1
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Liu M, Li S. Nitrile biosynthesis in nature: how and why? Nat Prod Rep 2024; 41:649-671. [PMID: 38193577 DOI: 10.1039/d3np00028a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.
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Affiliation(s)
- Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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2
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Křístková B, Martínková L, Rucká L, Kotik M, Kulik N, Rädisch R, Winkler M, Pátek M. Immobilization of aldoxime dehydratases on metal affinity resins and use of the immobilized catalysts for the synthesis of nitriles important in fragrance industry. J Biotechnol 2024; 384:12-19. [PMID: 38373531 DOI: 10.1016/j.jbiotec.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Nitriles have a wide range of uses as building blocks, solvents, and alternative fuels, but also as intermediates and components of flavors and fragrances. The enzymatic synthesis of nitriles by aldoxime dehydratase (Oxd) is an emerging process with significant advantages over conventional approaches. Here we focus on the immobilization of His-tagged Oxds on metal affinity resins, an approach that has not been used previously for these enzymes. The potential of the immobilized Oxd was demonstrated for the synthesis of phenylacetonitrile (PAN) and E-cinnamonitrile, compounds applicable in the fragrance industry. A comparison of Talon and Ni-NTA resins showed that Ni-NTA with its higher binding capacity was more suitable for the immobilization of Oxd. Immobilized Oxds were prepared from purified enzymes (OxdFv from Fusarium vanettenii and OxdBr1 from Bradyrhizobium sp.) or the corresponding cell-free extracts. The immobilization of cell-free extracts reduced time and cost of the catalyst production. The immobilized OxdBr1 was superior in terms of recyclability (22 cycles) in the synthesis of PAN from 15 mM E/Z-phenylacetaldoxime at pH 7.0 and 30 °C (100% conversion, 61% isolated yield after product purification). The volumetric and catalyst productivity was 10.5 g/L/h and 48.3 g/g of immobilized protein, respectively.
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Affiliation(s)
- Barbora Křístková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technická 5, Prague CZ-166 28, Czech Republic
| | - Ludmila Martínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic.
| | - Lenka Rucká
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic
| | - Michael Kotik
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic
| | - Natalia Kulik
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradská 237, Třeboň CZ-37981, Czech Republic
| | - Robert Rädisch
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, Prague CZ-128 44, Czech Republic
| | - Margit Winkler
- Institute of Molecular Biotechnology, Faculty of Technical Chemistry, Chemical and Process Engineering, Biotechnology, Graz University of Technology, Petersgasse 14, Graz A-8010, Austria; Austrian Center of Industrial Biotechnology GmbH, Krenngasse 37, Graz A-8010, Austria
| | - Miroslav Pátek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic
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3
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Yamaguchi T, Asano Y. Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review. J Biotechnol 2024; 384:20-28. [PMID: 38395363 DOI: 10.1016/j.jbiotec.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.
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Affiliation(s)
- Takuya Yamaguchi
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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4
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Ruiz-Pernía JJ, Świderek K, Bertran J, Moliner V, Tuñón I. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J Chem Theory Comput 2024; 20:1783-1795. [PMID: 38410913 PMCID: PMC10938506 DOI: 10.1021/acs.jctc.3c01395] [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: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.
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Affiliation(s)
| | - Katarzyna Świderek
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Moliner
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
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5
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Advances in the One-Step Approach of Polymeric Materials Using Enzymatic Techniques. Polymers (Basel) 2023; 15:polym15030703. [PMID: 36772002 PMCID: PMC9922006 DOI: 10.3390/polym15030703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The formulation in which biochemical enzymes are administered in polymer science plays a key role in retaining their catalytic activity. The one-step synthesis of polymers with highly sequence-controlled enzymes is a strategy employed to provide enzymes with higher catalytic activity and thermostability in material sustainability. Enzyme-catalyzed chain growth polymerization reactions using activated monomers, protein-polymer complexation techniques, covalent and non-covalent interaction, and electrostatic interactions can provide means to develop formulations that maintain the stability of the enzyme during complex material processes. Multifarious applications of catalytic enzymes are usually attributed to their efficiency, pH, and temperature, thus, progressing with a critical structure-controlled synthesis of polymer materials. Due to the obvious economics of manufacturing and environmental sustainability, the green synthesis of enzyme-catalyzed materials has attracted significant interest. Several enzymes from microorganisms and plants via enzyme-mediated material synthesis have provided a viable alternative for the appropriate synthesis of polymers, effectively utilizing the one-step approach. This review analyzes more and deeper strategies and material technologies widely used in multi-enzyme cascade platforms for engineering polymer materials, as well as their potential industrial applications, to provide an update on current trends and gaps in the one-step synthesis of materials using catalytic enzymes.
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6
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Bhattacharya S, Margheritis EG, Takahashi K, Kulesha A, D'Souza A, Kim I, Yoon JH, Tame JRH, Volkov AN, Makhlynets OV, Korendovych IV. NMR-guided directed evolution. Nature 2022; 610:389-393. [PMID: 36198791 PMCID: PMC10116341 DOI: 10.1038/s41586-022-05278-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/25/2022] [Indexed: 11/09/2022]
Abstract
Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins1-4. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20100 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins5. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations6-9. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzyme10. Machine learning methods have recently showed promise in predicting productive mutations11, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.
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Affiliation(s)
| | - Eleonora G Margheritis
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Katsuya Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alona Kulesha
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Inhye Kim
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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7
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Gao H, Chen JY, Peng Z, Feng L, Tung CH, Wang W. Bioinspired Iron-Catalyzed Dehydration of Aldoximes to Nitriles: A General N-O Redox-Cleavage Method. J Org Chem 2022; 87:10848-10857. [PMID: 35914249 DOI: 10.1021/acs.joc.2c01122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inspired by OxdA that operates biocatalytic aldoxime dehydration, we have developed an efficient iron catalyst, Cp*Fe(1,2-Cy2PC6H4O) (1), which rapidly converts various aliphatic and aromatic aldoximes to nitriles with release of H2O at room temperature. The catalysis involves redox activation of the N-O bond by a 1e- transfer from the iron catalyst to the oxime. Such redox-mediated N-O cleavage was demonstrated by the isolation of a ferrous iminato intermediate from the reaction of the ketoxime substrate. This iron-catalyzed acceptorless dehydration approach represents a general method for the preparation of nitriles, and it also delivers salicylonitriles by catalyzing the Kemp elimination reaction.
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Affiliation(s)
- Hongjie Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jia-Yi Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhiqiang Peng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lei Feng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Wenguang Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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8
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Matsui D, Muraki N, Chen K, Mori T, Ingram AA, Oike K, Gröger H, Aono S, Asano Y. Crystal structural analysis of aldoxime dehydratase from Bacillus sp. OxB-1: Importance of surface residues in optimization for crystallization. J Inorg Biochem 2022; 230:111770. [DOI: 10.1016/j.jinorgbio.2022.111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
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9
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Horvat M, Weilch V, Rädisch R, Hecko S, Schiefer A, Rudroff F, Wilding B, Klempier N, Pátek M, Martínková L, Winkler M. Chemoenzymatic one-pot reaction from carboxylic acid to nitrile via oxime. Catal Sci Technol 2022; 12:62-66. [PMID: 35126993 PMCID: PMC8725990 DOI: 10.1039/d1cy01694f] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/28/2021] [Indexed: 12/23/2022]
Abstract
We report a new chemoenzymatic cascade starting with aldehyde synthesis by carboxylic acid reductase (CAR) followed by chemical in situ oxime formation. The final step to the nitrile is catalyzed by aldoxime dehydratase (Oxd). Full conversions of phenylacetic acid and hexanoic acid were achieved in a two-phase mode. We report a new chemoenzymatic cascade starting with aldehyde synthesis by carboxylic acid reductase (CAR) followed by chemical in situ oxime formation and enzymatic dehydration by aldoxime dehydratase (Oxd).![]()
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Affiliation(s)
- Melissa Horvat
- Institute of Molecular Biotechnology, Graz University of Technology Petersgasse 14 A-8010 Graz Austria
| | - Victoria Weilch
- Institute of Molecular Biotechnology, Graz University of Technology Petersgasse 14 A-8010 Graz Austria
| | - Robert Rädisch
- Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 CZ-142 20 Prague Czech Republic .,Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 CZ-12844 Prague 2 Czech Republic
| | - Sebastian Hecko
- Institute of Applied Synthetic Chemistry, TU Wien Getreidemarkt 9/OC-163 A-1060 Vienna Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, TU Wien Getreidemarkt 9/OC-163 A-1060 Vienna Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien Getreidemarkt 9/OC-163 A-1060 Vienna Austria
| | - Birgit Wilding
- Acib GmbH Krenngasse 37 A-8010 Graz Austria.,Institute of Organic Chemistry, Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
| | - Norbert Klempier
- Institute of Organic Chemistry, Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
| | - Miroslav Pátek
- Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 CZ-142 20 Prague Czech Republic
| | - Ludmila Martínková
- Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 CZ-142 20 Prague Czech Republic
| | - Margit Winkler
- Institute of Molecular Biotechnology, Graz University of Technology Petersgasse 14 A-8010 Graz Austria .,Acib GmbH Krenngasse 37 A-8010 Graz Austria
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10
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Zheng D, Asano Y. A Cyanide‐free Biocatalytic Process for Synthesis of Complementary Enantiomers of 4‐Chloro‐3‐hydroxybutanenitrile From Allyl Chloride. ChemCatChem 2021. [DOI: 10.1002/cctc.202100835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daijun Zheng
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University 5180 Kurokawa Imizu Toyama 939-0398 Japan)
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University 5180 Kurokawa Imizu Toyama 939-0398 Japan)
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11
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Yavuzer H, Asano Y, Gröger H. Rationalizing the Unprecedented Stereochemistry of an Enzymatic Nitrile Synthesis through a Combined Computational and Experimental Approach. Angew Chem Int Ed Engl 2021; 60:19162-19168. [PMID: 33886145 PMCID: PMC8456930 DOI: 10.1002/anie.202017234] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/08/2023]
Abstract
In this contribution, the unique and unprecedented stereochemical phenomenon of an aldoxime dehydratase‐catalyzed enantioselective dehydration of racemic E‐ and Z‐aldoximes with selective formation of both enantiomeric forms of a chiral nitrile is rationalized by means of molecular modelling, comprising in silico mutations and docking studies. This theoretical investigation gave detailed insight into why with the same enzyme the use of racemic E‐ and Z‐aldoximes leads to opposite forms of the chiral nitrile. The calculated mutants with a larger or smaller cavity in the active site were then prepared and used in biotransformations, showing the theoretically predicted decrease and increase of the enantioselectivities in these nitrile syntheses. This validated model also enabled the rational design of mutants with a smaller cavity, which gave superior enantioselectivities compared to the known wild‐type enzyme, with excellent E‐values of up to E>200 when the mutant OxdRE‐Leu145Phe was utilized.
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Affiliation(s)
- Hilmi Yavuzer
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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12
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Yavuzer H, Asano Y, Gröger H. Rationalizing the Unprecedented Stereochemistry of an Enzymatic Nitrile Synthesis through a Combined Computational and Experimental Approach. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hilmi Yavuzer
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Yasuhisa Asano
- Biotechnology Research Center Toyama Prefectural University 5180 Kurokawa Imizu Toyama 939-0398 Japan
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
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13
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Hall M. Enzymatic strategies for asymmetric synthesis. RSC Chem Biol 2021; 2:958-989. [PMID: 34458820 PMCID: PMC8341948 DOI: 10.1039/d1cb00080b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Enzymes, at the turn of the 21st century, are gaining a momentum. Especially in the field of synthetic organic chemistry, a broad variety of biocatalysts are being applied in an increasing number of processes running at up to industrial scale. In addition to the advantages of employing enzymes under environmentally friendly reaction conditions, synthetic chemists are recognizing the value of enzymes connected to the exquisite selectivity of these natural (or engineered) catalysts. The use of hydrolases in enantioselective protocols paved the way to the application of enzymes in asymmetric synthesis, in particular in the context of biocatalytic (dynamic) kinetic resolutions. After two decades of impressive development, the field is now mature to propose a panel of catalytically diverse enzymes for (i) stereoselective reactions with prochiral compounds, such as double bond reduction and bond forming reactions, (ii) formal enantioselective replacement of one of two enantiotopic groups of prochiral substrates, as well as (iii) atroposelective reactions with noncentrally chiral compounds. In this review, the major enzymatic strategies broadly applicable in the asymmetric synthesis of optically pure chiral compounds are presented, with a focus on the reactions developed within the past decade.
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Affiliation(s)
- Mélanie Hall
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
- Field of Excellence BioHealth - University of Graz Austria
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14
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Domínguez de María P. Nitrile Synthesis with Aldoxime Dehydratases: A Biocatalytic Platform with Applications in Asymmetric Synthesis, Bulk Chemicals, and Biorefineries. Molecules 2021; 26:molecules26154466. [PMID: 34361620 PMCID: PMC8347273 DOI: 10.3390/molecules26154466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/17/2021] [Accepted: 07/22/2021] [Indexed: 12/05/2022] Open
Abstract
Nitriles comprise a broad group of chemicals that are currently being industrially produced and used in fine chemicals and pharmaceuticals, as well as in bulk applications, polymer chemistry, solvents, etc. Aldoxime dehydratases catalyze the cyanide-free synthesis of nitriles starting from aldoximes under mild conditions, holding potential to become sustainable alternatives for industrial processes. Different aldoxime dehydratases accept a broad range of aldoximes with impressive high substrate loadings of up to >1 Kg L−1 and can efficiently catalyze the reaction in aqueous media as well as in non-aqueous systems, such as organic solvents and solvent-free (neat substrates). This paper provides an overview of the recent developments in this field with emphasis on strategies that may be of relevance for industry and sustainability. When possible, potential links to biorefineries and to the use of biogenic raw materials are discussed.
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Affiliation(s)
- Pablo Domínguez de María
- Sustainable Momentum, SL, Av. Ansite 3, 4-6, 35011 Las Palmas de Gran Canaria, Canary Islands, Spain
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15
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Protein engineering of the aldoxime dehydratase from Bacillus sp. OxB-1 based on a rational sequence alignment approach. Sci Rep 2021; 11:14316. [PMID: 34253740 PMCID: PMC8275659 DOI: 10.1038/s41598-021-92749-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 06/08/2021] [Indexed: 12/31/2022] Open
Abstract
Recently, the program INTMSAlign_HiSol for identifying aggregation hotspots in proteins only requiring secondary structure data was introduced. We explored the utility of this program further and applied it for engineering of the aldoxime dehydratase from Bacillus sp. OxB-1. Towards this end, the effect of inverting the hydropathy at selected positions of the amino acid sequence on the enzymatic activity was studied leading to 60% of our constructed variants, which showed improved activity. In part, this activity increase can be rationalised by an improved heme incorporation of the variants. For example, a single mutation gave a 1.8 fold increased enzymatic activity and 30% improved absolute heme incorporation.
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16
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Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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17
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Tseliou V, Schilder D, Masman MF, Knaus T, Mutti FG. Generation of Oxidoreductases with Dual Alcohol Dehydrogenase and Amine Dehydrogenase Activity. Chemistry 2021; 27:3315-3325. [PMID: 33073866 PMCID: PMC7898336 DOI: 10.1002/chem.202003140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/17/2020] [Indexed: 11/12/2022]
Abstract
The l-lysine-ϵ-dehydrogenase (LysEDH) from Geobacillus stearothermophilus naturally catalyzes the oxidative deamination of the ϵ-amino group of l-lysine. We previously engineered this enzyme to create amine dehydrogenase (AmDH) variants that possess a new hydrophobic cavity in their active site such that aromatic ketones can bind and be converted into α-chiral amines with excellent enantioselectivity. We also recently observed that LysEDH was capable of reducing aromatic aldehydes into primary alcohols. Herein, we harnessed the promiscuous alcohol dehydrogenase (ADH) activity of LysEDH to create new variants that exhibited enhanced catalytic activity for the reduction of substituted benzaldehydes and arylaliphatic aldehydes to primary alcohols. Notably, these novel engineered dehydrogenases also catalyzed the reductive amination of a variety of aldehydes and ketones with excellent enantioselectivity, thus exhibiting a dual AmDH/ADH activity. We envisioned that the catalytic bi-functionality of these enzymes could be applied for the direct conversion of alcohols into amines. As a proof-of-principle, we performed an unprecedented one-pot "hydrogen-borrowing" cascade to convert benzyl alcohol to benzylamine using a single enzyme. Conducting the same biocatalytic cascade in the presence of cofactor recycling enzymes (i.e., NADH-oxidase and formate dehydrogenase) increased the reaction yields. In summary, this work provides the first examples of enzymes showing "alcohol aminase" activity.
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Affiliation(s)
- Vasilis Tseliou
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Don Schilder
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Marcelo F. Masman
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tanja Knaus
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Francesco G. Mutti
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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18
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Hinzmann A, Betke T, Asano Y, Gröger H. Synthetic Processes toward Nitriles without the Use of Cyanide: A Biocatalytic Concept Based on Dehydration of Aldoximes in Water. Chemistry 2021; 27:5313-5321. [PMID: 33112445 PMCID: PMC8049032 DOI: 10.1002/chem.202001647] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/22/2020] [Indexed: 11/29/2022]
Abstract
While belonging to the most fundamental functional groups, nitriles represent a class of compound that still raises challenges in terms of an efficient, cost‐effective, general and, at the same time, sustainable way for their synthesis. Complementing existing chemical routes, recently a cyanide‐free enzymatic process technology based on the use of an aldoxime dehydratase (Oxd) as a biocatalyst component has been developed and successfully applied for the synthesis of a range of nitrile products. In these biotransformations, the Oxd enzymes catalyze the dehydration of aldoximes as readily available substrates to the nitrile products. Herein, these developments with such enzymes are summarized, with a strong focus on synthetic applications. It is demonstrated that this biocatalytic technology has the potential to “cross the bridge” between the production of fine chemicals and pharmaceuticals, on one hand, and bulk and commodity chemicals, on the other.
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Affiliation(s)
- Alessa Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Tobias Betke
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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19
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Rani S, Dasgupta B, Bhati GK, Tomar K, Rakshit S, Maiti S. Superior Proton-Transfer Catalytic Promiscuity of Cytochrome c in Self-Organized Media. Chembiochem 2020; 22:1285-1291. [PMID: 33175409 DOI: 10.1002/cbic.202000768] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid-base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6-7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.
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Affiliation(s)
- Sheetal Rani
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Basundhara Dasgupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Gaurav Kumar Bhati
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Kalpana Tomar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
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20
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Martí S, Tuñón I, Moliner V, Bertran J. Are Heme-Dependent Enzymes Always Using a Redox Mechanism? A Theoretical Study of the Kemp Elimination Catalyzed by a Promiscuous Aldoxime Dehydratase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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21
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Kemp Elimination Reaction Catalyzed by Electric Fields. Chemphyschem 2020; 21:295-306. [PMID: 31840917 DOI: 10.1002/cphc.201901155] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/12/2019] [Indexed: 12/20/2022]
Abstract
The Kemp elimination reaction is the most widely used in the de novo design of new enzymes. The effect of two different kinds of electric fields in the reactions of acetate as a base with benzisoxazole and 5-nitrobenzisoxazole as substrates have been theoretically studied. The effect of the solvent reaction field has been calculated using the SMD continuum model for several solvents; we have shown that solvents inhibit both reactions, the decrease of the reaction rate being larger as far as the dielectric constant is increased. The diminution of the reaction rate is especially remarkable between aprotic organic solvents and protic solvents as water, the electrostatic term of the hydrogen bonds being the main factor for the large inhibitory effect of water. The presence of an external electric field oriented in the direction of the charge transfer (z axis) increases it and, so, the reaction rate. In the reaction of the nitro compound, if the electric field is oriented in an orthogonal direction (x axis) the charge transfer to the NO2 group is favored and there is a subsequent increase of the reaction rate. However, this increase is smaller than the one produced by the field in the z axis. It is worthwhile mentioning that one of the main effects of external electric fields of intermediate intensity is the reorientation of the reactants. Finally, the implications of our results in the de novo design of enzymes are discussed.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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22
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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23
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Tseliou V, Masman MF, Böhmer W, Knaus T, Mutti FG. Mechanistic Insight into the Catalytic Promiscuity of Amine Dehydrogenases: Asymmetric Synthesis of Secondary and Primary Amines. Chembiochem 2019; 20:800-812. [PMID: 30489013 PMCID: PMC6472184 DOI: 10.1002/cbic.201800626] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 12/18/2022]
Abstract
Biocatalytic asymmetric amination of ketones, by using amine dehydrogenases (AmDHs) or transaminases, is an efficient method for the synthesis of α-chiral primary amines. A major challenge is to extend amination to the synthesis of secondary and tertiary amines. Herein, for the first time, it is shown that AmDHs are capable of accepting other amine donors, thus giving access to enantioenriched secondary amines with conversions up to 43 %. Surprisingly, in several cases, the promiscuous formation of enantiopure primary amines, along with the expected secondary amines, was observed. By conducting practical laboratory experiments and computational experiments, it is proposed that the promiscuous formation of primary amines along with secondary amines is due to an unprecedented nicotinamide (NAD)-dependent formal transamination catalysed by AmDHs. In nature, this type of mechanism is commonly performed by pyridoxal 5'-phosphate aminotransferase and not by dehydrogenases. Finally, a catalytic pathway that rationalises the promiscuous NAD-dependent formal transamination activity and explains the formation of the observed mixture of products is proposed. This work increases the understanding of the catalytic mechanism of NAD-dependent aminating enzymes, such as AmDHs, and will aid further research into the rational engineering of oxidoreductases for the synthesis of α-chiral secondary and tertiary amines.
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Affiliation(s)
- Vasilis Tseliou
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Marcelo F. Masman
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Wesley Böhmer
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tanja Knaus
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Francesco G. Mutti
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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24
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Betke T, Maier M, Gruber-Wölfler H, Gröger H. Biocatalytic production of adiponitrile and related aliphatic linear α,ω-dinitriles. Nat Commun 2018; 9:5112. [PMID: 30504854 PMCID: PMC6269433 DOI: 10.1038/s41467-018-07434-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022] Open
Abstract
Linear α,ω-dinitriles are important precursors for the polymer industry. Most prominently, adiponitrile is produced on an annual scale of ca. 1 million tons. However, a drawback of today’s dominating process is the need for large amounts of highly toxic hydrogen cyanide. In this contribution, an alternative approach towards such linear dinitriles is presented based on dehydration of readily available α,ω-dialdoximes at ambient conditions by means of aldoxime dehydratases. In contrast to existing production routes this biocatalytic route enables a highly regio- and chemoselective approach towards dinitriles without the use of hydrogen cyanide or harsh reaction conditions. In addition, a selective synthesis of adiponitrile with substrate loadings of up to 100 g/L and high yields of up to 80% was achieved. Furthermore, a lab scale process on liter scale leading to > 99% conversion at 50 g/L underlines the potential and robustness of this method for technical applicability. Typically, preparation of the polymer precursors α,ω-dinitriles requires hydrogen cyanide. Here, the authors use aldoxime hydratase to produce adiponitrile and related aliphatic linear dinitriles under ambient conditions starting from readily available substrates without needing hydrogen cyanide.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Manuel Maier
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13/III, 8010, Graz, Austria
| | - Heidrun Gruber-Wölfler
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13/III, 8010, Graz, Austria
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.
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25
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Vilím J, Knaus T, Mutti FG. Catalytic Promiscuity of Galactose Oxidase: A Mild Synthesis of Nitriles from Alcohols, Air, and Ammonia. Angew Chem Int Ed Engl 2018; 57:14240-14244. [PMID: 30176101 PMCID: PMC6220830 DOI: 10.1002/anie.201809411] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 11/26/2022]
Abstract
We report an unprecedented catalytically promiscuous activity of the copper-dependent enzyme galactose oxidase. The enzyme catalyses the one-pot conversion of alcohols into the related nitriles under mild reaction conditions in ammonium buffer, consuming ammonia as the source of nitrogen and dioxygen (from air at atmospheric pressure) as the only oxidant. Thus, this green method does not require either cyanide salts, toxic metals, or undesired oxidants in stoichiometric amounts. The substrate scope of the reaction includes benzyl and cinnamyl alcohols as well as 4- and 3-pyridylmethanol, giving access to valuable chemical compounds. The oxidation proceeds through oxidation from alcohol to aldehyde, in situ imine formation, and final direct oxidation to nitrile.
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Affiliation(s)
- Jan Vilím
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tanja Knaus
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Francesco G. Mutti
- Van't Hoff Institute for Molecular Sciences, HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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26
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Vilím J, Knaus T, Mutti FG. Catalytic Promiscuity of Galactose Oxidase: A Mild Synthesis of Nitriles from Alcohols, Air, and Ammonia. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jan Vilím
- Van't Hoff Institute for Molecular Sciences, HIMS-Biocat; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Tanja Knaus
- Van't Hoff Institute for Molecular Sciences, HIMS-Biocat; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Francesco G. Mutti
- Van't Hoff Institute for Molecular Sciences, HIMS-Biocat; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
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27
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Hong NS, Petrović D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ. The evolution of multiple active site configurations in a designed enzyme. Nat Commun 2018; 9:3900. [PMID: 30254369 PMCID: PMC6156567 DOI: 10.1038/s41467-018-06305-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.
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Affiliation(s)
- Nan-Sook Hong
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Dušan Petrović
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Richmond Lee
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Ganna Gryn'ova
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.,Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Miha Purg
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Jake Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Paul Bauer
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Ching-Yeh Lin
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Peter D Mabbitt
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - William Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Timothy Altamore
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Chris Easton
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Michelle L Coote
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Shina C L Kamerlin
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden.
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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28
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Tang M, Chu B, Chang X. Direct N-Alkylation and Kemp Elimination Reactions of 1-Sulfonyl-1H-Indazoles. Chem Asian J 2018; 13:2109-2116. [PMID: 30020558 DOI: 10.1002/asia.201800741] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/05/2018] [Indexed: 02/28/2024]
Abstract
The reactions of 1-sulfonyl-1H-indazoles under basic conditions are discussed, and the direct N-alkylation and Kemp elimination reactions of these compounds are reported. A series of 2-(p-tosylamino)benzonitriles and N-alkyl indazoles were prepared in good yields. Moreover, the 2-(p-tosylamino)benzonitriles could be transformed into a diverse range of important derivatives in a one-pot reaction. This method was successfully applied to the total syntheses of quindolinone and cryptolepinone; quindolinone was prepared in a one-pot reaction from 1-sulfonyl-1H-indazole.
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Affiliation(s)
- Meng Tang
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, P. R. China
| | - Bingjie Chu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, P. R. China
| | - Xiaowei Chang
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, P. R. China
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29
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Overproduction and characterization of the first enzyme of a new aldoxime dehydratase family in Bradyrhizobium sp. Int J Biol Macromol 2018; 115:746-753. [PMID: 29698761 DOI: 10.1016/j.ijbiomac.2018.04.103] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/23/2022]
Abstract
Almost 100 genes within the genus Bradyrhizobium are known to potentially encode aldoxime dehydratases (Oxds), but none of the corresponding proteins have been characterized yet. Aldoximes are natural substances involved in plant defense and auxin synthesis, and Oxds are components of enzymatic cascades enabling bacteria to transform, utilize and detoxify them. The aim of this work was to characterize a representative of the highly conserved Oxds in Bradyrhizobium spp. which include both plant symbionts and members of the soil communities. The selected oxd gene from Bradyrhizobium sp. LTSPM299 was expressed in Escherichia coli, and the corresponding gene product (OxdBr1; GenBank: WP_044589203) was obtained as an N-His6-tagged protein (monomer, 40.7 kDa) with 30-47% identity to Oxds characterized previously. OxdBr1 was most stable at pH ca. 7.0-8.0 and at up to 30 °C. As substrates, the enzyme acted on (aryl)aliphatic aldoximes such as E/Z-phenylacetaldoxime, E/Z-2-phenylpropionaldoxime, E/Z-3-phenylpropionaldoxime, E/Z-indole-3-acetaldoxime, E/Z-propionaldoxime, E/Z-butyraldoxime, E/Z-valeraldoxime and E/Z-isovaleraldoxime. Some of the reaction products of OxdBr1 are substrates of nitrilases occurring in the same genus. Regions upstream of the oxd gene contained genes encoding a putative aliphatic nitrilase and its transcriptional activator, indicating the participation of OxdBr1 in the metabolic route from aldoximes to carboxylic acids.
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30
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Betke T, Higuchi J, Rommelmann P, Oike K, Nomura T, Kato Y, Asano Y, Gröger H. Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases. Chembiochem 2018; 19:768-779. [PMID: 29333684 DOI: 10.1002/cbic.201700571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Indexed: 11/05/2022]
Abstract
Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high-volume, low-price sectors, such as polymers, to low-volume, high-price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas-phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a "synthetic platform technology". Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2-arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.,Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Jun Higuchi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Philipp Rommelmann
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Keiko Oike
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Taiji Nomura
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
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