMID: 33045418 DOI: 10.1016/j.nbt.2020.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/07/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland; Swiss Coordination Committee on Biotechnology (SKB), Nordstrasse 15, 8021 Zürich, Switzerland.
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20
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Hahn F, Guth FM. The ambruticins and jerangolids - chemistry, biology and chemoenzymatic synthesis of potent antifungal drug candidates. Nat Prod Rep 2020; 37:1300-1315. [PMID: 32420573 DOI: 10.1039/d0np00012d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 1977 to 2020The ambruticins and jerangolids are myxobacterial reduced polyketides, which are produced via highly unusual biosynthetic pathways containing a plethora of non-canonical enzymatic transformations. Since the discovery of the first congeners in the late 1970s, they have been in the focus of drug development due to their good antifungal activity and low toxicity in mammals, which result from interaction with an unusual innercellular target in fungi. Despite significant efforts, which have led to the development of various total syntheses, their structural complexity has yet avoided full exploitation of their pharmacological potential. This article summarises biological, total and semisynthetic as well as biosynthetic studies on both compounds. An outlook on the biosynthesis-based approaches to them and their derivatives is presented. Due to the structural and biosynthetic characteristics of the ambruticins and jerangolids, chemoenzymatic processes that make use of their biosynthetic pathway enzymes are particularly promising to gain efficient access to derivative libraries for structure activity relationship studies.
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Affiliation(s)
- Frank Hahn
- Department of Chemistry, University of Bayreuth, 51427 Bayreuth, Germany.
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21
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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22
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Abstract
Quinolone-containing natural products are widely found in bacteria, fungi, and plants. The fungal quinolactacins, which are N-methyl-4-quinolones, display a wide spectrum of biological activities. Here we uncovered a concise nonribosomal peptide synthetase pathway involved in quinolactacin A biosynthesis from Penicillium by using heterologous reconstitution and in vitro enzymatic synthesis. The N-desmethyl analog of quinolactacin A was accessed through the construction of a hybrid bacterial and fungi pathway in the heterologous host.
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Affiliation(s)
- Mengting Liu
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry University of California, Los Angeles, California 90095, United States.,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry University of California, Los Angeles, California 90095, United States
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23
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Cowled MS, Vuong D, Crombie A, Lacey E, Karuso P, Piggott AM. The chemical gymnastics of enterocin: evidence for stereodivergence in Nature. Org Biomol Chem 2020; 18:5879-5890. [PMID: 32672321 DOI: 10.1039/d0ob01099e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Stereodivergence in Nature encapsulates both enzymatic (biosynthetic) and non-enzymatic (chemical) diversification of natural product scaffolds arising from a single biosynthetic pathway. Herein, we report a fascinating example of stereodivergence for the bacterial polyketide enterocin, which we observed to undergo a series of facile skeletal rearrangements in solution, leading to four distinct isomeric structures. The final distribution of the four isomers was found to be highly sensitive to the conditions used, including solvent, temperature and pH. In this study, we have investigated the kinetics of these isomeric conversions, and using a combination of DFT and thermochemical calculations, were able to establish a mechanism detailing a concerted rearrangement and an unusual "gymnastic" sequence of pseudo-chair-boat conformational interconversions. In addition to these kinetic and mechanistic studies, we also performed a semisynthetic study aimed at stabilising the enterocin scaffold. In total, seven analogues of enterocin were synthesised and investigated for their stability and in vitro activity against a panel of bacteria, fungi, plants and mammalian cells.
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Affiliation(s)
- Michael S Cowled
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia. and Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
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24
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Salim AA, Samarasekera K, Khalil ZG, Capon RJ. Exploring Natural Product Artifacts: The Polyketide Enterocin Warms to a Ballet of Isomers. Org Lett 2020; 22:4828-4832. [PMID: 32511935 DOI: 10.1021/acs.orglett.0c01629] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The polyketide enterocin is responsive to environmental stimuli, where mild heating promotes an equilibrium mixture of the isomeric acetals enterocins B and C, which subsequently undergo pseudo-chair-boat inversion to enterocin D. When exposed to aqueous base, enterocin is converted to the isomeric Michael acceptor enterocin F. These studies demonstrate that knowledge of environmental stimuli and associated artifacts is critical to understanding the chemical and ecological properties of enterocins and other classes of natural products.
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Affiliation(s)
- Angela A Salim
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Kaumadi Samarasekera
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zeinab G Khalil
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert J Capon
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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25
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Zhuang L, Huang S, Liu WQ, Karim AS, Jewett MC, Li J. Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin. Metab Eng 2020; 60:37-44. [PMID: 32224263 DOI: 10.1016/j.ymben.2020.03.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/20/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022]
Abstract
Natural products are important because of their significant pharmaceutical properties such as antiviral, antimicrobial, and anticancer activity. Recent breakthroughs in DNA sequencing reveal that a great number of cryptic natural product biosynthetic gene clusters are encoded in microbial genomes, for example, those of Streptomyces species. However, it is still challenging to access compounds from these clusters because many source organisms are uncultivable or the genes are silent during laboratory cultivation. To address this challenge, we develop an efficient cell-free platform for the rapid, in vitro total biosynthesis of the nonribosomal peptide valinomycin as a model. We achieve this goal in two ways. First, we used a cell-free protein synthesis (CFPS) system to express the entire valinomycin biosynthetic gene cluster (>19 kb) in a single-pot reaction, giving rise to approximately 37 μg/L of valinomycin after optimization. Second, we coupled CFPS with cell-free metabolic engineering system by mixing two enzyme-enriched cell lysates to perform a two-stage biosynthesis. This strategy improved valinomycin production ~5000-fold to nearly 30 mg/L. We expect that cell-free biosynthetic systems will provide a new avenue to express, discover, and characterize natural product gene clusters of interest in vitro.
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Affiliation(s)
- Lei Zhuang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, United States.
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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26
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Hoang M, Kumar RA, Buisson DA, Ling WL, Gravel E, Doris E. Self‐assembled Polydiacetylene Nanoribbons for Semi‐heterogeneous and Enantioselective Organocatalysis of Aldol Reactions in Water. ChemCatChem 2019. [DOI: 10.1002/cctc.201901960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Minh‐Duc Hoang
- Service de Chimie Bioorganique et de Marquage (SCBM) CEAUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Ramar Arun Kumar
- Service de Chimie Bioorganique et de Marquage (SCBM) CEAUniversité Paris-Saclay 91191 Gif-sur-Yvette France
- SRM Research Institute, Department of ChemistrySRM Institute of Science and Technology Kattankulathur 603203 Chennai India
| | - David A. Buisson
- Service de Chimie Bioorganique et de Marquage (SCBM) CEAUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Wai Li Ling
- Univ. Grenoble Alpes, CEA, CNRS, IBS 38000 Grenoble France
| | - Edmond Gravel
- Service de Chimie Bioorganique et de Marquage (SCBM) CEAUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Eric Doris
- Service de Chimie Bioorganique et de Marquage (SCBM) CEAUniversité Paris-Saclay 91191 Gif-sur-Yvette France
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27
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Enzyme alchemy: cell-free synthetic biochemistry for natural products. Emerg Top Life Sci 2019; 3:529-535. [PMID: 33523168 DOI: 10.1042/etls20190083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022]
Abstract
Cell-free synthetic biochemistry aims to engineer chemical biology by exploiting biosynthetic dexterity outside of the constraints of a living cell. One particular use is for making natural products, where cell-free systems have initially demonstrated feasibility in the biosynthesis of a range of complex natural products classes. This has shown key advantages over total synthesis, such as increased yield, enhanced regioselectivity, use of reduced temperatures and less reaction steps. Uniquely, cell-free synthetic biochemistry represents a new area that seeks to advance upon these efforts and is particularly useful for defining novel synthetic pathways to replace natural routes and optimising the production of complex natural product targets from low-cost precursors. Key challenges and opportunities will include finding solutions to scaled-up cell-free biosynthesis, as well as the targeting of high value and toxic natural products that remain challenging to make either through whole-cell biotransformation platforms or total synthesis routes. Although underexplored, cell-free synthetic biochemistry could also be used to develop 'non-natural' natural products or so-called xenobiotics for novel antibiotics and drugs, which can be difficult to engineer directly within a living cell.
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28
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Zheng L, Jiang X, Zhang Q, Zhu Y, Zhang H, Zhang W, Saurav K, Liu J, Zhang C. Discovery and Biosynthesis of Neoenterocins Indicate a Skeleton Rearrangement of Enterocin. Org Lett 2019; 21:9066-9070. [PMID: 31657934 DOI: 10.1021/acs.orglett.9b03460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Liujuan Zheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaodong Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Kumar Saurav
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jinsong Liu
- Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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29
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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30
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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31
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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32
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Dudley QM, Nash CJ, Jewett MC. Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol (Oxf) 2019; 4:ysz003. [PMID: 30873438 PMCID: PMC6407499 DOI: 10.1093/synbio/ysz003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 11/25/2022] Open
Abstract
Isoprenoids are an attractive class of metabolites for enzymatic synthesis from renewable substrates. However, metabolic engineering of microorganisms for monoterpenoid production is limited by the need for time-consuming, and often non-intuitive, combinatorial tuning of biosynthetic pathway variations to meet design criteria. Towards alleviating this limitation, the goal of this work was to build a modular, cell-free platform for construction and testing of monoterpenoid pathways, using the fragrance and flavoring molecule limonene as a model. In this platform, multiple Escherichia coli lysates, each enriched with a single overexpressed pathway enzyme, are mixed to construct the full biosynthetic pathway. First, we show the ability to synthesize limonene from six enriched lysates with mevalonate substrate, an adenosine triphosphate (ATP) source, and cofactors. Next, we extend the pathway to use glucose as a substrate, which relies on native metabolism in the extract to convert glucose to acetyl-CoA along with three additional enzymes to convert acetyl-CoA to mevalonate. We find that the native E. coli farnesyl diphosphate synthase (IspA) is active in the lysate and diverts flux from the pathway intermediate geranyl pyrophospahte to farnesyl pyrophsophate and the byproduct farnesol. By adjusting the relative levels of cofactors NAD+, ATP and CoA, the system can synthesize 0.66 mM (90.2 mg l-1) limonene over 24 h, a productivity of 3.8 mg l-1 h-1. Our results highlight the flexibility of crude lysates to sustain complex metabolism and, by activating a glucose-to-limonene pathway with 9 heterologous enzymes encompassing 20 biosynthetic steps, expands an approach of using enzyme-enriched lysates for constructing, characterizing and prototyping enzymatic pathways.
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Affiliation(s)
- Quentin M Dudley
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Connor J Nash
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute Northwestern University, Chicago, IL, USA
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33
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Rizzo A, Mayer RJ, Trauner D. Biomimetic Approach Toward Enterocin and Deoxyenterocin. J Org Chem 2018; 84:1162-1175. [DOI: 10.1021/acs.joc.8b02273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Antonio Rizzo
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5−13, 81377 München, Germany
| | - Robert J. Mayer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5−13, 81377 München, Germany
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5−13, 81377 München, Germany
- Department of Chemistry, New York University 100 Washington Square East, Room 712, New York, New York 10003, United States
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Insights into the enzymatic formation, chemical features, and biological role of the flavin-N5-oxide. Curr Opin Chem Biol 2018; 47:47-53. [DOI: 10.1016/j.cbpa.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 11/22/2022]
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35
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Zhang Z, He Y, Huang Y, Ding L, Chen L, Liu Y, Nie Y, Zhang X. Development and Optimization of an In Vitro Multienzyme Synthetic System for Production of Kaempferol from Naringenin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8272-8279. [PMID: 30019587 DOI: 10.1021/acs.jafc.8b01299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
An in vitro multienzyme synthetic system was developed and optimized to efficiently produce kaempferol in a single reaction tube. Two key genes, Atf3h and Atfls1, in the biosynthetic pathway of kaempferol were cloned into a prokaryotic expression vector and overexpressed in Escherichia coli. The recombinant proteins were purified through affinity chromatography and showed activities of flavanone 3-hydroxylase and flavonol synthase, respectively, followed by development of an in vitro synthetic system for producing kaempferol. The system contains 8.2 mM α-ketoglutaric acid, 0.01 mM ferrous ion, 0.4% sodium ascorbate, 25 μg/mL of each recombinant enzyme, and 10% glycerol in 100 mM Tris-HCl (pH 7.2). When the reaction was carried out at 40 °C for 40-50 min, the yield of kaempferol was 37.55 ± 1.62 mg/L and the conversion rate from NRN to KMF was 55.89% ± 2.74%. Overall, this system provides a promising and efficient approach to produce kaempferol economically.
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Affiliation(s)
- Zhiping Zhang
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Yanzhi He
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Yue Huang
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Li Ding
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Lei Chen
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Yaxian Liu
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Yesen Nie
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
| | - Xinyue Zhang
- College of Bioscience and Biotechnology , Yangzhou University , Yangzhou , Jiangsu 225009 , China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China , Yangzhou University (26116120), Yangzhou , Jiangsu 225009 , China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety , Yangzhou University , Yangzhou , Jiangsu 225009 , China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu 225009 , China
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36
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Cell-free synthetic biology for in vitro biosynthesis of pharmaceutical natural products. Synth Syst Biotechnol 2018; 3:83-89. [PMID: 29900420 PMCID: PMC5995452 DOI: 10.1016/j.synbio.2018.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Natural products with significant biological activities continuously act as rich sources for drug discovery and development. To harness the potential of these valuable compounds, robust methods need to be developed for their rapid and sustainable production. Cell-free biosynthesis of pharmaceutical natural products by in vitro reconstruction of the entire biosynthetic pathways represents one such solution. In this review, we focus on in vitro biosynthesis of two important classes of natural products, polyketides (PKs) and nonribosomal peptides (NRPs). First, we summarize purified enzyme-based systems for the biosynthesis of PKs, NRPs, and PK/NRP hybrids. Then, we introduce the cell-free protein synthesis (CFPS)-based technology for natural product production. With that, we discuss challenges and opportunities of cell-free synthetic biology for in vitro biosynthesis of natural products.
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37
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Preparation and Characterization of the Favorskiiase Flavoprotein EncM and Its Distinctive Flavin-N5-Oxide Cofactor. Methods Enzymol 2018; 604:523-540. [DOI: 10.1016/bs.mie.2018.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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38
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Miyanaga A. Structure and function of polyketide biosynthetic enzymes: various strategies for production of structurally diverse polyketides. Biosci Biotechnol Biochem 2017; 81:2227-2236. [DOI: 10.1080/09168451.2017.1391687] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Polyketides constitute a large family of natural products that display various biological activities. Polyketides exhibit a high degree of structural diversity, although they are synthesized from simple acyl building blocks. Recent biochemical and structural studies provide a better understanding of the biosynthetic logic of polyketide diversity. This review highlights the biosynthetic mechanisms of structurally unique polyketides, β-amino acid-containing macrolactams, enterocin, and phenolic lipids. Functional and structural studies of macrolactam biosynthetic enzymes have revealed the unique biosynthetic machinery used for selective incorporation of a rare β-amino acid starter unit into the polyketide skeleton. Biochemical and structural studies of cyclization enzymes involved in the biosynthesis of enterocin and phenolic lipids provide mechanistic insights into how these enzymes diversify the carbon skeletons of their products.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
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39
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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40
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Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules. ACS Chem Biol 2017; 12:2157-2163. [PMID: 28617580 DOI: 10.1021/acschembio.7b00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.
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Affiliation(s)
| | - René F. Ramos Alvarenga
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Thomas P. Wyche
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biological
Chemistry and Molecular Pharmacology Department, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | | | | | | | - Charles D. Schwieters
- Center for
Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, United States
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41
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Dhakal D, Pokhrel AR, Shrestha B, Sohng JK. Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds. Front Microbiol 2017; 8:1106. [PMID: 28663748 PMCID: PMC5471306 DOI: 10.3389/fmicb.2017.01106] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/31/2017] [Indexed: 12/28/2022] Open
Abstract
Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications.
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Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Anaya Raj Pokhrel
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University Asan-siSouth Korea
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42
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Taniguchi H, Okano K, Honda K. Modules for in vitro metabolic engineering: Pathway assembly for bio-based production of value-added chemicals. Synth Syst Biotechnol 2017; 2:65-74. [PMID: 29062963 PMCID: PMC5636945 DOI: 10.1016/j.synbio.2017.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/02/2017] [Indexed: 11/17/2022] Open
Abstract
Bio-based chemical production has drawn attention regarding the realization of a sustainable society. In vitro metabolic engineering is one of the methods used for the bio-based production of value-added chemicals. This method involves the reconstitution of natural or artificial metabolic pathways by assembling purified/semi-purified enzymes in vitro. Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel, enabling easier pathway design with high modularity. Multiple modules have been designed, built, tested, and improved by different groups for different purpose. In this review, we focus on these in vitro metabolic engineering modules, especially focusing on the carbon metabolism, and present an overview of input modules, output modules, and other modules related to cofactor management.
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43
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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44
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Palanisamy SK, Rajendran NM, Marino A. Natural Products Diversity of Marine Ascidians (Tunicates; Ascidiacea) and Successful Drugs in Clinical Development. NATURAL PRODUCTS AND BIOPROSPECTING 2017; 7:1-111. [PMID: 28097641 PMCID: PMC5315671 DOI: 10.1007/s13659-016-0115-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
This present study reviewed the chemical diversity of marine ascidians and their pharmacological applications, challenges and recent developments in marine drug discovery reported during 1994-2014, highlighting the structural activity of compounds produced by these specimens. Till date only 5% of living ascidian species were studied from <3000 species, this study represented from family didemnidae (32%), polyclinidae (22%), styelidae and polycitoridae (11-12%) exhibiting the highest number of promising MNPs. Close to 580 compound structures are here discussed in terms of their occurrence, structural type and reported biological activity. Anti-cancer drugs are the main area of interest in the screening of MNPs from ascidians (64%), followed by anti-malarial (6%) and remaining others. FDA approved ascidian compounds mechanism of action along with other compounds status of clinical trials (phase 1 to phase 3) are discussed here in. This review highlights recent developments in the area of natural products chemistry and biotechnological approaches are emphasized.
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Affiliation(s)
- Satheesh Kumar Palanisamy
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98166, Messina, Italy.
| | - N M Rajendran
- Key Laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Angela Marino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98166, Messina, Italy
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45
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Greunke C, Glöckle A, Antosch J, Gulder TAM. Biokatalytische Totalsynthese von Ikarugamycin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christian Greunke
- Gulder Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstraße 4 85748 Garching Deutschland
| | - Anna Glöckle
- Gulder Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstraße 4 85748 Garching Deutschland
| | - Janine Antosch
- Gulder Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstraße 4 85748 Garching Deutschland
| | - Tobias A. M. Gulder
- Gulder Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstraße 4 85748 Garching Deutschland
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46
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Greunke C, Glöckle A, Antosch J, Gulder TAM. Biocatalytic Total Synthesis of Ikarugamycin. Angew Chem Int Ed Engl 2017; 56:4351-4355. [DOI: 10.1002/anie.201611063] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Christian Greunke
- Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstrasse 4 85748 Garching Germany
| | - Anna Glöckle
- Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstrasse 4 85748 Garching Germany
| | - Janine Antosch
- Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstrasse 4 85748 Garching Germany
| | - Tobias A. M. Gulder
- Biosystems Chemistry; Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM); Lichtenbergstrasse 4 85748 Garching Germany
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47
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Friedrich S, Hemmerling F, Lindner F, Warnke A, Wunderlich J, Berkhan G, Hahn F. Characterisation of the Broadly-Specific O-Methyl-transferase JerF from the Late Stages of Jerangolid Biosynthesis. Molecules 2016; 21:molecules21111443. [PMID: 27801873 PMCID: PMC6273487 DOI: 10.3390/molecules21111443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 12/03/2022] Open
Abstract
We describe the characterisation of the O-methyltransferase JerF from the late stages of jerangolid biosynthesis. JerF is the first known example of an enzyme that catalyses the formation of a non-aromatic, cyclic methylenolether. The enzyme was overexpressed in E. coli and the cell-free extracts were used in bioconversion experiments. Chemical synthesis gave access to a series of substrate surrogates that covered a broad structural space. Enzymatic assays revealed a broad substrate tolerance and high regioselectivity of JerF, which makes it an attractive candidate for an application in chemoenzymatic synthesis with particular usefulness for late stage application on 4-methoxy-5,6-dihydro-2H-pyran-2-one-containing natural products.
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Affiliation(s)
- Steffen Friedrich
- Zentrum für Biomolekulare Wirkstoffe, Leibniz-Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany.
| | - Franziska Hemmerling
- Zentrum für Biomolekulare Wirkstoffe, Leibniz-Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany.
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Universitätsstraße 30, 95447 Bayreuth, Germany.
| | - Frederick Lindner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Universitätsstraße 30, 95447 Bayreuth, Germany.
| | - Anna Warnke
- Zentrum für Biomolekulare Wirkstoffe, Leibniz-Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany.
| | - Johannes Wunderlich
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Universitätsstraße 30, 95447 Bayreuth, Germany.
| | - Gesche Berkhan
- Zentrum für Biomolekulare Wirkstoffe, Leibniz-Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany.
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Universitätsstraße 30, 95447 Bayreuth, Germany.
| | - Frank Hahn
- Zentrum für Biomolekulare Wirkstoffe, Leibniz-Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany.
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Universitätsstraße 30, 95447 Bayreuth, Germany.
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48
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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49
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Krauser S, Weyler C, Blaß LK, Heinzle E. Directed multistep biocatalysis using tailored permeabilized cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 137:185-234. [PMID: 23989897 DOI: 10.1007/10_2013_240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
: Recent developments in the field of biocatalysis using permeabilized cells are reviewed here, with a special emphasis on the newly emerging area of multistep biocatalysis using permeabilized cells. New methods of metabolic engineering using in silico network design and new methods of genetic engineering provide the opportunity to design more complex biocatalysts for the synthesis of complex biomolecules. Methods for the permeabilization of cells are thoroughly reviewed. We provide an extended review of useful available databases and bioinformatics tools, particularly for setting up genome-scale reconstructed networks. Examples described include phosphorylated carbohydrates, sugar nucleotides, and polyketides.
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Affiliation(s)
- Steffen Krauser
- Biochemical Engineering Institute, Saarland University, 66123, Saarbrücken, Germany
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50
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Morgado G, Gerngross D, Roberts TM, Panke S. Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:117-146. [PMID: 27757475 DOI: 10.1007/10_2016_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).
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Affiliation(s)
- Gaspar Morgado
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Daniel Gerngross
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania M Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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