1
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Cancellieri MC, Nobbio C, Gatti FG, Brenna E, Parmeggiani F. Applications of biocatalytic CC bond reductions in the synthesis of flavours and fragrances. J Biotechnol 2024; 390:13-27. [PMID: 38761886 DOI: 10.1016/j.jbiotec.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Industrial biotechnology and biocatalysis can provide very effective synthetic tools to increase the sustainability of the production of fine chemicals, especially flavour and fragrance (F&F) ingredients, the market demand of which has been constantly increasing in the last years. One of the most important transformations in F&F chemistry is the reduction of CC bonds, typically carried out with metal-catalysed hydrogenations or hydride-based reagents. Its biocatalytic counterpart is a competitive alternative, showcasing a range of advantages such as excellent chemo-, regio- and stereoselectivity, ease of implementation, mild reaction conditions and modest environmental impact. In the present review, the application of biocatalysed alkene reductions (from microbial fermentations with wild-type strains to engineered isolated ene-reductase enzymes) to synthetic processes useful for the F&F industry will be described, highlighting not only the exquisite stereoselectivity achieved, but also the overall improvement when chirality is not involved. Multi-enzymatic cascades involving CC bioreductions are also examined, which allow much greater chemical complexity to be built in one-pot biocatalytic systems.
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Affiliation(s)
- Maria C Cancellieri
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Celeste Nobbio
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Francesco G Gatti
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Elisabetta Brenna
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy.
| | - Fabio Parmeggiani
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy.
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2
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Sebastianelli L, Kaur H, Chen Z, Krishnamurthy R, Mansy SS. A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides. Chemistry 2024; 30:e202400411. [PMID: 38640109 DOI: 10.1002/chem.202400411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/21/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3-(aminocarbonyl)-1-(2,3-dihydroxypropyl)pyridinium, 1-methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules.
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Affiliation(s)
- Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Harpreet Kaur
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Ziniu Chen
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
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3
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Black WB, Perea S, Li H. Design, construction, and application of noncanonical redox cofactor infrastructures. Curr Opin Biotechnol 2023; 84:103019. [PMID: 37939631 DOI: 10.1016/j.copbio.2023.103019] [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: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Controlling the flow of carbon and reducing power in biological systems is a central theme in metabolic engineering. Often, trade-offs in pushing carbon flux through targeted pathways while operating in conditions agreeable to the host are required due to the central pools of the shared native redox cofactors NAD(P)/H. Noncanonical redox cofactors (NRCs) have emerged as promising tools to transform how engineers develop biotransformation systems. These new-to-Nature redox cofactors have been demonstrated to function orthogonally to the endogenous cofactors, support pathway thermodynamics optimization, and achieve product scopes previously difficult to reach due to endogenous pathway crosstalk. This review will discuss the development of NRC infrastructures, comprising NRC pools, cofactor reduction sources, and cofactor oxidation sinks, the (pool-source-sink) infrastructure.
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Affiliation(s)
- William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America; Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-3900, United States of America.
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4
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Bruggeman C, Gregurash K, Hickey DP. Impact of sodium pyruvate on the electrochemical reduction of NAD + biomimetics. Faraday Discuss 2023; 247:87-100. [PMID: 37496434 DOI: 10.1039/d3fd00047h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Biomimetics of nicotinamide adenine dinucleotide (mNADH) are promising cost-effective alternatives to their natural counterpart for biosynthetic applications; however, attempts to recycle mNADH often rely on coenzymes or precious metal catalysts. Direct electrolysis is an attractive approach for recycling mNADH, but electrochemical reduction of the oxidized mimetic (mNAD+) primarily results in the formation of an enzymatically inactive dimer. Herein, we find that aqueous electrochemical reduction of an NAD+ mimetic, 1-n-butyl-3-carbamoylpyridinium bromide (1+), to its enzymatically active form, 1,4-dihydro-1-n-butyl nicotinamide (1H), is favored in the presence of sodium pyruvate as a supporting electrolyte. Maximum formation of 1H is achieved in the presence of a large excess of pyruvate in combination with a large excess of a co-supporting electrolyte. Formation of 1H is found to be favored at pH 7, with an optimized product ratio of ∼50/50 dimer/1H observed by cyclic voltammetry. Furthermore, sodium pyruvate is shown to promote electroreductive generation of the 1,4-dihydro form of several additional mNADH as well as NADH itself. This method provides a general strategy for regenerating 1,4-dihydro-nicotinamide mimetics of NADH from their oxidized forms.
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Affiliation(s)
- Chase Bruggeman
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA.
| | - Karissa Gregurash
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA.
| | - David P Hickey
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA.
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5
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Guo YY, Tian ZH, Han YC, Ma D, Shao T, Jiang Z. Hantzsch Ester as Efficient and Economical NAD(P)H Mimic for In Vitro Bioredox Reactions. Chemistry 2023; 29:e202301180. [PMID: 37263982 DOI: 10.1002/chem.202301180] [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: 04/14/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/03/2023]
Abstract
Biocatalysis has emerged as a valuable and reliable tool for industrial and academic societies, particularly in fields related to bioredox reactions. The cost of cofactors, especially those needed to be replenished at stoichiometric amounts or more, is the chief economic concern for bioredox reactions. In this study, a readily accessible, inexpensive, and bench-stable Hantzsch ester is verified as the viable and efficient NAD(P)H mimic by four enzymatic redox transformations, including two non-heme diiron N-oxygenases and two flavin-dependent reductases. This finding provides the potential to significantly reduce the costs of NAD(P)H-relying bioredox reactions.
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Affiliation(s)
- Yuan-Yang Guo
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Ze-Hua Tian
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Yu-Chen Han
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Dandan Ma
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Tianju Shao
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Zhiyong Jiang
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
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6
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Xie W, Xu J, Md Idros U, Katsuhira J, Fuki M, Hayashi M, Yamanaka M, Kobori Y, Matsubara R. Metal-free reduction of CO 2 to formate using a photochemical organohydride-catalyst recycling strategy. Nat Chem 2023:10.1038/s41557-023-01157-6. [PMID: 36959509 DOI: 10.1038/s41557-023-01157-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/09/2023] [Indexed: 03/25/2023]
Abstract
Increasing levels of CO2 in the atmosphere is a problem that must be urgently resolved if the rise in current global temperatures is to be slowed. Chemically reducing CO2 into compounds that are useful as energy sources and carbon-based materials could be helpful in this regard. However, for the CO2 reduction reaction (CO2RR) to be operational on a global scale, the catalyst system must: use only renewable energy, be built from abundantly available elements and not require high-energy reactants. Although light is an attractive renewable energy source, most existing CO2RR methods use electricity and many of the catalysts used are based on rare heavy metals. Here we present a transition-metal-free catalyst system that uses an organohydride catalyst based on benzimidazoline for the CO2RR that can be regenerated using a carbazole photosensitizer and visible light. The system is capable of producing formate with a turnover number exceeding 8,000 and generates no other reduced products (such as H2 and CO).
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Affiliation(s)
- Weibin Xie
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Jiasheng Xu
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Ubaidah Md Idros
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Jouji Katsuhira
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Masaaki Fuki
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
- Molecular Photoscience Research Center, Kobe University, Kobe, Japan
| | - Masahiko Hayashi
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Masahiro Yamanaka
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Tokyo, Japan.
| | - Yasuhiro Kobori
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan.
- Molecular Photoscience Research Center, Kobe University, Kobe, Japan.
| | - Ryosuke Matsubara
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan.
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7
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Li N, Yao SJ, Wei MJ, He J, Chi W, Lan YQ. CO 2 Photoactivation Study of Adenine Nucleobase: Role of Hydrogen-Bonding Traction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206724. [PMID: 36436832 DOI: 10.1002/smll.202206724] [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: 11/02/2022] [Revised: 11/12/2022] [Indexed: 06/16/2023]
Abstract
The discovery and in-depth study of non-biocatalytic applications of active biomolecules are essential for the development of biomimicry. Here, the effect of intermolecular hydrogen-bonding traction on the CO2 photoactivation performance of adenine nucleobase by means of an adenine-containing model system (AMOF-1-4) is uncovered. Remarkably, the hydrogen-bonding schemes around adenines are regularly altered with the increase in the alkyl (methyl, ethyl, isopropyl, and tert-butyl) electron-donating capacity of the coordinated aliphatic carboxylic acids, and thus, lead to a stepwise improvement in CO2 photoreduction activity. Density functional theory calculations demonstrate that strong intermolecular hydrogen-bonding traction surrounding adenine can obviously increase the adenine-CO2 interaction energy and, therefore, result in a smoother CO2 activation process. Significantly, this work also provides new inspiration for expanding the application of adenine to more small-molecule catalytic reactions.
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Affiliation(s)
- Ning Li
- Department School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong, 510006, China
| | - Su-Juan Yao
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Mei-Jie Wei
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China
| | - Jun He
- Department School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong, 510006, China
| | - Weijie Chi
- School of Science, Hainan university, No. 58 Renmin Avenue, Meilan District, Haikou, 570228, China
| | - Ya-Qian Lan
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
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8
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Gu ZY, Li WD, Li YL, Cui K, Xia JB. Selective Reductive Coupling of Vinyl Azaarenes and Alkynes via Photoredox Cobalt Dual Catalysis. Angew Chem Int Ed Engl 2023; 62:e202213281. [PMID: 36178079 DOI: 10.1002/anie.202213281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Indexed: 12/30/2022]
Abstract
A visible light-induced Co-catalyzed highly regio- and stereoselective reductive coupling of vinyl azaarenes and alkynes has been developed. Notably, Hünig's base together with simple ethanol has been successfully applied as the hydrogen sources instead of commonly used Hantzsch esters in this catalytic photoredox reaction. This approach has considerable advantages for the straightforward synthesis of stereodefined multiple substituted alkenes bearing an azaarene motif, such as excellent regioselectivity (>20 : 1 for >30 examples) and stereoselectivity (>20 : 1 E/Z), broad substrate scope and good functional group compatibility under mild reaction conditions, which has been utilized in the concise synthesis of natural product monomorine I. A reasonable catalytic reaction pathway involving protolysis of the cobaltacyclopentene intermediate has been proposed based on the mechanistic studies.
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Affiliation(s)
- Zheng-Yang Gu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Textiles and Clothing, Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224003, China
| | - Wen-Duo Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yan-Lin Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Kun Cui
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Ji-Bao Xia
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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9
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Fu Y, Wang B, Cao Z. Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O–O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations. Inorg Chem 2022; 61:20501-20512. [DOI: 10.1021/acs.inorgchem.2c03229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuzhuang Fu
- 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, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- 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, China
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10
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Cofactor and Process Engineering for Nicotinamide Recycling and Retention in Intensified Biocatalysis. Catalysts 2022. [DOI: 10.3390/catal12111454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
There is currently considerable interest in the intensification of biocatalytic processes to reduce the cost of goods for biocatalytically produced chemicals, including pharmaceuticals and advanced pharmaceutical intermediates. Continuous-flow biocatalysis shows considerable promise as a method for process intensification; however, the reliance of some reactions on the use of diffusible cofactors (such as the nicotinamide cofactors) has proven to be a technical barrier for key enzyme classes. This minireview covers attempts to overcome this limitation, including the cofactor recapture and recycling retention of chemically modified cofactors. For the latter, we also consider the state of science for cofactor modification, a field reinvigorated by the current interest in continuous-flow biocatalysis.
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11
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Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nat Commun 2022; 13:5021. [PMID: 36028482 PMCID: PMC9418148 DOI: 10.1038/s41467-022-32727-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/13/2022] [Indexed: 11/09/2022] Open
Abstract
Noncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN+). We achieve this by engineering the life-essential glutathione reductase in Escherichia coli to exclusively rely on the reduced NMN+ (NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN+ with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA+), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P)+.
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Affiliation(s)
- Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - William B Black
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Christian M Heckmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Allison Wolder
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Francis Nicklen
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, CA, 95817, USA
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Ray Luo
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department Materials Science and Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA.
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12
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Improving the Enzymatic Cascade of Reactions for the Reduction of CO2 to CH3OH in Water: From Enzymes Immobilization Strategies to Cofactor Regeneration and Cofactor Suppression. Molecules 2022; 27:molecules27154913. [PMID: 35956865 PMCID: PMC9370104 DOI: 10.3390/molecules27154913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
The need to decrease the concentration of CO2 in the atmosphere has led to the search for strategies to reuse such molecule as a building block for chemicals and materials or a source of carbon for fuels. The enzymatic cascade of reactions that produce the reduction of CO2 to methanol seems to be a very attractive way of reusing CO2; however, it is still far away from a potential industrial application. In this review, a summary was made of all the advances that have been made in research on such a process, particularly on two salient points: enzyme immobilization and cofactor regeneration. A brief overview of the process is initially given, with a focus on the enzymes and the cofactor, followed by a discussion of all the advances that have been made in research, on the two salient points reported above. In particular, the enzymatic regeneration of NADH is compared to the chemical, electrochemical, and photochemical conversion of NAD+ into NADH. The enzymatic regeneration, while being the most used, has several drawbacks in the cost and life of enzymes that suggest attempting alternative solutions. The reduction in the amount of NADH used (by converting CO2 electrochemically into formate) or even the substitution of NADH with less expensive mimetic molecules is discussed in the text. Such an approach is part of the attempt made to take stock of the situation and identify the points on which work still needs to be conducted to reach an exploitation level of the entire process.
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13
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Wang Z, Hu Y, Zhang S, Sun Y. Artificial photosynthesis systems for solar energy conversion and storage: platforms and their realities. Chem Soc Rev 2022; 51:6704-6737. [PMID: 35815740 DOI: 10.1039/d1cs01008e] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In natural photosynthesis, photosynthetic organisms such as green plants realize efficient solar energy conversion and storage by integrating photosynthetic components on the thylakoid membrane of chloroplasts. Inspired by natural photosynthesis, researchers have developed many artificial photosynthesis systems (APS's) that integrate various photocatalysts and biocatalysts to convert and store solar energy in the fields of resource, environment, food, and energy. To improve the system efficiency and reduce the operation cost, reaction platforms are introduced in APS's since they allow for great stability and continuous processing. A systematic understanding of how a reaction platform affects the performance of artificial photosynthesis is conducive for designing an APS with superb solar energy utilization. In this review, we discuss the recent APS's researches, especially those confined on/in platforms. The importance of different platforms and their influences on APS's performance are emphasized. Generally, confined platforms can enhance the stability and repeatability of both photocatalysts and biocatalysts in APS's as well as improve the photosynthetic performance due to the proximity effect. For functional platforms that can participate in the artificial photosynthesis reactions as active parts, a high integration of APS's components on/in these platforms can lead to efficient electron transfer, enhanced light-harvesting, or synergistic catalysis, resulting in superior photosynthesis performance. Therefore, the integration of APS's components is beneficial for the transfer of substrates and photoexcited electrons in artificial photosynthesis. We finally summarize the current challenges of APS's development and further efforts on the improvement of APS's.
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Affiliation(s)
- Zhenfu Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Yang Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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14
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Borah B, Patat M, Swain S, Chowhan LR. Recent Advances and Prospects in the Transition‐Metal‐Free Synthesis of 1,4‐Dihydropyridines. ChemistrySelect 2022. [DOI: 10.1002/slct.202202484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Biplob Borah
- School of Applied Material Sciences Centre for Applied Chemistry Central University of Gujarat, Sector-30 Gandhinagar India- 382030
| | - Mihir Patat
- School of Applied Material Sciences Centre for Applied Chemistry Central University of Gujarat, Sector-30 Gandhinagar India- 382030
| | - Sidhartha Swain
- School of Applied Material Sciences Centre for Applied Chemistry Central University of Gujarat, Sector-30 Gandhinagar India- 382030
| | - L. Raju Chowhan
- School of Applied Material Sciences Centre for Applied Chemistry Central University of Gujarat, Sector-30 Gandhinagar India- 382030
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15
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King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. ACS Catal 2022; 12:8582-8592. [PMID: 37622090 PMCID: PMC10449333 DOI: 10.1021/acscatal.2c01837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical cofactors such as nicotinamide mononucleotide (NMN+) supplant the electron-transfer functionality of the natural cofactors, NAD(P)+, at a lower cost in cell-free biomanufacturing and enable orthogonal electron delivery in whole-cell metabolic engineering. Here, we redesign the high-flux Embden-Meyerhof-Parnas (EMP) glycolytic pathway to generate NMN+-based reducing power, by engineering Streptococcus mutans glyceraldehyde-3-phosphate dehydrogenase (Sm GapN) to utilize NMN+. Through iterative rounds of rational design, we discover the variant GapN Penta (P179K-F153S-S330R-I234E-G210Q) with high NMN+-dependent activity and GapN Ortho (P179K-F153S-S330R-I234E-G214E) with ~3.4 × 106-fold switch in cofactor specificity from its native cofactor NADP+ to NMN+. GapN Ortho is further demonstrated to function in Escherichia coli only in the presence of NMN+, enabling orthogonal control of glucose utilization. Molecular dynamics simulation and residue network connectivity analysis indicate that mutations altering cofactor specificity must be coordinated to maintain the appropriate degree of backbone flexibility to position the catalytic cysteine. These results provide a strategy to guide future designs of NMN+-dependent enzymes and establish the initial steps toward an orthogonal EMP pathway with biomanufacturing potential.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Frances Nicklen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Justin B Siegel
- Department of Chemistry, Genome Center, and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
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16
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Charlton SN, Hayes MA. Oxygenating Biocatalysts for Hydroxyl Functionalisation in Drug Discovery and Development. ChemMedChem 2022; 17:e202200115. [PMID: 35385205 PMCID: PMC9323455 DOI: 10.1002/cmdc.202200115] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Indexed: 11/12/2022]
Abstract
C-H oxyfunctionalisation remains a distinct challenge for synthetic organic chemists. Oxygenases and peroxygenases (grouped here as "oxygenating biocatalysts") catalyse the oxidation of a substrate with molecular oxygen or hydrogen peroxide as oxidant. The application of oxygenating biocatalysts in organic synthesis has dramatically increased over the last decade, producing complex compounds with potential uses in the pharmaceutical industry. This review will focus on hydroxyl functionalisation using oxygenating biocatalysts as a tool for drug discovery and development. Established oxygenating biocatalysts, such as cytochrome P450s and flavin-dependent monooxygenases, have widely been adopted for this purpose, but can suffer from low activity, instability or limited substrate scope. Therefore, emerging oxygenating biocatalysts which offer an alternative will also be covered, as well as considering the ways in which these hydroxylation biotransformations can be applied in drug discovery and development, such as late-stage functionalisation (LSF) and in biocatalytic cascades.
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Affiliation(s)
- Sacha N. Charlton
- School of ChemistryUniversity of Bristol, Cantock's CloseBristolBS8 1TSUK
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery SciencesBiopharmaceuticals R&DAstraZenecaGothenburgSweden
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17
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Lechner H, Oberdorfer G. Derivatives of natural organocatalytic cofactors and artificial organocatalytic cofactors as catalysts in enzymes. Chembiochem 2022; 23:e202100599. [PMID: 35302276 PMCID: PMC9401024 DOI: 10.1002/cbic.202100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/14/2022] [Indexed: 11/11/2022]
Abstract
Catalytically active non-metal cofactors in enzymes carry out a variety of different reactions. The efforts to develop derivatives of natural occurring cofactors such as flavins or pyridoxal phosphate and the advances to design new, non-natural cofactors are reviewed here. We report the status quo for enzymes harboring organocatalysts as derivatives of natural cofactors or as artificial ones and their application in the asymmetric synthesis of various compounds.
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Affiliation(s)
- Horst Lechner
- Graz University of Technology: Technische Universitat Graz, Institute of Biochemistry, Petersgasse 12/2, 8010, Graz, AUSTRIA
| | - Gustav Oberdorfer
- Graz University of Technology: Technische Universitat Graz, Institute of Biochemistry, Petersgasse 12/2, 8010, Graz, AUSTRIA
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18
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Kim J, Um Y, Han S, Hilberath T, Kim YH, Hollmann F, Park CB. Unbiased Photoelectrode Interfaces for Solar Coupling of Lignin Oxidation with Biocatalytic C═C Bond Hydrogenation. ACS APPLIED MATERIALS & INTERFACES 2022; 14:11465-11473. [PMID: 35196006 DOI: 10.1021/acsami.1c24342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The pulp and paper manufacturers generate approximately 50 million metric tons of lignin per annum, most of which has been abandoned or incinerated because of lignin's recalcitrant nature. Here, we report bias-free photoelectrochemical (PEC) oxidation of lignin coupled with asymmetric hydrogenation of C═C bonds. The PEC platform consists of a hematite (α-Fe2O3) photoanode and a silicon photovoltaic-wired mesoporous indium tin oxide (Si/mesoITO) photocathode. We substantiate a new function of photoelectroactivated α-Fe2O3 to extract electrons from lignin. The extracted electrons are transferred to the Si/mesoITO photocathode for regenerating synthetic nicotinamide cofactor analogues (mNADHs). We demonstrate that the reduction kinetics of mNAD+s depend on their reduction peak potentials. The regenerated mNADHs activate ene-reductases from the old yellow enzyme (OYE) family, which catalyze enantioselective reduction of α,β-unsaturated hydrocarbons. This lignin-fueled biocatalytic PEC system exhibits an excellent OYE's turnover frequency and total turnover number for photobiocatalytic trans-hydrogenation through cofactor regeneration. This work presents the first example of PEC regeneration of mNADHs and opens up a sustainable route for bias-free chemical synthesis using renewable lignin waste as an electron feedstock.
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Affiliation(s)
- Jinhyun Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| | - Yunna Um
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| | - Seunghyun Han
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Thomas Hilberath
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands
| | - Chan Beum Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
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19
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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20
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Reeve HA, Nicholson J, Altaf F, Lonsdale TH, Preissler J, Lauterbach L, Lenz O, Leimkühler S, Hollmann F, Paul CE, Vincent KA. A hydrogen-driven biocatalytic approach to recycling synthetic analogues of NAD(P)H. Chem Commun (Camb) 2022; 58:10540-10543. [DOI: 10.1039/d2cc02411j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Soluble hydrogenase enables atom efficient, H2-driven, recycling of synthetic nicotinamide cofactors.
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Affiliation(s)
- Holly A. Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Jake Nicholson
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Farieha Altaf
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Thomas H. Lonsdale
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Janina Preissler
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Lars Lauterbach
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
- RWTH Aachen University iAMB – Institute of Applied Microbiology Worringer Weg 1, 52074 Aachen, Germany
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Caroline E. Paul
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
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21
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Abstract
Noncanonical redox cofactor systems utilize nicotinamide adenine dinucleotide (phosphate), NAD(P)H, mimics to perform biotransformation reactions. Compared to systems utilizing native NAD(P)H, these noncanonical redox cofactors can offer decreased cost of cofactor supply, improved system activities, and can even supply reducing power directly to targeted reactions in complex biological environments. When these systems are operated in cell-free settings, the high level of user control afforded by direct access to the reaction system enables specific tuning of cofactor parameters, enzyme activity, and reaction progression to maximize system productivity. In this chapter, we will describe methods for constructing these cell-free noncanonical redox cofactor systems. Specifically, methods, design concepts, and system adaptation will be discussed for applying noncanonical redox cofactors to both purified protein-based and crude lysate-based biotransformation systems.
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Affiliation(s)
- William B Black
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, USA
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, USA.
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22
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Tan Z, Han Y, Fu Y, Zhang X, Xu M, Na Q, Zhuang W, Qu X, Ying H, Zhu C. Investigating the Structure‐Reactivity Relationships Between Nicotinamide Coenzyme Biomimetics and Pentaerythritol Tetranitrate Reductase. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhuotao Tan
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Yaoying Han
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Yaping Fu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Xiaowang Zhang
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Mengjiao Xu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Qi Na
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Xudong Qu
- School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai People's Republic of China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Chenjie Zhu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
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23
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Drenth J, Yang G, Paul CE, Fraaije MW. A Tailor-Made Deazaflavin-Mediated Recycling System for Artificial Nicotinamide Cofactor Biomimetics. ACS Catal 2021; 11:11561-11569. [PMID: 34557329 PMCID: PMC8453485 DOI: 10.1021/acscatal.1c03033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/22/2021] [Indexed: 12/13/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) and its 2'-phosphorylated form NADP are crucial cofactors for a large array of biocatalytically important redox enzymes. Their high cost and relatively poor stability, however, make them less attractive electron mediators for industrial processes. Nicotinamide cofactor biomimetics (NCBs) are easily synthesized, are inexpensive, and are also generally more stable than their natural counterparts. A bottleneck for the application of these artificial hydride carriers is the lack of efficient cofactor recycling methods. Therefore, we engineered the thermostable F420:NADPH oxidoreductase from Thermobifida fusca (Tfu-FNO), by structure-inspired site-directed mutagenesis, to accommodate the unnatural N1 substituents of eight NCBs. The extraordinarily low redox potential of the natural cofactor F420H2 was then exploited to reduce these NCBs. Wild-type enzyme had detectable activity toward all selected NCBs, with K m values in the millimolar range and k cat values ranging from 0.09 to 1.4 min-1. Saturation mutagenesis at positions Gly-29 and Pro-89 resulted in mutants with up to 139 times higher catalytic efficiencies. Mutant G29W showed a k cat value of 4.2 s-1 toward 1-benzyl-3-acetylpyridine (BAP+), which is similar to the k cat value for the natural substrate NADP+. The best Tfu-FNO variants for a specific NCB were then used for the recycling of catalytic amounts of these nicotinamides in conversion experiments with the thermostable ene-reductase from Thermus scotoductus (TsOYE). We were able to fully convert 10 mM ketoisophorone with BAP+ within 16 h, using F420 or its artificial biomimetic FOP (FO-2'-phosphate) as an efficient electron mediator and glucose-6-phosphate as an electron donor. The generated toolbox of thermostable and NCB-dependent Tfu-FNO variants offers powerful cofactor regeneration biocatalysts for the reduction of several artificial nicotinamide biomimetics at both ambient and high temperatures. In fact, to our knowledge, this enzymatic method seems to be the best-performing NCB-recycling system for BNAH and BAPH thus far.
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Affiliation(s)
- Jeroen Drenth
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Guang Yang
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Caroline E. Paul
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Marco W. Fraaije
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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24
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Yang N, Tian Y, Zhang M, Peng X, Li F, Li J, Li Y, Fan B, Wang F, Song H. Photocatalyst-enzyme hybrid systems for light-driven biotransformation. Biotechnol Adv 2021; 54:107808. [PMID: 34324993 DOI: 10.1016/j.biotechadv.2021.107808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/26/2021] [Accepted: 07/21/2021] [Indexed: 11/02/2022]
Abstract
Enzymes catalyse target reactions under mild conditions with high efficiency, as well as excellent regional-, stereo-, and enantiomeric selectivity. Photocatalysis utilises sustainable and environment-friendly light power to realise efficient chemical conversion. By combining the interdisciplinary advantages of photo- and enzymatic catalysis, the photocatalyst-enzyme hybrid systems have proceeded various light-driven biotransformation with high efficiency under environmentally benign conditions, thus, attracting unparalleled focus during the last decades. It has also been regarded as a promising pathway towards green chemistry utilising ubiquitous solar energy. This systematic review gives insight into this research field by classifying the existing photocatalyst-enzyme hybrid systems into three sections based on different hybridizing modes between photo- and enzymatic catalysis. Furthermore, existing challenges and proposed strategies are discussed within this context. The first system summarised is the cofactor-mediated hybrid system, in which natural/artificial cofactors act as reducing equivalents that connect photocatalysts with enzymes for light-driven enzymatic biotransformation. Second, the direct contact-based photocatalyst-enzyme hybrid systems are described, including two different kinds of electron exchange sites on the enzyme molecules. Third, some cases where photocatalysts and enzymes are integrated into a reaction cascade with specific intermediates will be discussed in the following chapter. Finally, we provide perspective concerning the future of this field.
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Affiliation(s)
- Nan Yang
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Yao Tian
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Mai Zhang
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Xiting Peng
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Feng Li
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Jianxun Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Yi Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Bei Fan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Fengzhong Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China.
| | - Hao Song
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China.
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25
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Li Q, Liu W, Zhao ZK. Synthesis of proteogenic amino acid-based NAD analogs. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Basle M, Padley HAW, Martins FL, Winkler GS, Jäger CM, Pordea A. Design of artificial metalloenzymes for the reduction of nicotinamide cofactors. J Inorg Biochem 2021; 220:111446. [PMID: 33865209 DOI: 10.1016/j.jinorgbio.2021.111446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022]
Abstract
Artificial metalloenzymes result from the insertion of a catalytically active metal complex into a biological scaffold, generally a protein devoid of other catalytic functionalities. As such, their design requires efforts to engineer substrate binding, in addition to accommodating the artificial catalyst. Here we constructed and characterised artificial metalloenzymes using alcohol dehydrogenase as starting point, an enzyme which has both a cofactor and a substrate binding pocket. A docking approach was used to determine suitable positions for catalyst anchoring to single cysteine mutants, leading to an artificial metalloenzyme capable to reduce both natural cofactors and the hydrophobic 1-benzylnicotinamide mimic. Kinetic studies revealed that the new construct displayed a Michaelis-Menten behaviour with the native nicotinamide cofactors, which were suggested by docking to bind at a surface exposed site, different compared to their native binding position. On the other hand, the kinetic and docking data suggested that a typical enzyme behaviour was not observed with the hydrophobic 1-benzylnicotinamide mimic, with which binding events were plausible both inside and outside the protein. This work demonstrates an extended substrate scope of the artificial metalloenzymes and provides information about the binding sites of the nicotinamide substrates, which can be exploited to further engineer artificial metalloenzymes for cofactor regeneration. SYNOPSIS ABOUT GRAPHICAL ABSTRACT: The manuscript provides information on the design of artificial metalloenzymes based on the bioconjugation of rhodium complexes to alcohol dehydrogenase, to improve their ability to reduce hydrophobic substrates. The graphical abstract presents different binding modes and results observed with native cofactors as substrates, compared to the hydrophobic benzylnicotinamide.
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Affiliation(s)
- Mattias Basle
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Henry A W Padley
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Floriane L Martins
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | | | - Christof M Jäger
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Anca Pordea
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom.
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27
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Liu Y, Guo X, Liu W, Wang J, Kent Zhao Z. Structural Insights into Malic Enzyme Variants Favoring an Unnatural Redox Cofactor. Chembiochem 2021; 22:1765-1768. [PMID: 33523590 DOI: 10.1002/cbic.202000800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Indexed: 01/07/2023]
Abstract
The use of nicotinamide cytosine dinucleotide (NCD), a biocompatible nicotinamide adenosine dinucleotide (NAD) analogue, is of great scientific and biotechnological interest. Several redox enzymes have been devised to favor NCD, and have been successfully applied in creating NCD-dependent redox systems. However, molecular interactions between cofactor and protein have still to be disclosed in order to guide further engineering efforts. Here we report the structural analysis of an NCD-favoring malic enzyme (ME) variant derived from Escherichia coli. The X-ray crystal structure data revealed that the residues located at position 346 and 401 in ME acted as the "gatekeepers" of the adenine moiety binding cavity. When Arg346 was substituted with either acidic or aromatic residues, the corresponding mutants showed substantially reduced NCD preference. Inspired by these observations, we generated Lactobacillus helveticus derived d-lactate dehydrogenase variants at Ile177, the counterpart to Arg346 in ME, and found a similar trend in terms of cofactor preference changes. As many NAD-dependent oxidoreductases share key structural features, our results provide guidance for protein engineering to obtain more NCD-favoring variants.
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Affiliation(s)
- Yuxue Liu
- College of Life Sciences, Henan Normal University, 46 East of Construction Road, Xinxiang, 453007, P. R. China.,Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Xiaojia Guo
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,Present address: Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, P. R. China
| | - Junting Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Zongbao Kent Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P. R. China
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28
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Abstract
The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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29
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Hollmann F, Opperman DJ, Paul CE. Biocatalytic Reduction Reactions from a Chemist's Perspective. Angew Chem Int Ed Engl 2021; 60:5644-5665. [PMID: 32330347 PMCID: PMC7983917 DOI: 10.1002/anie.202001876] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 11/09/2022]
Abstract
Reductions play a key role in organic synthesis, producing chiral products with new functionalities. Enzymes can catalyse such reactions with exquisite stereo-, regio- and chemoselectivity, leading the way to alternative shorter classical synthetic routes towards not only high-added-value compounds but also bulk chemicals. In this review we describe the synthetic state-of-the-art and potential of enzymes that catalyse reductions, ranging from carbonyl, enone and aromatic reductions to reductive aminations.
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Affiliation(s)
- Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
- Department of BiotechnologyUniversity of the Free State205 Nelson Mandela DriveBloemfontein9300South Africa
| | - Diederik J. Opperman
- Department of BiotechnologyUniversity of the Free State205 Nelson Mandela DriveBloemfontein9300South Africa
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
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30
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Recent advance of chemoenzymatic catalysis for the synthesis of chemicals: Scope and challenge. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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31
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Röllig R, Paul CE, Claeys-Bruno M, Duquesne K, Kara S, Alphand V. Divorce in the two-component BVMO family: the single oxygenase for enantioselective chemo-enzymatic Baeyer-Villiger oxidations. Org Biomol Chem 2021; 19:3441-3450. [PMID: 33899864 DOI: 10.1039/d1ob00015b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two-component flavoprotein monooxygenases consist of a reductase and an oxygenase enzyme. The proof of functionality of the latter without its counterpart as well as the mechanism of flavin transfer remains unanswered beyond doubt. To tackle this question, we utilized a reductase-free reaction system applying purified 2,5-diketocamphane-monooxygenase I (2,5-DKCMO), a FMN-dependent type II Baeyer-Villiger monooxygenase, and synthetic nicotinamide analogues (NCBs) as dihydropyridine derivatives for FMN reduction. This system demonstrated the stand-alone quality of the oxygenase, as well as the mechanism of FMNH2 transport by free diffusion. The efficiency of this reductase-free system strongly relies on the balance of FMN reduction and enzymatic (re)oxidation, since reduced FMN in solution causes undesired side reactions, such as hydrogen peroxide formation. Design of experiments allowed us to (i) investigate the effect of various reaction parameters, underlining the importance to balance the FMN/FMNH2 cycle, (ii) optimize the reaction system for the enzymatic Baeyer-Villiger oxidation of rac-bicyclo[3.2.0]hept-2-en-6-one, rac-camphor, and rac-norcamphor. Finally, this study not only demonstrates the reductase-independence of 2,5-DKCMO, but also revisits the terminology of two-component flavoprotein monooxygenases for this specific case.
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Affiliation(s)
- Robert Röllig
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 UMR 7313, Marseille, France. and Aarhus University, Denmark
| | | | | | - Katia Duquesne
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 UMR 7313, Marseille, France.
| | | | - Véronique Alphand
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 UMR 7313, Marseille, France.
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32
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Pothikumar R, Bhat VT, Namitharan K. Pyridine mediated transition-metal-free direct alkylation of anilines using alcohols via borrowing hydrogen conditions. Chem Commun (Camb) 2020; 56:13607-13610. [PMID: 33057478 DOI: 10.1039/d0cc05912a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Herein, we report pyridine and other similar azaaromatics as efficient biomimetic hydrogen shuttles for a transition-metal-free direct N-alkylation of aryl and heteroaryl amines using a variety of benzylic and straight chain alcohols. Mechanistic studies including deuterium labeling and the isolation of dihydro-intermediates of the benzannulated pyridine confirmed the role of pyridine and a borrowing hydrogen process operating in these reactions. In addition, we have extended this methodology for the development of dehydrogenative synthesis of quinolines and indoles, as well as the transfer hydrogenation of ketones.
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Affiliation(s)
- Rajagopal Pothikumar
- Organic Synthesis and Catalysis Laboratory SRM Research Institute and Department of Chemistry SRM Institute of Science and Technology, Chennai, India.
| | - Venugopal T Bhat
- Organic Synthesis and Catalysis Laboratory SRM Research Institute and Department of Chemistry SRM Institute of Science and Technology, Chennai, India.
| | - Kayambu Namitharan
- Organic Synthesis and Catalysis Laboratory SRM Research Institute and Department of Chemistry SRM Institute of Science and Technology, Chennai, India.
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33
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Hollmann F, Opperman DJ, Paul CE. Biokatalytische Reduktionen aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frank Hollmann
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft Niederlande
- Department of Biotechnology University of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 Südafrika
| | - Diederik J. Opperman
- Department of Biotechnology University of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 Südafrika
| | - Caroline E. Paul
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft Niederlande
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34
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
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35
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Song H, Ma C, Wang L, Zhu Z. Platinum nanoparticle-deposited multi-walled carbon nanotubes as a NADH oxidase mimic: characterization and applications. NANOSCALE 2020; 12:19284-19292. [PMID: 32935692 DOI: 10.1039/d0nr04060f] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The effective regeneration of bioactive NAD+ plays an important role in numerous dehydrogenase-dependent applications including biocatalysis and biosensing. However, this process usually suffers from high thermodynamic barrier, instability and high cost associated with natural enzymes. The emergence of nanomaterials with enzyme mimic characteristics has offered a potential alternative to many enzyme-catalyzed processes. Platinum nanoparticles (PtNPs), for example, have been extensively studied for their peroxidase- and oxidase-like activities. However, their behavior as a NADH oxidase mimic has barely been characterized in detail. Herein, we report a facile approach for preparing PtNP-deposited multi-walled carbon nanotubes (PtNPs@MWCNTs) as the nanozyme for NADH oxidation. Its enzymatic activity was investigated in depth, revealing that it is a NADH oxidase instead of a peroxidase and the catalytic process generates O2˙-, rather than OH˙ or 1O2, from dissolved O2. The recovery yield of bioactive NAD+ regeneration by the nanozyme could reach ∼100% with a total turnover number of ∼6000. Besides, it exhibited terrific electrochemical performance for NADH oxidation and sensing by greatly boosting the response and lowering the oxidation overpotential. It could also work on biomimetic cofactors with even higher activity. Finally, xylose dehydrogenase was immobilized with the nanozyme to constitute a hybrid bioelectrode for xylose sensing. The biosensor had a xylose detecting range of 5-400 μM with the limit of detection as low as 1 μM and can retain its performance after being reused several times. Our results suggest that the PtNPs@MWCNTs characterized as a NADH oxidase nanozyme hold great promise in the applications of biocatalysis and biosensing, which intensively deal with dehydrogenases and natural or biomimetic cofactors.
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Affiliation(s)
- Haiyan Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China.
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China.
| | - Lei Wang
- National Human Genetic Resource Center, 12 Dahuisi Road, Haidian District, Beijing 100081, P.R. China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China. and School of Chemical Engineering, University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, P. R. China
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36
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Weusthuis RA, Folch PL, Pozo-Rodríguez A, Paul CE. Applying Non-canonical Redox Cofactors in Fermentation Processes. iScience 2020; 23:101471. [PMID: 32891057 PMCID: PMC7479625 DOI: 10.1016/j.isci.2020.101471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/29/2023] Open
Abstract
Fermentation processes are used to sustainably produce chemicals and as such contribute to the transition to a circular economy. The maximum theoretical yield of a conversion can only be approached if all electrons present in the substrate end up in the product. Control over the electrons is therefore crucial. However, electron transfer via redox cofactors results in a diffuse distribution of electrons over metabolism. To overcome this challenge, we propose to apply non-canonical redox cofactors (NRCs) in metabolic networks: cofactors that channel electrons exclusively from substrate to product, forming orthogonal circuits for electron transfer.
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Affiliation(s)
- Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Pauline L. Folch
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Ana Pozo-Rodríguez
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Caroline E. Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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37
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Black WB, Aspacio D, Bever D, King E, Zhang L, Li H. Metabolic engineering of Escherichia coli for optimized biosynthesis of nicotinamide mononucleotide, a noncanonical redox cofactor. Microb Cell Fact 2020; 19:150. [PMID: 32718347 PMCID: PMC7384224 DOI: 10.1186/s12934-020-01415-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/20/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Noncanonical redox cofactors are emerging as important tools in cell-free biosynthesis to increase the economic viability, to enable exquisite control, and to expand the range of chemistries accessible. However, these noncanonical redox cofactors need to be biologically synthesized to achieve full integration with renewable biomanufacturing processes. RESULTS In this work, we engineered Escherichia coli cells to biosynthesize the noncanonical cofactor nicotinamide mononucleotide (NMN+), which has been efficiently used in cell-free biosynthesis. First, we developed a growth-based screening platform to identify effective NMN+ biosynthetic pathways in E. coli. Second, we explored various pathway combinations and host gene disruption to achieve an intracellular level of ~ 1.5 mM NMN+, a 130-fold increase over the cell's basal level, in the best strain, which features a previously uncharacterized nicotinamide phosphoribosyltransferase (NadV) from Ralstonia solanacearum. Last, we revealed mechanisms through which NMN+ accumulation impacts E. coli cell fitness, which sheds light on future work aiming to improve the production of this noncanonical redox cofactor. CONCLUSION These results further the understanding of effective production and integration of NMN+ into E. coli. This may enable the implementation of NMN+-directed biocatalysis without the need for exogenous cofactor supply.
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Affiliation(s)
- William B Black
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Derek Aspacio
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Danielle Bever
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Edward King
- Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Linyue Zhang
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Han Li
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States.
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38
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Mordhorst S, Andexer JN. Round, round we go - strategies for enzymatic cofactor regeneration. Nat Prod Rep 2020; 37:1316-1333. [PMID: 32582886 DOI: 10.1039/d0np00004c] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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39
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Photoinduced monooxygenation involving NAD(P)H-FAD sequential single-electron transfer. Nat Commun 2020; 11:2600. [PMID: 32451409 PMCID: PMC7248105 DOI: 10.1038/s41467-020-16450-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/28/2020] [Indexed: 01/09/2023] Open
Abstract
Light-dependent or light-stimulated catalysis provides a multitude of perspectives for implementation in technological or biomedical applications. Despite substantial progress made in the field of photobiocatalysis, the number of usable light-responsive enzymes is still very limited. Flavoproteins have exceptional potential for photocatalytic applications because the name-giving cofactor intrinsically features light-dependent reactivity, undergoing photoreduction with a variety of organic electron donors. However, in the vast majority of these enzymes, photoreactivity of the enzyme-bound flavin is limited or even suppressed. Here, we present a flavoprotein monooxygenase in which catalytic activity is controllable by blue light illumination. The reaction depends on the presence of nicotinamide nucleotide-type electron donors, which do not support the reaction in the absence of light. Employing various experimental approaches, we demonstrate that catalysis depends on a protein-mediated photoreduction of the flavin cofactor, which proceeds via a radical mechanism and a transient semiquinone intermediate.
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40
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Enantioselective Epoxidation by Flavoprotein Monooxygenases Supported by Organic Solvents. Catalysts 2020. [DOI: 10.3390/catal10050568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Styrene and indole monooxygenases (SMO and IMO) are two-component flavoprotein monooxygenases composed of a nicotinamide adenine dinucleotide (NADH)-dependent flavin adenine dinucleotide (FAD)-reductase (StyB or IndB) and a monooxygenase (StyA or IndA). The latter uses reduced FAD to activate oxygen and to oxygenate the substrate while releasing water. We circumvented the need for the reductase by direct FAD reduction in solution using the NAD(P)H-mimic 1-benzyl-1,4-dihydronicotinamide (BNAH) to fuel monooxygenases without NADH requirement. Herein, we report on the hitherto unknown solvent tolerance for the indole monooxygenase from Gemmobacter nectariphilus DSM15620 (GnIndA) and the styrene monooxygenase from Gordonia rubripertincta CWB2 (GrStyA). These enzymes were shown to convert bulky and rather hydrophobic styrene derivatives in the presence of organic cosolvents. Subsequently, BNAH-driven biotransformation was furthermore optimized with regard to the applied cosolvent and its concentration as well as FAD and BNAH concentration. We herein demonstrate that GnIndA and GrStyA enable selective epoxidations of allylic double bonds (up to 217 mU mg−1) in the presence of organic solvents such as tetrahydrofuran, acetonitrile, or several alcohols. Notably, GnIndA was found to resist methanol concentrations up to 25 vol.%. Furthermore, a diverse substrate preference was determined for both enzymes, making their distinct use very interesting. In general, our results seem representative for many IMOs as was corroborated by in silico mutagenetic studies.
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41
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Phonbuppha J, Tinikul R, Wongnate T, Intasian P, Hollmann F, Paul CE, Chaiyen P. A Minimized Chemoenzymatic Cascade for Bacterial Luciferase in Bioreporter Applications. Chembiochem 2020; 21:2073-2079. [PMID: 32187433 DOI: 10.1002/cbic.202000100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Indexed: 12/17/2022]
Abstract
Bacterial luciferase (Lux) catalyzes a bioluminescence reaction by using long-chain aldehyde, reduced flavin and molecular oxygen as substrates. The reaction can be applied in reporter gene systems for biomolecular detection in both prokaryotic and eukaryotic organisms. Because reduced flavin is unstable under aerobic conditions, another enzyme, flavin reductase, is needed to supply reduced flavin to the Lux-catalyzed reaction. To create a minimized cascade for Lux that would have greater ease of use, a chemoenzymatic reaction with a biomimetic nicotinamide (BNAH) was used in place of the flavin reductase reaction in the Lux system. The results showed that the minimized cascade reaction can be applied to monitor bioluminescence of the Lux reporter in eukaryotic cells effectively, and that it can achieve higher efficiencies than the system with flavin reductase. This development is useful for future applications as high-throughput detection tools for drug screening applications.
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Affiliation(s)
- Jittima Phonbuppha
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Pattarawan Intasian
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft (The, Netherlands
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft (The, Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
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42
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Affiliation(s)
- Mathias Ziegler
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Andrey A Nikiforov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
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43
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Liu Y, Li Q, Wang L, Guo X, Wang J, Wang Q, Zhao ZK. Engineering d-Lactate Dehydrogenase to Favor an Non-natural Cofactor Nicotinamide Cytosine Dinucleotide. Chembiochem 2020; 21:1972-1975. [PMID: 32175634 DOI: 10.1002/cbic.201900766] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/08/2020] [Indexed: 12/29/2022]
Abstract
Synthetic nicotinamide adenine dinucleotide (NAD) analogues are of great scientific and biotechnological interest. One such analogue, nicotinamide cytosine dinucleotide (NCD), has been successfully applied to creating bioorthogonal redox systems. Yet, only a few redox enzymes have been devised to favor NCD. We have engineered Lactobacillus helveticus-derived NAD-dependent d-lactate dehydrogenase (LhDLDH) to favor NCD by semirational design. Sequence alignment and structural analysis revealed that amino acid residues I177 and N213 form a "gate" guarding the NAD adenine moiety binding cavity. Saturated mutagenesis libraries were constructed by using the mutant LhDLDH-V152R as the parental sequence. Mutants were obtained with good catalytic efficiency, and NCD preference increased by up to 940-fold. Experiments showed that Escherichia coli cells expressing mutants with higher NCD preference afforded much less d-lactate, thus suggesting the potential to construct NCD-mediated orthogonal metabolism.
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Affiliation(s)
- Yuxue Liu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Qing Li
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Lei Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Xiaojia Guo
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Junting Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Qian Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P. R. China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P. R. China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P. R. China
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44
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Guarneri A, Westphal AH, Leertouwer J, Lunsonga J, Franssen MCR, Opperman DJ, Hollmann F, Berkel WJH, Paul CE. Flavoenzyme‐mediated Regioselective Aromatic Hydroxylation with Coenzyme Biomimetics. ChemCatChem 2020. [DOI: 10.1002/cctc.201902044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Alice Guarneri
- Laboratory of Organic ChemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Adrie H. Westphal
- Laboratory of BiochemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Jos Leertouwer
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
| | - Joy Lunsonga
- Laboratory of Organic ChemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Maurice C. R. Franssen
- Laboratory of Organic ChemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Diederik J. Opperman
- Department of BiotechnologyUniversity of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 South Africa
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
| | - Willem J. H. Berkel
- Laboratory of Food ChemistryWageningen University Bornse Weilanden 9 Wageningen 6708 WG The Netherlands
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
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45
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Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nat Chem Biol 2020; 16:87-94. [PMID: 31768035 PMCID: PMC7546441 DOI: 10.1038/s41589-019-0402-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/07/2019] [Indexed: 01/29/2023]
Abstract
Biological production of chemicals often requires the use of cellular cofactors, such as nicotinamide adenine dinucleotide phosphate (NADP+). These cofactors are expensive to use in vitro and difficult to control in vivo. We demonstrate the development of a noncanonical redox cofactor system based on nicotinamide mononucleotide (NMN+). The key enzyme in the system is a computationally designed glucose dehydrogenase with a 107-fold cofactor specificity switch toward NMN+ over NADP+ based on apparent enzymatic activity. We demonstrate that this system can be used to support diverse redox chemistries in vitro with high total turnover number (~39,000), to channel reducing power in Escherichia coli whole cells specifically from glucose to a pharmaceutical intermediate, levodione, and to sustain the high metabolic flux required for the central carbon metabolism to support growth. Overall, this work demonstrates efficient use of a noncanonical cofactor in biocatalysis and metabolic pathway design.
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Affiliation(s)
- William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Wai Shun Mak
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bonnie Fong
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Alicia Sanchez Martinez
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA.
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA.
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Huang R, Chen H, Upp DM, Lewis JC, Zhang YHPJ. A High-Throughput Method for Directed Evolution of NAD(P) +-Dependent Dehydrogenases for the Reduction of Biomimetic Nicotinamide Analogues. ACS Catal 2019; 9:11709-11719. [PMID: 34765284 DOI: 10.1021/acscatal.9b03840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineering flavin-free NAD(P)+-dependent dehydrogenases to reduce biomimetic nicotinamide analogues (mNAD+s) is of importance for eliminating the need for costly NAD(P)+ in coenzyme regeneration systems. Current redox dye-based screening methods for engineering the mNAD+ specificity of dehydrogenases are frequently encumbered by a background signal from endogenous NAD(P) and intracellular reducing compounds, making the detection of low mNAD+-based activities a limiting factor for directed evolution. Here, we develop a high-throughput screening method, NAD(P)-eliminated solid-phase assay (NESPA), which can reliably identify mNAD+-active mutants of dehydrogenases with a minimal background signal. This method involves (1) heat lysis of colonies to permeabilize the cell membrane, (2) colony transfer onto filter paper, (3) washing to remove endogenous NAD(P) and reducing compounds, (4) enzyme-coupled assay for mNADH-dependent color production, and (5) digital imaging of colonies to identify mNAD+-active mutants. This method was used to improve the activity of 6-phosphogluconate dehydrogenase on nicotinamide mononucleotide (NMN+). The best mutant obtained after six rounds of directed evolution exhibits a 50-fold enhancement in catalytic efficiency (k cat/K M) and a specific activity of 17.7 U/mg on NMN+, which is comparable to the wild-type enzyme on its natural coenzyme, NADP+. The engineered dehydrogenase was then used to construct an NMNH regeneration system to drive an ene-reductase catalysis. A comparable level of turnover frequency and product yield was observed using the engineered system relative to NADPH regeneration by using the wild-type dehydrogenase. NESPA provides a simple and accurate readout of mNAD+-based activities and the screening at high-throughput levels (approximately tens of thousands per round), thus opening up an avenue for the evolution of dehydrogenases with specific activities on mNAD+s similar to the levels of natural enzyme/coenzyme pairs.
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Affiliation(s)
- Rui Huang
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Hui Chen
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David M. Upp
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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Depaix A, Kowalska J. NAD Analogs in Aid of Chemical Biology and Medicinal Chemistry. Molecules 2019; 24:molecules24224187. [PMID: 31752261 PMCID: PMC6891637 DOI: 10.3390/molecules24224187] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/06/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) serves as an essential redox co-factor and mediator of multiple biological processes. Besides its well-established role in electron transfer reactions, NAD serves as a substrate for other biotransformations, which, at the molecular level, can be classified as protein post-translational modifications (protein deacylation, mono-, and polyADP-ribosylation) and formation of signaling molecules (e.g., cyclic ADP ribose). These biochemical reactions control many crucial biological processes, such as cellular signaling and recognition, DNA repair and epigenetic modifications, stress response, immune response, aging and senescence, and many others. However, the links between the biological effects and underlying molecular processes are often poorly understood. Moreover, NAD has recently been found to tag the 5′-ends of some cellular RNAs, but the function of these NAD-capped RNAs remains largely unrevealed. Synthetic NAD analogs are invaluable molecular tools to detect, monitor, structurally investigate, and modulate activity of NAD-related enzymes and biological processes in order to aid their deeper understanding. Here, we review the recent advances in the design and development of NAD analogs as probes for various cellular NAD-related enzymes, enzymatic inhibitors with anticancer or antimicrobial therapeutic potential, and other NAD-related chemical biology tools. We focus on research papers published within the last 10 years.
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48
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Desage‐El Murr M. Nature is the Cure: Engineering Natural Redox Cofactors for Biomimetic and Bioinspired Catalysis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Marine Desage‐El Murr
- Institut de Chimie UMR 7177Université de Strasbourg 1 rue Blaise Pascal Strasbourg 67000 France
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Seel CJ, Gulder T. Biocatalysis Fueled by Light: On the Versatile Combination of Photocatalysis and Enzymes. Chembiochem 2019; 20:1871-1897. [PMID: 30864191 DOI: 10.1002/cbic.201800806] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Enzymes catalyze a plethora of highly specific transformations under mild and environmentally benign reaction conditions. Their fascinating performances attest to high synthetic potential that is often hampered by operational obstacles such as in vitro cofactor supply and regeneration. Exploiting light and combining it with biocatalysis not only helps in overcoming these drawbacks, but the fruitful liaison of these two fields of "green chemistry" also offers opportunities to unlock new synthetic reactivities. In this review we provide an overview of the wide variety of photo-biocatalysis, ranging from the photochemical delivery of electrons required in redox biocatalysis and photochemical cofactor and reagent (re)generation to direct photoactivation of enzymes enabling reactions unknown in nature. We highlight synthetically relevant transformations such as asymmetric reactions facilitated by the combination of light as energy source and enzymes' catalytic power.
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Affiliation(s)
- Catharina J Seel
- Department of Chemistry and Catalysis Research Center (CRC), Technical University Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Tanja Gulder
- Department of Chemistry and Catalysis Research Center (CRC), Technical University Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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50
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Fukuzumi S, Lee YM, Nam W. Catalytic recycling of NAD(P)H. J Inorg Biochem 2019; 199:110777. [PMID: 31376683 DOI: 10.1016/j.jinorgbio.2019.110777] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022]
Abstract
A large number of industrially relevant enzymes depend upon dihydronicotinamide adenine dinucleotide (NADH) and dihydronicotinamide adenine dinucleotide phosphate (NADPH) cofactors, which are too expensive to be added in stoichiometric amounts. Existing NAD(P)H-recycling systems suffer from low activity, or the generation of side products. This review focuses on NAD(P)H cofactor regeneration catalyzed by transition metal complexes such as rhodium, ruthenium and iridium complexes using cheap reducing agents such as hydrogen (H2) and ethanol, which have attracted increasing attention as sustainable energy carriers. The catalytic mechanisms for the regioselective reduction of NAD(P)+ are discussed with emphasis on identification of catalytically active intermediates such as transition metal hydride complexes. Applications of NAD(P)H-recycling systems to develop artificial photosynthesis are also discussed.
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Affiliation(s)
- Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea; Faculty of Science and Engineering, Meijo University, Nagoya, Aichi 468-8502, Japan.
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea; Research Institute for Basic Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea; State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
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