1
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Yuan B, Yang D, Qu G, Turner NJ, Sun Z. Biocatalytic reductive aminations with NAD(P)H-dependent enzymes: enzyme discovery, engineering and synthetic applications. Chem Soc Rev 2024; 53:227-262. [PMID: 38059509 DOI: 10.1039/d3cs00391d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Chiral amines are pivotal building blocks for the pharmaceutical industry. Asymmetric reductive amination is one of the most efficient and atom economic methodologies for the synthesis of optically active amines. Among the various strategies available, NAD(P)H-dependent amine dehydrogenases (AmDHs) and imine reductases (IREDs) are robust enzymes that are available from various sources and capable of utilizing a broad range of substrates with high activities and stereoselectivities. AmDHs and IREDs operate via similar mechanisms, both involving a carbinolamine intermediate followed by hydride transfer from the co-factor. In addition, both groups catalyze the formation of primary and secondary amines utilizing both organic and inorganic amine donors. In this review, we discuss advances in developing AmDHs and IREDs as biocatalysts and focus on evolutionary history, substrate scope and applications of the enzymes to provide an outlook on emerging industrial biotechnologies of chiral amine production.
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Affiliation(s)
- Bo Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Dameng Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Nicholas J Turner
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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2
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Igareta NV, Tachibana R, Spiess DC, Peterson RL, Ward TR. Spiers Memorial Lecture: Shielding the active site: a streptavidin superoxide-dismutase chimera as a host protein for asymmetric transfer hydrogenation. Faraday Discuss 2023; 244:9-20. [PMID: 36924204 PMCID: PMC10416703 DOI: 10.1039/d3fd00034f] [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: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 03/17/2023]
Abstract
By anchoring a metal cofactor within a host protein, so-called artificial metalloenzymes can be generated. Such hybrid catalysts combine the versatility of transition metals in catalyzing new-to-nature reactions with the power of genetic-engineering to evolve proteins. With the aim of gaining better control over second coordination-sphere interactions between a streptavidin host-protein (Sav) and a biotinylated cofactor, we engineered a hydrophobic dimerization domain, borrowed from superoxide dismutase C (SOD), on Sav's biotin-binding vestibule. The influence of the SOD dimerization domain (DD) on the performance of an asymmetric transfer hydrogenase (ATHase) resulting from anchoring a biotinylated Cp*Ir-cofactor - [Cp*Ir(biot-p-L)Cl] (1-Cl) - within Sav-SOD is reported herein. We show that, depending on the nature of the residue at position Sav S112, the introduction of the SOD DD on the biotin-binding vestibule leads to an inversion of configuration of the reduction product, as well as a fivefold increase in catalytic efficiency. The findings are rationalized by QM/MM calculations, combined with X-ray crystallography.
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Affiliation(s)
- Nico V Igareta
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, CH-4058, Switzerland.
- National Center of Competence in Research (NCCR) "Molecular Systems Engineering", 4058 Basel, Switzerland.
| | - Ryo Tachibana
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, CH-4058, Switzerland.
| | - Daniel C Spiess
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, CH-4058, Switzerland.
| | - Ryan L Peterson
- National Center of Competence in Research (NCCR) "Molecular Systems Engineering", 4058 Basel, Switzerland.
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, CH-4058, Switzerland.
- National Center of Competence in Research (NCCR) "Molecular Systems Engineering", 4058 Basel, Switzerland.
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3
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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4
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Kato S, Onoda A, Schwaneberg U, Hayashi T. Evolutionary Engineering of a Cp*Rh(III) Complex-Linked Artificial Metalloenzyme with a Chimeric β-Barrel Protein Scaffold. J Am Chem Soc 2023; 145. [PMID: 36892401 PMCID: PMC10119979 DOI: 10.1021/jacs.3c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 03/10/2023]
Abstract
Evolutionary engineering of our previously reported Cp*Rh(III)-linked artificial metalloenzyme was performed based on a DNA recombination strategy to improve its catalytic activity toward C(sp2)-H bond functionalization. Improved scaffold design was achieved with α-helical cap domains of fatty acid binding protein (FABP) embedded within the β-barrel structure of nitrobindin (NB) as a chimeric protein scaffold for the artificial metalloenzyme. After optimization of the amino acid sequence by directed evolution methodology, an engineered variant, designated NBHLH1(Y119A/G149P) with enhanced performance and enhanced stability was obtained. Additional rounds of metalloenzyme evolution provided a Cp*Rh(III)-linked NBHLH1(Y119A/G149P) variant with a >35-fold increase in catalytic efficiency (kcat/KM) for cycloaddition of oxime and alkyne. Kinetic studies and MD simulations revealed that aromatic amino acid residues in the confined active-site form a hydrophobic core which binds to aromatic substrates adjacent to the Cp*Rh(III) complex. The metalloenzyme engineering process based on this DNA recombination strategy will serve as a powerful method for extensive optimization of the active-sites of artificial metalloenzymes.
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Affiliation(s)
- Shunsuke Kato
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Akira Onoda
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute
of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Takashi Hayashi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
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5
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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6
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Feng X, Cao Y, Liu W, Xian M. Identification of Two Novel Fluorinases From Amycolatopsis sp. CA-128772 and Methanosaeta sp. PtaU1.Bin055 and a Mutant With Improved Catalytic Efficiency With Native Substrate. Front Bioeng Biotechnol 2022; 10:881326. [PMID: 35769103 PMCID: PMC9234330 DOI: 10.3389/fbioe.2022.881326] [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: 02/22/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022] Open
Abstract
Fluoride plays an important role in the fields of materials and medicine. Compared with chemical synthesis, fluorinases are natural catalysts with more application potential, which provide a green and effective way to obtain organofluorine. However, the application of fluorinases is limited by certain factors, such as the limited number of enzymes and their low activity. In this work, two new fluorinases from Amycolatopsis sp. CA-128772 and Methanosaeta sp. PtaU1.Bin055 were identified by gene mining and named Fam and Fme, respectively. The activities of these two enzymes were reported for the first time, and Fme showed good thermal stability, which was different from the reported fluorinases. In addition, the activity toward natural substrate of Fam was improved by site-directed mutagenesis, the catalytic efficiency (kcat/Km) of the best mutant containing two amino acid substitutions (T72A and S164G) toward the substrate S-adenosyl-L-methionine was improved by 2.2-fold compared to the wild-type. Structural modeling analysis revealed that the main reason for the increased enzyme activity might be the formation of a new substrate channel. Experimental evidence suggests that the substrate channel may indeed play a key role in regulating the function of the fluorinases.
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Affiliation(s)
- Xinming Feng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujin Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Yujin Cao, ; Wei Liu, ; Mo Xian,
| | - Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Yujin Cao, ; Wei Liu, ; Mo Xian,
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Yujin Cao, ; Wei Liu, ; Mo Xian,
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7
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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8
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Martins FL, Pordea A, Jäger CM. Computationally driven design of an artificial metalloenzyme using supramolecular anchoring strategies of iridium complexes to alcohol dehydrogenase. Faraday Discuss 2022; 234:315-335. [PMID: 35156975 DOI: 10.1039/d1fd00070e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial metalloenzymes (ArMs) confer non-biological reactivities to biomolecules, whilst taking advantage of the biomolecular architecture in terms of their selectivity and renewable origin. In particular, the design of ArMs by the supramolecular anchoring of metal catalysts to protein hosts provides flexible and easy to optimise systems. The use of cofactor dependent enzymes as hosts gives the advantage of both a (hydrophobic) binding site for the substrate and a cofactor pocket to accommodate the catalyst. Here, we present a computationally driven design approach of ArMs for the transfer hydrogenation reaction of cyclic imines, starting from the NADP+-dependent alcohol dehydrogenase from Thermoanaerobacter brockii (TbADH). We tested and developed a molecular docking workflow to define and optimize iridium catalysts with high affinity for the cofactor binding site of TbADH. The workflow uses high throughput docking of compound libraries to identify key structural motifs for high affinity, followed by higher accuracy docking methods on smaller, focused ligand and catalyst libraries. Iridium sulfonamide catalysts were selected and synthesised, containing either a triol, a furane, or a carboxylic acid to provide the interaction with the cofactor binding pocket. IC50 values of the resulting complexes during TbADH-catalysed alcohol oxidation were determined by competition experiments and were between 4.410 mM and 0.052 mM, demonstrating the affinity of the iridium complexes for either the substrate or the cofactor binding pocket of TbADH. The catalytic activity of the free iridium complexes in solution showed a maximal turnover number (TON) of 90 for the reduction of salsolidine by the triol-functionalised iridium catalyst, whilst in the presence of TbADH, only the iridium catalyst with the triol anchoring functionality showed activity for the same reaction (TON of 36 after 24 h). The observation that the artificial metalloenzymes developed here lacked stereoselectivity demonstrates the need for the further investigation and optimisation of the ArM. Our results serve as a starting point for the design of robust artificial metalloenzymes, exploiting supramolecular anchoring to natural NAD(P)H binding pockets.
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Affiliation(s)
- Floriane L Martins
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, UK.
| | - Anca Pordea
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, UK.
| | - Christof M Jäger
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, UK.
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9
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Hassan IS, Fuller JT, Dippon VN, Ta AN, Danneman MW, McNaughton BR, Alexandrova AN, Rovis T. Tuning Through-Space Interactions via the Secondary Coordination Sphere of an Artificial Metalloenzyme Leads to Enhanced Rh(III)-Catalysis. Chem Sci 2022; 13:9220-9224. [PMID: 36093000 PMCID: PMC9384688 DOI: 10.1039/d2sc03674f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
We report computationally-guided protein engineering of monomeric streptavidin Rh(iii) artificial metalloenzyme to enhance catalysis of the enantioselective coupling of acrylamide hydroxamate esters and styrenes. Increased TON correlates with calculated distances between the Rh(iii) metal and surrounding residues, underscoring an artificial metalloenzyme's propensity for additional control in metal-catalyzed transformations by through-space interactions. We report computationally-guided protein engineering of monomeric streptavidin Rh(iii) artificial metalloenzyme to enhance catalysis of the enantioselective coupling of acrylamide hydroxamate esters and styrenes.![]()
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Affiliation(s)
- Isra S Hassan
- Department of Chemistry, Columbia University New York NY 10027 USA
| | - Jack T Fuller
- Department of Chemistry & Biochemistry, University of California Los Angeles Los Angeles CA 90095 USA
| | - Vanessa N Dippon
- Department of Chemistry, Columbia University New York NY 10027 USA
| | - Angeline N Ta
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
| | | | - Brian R McNaughton
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
| | - Anastassia N Alexandrova
- Department of Chemistry & Biochemistry, University of California Los Angeles Los Angeles CA 90095 USA
| | - Tomislav Rovis
- Department of Chemistry, Columbia University New York NY 10027 USA
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10
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Nödling AR, Santi N, Castillo R, Lipka-Lloyd M, Jin Y, Morrill LC, Świderek K, Moliner V, Luk LYP. The role of streptavidin and its variants in catalysis by biotinylated secondary amines. Org Biomol Chem 2021; 19:10424-10431. [PMID: 34825690 PMCID: PMC8652411 DOI: 10.1039/d1ob01947c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022]
Abstract
Here, we combine the use of host screening, protein crystallography and QM/MM molecular dynamics simulations to investigate how the protein structure affects iminium catalysis by biotinylated secondary amines in a model 1,4 conjugate addition reaction. Monomeric streptavidin (M-Sav) lacks a quaternary structure and the solvent-exposed reaction site resulted in poor product conversion in the model reaction with low enantio- and regioselectivities. These parameters were much improved when the tetrameric host T-Sav was used; indeed, residues at the symmetrical subunit interface were proven to be critical for catalysis through a mutagenesis study. The use of QM/MM simulations and the asymmetric dimeric variant D-Sav revealed that both Lys121 residues which are located in the hosting and neighboring subunits play a critical role in controlling the stereoselectivity and reactivity. Lastly, the D-Sav template, though providing a lower conversion than that of the symmetric tetrameric counterpart, is likely a better starting point for future protein engineering because each surrounding residue within the asymmetric scaffold can be refined for secondary amine catalysis.
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Affiliation(s)
- Alexander R Nödling
- School of Chemistry, Main Building, Cardiff University, Cardiff, CF10 3AT, UK.
| | - Nicolò Santi
- School of Chemistry, Main Building, Cardiff University, Cardiff, CF10 3AT, UK.
| | - Raquel Castillo
- Department de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain.
| | | | - Yi Jin
- School of Chemistry, Main Building, Cardiff University, Cardiff, CF10 3AT, UK.
| | - Louis C Morrill
- Cardiff Catalysis Institute, School of Chemistry, Main Building, Cardiff University, Cardiff, CF10 3AT, UK
| | - Katarzyna Świderek
- Department de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain.
| | - Vicent Moliner
- Department de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain.
| | - Louis Y P Luk
- School of Chemistry, Main Building, Cardiff University, Cardiff, CF10 3AT, UK.
- Cardiff Catalysis Institute, School of Chemistry, Main Building, Cardiff University, Cardiff, CF10 3AT, UK
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11
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12
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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14
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An integrative approach to improving the biocatalytic reactions of whole cells expressing recombinant enzymes. World J Microbiol Biotechnol 2021; 37:105. [PMID: 34037845 DOI: 10.1007/s11274-021-03075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
Biotransformation is a selective, stereospecific, efficient, and environment friendly method, compared to chemical synthesis, and a feasible tool for industrial and pharmaceutical applications. The design of biocatalysts using enzyme engineering and metabolic engineering tools has been widely reviewed. However, less importance has been given to the biocatalytic reaction of whole cells expressing recombinant enzymes. Along with the remarkable development of biotechnology tools, a variety of techniques have been applied to improve the biocatalytic reaction of whole cell biotransformation. In this review, techniques related to the biocatalytic reaction are examined, reorganized, and summarized via an integrative approach. Moreover, equilibrium-shifted biotransformation is reviewed for the first time.
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15
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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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16
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Punt PM, Langenberg MD, Altan O, Clever GH. Modular Design of G-Quadruplex MetalloDNAzymes for Catalytic C-C Bond Formations with Switchable Enantioselectivity. J Am Chem Soc 2021; 143:3555-3561. [PMID: 33630569 DOI: 10.1021/jacs.0c13251] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of (S) and (R) enantiomeric reaction products, respectively.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Marie D Langenberg
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Okan Altan
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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17
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Facchetti G, Bucci R, Fusè M, Erba E, Gandolfi R, Pellegrino S, Rimoldi I. Alternative Strategy to Obtain Artificial Imine Reductase by Exploiting Vancomycin/D-Ala-D-Ala Interactions with an Iridium Metal Complex. Inorg Chem 2021; 60:2976-2982. [PMID: 33550804 DOI: 10.1021/acs.inorgchem.0c02969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on the supramolecular interaction between vancomycin (Van), an antibiotic glycopeptide, and D-Ala-D-Ala (DADA) dipeptides, a novel class of artificial metalloenzymes was synthesized and characterized. The presence of an iridium(III) ligand at the N-terminus of DADA allowed the use of the metalloenzyme as a catalyst in the asymmetric transfer hydrogenation of cyclic imines. In particular, the type of link between DADA and the metal-chelating moiety was found to be fundamental for inducing asymmetry in the reaction outcome, as highlighted by both computational studies and catalytic results. Using the [IrCp*(m-I)Cl]Cl ⊂ Van complex in 0.1 M CH3COONa buffer at pH 5, a significant 70% (S) e.e. was obtained in the reduction of quinaldine B.
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Affiliation(s)
- Giorgio Facchetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Raffaella Bucci
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Emanuela Erba
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Raffaella Gandolfi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Sara Pellegrino
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Isabella Rimoldi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
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18
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Vong K, Nasibullin I, Tanaka K. Exploring and Adapting the Molecular Selectivity of Artificial Metalloenzymes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kenward Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
| | - Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
| | - Katsunori Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
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19
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Tang J, Dong W, Chen F, Deng L, Xian M. Rhodium catalysts with cofactor mimics for the biomimetic reduction of CN bonds. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00904d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bio-inspired reduction of CN bonds was successfully performed using rhodium catalysts containing cofactor mimics. The intramolecular cooperation between rhodium and cofactor mimics enabled the transformation with good selectivity. A plausible mechanism was also proposed.
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Affiliation(s)
- Jie Tang
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P.R. China
| | - Wenjin Dong
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P.R. China
| | - Fushan Chen
- College of Chemical Engineering
- Qingdao University of Sciences & Technology
- Qingdao
- P.R. China
| | - Li Deng
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P.R. China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P.R. China
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20
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Mukherjee P, Maiti D. Evolution of strept(avidin)-based artificial metalloenzymes in organometallic catalysis. Chem Commun (Camb) 2020; 56:14519-14540. [PMID: 33150893 DOI: 10.1039/d0cc05450j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Artificial metalloenzymes have been recently established as efficient alternatives to traditional transition metal catalysts. The presence of a secondary coordination sphere in artificial metalloenzymes makes them advantageous over transition metal catalysts, which rely essentially on their first coordination sphere to exhibit their catalytic activity. Recent developments on streptavidin- and avidin-based artificial metalloenzymes have made them highly chemically and genetically evolved for selective organometallic transformations. In this review, we discuss the chemo-genetic optimization of streptavidin- and avidin-based artificial metalloenzymes for the enhancement of their catalytic activities towards a wide range of synthetic transformations. Considering the high impact in vivo applications of artificial metalloenzymes, their catalytic efficacies to promote abiological reactions in intracellular as well as periplasmic environment are also discussed. Overall, this review can provide an insight to readers regarding the design and systematic optimization of strept(avidin)-based artificial metalloenzymes for specific reactions.
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Affiliation(s)
- Prasun Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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21
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Booth RL, Grogan G, Wilson KS, Duhme-Klair AK. Artificial imine reductases: developments and future directions. RSC Chem Biol 2020; 1:369-378. [PMID: 34458768 PMCID: PMC8341917 DOI: 10.1039/d0cb00113a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
Biocatalytic imine reduction has been a topic of intense research by the artificial metalloenzyme community in recent years. Artificial constructs, together with natural enzymes, have been engineered to produce chiral amines with high enantioselectivity. This review examines the design of the main classes of artificial imine reductases reported thus far and summarises approaches to enhancing their catalytic performance using complementary methods. Examples of utilising these biocatalysts in vivo or in multi-enzyme cascades have demonstrated the potential that artIREDs can offer, however, at this time their use in biocatalysis remains limited. This review explores the current scope of artIREDs and the strategies used for catalyst improvement, and examines the potential for artIREDs in the future.
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Affiliation(s)
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York UK
| | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York UK
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22
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Roddan R, Sula A, Méndez-Sánchez D, Subrizi F, Lichman BR, Broomfield J, Richter M, Andexer JN, Ward JM, Keep NH, Hailes HC. Single step syntheses of (1S)-aryl-tetrahydroisoquinolines by norcoclaurine synthases. Commun Chem 2020; 3:170. [PMID: 36703392 PMCID: PMC9814250 DOI: 10.1038/s42004-020-00416-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/14/2020] [Indexed: 01/29/2023] Open
Abstract
The 1-aryl-tetrahydroisoquinoline (1-aryl-THIQ) moiety is found in many biologically active molecules. Single enantiomer chemical syntheses are challenging and although some biocatalytic routes have been reported, the substrate scope is limited to certain structural motifs. The enzyme norcoclaurine synthase (NCS), involved in plant alkaloid biosynthesis, has been shown to perform stereoselective Pictet-Spengler reactions between dopamine and several carbonyl substrates. Here, benzaldehydes are explored as substrates and found to be accepted by both wild-type and mutant constructs of NCS. In particular, the variant M97V gives a range of (1 S)-aryl-THIQs in high yields (48-99%) and e.e.s (79-95%). A co-crystallised structure of the M97V variant with an active site reaction intermediate analogue is also obtained with the ligand in a pre-cyclisation conformation, consistent with (1 S)-THIQs formation. Selected THIQs are then used with catechol O-methyltransferases with exceptional regioselectivity. This work demonstrates valuable biocatalytic approaches to a range of (1 S)-THIQs.
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Affiliation(s)
- Rebecca Roddan
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Altin Sula
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK
| | - Daniel Méndez-Sánchez
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Fabiana Subrizi
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Benjamin R Lichman
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, WC1E 6BT, UK
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joseph Broomfield
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Michael Richter
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Schulgasse 11a, 94315, Straubing, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - John M Ward
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, WC1E 6BT, UK.
| | - Nicholas H Keep
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK.
| | - Helen C Hailes
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK.
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23
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Kato S, Onoda A, Taniguchi N, Schwaneberg U, Hayashi T. Directed Evolution of a Cp*Rh III -Linked Biohybrid Catalyst Based on a Screening Platform with Affinity Purification. Chembiochem 2020; 22:679-685. [PMID: 33026156 PMCID: PMC7894531 DOI: 10.1002/cbic.202000681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Directed evolution of Cp*RhIII‐linked nitrobindin (NB), a biohybrid catalyst, was performed based on an in vitro screening approach. A key aspect of this effort was the establishment of a high‐throughput screening (HTS) platform that involves an affinity purification step employing a starch‐agarose resin for a maltose binding protein (MBP) tag. The HTS platform enables efficient preparation of the purified MBP‐tagged biohybrid catalysts in a 96‐well format and eliminates background influence of the host E. coli cells. Three rounds of directed evolution and screening of more than 4000 clones yielded a Cp*RhIII‐linked NB(T98H/L100K/K127E) variant with a 4.9‐fold enhanced activity for the cycloaddition of acetophenone oximes with alkynes. It is confirmed that this HTS platform for directed evolution provides an efficient strategy for generating highly active biohybrid catalysts incorporating a synthetic metal cofactor.
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Affiliation(s)
- Shunsuke Kato
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akira Onoda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Naomasa Taniguchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen, 52074, Germany
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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24
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Kariyawasam K, Di Meo T, Hammerer F, Valerio-Lepiniec M, Sciortino G, Maréchal JD, Minard P, Mahy JP, Urvoas A, Ricoux R. An Artificial Hemoprotein with Inducible Peroxidase- and Monooxygenase-Like Activities. Chemistry 2020; 26:14929-14937. [PMID: 32588931 DOI: 10.1002/chem.202002434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/25/2020] [Indexed: 12/24/2022]
Abstract
A novel inducible artificial metalloenzyme obtained by covalent attachment of a manganese(III)-tetraphenylporphyrin (MnTPP) to the artificial bidomain repeat protein, (A3A3')Y26C, is reported. The protein is part of the αRep family. The biohybrid was fully characterized by MALDI-ToF mass spectrometry, circular dichroism and UV/Vis spectroscopies. The peroxidase and monooxygenase activities were evaluated on the original and modified scaffolds including those that have a) an additional imidazole, b) a specific αRep bA3-2 that is known to induce the opening of the (A3A3') interdomain region and c) a derivative of the αRep bA3-2 inducer extended with a His6 -Tag (His6 -bA3-2). Catalytic profiles are highly dependent on the presence of co-catalysts with the best activity obtained with His6 -bA3-2. The entire mechanism was rationalized by an integrative molecular modeling study that includes protein-ligand docking and large-scale molecular dynamics. This constitutes the first example of an entirely artificial metalloenzyme with inducible peroxidase and monooxygenase activities, reminiscent of allosteric regulation of natural enzymatic pathways.
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Affiliation(s)
- Kalani Kariyawasam
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Thibault Di Meo
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Fabien Hammerer
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdanyola del Vallés, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdanyola del Vallés, Barcelona, Spain
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
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25
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Nödling AR, Santi N, Williams TL, Tsai YH, Luk LYP. Enabling protein-hosted organocatalytic transformations. RSC Adv 2020; 10:16147-16161. [PMID: 33184588 PMCID: PMC7654312 DOI: 10.1039/d0ra01526a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/25/2020] [Indexed: 12/30/2022] Open
Abstract
In this review, the development of organocatalytic artificial enzymes will be discussed. This area of protein engineering research has underlying importance, as it enhances the biocompatibility of organocatalysis for applications in chemical and synthetic biology research whilst expanding the catalytic repertoire of enzymes. The approaches towards the preparation of organocatalytic artificial enzymes, techniques used to improve their performance (selectivity and reactivity) as well as examples of their applications are presented. Challenges and opportunities are also discussed.
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Affiliation(s)
- Alexander R Nödling
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Nicolò Santi
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
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26
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Alonso-Cotchico L, Rodrı́guez-Guerra J, Lledós A, Maréchal JD. Molecular Modeling for Artificial Metalloenzyme Design and Optimization. Acc Chem Res 2020; 53:896-905. [PMID: 32233391 DOI: 10.1021/acs.accounts.0c00031] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Artificial metalloenzymes (ArMs) are obtained by inserting homogeneous catalysts into biological scaffolds and are among the most promising strategies in the quest for new-to-nature biocatalysts. The quality of their design strongly depends on how three partners interact: the biological host, the "artificial cofactor," and the substrate. However, structural characterization of functional artificial metalloenzymes by X-ray or NMR is often partial, elusive, or absent. How the cofactor binds to the protein, how the receptor reorganizes upon the binding of the cofactor and the substrate, and which are the binding mode(s) of the substrate for the reaction to proceed are key questions that are frequently unresolved yet crucial for ArM design. Such questions may eventually be solved by molecular modeling but require a step change beyond the current state-of-the-art methodologies.Here, we summarize our efforts in the study of ArMs, presenting both the development of computational strategies and their application. We first focus on our integrative computational framework that incorporates a variety of methods such as protein-ligand docking, classical molecular dynamics (MD), and pure quantum mechanical (QM) methods, which, when properly combined, are able to depict questions that range from host-cofactor binding predictions to simulations of entire catalytic mechanisms. We also pay particular attention to the protein-ligand docking strategies that we have developed to accurately predict the binding of transition metal-containing molecules to proteins. While this aspect is fundamental to many bioinorganic fields beyond ArMs, it has been disregarded from the molecular modeling landscape until very recently.Next we describe how to apply this computational framework to particular ArMs including systems previously characterized experimentally as well as others where computation served to guide the design. We start with the prediction of the interactions between homogeneous catalysts and biological hosts. Protein-ligand docking is pivotal at that stage, but it needs to be combined with QM/MM or MD approaches when the binding of the cofactor implies significant conformational changes of the protein or involve changes of the electronic state of the metal.Then, we summarize molecular modeling studies aimed at identifying cofactor-substrate arrangements inside the ArM active pocket that are consistent with its reactivity. These calculations stand on "Theozyme"-like dockings, MD-refined or not, which provide molecular rationale of the catalytic profiles of the artificial systems.In the third section, we present case studies to decode the entire catalytic mechanism of two ArMs: (1) an iridium based asymmetric transfer hydrogenase obtained by insertion of Noyori's catalyst into streptavidin and (2) a metallohydrolase achieved by including a receptor. Transition states, second coordination sphere effects, as well as motions of the cofactors are identified as drivers of the enantiomeric profiles.Finally, we report computer-aided designs of ArMs to guide experiments toward chemical and mutational changes that improve their activity and/or enantioselective profiles and expand toward future directions.
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Affiliation(s)
- Lur Alonso-Cotchico
- Departament de Quı́mica, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallès, Barcelona Spain
| | - Jaime Rodrı́guez-Guerra
- Departament de Quı́mica, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallès, Barcelona Spain
| | - Agustí Lledós
- Departament de Quı́mica, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallès, Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Quı́mica, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallès, Barcelona Spain
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27
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Pilar Lamata M, Passarelli V, Carmona D. Recent Advances in Iridium-Catalysed Transfer Hydrogenation Reactions. TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Wu S, Zhou Y, Rebelein JG, Kuhn M, Mallin H, Zhao J, Igareta NV, Ward TR. Breaking Symmetry: Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes. J Am Chem Soc 2019; 141:15869-15878. [PMID: 31509711 PMCID: PMC6805045 DOI: 10.1021/jacs.9b06923] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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The biotin–streptavidin technology
has been extensively
exploited to engineer artificial metalloenzymes (ArMs) that catalyze
a dozen different reactions. Despite its versatility, the homotetrameric
nature of streptavidin (Sav) and the noncooperative binding of biotinylated
cofactors impose two limitations on the genetic optimization of ArMs:
(i) point mutations are reflected in all four subunits of Sav, and
(ii) the noncooperative binding of biotinylated cofactors to Sav may
lead to an erosion in the catalytic performance, depending on the
cofactor:biotin-binding site ratio. To address these challenges, we
report on our efforts to engineer a (monovalent) single-chain dimeric
streptavidin (scdSav) as scaffold for Sav-based ArMs. The versatility
of scdSav as host protein is highlighted for the asymmetric transfer
hydrogenation of prochiral imines using [Cp*Ir(biot-p-L)Cl] as cofactor. By capitalizing on a more precise genetic fine-tuning
of the biotin-binding vestibule, unrivaled levels of activity and
selectivity were achieved for the reduction of challenging prochiral
imines. Comparison of the saturation kinetic data and X-ray structures
of [Cp*Ir(biot-p-L)Cl]·scdSav with a structurally
related [Cp*Ir(biot-p-L)Cl]·monovalent scdSav
highlights the advantages of the presence of a single biotinylated
cofactor precisely localized within the biotin-binding vestibule of
the monovalent scdSav. The practicality of scdSav-based ArMs was illustrated
for the reduction of the salsolidine precursor (500 mM) to afford
(R)-salsolidine in 90% ee and >17 000 TONs.
Monovalent scdSav thus provides a versatile scaffold to evolve more
efficient ArMs for in vivo catalysis and large-scale applications.
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Affiliation(s)
- Shuke Wu
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Yi Zhou
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Johannes G Rebelein
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Miriam Kuhn
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Hendrik Mallin
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Jingming Zhao
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Nico V Igareta
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Thomas R Ward
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
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29
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Davis H, Ward TR. Artificial Metalloenzymes: Challenges and Opportunities. ACS CENTRAL SCIENCE 2019; 5:1120-1136. [PMID: 31404244 PMCID: PMC6661864 DOI: 10.1021/acscentsci.9b00397] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Indexed: 05/04/2023]
Abstract
Artificial metalloenzymes (ArMs) result from the incorporation of an abiotic metal cofactor within a protein scaffold. From the earliest techniques of transition metals adsorbed on silk fibers, the field of ArMs has expanded dramatically over the past 60 years to encompass a range of reaction classes and inspired approaches: Assembly of the ArMs has taken multiple forms with both covalent and supramolecular anchoring strategies, while the scaffolds have been intuitively selected and evolved, repurposed, or designed in silico. Herein, we discuss some of the most prominent recent examples of ArMs to highlight the challenges and opportunities presented by the field.
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30
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Liang AD, Serrano-Plana J, Peterson RL, Ward TR. Artificial Metalloenzymes Based on the Biotin-Streptavidin Technology: Enzymatic Cascades and Directed Evolution. Acc Chem Res 2019; 52:585-595. [PMID: 30735358 PMCID: PMC6427477 DOI: 10.1021/acs.accounts.8b00618] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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Artificial metalloenzymes (ArMs) result from
anchoring a metal-containing
moiety within a macromolecular scaffold (protein or oligonucleotide).
The resulting hybrid catalyst combines attractive features of both
homogeneous catalysts and enzymes. This strategy includes the possibility
of optimizing the reaction by both chemical (catalyst design) and
genetic means leading to achievement of a novel degree of (enantio)selectivity,
broadening of the substrate scope, or increased activity, among others.
In the past 20 years, the Ward group has exploited, among others,
the biotin–(strept)avidin technology to localize a catalytic
moiety within a well-defined protein environment. Streptavidin has
proven versatile for the implementation of ArMs as it offers the following
features: (i) it is an extremely robust protein scaffold, amenable
to extensive genetic manipulation and mishandling, (ii) it can be
expressed in E. coli to very high titers (up to >8
g·L–1 in fed-batch cultures), and (iii) the
cavity surrounding the biotinylated cofactor is commensurate with
the size of a typical metal-catalyzed transition state. Relying on
a chemogenetic optimization strategy, varying the orientation and
the nature of the biotinylated cofactor within genetically engineered
streptavidin, 12 reactions have been reported by the Ward group thus
far. Recent efforts within our group have focused on extending the
ArM technology to create complex systems for integration into biological
cascade reactions and in vivo. With the long-term
goal of complementing in vivo natural enzymes with
ArMs, we summarize herein three complementary
research lines: (i) With the aim of mimicking complex cross-regulation
mechanisms prevalent in metabolism, we have engineered enzyme cascades,
including cross-regulated reactions, that rely on ArMs. These efforts
highlight the remarkable (bio)compatibility and complementarity of
ArMs with natural enzymes. (ii) Additionally, multiple-turnover catalysis
in the cytoplasm of aerobic organisms was achieved with ArMs that
are compatible with a glutathione-rich environment. This feat is demonstrated
in HEK-293T cells that are engineered with a gene switch that is upregulated
by an ArM equipped with a cell-penetrating module. (iii) Finally,
ArMs offer the fascinating prospect of “endowing organometallic
chemistry with a genetic memory.” With this goal in mind, we
have identified E. coli’s periplasmic space
and surface display to compartmentalize an ArM, while maintaining
the critical phenotype–genotype linkage. This strategy offers
a straightforward means to optimize by directed evolution the catalytic
performance of ArMs. Five reactions have been optimized following
these compartmentalization strategies: ruthenium-catalyzed olefin
metathesis, ruthenium-catalyzed deallylation, iridium-catalyzed transfer
hydrogenation, dirhodium-catalyzed cyclopropanation and carbene insertion
in C–H bonds. Importantly, >100 turnovers were achieved
with
ArMs in E. coli whole cells, highlighting the multiple
turnover catalytic nature of these systems.
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Affiliation(s)
- Alexandria Deliz Liang
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Joan Serrano-Plana
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Ryan L. Peterson
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
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31
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Markel U, Sauer DF, Schiffels J, Okuda J, Schwaneberg U. Towards the Evolution of Artificial Metalloenzymes—A Protein Engineer's Perspective. Angew Chem Int Ed Engl 2019; 58:4454-4464. [DOI: 10.1002/anie.201811042] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Daniel F. Sauer
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Johannes Schiffels
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry RWTH Aachen University Landoltweg 1 52056 Aachen Germany
| | - Ulrich Schwaneberg
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
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32
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Markel U, Sauer DF, Schiffels J, Okuda J, Schwaneberg U. Auf dem Weg zur Evolution artifizieller Metalloenzyme – aus einem Protein‐Engineering‐Blickwinkel. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ulrich Markel
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
| | - Daniel F. Sauer
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
| | - Johannes Schiffels
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
| | - Jun Okuda
- Institut für Anorganische Chemie RWTH Aachen Landoltweg 1 52056 Aachen Deutschland
| | - Ulrich Schwaneberg
- DWI Leibniz-Institut für Interaktive Materialien Forckenbeckstraße 50 52074 Aachen Deutschland
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
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33
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Wang Y, Astruc D, Abd-El-Aziz AS. Metallopolymers for advanced sustainable applications. Chem Soc Rev 2019; 48:558-636. [PMID: 30506080 DOI: 10.1039/c7cs00656j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Since the development of metallopolymers, there has been tremendous interest in the applications of this type of materials. The interest in these materials stems from their potential use in industry as catalysts, biomedical agents in healthcare, energy storage and production as well as climate change mitigation. The past two decades have clearly shown exponential growth in the development of many new classes of metallopolymers that address these issues. Today, metallopolymers are considered to be at the forefront for discovering new and sustainable heterogeneous catalysts, therapeutics for drug-resistant diseases, energy storage and photovoltaics, molecular barometers and thermometers, as well as carbon dioxide sequesters. The focus of this review is to highlight the advances in design of metallopolymers with specific sustainable applications.
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Affiliation(s)
- Yanlan Wang
- Liaocheng University, Department of Chemistry and Chemical Engineering, 252059, Liaocheng, China.
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34
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Chan HCS, Pan L, Li Y, Yuan S. Rationalization of stereoselectivity in enzyme reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- H. C. Stephen Chan
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
- Faculty of Life Sciences University of Bradford Bradford UK
| | - Lu Pan
- Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai China
| | - Yi Li
- Department of Neurology University of Southern California Los Angeles California
| | - Shuguang Yuan
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
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35
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Zhao J, Rebelein JG, Mallin H, Trindler C, Pellizzoni MM, Ward TR. Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in Escherichia coli's Periplasm. J Am Chem Soc 2018; 140:13171-13175. [PMID: 30272972 DOI: 10.1021/jacs.8b07189] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Artificial metalloenzymes (ArMs), which combine an abiotic metal cofactor with a protein scaffold, catalyze various synthetically useful transformations. To complement the natural enzymes' repertoire, effective optimization protocols to improve ArM's performance are required. Here we report on our efforts to optimize the activity of an artificial transfer hydrogenase (ATHase) using Escherichia coli whole cells. For this purpose, we rely on a self-immolative quinolinium substrate which, upon reduction, releases fluorescent umbelliferone, thus allowing efficient screening. Introduction of a loop in the immediate proximity of the Ir-cofactor afforded an ArM with up to 5-fold increase in transfer hydrogenation activity compared to the wild-type ATHase using purified mutants.
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Affiliation(s)
- Jingming Zhao
- Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland
| | - Johannes G Rebelein
- Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland
| | - Hendrik Mallin
- Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland
| | - Christian Trindler
- Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland
| | - Michela M Pellizzoni
- Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland
| | - Thomas R Ward
- Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland
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36
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Leurs M, Dorn B, Wilhelm S, Manisegaran M, Tiller JC. Multicore Artificial Metalloenzymes Derived from Acylated Proteins as Catalysts for the Enantioselective Dihydroxylation and Epoxidation of Styrene Derivatives. Chemistry 2018; 24:10859-10867. [DOI: 10.1002/chem.201802185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Melanie Leurs
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Bjoern Dorn
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Sascha Wilhelm
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Magiliny Manisegaran
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Joerg. C. Tiller
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
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37
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Heinisch T, Schwizer F, Garabedian B, Csibra E, Jeschek M, Vallapurackal J, Pinheiro VB, Marlière P, Panke S, Ward TR. E. coli surface display of streptavidin for directed evolution of an allylic deallylase. Chem Sci 2018; 9:5383-5388. [PMID: 30079176 PMCID: PMC6048633 DOI: 10.1039/c8sc00484f] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022] Open
Abstract
Artificial metalloenzymes (ArMs hereafter) combine attractive features of both homogeneous catalysts and enzymes and offer the potential to implement new-to-nature reactions in living organisms. Herein we present an E. coli surface display platform for streptavidin (Sav hereafter) relying on an Lpp-OmpA anchor. The system was used for the high throughput screening of a bioorthogonal CpRu-based artificial deallylase (ADAse) that uncages an allylcarbamate-protected aminocoumarin 1. Two rounds of directed evolution afforded the double mutant S112M-K121A that displayed a 36-fold increase in surface activity vs. cellular background and a 5.7-fold increased in vitro activity compared to the wild type enzyme. The crystal structure of the best ADAse reveals the importance of mutation S112M to stabilize the cofactor conformation inside the protein.
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Affiliation(s)
- Tillmann Heinisch
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Fabian Schwizer
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Brett Garabedian
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Eszter Csibra
- Institute of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , UK
| | - Markus Jeschek
- Department of Biosystems Science and Engineering , ETH Zurich , Mattenstrasse 26 , Basel CH-4058 , Switzerland
| | - Jaicy Vallapurackal
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Vitor B Pinheiro
- Institute of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , UK
| | | | - Sven Panke
- Department of Biosystems Science and Engineering , ETH Zurich , Mattenstrasse 26 , Basel CH-4058 , Switzerland
| | - Thomas R Ward
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
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38
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Facchetti G, Rimoldi I. 8-Amino-5,6,7,8-tetrahydroquinoline in iridium(iii) biotinylated Cp* complex as artificial imine reductase. NEW J CHEM 2018. [DOI: 10.1039/c8nj04558e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The imine reductase formed by the (R)-CAMPY ligand bound to the S112M Sav mutant showed an 83% ee in the asymmetric transfer hydrogenation of 6,7-dimethoxy-1-methyl-3,4-dihydroisoquinoline.
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Affiliation(s)
- Giorgio Facchetti
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 10033 Milano
- Italy
| | - Isabella Rimoldi
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 10033 Milano
- Italy
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39
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Hestericová M, Heinisch T, Lenz M, Ward TR. Ferritin encapsulation of artificial metalloenzymes: engineering a tertiary coordination sphere for an artificial transfer hydrogenase. Dalton Trans 2018; 47:10837-10841. [DOI: 10.1039/c8dt02224k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Creating a tertiary coordination sphere around a transition metal catalyst incorporated within a protein affects its catalytic turnover and enantioselectivity.
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Affiliation(s)
| | | | - Markus Lenz
- Institute for Ecopreneurship
- School of Life Sciences
- University of Applied Sciences and Arts Northwestern Switzerland
- Muttenz
- Switzerland
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