1
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Kawamura Y, Ishida C, Miyata R, Miyata A, Hayashi S, Fujinami D, Ito S, Nakano S. Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction. Commun Chem 2023; 6:200. [PMID: 37737277 PMCID: PMC10517122 DOI: 10.1038/s42004-023-01005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Production of D-amino acids (D-AAs) on a large-scale enables to provide precursors of peptide therapeutics. In this study, we designed a novel L-amino acid oxidase, HTAncLAAO2, by ancestral sequence reconstruction, exhibiting high thermostability and long-term stability. The crystal structure of HTAncLAAO2 was determined at 2.2 Å by X-ray crystallography, revealing that the enzyme has an octameric form like a "ninja-star" feature. Enzymatic property analysis demonstrated that HTAncLAAO2 exhibits three-order larger kcat/Km values towards four L-AAs (L-Phe, L-Leu, L-Met, and L-Ile) than that of L-Trp. Through screening the variants, we obtained the HTAncLAAO2(W220A) variant, which shows a > 6-fold increase in kcat value toward L-Trp compared to the original enzyme. This variant applies to synthesizing enantio-pure D-Trp derivatives from L- or rac-forms at a preparative scale. Given its excellent properties, HTAncLAAO2 would be a starting point for designing novel oxidases with high activity toward various amines and AAs.
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Affiliation(s)
- Yui Kawamura
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Chiharu Ishida
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Ryo Miyata
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 2217-14 Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan
| | - Azusa Miyata
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Seiichiro Hayashi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Daisuke Fujinami
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
- PREST, Japan Science and Technology Agency, Saitama, Japan.
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2
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Xu S, Chu M, Zhang F, Zhao J, Zhang J, Cao Y, He G, Israr M, Zhao B, Ju J. Enhancement in the catalytic efficiency of D-amino acid oxidase from Glutamicibacter protophormiae by multiple amino acid substitutions. Enzyme Microb Technol 2023; 166:110224. [PMID: 36889103 DOI: 10.1016/j.enzmictec.2023.110224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
D-Amino acid oxidase (DAAO) is an imperative oxidoreductase that oxidizes D-amino acids to corresponding keto acids, producing ammonia and hydrogen peroxide. Previously, based on the sequence alignment of DAAO from Glutamicibacter protophormiae (GpDAAO-1) and (GpDAAO-2), 4 residues (E115, N119, T256, T286) at the surface regions of GpDAAO-2, were subjected to site-directed mutagenesis and achieved 4 single-point mutants with enhanced catalytic efficiency (kcat/Km) compared to parental GpDAAO-2. In the present study, to further enhance the catalytic efficiency of GpDAAO-2, a total of 11 (6 double, 4 triple, and 1 quadruple-point) mutants were prepared by the different combinations of 4 single-point mutants. All mutants and wild types were overexpressed, purified and enzymatically characterized. A triple-point mutant E115A/N119D/T286A exhibited the most significant improvement in catalytic efficiency as compared to wild-type GpDAAO-1 and GpDAAO-2. Structural modeling analysis elucidated that residue Y213 in loop region C209-Y219 might act as the active-site lid for controlling substrate access, the residue K256 substituted by threonine (K256T) might change the hydrogen bonding interaction between residue Y213 and the surrounding residues, and switch the conformation of the active-site lid from the closed state to the open state, resulting in the enhancement in substrate accessibility and catalytic efficiency.
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Affiliation(s)
- Shujing Xu
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Mengqiu Chu
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China; Hebei Collaborative Innovation Center for Eco-Environment, Shijiazhuang 050024, China
| | - Fa Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Jiawei Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Jiaqi Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Yuting Cao
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Guangzheng He
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Muhammad Israr
- Department of Biology, The University of Haripur, Haripur 22620, Pakistan.
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China; Hebei Collaborative Innovation Center for Eco-Environment, Shijiazhuang 050024, China.
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3
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Motoyama T, Yamamoto Y, Ishida C, Hasebe F, Kawamura Y, Shigeta Y, Ito S, Nakano S. Reaction Mechanism of Ancestral l-Lys α-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis. ACS OMEGA 2022; 7:44407-44419. [PMID: 36506213 PMCID: PMC9730747 DOI: 10.1021/acsomega.2c06334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The flavin-dependent amine oxidase superfamily contains various l-amino acid oxidases (LAAOs) bearing different substrate specificities and enzymatic properties. LAAOs catalyze the oxidation of the α-amino group of l-amino acids (L-AAs) to produce imino acids and H2O2. In this study, an ancestral l-Lys α-oxidase (AncLLysO2) was designed utilizing genome-mined sequences from the Caulobacter species. The AncLLysO2 exhibited high specificity toward l-Lys; the k cat/K m values toward l-Lys were one and two orders larger than those of l-Arg and l-ornithine, respectively. Liquid chromatography-high resolution mass spectrometry analysis indicated that AncLLysO2 released imino acid immediately from the active site after completion of oxidation of the α-amino group. Crystal structures of the ligand-free, l-Lys- and l-Arg-bound forms of AncLLysO2 were determined at 1.4-1.6 Å resolution, indicating that the active site of AncLLysO2 kept an open state during the reaction and more likely to release products. The structures also indicated the substrate recognition mechanism of AncLLysO2; ε-amino, α-amino, and carboxyl groups of l-Lys formed interactions with Q357, A551, and R77, respectively. Biochemical and molecular dynamics simulation analysis of AncLLysO2 indicated that active site residues that indirectly interact with the substrate are also important to exhibit high activity; for example, the aromatic group of Y219 is important to ensure that the l-Lys substrate is placed in the correct position to allow the reaction to proceed efficiently. Taken together, we propose the reaction mechanism of AncLLysO2.
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Affiliation(s)
- Tomoharu Motoyama
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yuta Yamamoto
- Department
of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Chiharu Ishida
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Fumihito Hasebe
- Department
of Bioscience, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Yui Kawamura
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
| | - Sohei Ito
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shogo Nakano
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- PREST, Japan Science and Technology
Agency, Saitama 332-0012, Japan
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4
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Novel Enzymatic Method for Imine Synthesis via the Oxidation of Primary Amines Using D-Amino Acid Oxidase from Porcine Kidney. Catalysts 2022. [DOI: 10.3390/catal12050511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
During studies on the oxidative cyanation reaction catalyzed by a variant of D-amino acid oxidase from porcine kidney (pkDAO) (Y228L/R283G), an unexpected formation of 1-phenyl-N-(1-phenylethylidene)ethanamine (PPEA) was detected. The optimal reaction conditions for the synthesis of PPEA and the reaction mechanism were investigated using the pkDAO variant. The highest PPEA synthesis was obtained in the reaction with 150 mM (R)-MBA at pH 9.0 and at 20 °C. Since PPEA synthesis proceeded by trapping the intermediate 1-phenylethanimine (1-PEI) by 15N-labeled n-hexylamine, which is not a substrate for the pKDAO variant, it was deduced that PPEA would be synthesized by a nucleophilic substitution of 1-PEI by another molecule of (R)-MBA. PPEA was further identified by its conversion to bis(1-phenylethyl)amine (BPEA) through reduction with NaBH4. Thus, a new enzymatic method of imine synthesis by oxidation of primary amine by the variant pkDAO was achieved for the first time.
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5
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Wahart AJC, Staniland J, Miller GJ, Cosgrove SC. Oxidase enzymes as sustainable oxidation catalysts. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211572. [PMID: 35242351 PMCID: PMC8753158 DOI: 10.1098/rsos.211572] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 05/03/2023]
Abstract
Oxidation is one of the most important processes used by the chemical industry. However, many of the methods that are used pose significant sustainability and environmental issues. Biocatalytic oxidation offers an alternative to these methods, with a now significant enzymatic oxidation toolbox on offer to chemists. Oxidases are one of these options, and as they only depend on molecular oxygen as a terminal oxidant offer perfect atom economy alongside the selectivity benefits afforded by enzymes. This review will focus on examples of oxidase biocatalysts that have been used for the sustainable production of important molecules and highlight some important processes that have been significantly improved through the use of oxidases. It will also consider emerging classes of oxidases, and how they might fit in a future biorefinery approach for the sustainable production of important chemicals.
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Affiliation(s)
- Alice J. C. Wahart
- Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | | | - Gavin J. Miller
- Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5BG, UK
- The Keele Centre for Glycoscience Research and Training, Keele University, Staffordshire, ST5 5BG, UK
| | - Sebastian C. Cosgrove
- Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5BG, UK
- The Keele Centre for Glycoscience Research and Training, Keele University, Staffordshire, ST5 5BG, UK
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6
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Li BB, Zhang J, Chen FF, Chen Q, Xu JH, Zheng GW. Direct reductive amination of ketones with amines by reductive aminases. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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7
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Cigan E, Eggbauer B, Schrittwieser JH, Kroutil W. The role of biocatalysis in the asymmetric synthesis of alkaloids - an update. RSC Adv 2021; 11:28223-28270. [PMID: 35480754 PMCID: PMC9038100 DOI: 10.1039/d1ra04181a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022] Open
Abstract
Alkaloids are a group of natural products with interesting pharmacological properties and a long history of medicinal application. Their complex molecular structures have fascinated chemists for decades, and their total synthesis still poses a considerable challenge. In a previous review, we have illustrated how biocatalysis can make valuable contributions to the asymmetric synthesis of alkaloids. The chemo-enzymatic strategies discussed therein have been further explored and improved in recent years, and advances in amine biocatalysis have vastly expanded the opportunities for incorporating enzymes into synthetic routes towards these important natural products. The present review summarises modern developments in chemo-enzymatic alkaloid synthesis since 2013, in which the biocatalytic transformations continue to take an increasingly 'central' role.
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Affiliation(s)
- Emmanuel Cigan
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Bettina Eggbauer
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Joerg H Schrittwieser
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
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8
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Chen X, Zhao R, Liu Z, Sun S, Ma Y, Liu Q, Sun X, Liu L. Redox deracemization of α-substituted 1,3-dihydroisobenzofurans. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids. Commun Chem 2020; 3:181. [PMID: 36703379 PMCID: PMC9814856 DOI: 10.1038/s42004-020-00432-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
L-amino acid oxidases (LAAOs) can be applied to convert racemic amino acids to D-isomers, which are potential precursors of pharmaceuticals. However, this application is hampered by the lack of available stable and structure-determined LAAOs. In this study, we attempt to address this limitation by utilizing two ancestral LAAOs: AncLAAO-N4 and AncLAAO-N5. AncLAAO-N4 has the highest thermal and temporal stabilities among the designed LAAOs that can be used for deracemization and stereoinversion. AncLAAO-N5 can provide X-ray crystal structures, which are helpful to reveal substrate recognition and reaction mechanisms of LAAOs at the molecular level. Next, we attempted to improve activity of AncLAAO-N4 toward L-Val through a semi-rational protein engineering method. Three variants with enhanced activity toward L-Val were obtained. Taken together, we believe that the activity and substrate selectivity of AncLAAOs give them the potential to be key enzymes in various chemoenzymatic reactions.
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10
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Yasukawa K, Kawahara N, Motojima F, Nakano S, Asano Y. Porcine kidney d-amino acid oxidase-derived R-amine oxidases with new substrate specificities. Enzymes 2020; 47:117-136. [PMID: 32951821 DOI: 10.1016/bs.enz.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An R-stereoselective amine oxidase and variants with markedly altered substrate specificity toward (R)-amines were generated from porcine d-amino acid oxidase (pkDAO), based on the X-ray crystallographic analysis of the wild-type enzyme. The new R-amine oxidase, a pkDAO variant (Y228L/R283G), acted on α-MBA and its derivatives, α-ethylbenzylamine, alkylamine, and cyclic secondary amines, totally losing the activities toward the original substrates, d-amino acids. The variant is enantiocomplementary to the flavin-type S-stereoselective amine oxidase variant from Aspergillus niger. Moreover, we solved the structure of pkDAO variants and successfully applied the obtained information to generate more variants through rational protein engineering, and used them in the synthesis of pharmaceutically attractive chiral compounds. The pkDAO variant Y228L/R283G and a variant I230A/R283G were used to synthesize (S)-amine and (R)-4-CBHA through deracemization, from racemic α-methylbenzylamine and benzhydrylamine, respectively, by selective oxidation of one of the enantiomers in the presence of a chemical reductant such as NaBH4. From a mechanistic point of view, we speculated that the imine intermediate, synthesized by oxidases or dehydrogenases, could be converted into primary α-aminonitrile by nucleophilic addition of cyanide in aqueous solutions. Nitriles and some unnatural amino acids were synthesized through a cascade reaction by oxidative cyanation reaction with the variant and a wide substrate specificity nitrilase.
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Affiliation(s)
- Kazuyuki Yasukawa
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Nobuhiro Kawahara
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Fumihiro Motojima
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Shogo Nakano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan.
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11
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Chen X, Yan L, Zhang L, Zhao C, Feng G, Chen L, Sun S, Liu Q, Liu L. Aerobic redox deracemization of α-aryl glycine esters. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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12
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Mao Y, Wang Z, Wang G, Zhao R, Kan L, Pan X, Liu L. Redox Deracemization of Tertiary Stereocenters Adjacent to an Electron-Withdrawing Group. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ying Mao
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Zehua Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Gang Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Ran Zhao
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Linglong Kan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Xiaoguang Pan
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Lei Liu
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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13
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Zhang L, Zhu R, Feng A, Zhao C, Chen L, Feng G, Liu L. Redox deracemization of β,γ-alkynyl α-amino esters. Chem Sci 2020; 11:4444-4449. [PMID: 34122901 PMCID: PMC8159540 DOI: 10.1039/d0sc00944j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The first non-enzymatic redox deracemization method using molecular oxygen as the terminal oxidant has been described. The one-pot deracemization of β,γ-alkynyl α-amino esters consisted of a copper-catalyzed aerobic oxidation and chiral phosphoric acid-catalyzed asymmetric transfer hydrogenation with excellent functional group compatibility. By using benzothiazoline as the reducing reagent, an exclusive chemoselectivity at the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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N bond over the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C bond was achieved, allowing for efficient deracemization of a series of α-amino esters bearing diverse α-alkynyl substituent patterns. The origins of chemo- and enantio-selectivities were elucidated by experimental and computational mechanistic investigation. The generality of the strategy is further demonstrated by efficient deracemization of β,γ-alkenyl α-amino esters. A one-pot deracemization of β,γ-alkynyl α-amino esters consisting of an aerobic oxidation and chiral phosphoric acid-catalyzed asymmetric transfer hydrogenation has been described.![]()
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Affiliation(s)
- Lu Zhang
- School of Pharmaceutical Sciences, Shandong University Jinan 250012 China
| | - Rongxiu Zhu
- School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 China
| | - Aili Feng
- School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 China
| | - Changyin Zhao
- School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 China
| | - Lei Chen
- School of Pharmaceutical Sciences, Shandong University Jinan 250012 China
| | - Guidong Feng
- School of Pharmaceutical Sciences, Shandong University Jinan 250012 China
| | - Lei Liu
- School of Pharmaceutical Sciences, Shandong University Jinan 250012 China .,School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 China
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14
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Tseliou V, Knaus T, Vilím J, Masman MF, Mutti FG. Kinetic Resolution of Racemic Primary Amines Using Geobacillus stearothermophilus Amine Dehydrogenase Variant. ChemCatChem 2020; 12:2184-2188. [PMID: 32802214 PMCID: PMC7422701 DOI: 10.1002/cctc.201902085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/22/2020] [Indexed: 11/11/2022]
Abstract
A NADH-dependent engineered amine dehydrogenase from Geobacillus stearothermophilus (LE-AmDH-v1) was applied together with a NADH-oxidase from Streptococcus mutans (NOx) for the kinetic resolution of pharmaceutically relevant racemic α-chiral primary amines. The reaction conditions (e. g., pH, temperature, type of buffer) were optimised to yield S-configured amines with up to >99 % ee.
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Affiliation(s)
- Vasilis Tseliou
- van ‘t Hoff Institute for Molecular Sciences HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
| | - Tanja Knaus
- van ‘t Hoff Institute for Molecular Sciences HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
| | - Jan Vilím
- van ‘t Hoff Institute for Molecular Sciences HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
| | - Marcelo F. Masman
- van ‘t Hoff Institute for Molecular Sciences HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
| | - Francesco G. Mutti
- van ‘t Hoff Institute for Molecular Sciences HIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
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15
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Zhang YH, Chen FF, Li BB, Zhou XY, Chen Q, Xu JH, Zheng GW. Stereocomplementary Synthesis of Pharmaceutically Relevant Chiral 2-Aryl-Substituted Pyrrolidines Using Imine Reductases. Org Lett 2020; 22:3367-3372. [DOI: 10.1021/acs.orglett.0c00802] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yu-Hui Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Fei-Fei Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Bo-Bo Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xin-Yi Zhou
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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16
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Ma Y, Liu X, Mao Y, Huang J, Ma S, Liu L. Redox deracemization of diarylmethyl alkynes. Org Chem Front 2020. [DOI: 10.1039/d0qo00811g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A highly effective one-pot redox deracemization of diarylmethyl alkynes has been disclosed.
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Affiliation(s)
- Yingang Ma
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Cheeloo College of Medicine
- Shandong University
| | - Xigong Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P.R. China
| | - Ying Mao
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Cheeloo College of Medicine
- Shandong University
| | - Jiancheng Huang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P.R. China
| | - Shutao Ma
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Cheeloo College of Medicine
- Shandong University
| | - Lei Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Cheeloo College of Medicine
- Shandong University
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17
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Nakano S, Minamino Y, Hasebe F, Ito S. Deracemization and Stereoinversion to Aromatic d-Amino Acid Derivatives with Ancestral l-Amino Acid Oxidase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03418] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yuki Minamino
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Fumihito Hasebe
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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18
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Duan J, Li B, Qin Y, Dong Y, Ren J, Li G. Recent progress in directed evolution of stereoselective monoamine oxidases. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0272-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMonoamine oxidases (MAOs) use molecular dioxygen as oxidant to catalyze the oxidation of amines to imines. This type of enzyme can be employed for the synthesis of primary, secondary, and tertiary amines by an appropriate deracemization protocol. Consequently, MAOs are an attractive class of enzymes in biocatalysis. However, they also have limitations in enzyme-catalyzed processes due to the often-observed narrow substrate scope, low activity, or poor/wrong stereoselectivity. Therefore, directed evolution was introduced to eliminate these obstacles, which is the subject of this review. The main focus is on recent efforts concerning the directed evolution of four MAOs: monoamine oxidase (MAO-N), cyclohexylamine oxidase (CHAO),D-amino acid oxidase (pkDAO), and 6-hydroxy-D-nicotine oxidase (6-HDNO).
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19
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Musa MM, Hollmann F, Mutti FG. Synthesis of enantiomerically pure alcohols and amines via biocatalytic deracemisation methods. Catal Sci Technol 2019; 9:5487-5503. [PMID: 33628427 PMCID: PMC7116805 DOI: 10.1039/c9cy01539f] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Deracemisation via chemo-enzymatic or multi-enzymatic approaches is the optimum substitute for kinetic resolution, which suffers from the limitation of a theoretical maximum 50% yield albeit high enantiomeric excess is attainable. This review covers the recent progress in various deracemisation approaches applied to the synthesis of enantiomerically pure alcohols and amines, such as (1) dynamic kinetic resolution, (2) cyclic deracemisation, (3) linear deracemisation (including stereoinversion) and (4) enantioconvergent methods.
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Affiliation(s)
- Musa M Musa
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZDelft, The Netherlands
| | - Francesco G Mutti
- Van't HoffInstitute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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20
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Han SW, Jang Y, Shin JS. In Vitro and In Vivo One-Pot Deracemization of Chiral Amines by Reaction Pathway Control of Enantiocomplementary ω-Transaminases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
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21
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Asano Y, Yasukawa K. Identification and development of amino acid oxidases. Curr Opin Chem Biol 2019; 49:76-83. [DOI: 10.1016/j.cbpa.2018.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 12/23/2022]
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22
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Yoon S, Patil MD, Sarak S, Jeon H, Kim G, Khobragade TP, Sung S, Yun H. Deracemization of Racemic Amines to Enantiopure (
R
)‐ and (
S
)‐amines by Biocatalytic Cascade Employing ω‐Transaminase and Amine Dehydrogenase. ChemCatChem 2019. [DOI: 10.1002/cctc.201900080] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sanghan Yoon
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Mahesh D. Patil
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Sharad Sarak
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Hyunwoo Jeon
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Geon‐Hee Kim
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Taresh P. Khobragade
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Sihyong Sung
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
| | - Hyungdon Yun
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro, Gwanjin-gu Seoul 050-29 South Korea
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23
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Asano Y. Screening and development of enzymes for determination and transformation of amino acids. Biosci Biotechnol Biochem 2019; 83:1402-1416. [PMID: 30621552 DOI: 10.1080/09168451.2018.1559027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.
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Affiliation(s)
- Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Toyama , Japan
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24
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Affiliation(s)
- Mahesh D. Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Andreas Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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25
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Ball J, Gannavaram S, Gadda G. Structural determinants for substrate specificity of flavoenzymes oxidizing d-amino acids. Arch Biochem Biophys 2018; 660:87-96. [PMID: 30312594 DOI: 10.1016/j.abb.2018.10.002] [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: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022]
Abstract
The oxidation of d-amino acids is relevant to neurodegenerative diseases, detoxification, and nutrition in microorganisms and mammals. It is also important for the resolution of racemic amino acid mixtures and the preparation of chiral building blocks for the pharmaceutical and food industry. Considerable biochemical and structural knowledge has been accrued in recent years on the enzymes that carry out the oxidation of the Cα-N bond of d-amino acids. These enzymes contain FAD as a required coenzyme, share similar overall three-dimensional folds and highly conserved active sites, but differ in their specificity for substrates with neutral, anionic, or cationic side-chains. Here, we summarize the current biochemical and structural knowledge regarding substrate specificity on d-amino acid oxidase, d-aspartate oxidase, and d-arginine dehydrogenase for which a wealth of biochemical and structural studies is available.
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Affiliation(s)
- Jacob Ball
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Swathi Gannavaram
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Giovanni Gadda
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA; Departments of Biology, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302-3965, USA.
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26
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Li QH, Dong Y, Chen FF, Liu L, Li CX, Xu JH, Zheng GW. Reductive amination of ketones with ammonium catalyzed by a newly identified Brevibacterium epidermidis strain for the synthesis of (S)-chiral amines. CHINESE JOURNAL OF CATALYSIS 2018. [DOI: 10.1016/s1872-2067(18)63108-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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27
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Yasukawa K, Motojima F, Ono A, Asano Y. Expansion of the Substrate Specificity of Porcine Kidney D-Amino Acid Oxidase for S-Stereoselective Oxidation of 4-Cl-Benzhydrylamine. ChemCatChem 2018; 10:3500-3505. [PMID: 30333894 PMCID: PMC6174955 DOI: 10.1002/cctc.201800614] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Indexed: 11/11/2022]
Abstract
Discovery and development of enzymes for the synthesis of chiral amines have been a hot topic for basic and applied aspects of biocatalysts. Based on our X-ray crystallographic analyses of porcine kidney D-amino acid oxidase (pkDAO) and its variants, we rationally designed a new variant that catalyzed the oxidation of (S)-4-Cl-benzhydrylamine (CBHA) from pkDAO and obtained it by functional high-throughput screening with colorimetric assay. The variant I230A/R283G was constructed from the variant R283G which had completely lost the activity for D-amino acids, further gaining new activity toward (S)-chiral amines with the bulky substituents. The variant enzyme (I230A/R283G) was characterized to have a catalytic efficiency of 1.85 s-1 for (S)-CBHA, while that for (R)-1-phenylethylamine was diminished 10-fold as compared with the Y228L/R283G variant. The variant was efficiently used for the synthesis of (R)-CBHA in 96 % ee from racemic CBHA by the deracemization reaction in the presence of reducing agent such as NaBH4 in water. Furthermore, X-ray crystallographic analysis of the new variant complexed with (S)-CBHA, together with modelling study clearly showed the basis of understanding the structure-activity relationship of pkDAO.
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Affiliation(s)
- Kazuyuki Yasukawa
- Biotechnology Research Center and Department of BiotechnologyToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
- Asano Active Enzyme Molecule ProjectToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
| | - Fumihiro Motojima
- Biotechnology Research Center and Department of BiotechnologyToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
- Asano Active Enzyme Molecule ProjectToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
| | - Atsushi Ono
- Biotechnology Research Center and Department of BiotechnologyToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of BiotechnologyToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
- Asano Active Enzyme Molecule ProjectToyama Prefectural University5180 KurokawaImizu, Toyama939-0398Japan
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28
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Subramanian K, Góra A, Spruijt R, Mitusińska K, Suarez-Diez M, Martins dos Santos V, Schaap PJ. Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS One 2018; 13:e0198990. [PMID: 29906280 PMCID: PMC6003678 DOI: 10.1371/journal.pone.0198990] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 11/28/2022] Open
Abstract
D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.
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Affiliation(s)
- Kalyanasundaram Subramanian
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
| | - Ruud Spruijt
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
- Department of Chemistry, Silesian University of Technology, ks. Marcina Strzody, Gliwice, Poland
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
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29
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Nakano S, Motoyama T, Miyashita Y, Ishizuka Y, Matsuo N, Tokiwa H, Shinoda S, Asano Y, Ito S. Benchmark Analysis of Native and Artificial NAD +-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data. Biochemistry 2018; 57:3722-3732. [PMID: 29787243 DOI: 10.1021/acs.biochem.8b00339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full-consensus design (FCD) and ancestral-sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial l-threonine 3-dehydrogenases (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1, and AncTDH, using FCD and ASR, respectively. The artificial SDR-TDHs had excellent thermal stability and NAD+ recognition compared to native SDR-TDH from Cupriavidus necator (CnTDH); the melting temperatures of FcTDH-N1 and AncTDH were about 10 and 5 °C higher than that of CnTDH, respectively, and the dissociation constants toward NAD+ of FcTDH-N1 and AncTDH were 2- and 7-fold lower than that of CnTDH, respectively. Enzymatic efficiency of the artificial SDR-TDHs were comparable to that of CnTDH. Crystal structures of FcTDH-N1 and AncTDH were determined at 2.8 and 2.1 Å resolution, respectively. Structural and MD simulation analysis of the SDR-TDHs indicated that only the flexibility at specific regions was changed, suggesting that multiple mutations introduced in the artificial SDR-TDHs altered their flexibility and thereby affected their enzymatic properties. Benchmark analysis of the SDR-TDHs indicated that both FCD and ASR can generate highly functional proteins if a curated library is prepared appropriately.
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Affiliation(s)
- Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.,Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Tomoharu Motoyama
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Yurina Miyashita
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Yuki Ishizuka
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Naoya Matsuo
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Hiroaki Tokiwa
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Suguru Shinoda
- Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan.,Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Yasuhisa Asano
- Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan.,Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.,Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
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30
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Cosgrove SC, Hussain S, Turner NJ, Marsden SP. Synergistic Chemo/Biocatalytic Synthesis of Alkaloidal Tetrahydroquinolines. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01220] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian C. Cosgrove
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Institute of Process Research and Development and School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Shahed Hussain
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stephen P. Marsden
- Institute of Process Research and Development and School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
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31
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Chen FF, Zheng GW, Liu L, Li H, Chen Q, Li FL, Li CX, Xu JH. Reshaping the Active Pocket of Amine Dehydrogenases for Asymmetric Synthesis of Bulky Aliphatic Amines. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04135] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fei-Fei Chen
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Lei Liu
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Hao Li
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Qi Chen
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Fu-Long Li
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
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32
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Yao P, Cong P, Gong R, Li J, Li G, Ren J, Feng J, Lin J, Lau PCK, Wu Q, Zhu D. Biocatalytic Route to Chiral 2-Substituted-1,2,3,4-Tetrahydroquinolines Using Cyclohexylamine Oxidase Muteins. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03552] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Peiyuan Yao
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Peiqian Cong
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
| | - Rui Gong
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
| | - Jinlong Li
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Guangyue Li
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Jie Ren
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Jinhui Feng
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Jianping Lin
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Peter C. K. Lau
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Qiaqing Wu
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
| | - Dunming Zhu
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic
Area, Tianjin 300308, P.R. China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
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33
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Aleku GA, Mangas-Sanchez J, Citoler J, France SP, Montgomery SL, Heath RS, Thompson MP, Turner NJ. Kinetic Resolution and Deracemization of Racemic Amines Using a Reductive Aminase. ChemCatChem 2018. [DOI: 10.1002/cctc.201701484] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Godwin A. Aleku
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Juan Mangas-Sanchez
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Joan Citoler
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Scott P. France
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Sarah L. Montgomery
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Rachel S. Heath
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Matthew P. Thompson
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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34
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France SP, Aleku GA, Sharma M, Mangas-Sanchez J, Howard RM, Steflik J, Kumar R, Adams RW, Slabu I, Crook R, Grogan G, Wallace TW, Turner NJ. Biocatalytic Routes to Enantiomerically Enriched Dibenz[c
,e
]azepines. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708453] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Scott P. France
- School of Chemistry; University of Manchester; Manchester Institute of Biotechnology; 131 Princess Street Manchester M17DN UK
| | - Godwin A. Aleku
- School of Chemistry; University of Manchester; Manchester Institute of Biotechnology; 131 Princess Street Manchester M17DN UK
| | - Mahima Sharma
- York Structural Biology Laboratory; Department of Chemistry; University of York; Heslington York YO10 5DD UK
| | - Juan Mangas-Sanchez
- School of Chemistry; University of Manchester; Manchester Institute of Biotechnology; 131 Princess Street Manchester M17DN UK
| | - Roger M. Howard
- Groton Laboratories; Pfizer Worldwide Research and Development; 445 Eastern Point Road Groton CT 06340 USA
- Sandwich Laboratories; Pfizer Worldwide Research and Development; Discovery Park Sandwich, Kent CT13 9NJ UK
| | - Jeremy Steflik
- Groton Laboratories; Pfizer Worldwide Research and Development; 445 Eastern Point Road Groton CT 06340 USA
| | - Rajesh Kumar
- Groton Laboratories; Pfizer Worldwide Research and Development; 445 Eastern Point Road Groton CT 06340 USA
| | - Ralph W. Adams
- School of Chemistry; University of Manchester; Manchester M13 9PL UK
| | - Iustina Slabu
- School of Chemistry; University of Manchester; Manchester Institute of Biotechnology; 131 Princess Street Manchester M17DN UK
| | - Robert Crook
- Sandwich Laboratories; Pfizer Worldwide Research and Development; Discovery Park Sandwich, Kent CT13 9NJ UK
| | - Gideon Grogan
- York Structural Biology Laboratory; Department of Chemistry; University of York; Heslington York YO10 5DD UK
| | | | - Nicholas J. Turner
- School of Chemistry; University of Manchester; Manchester Institute of Biotechnology; 131 Princess Street Manchester M17DN UK
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35
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France SP, Aleku GA, Sharma M, Mangas-Sanchez J, Howard RM, Steflik J, Kumar R, Adams RW, Slabu I, Crook R, Grogan G, Wallace TW, Turner NJ. Biocatalytic Routes to Enantiomerically Enriched Dibenz[c,e]azepines. Angew Chem Int Ed Engl 2017; 56:15589-15593. [PMID: 29024400 DOI: 10.1002/anie.201708453] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Indexed: 11/11/2022]
Abstract
Biocatalytic retrosynthetic analysis of dibenz[c,e]azepines has highlighted the use of imine reductase (IRED) and ω-transaminase (ω-TA) biocatalysts to establish the key stereocentres of these molecules. Several enantiocomplementary IREDs were identified for the synthesis of (R)- and (S)-5-methyl-6,7-dihydro-5H-dibenz[c,e]azepine with excellent enantioselectivity, by reduction of the parent imines. Crystallographic evidence suggests that IREDs may be able to bind one conformer of the imine substrate such that, upon reduction, the major product conformer is generated directly. ω-TA biocatalysts were also successfully employed for the production of enantiopure 1-(2-bromophenyl)ethan-1-amine, thus enabling an orthogonal route for the installation of chirality into dibenz[c,e]azepine framework.
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Affiliation(s)
- Scott P France
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M17DN, UK
| | - Godwin A Aleku
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M17DN, UK
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Juan Mangas-Sanchez
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M17DN, UK
| | - Roger M Howard
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA.,Sandwich Laboratories, Pfizer Worldwide Research and Development, Discovery Park, Sandwich, Kent, CT13 9NJ, UK
| | - Jeremy Steflik
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA
| | - Rajesh Kumar
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA
| | - Ralph W Adams
- School of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Iustina Slabu
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M17DN, UK
| | - Robert Crook
- Sandwich Laboratories, Pfizer Worldwide Research and Development, Discovery Park, Sandwich, Kent, CT13 9NJ, UK
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Timothy W Wallace
- School of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Nicholas J Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M17DN, UK
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36
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PH-Dependent Enantioselectivity of D-amino Acid Oxidase in Aqueous Solution. Sci Rep 2017; 7:2994. [PMID: 28592826 PMCID: PMC5462808 DOI: 10.1038/s41598-017-03177-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/26/2017] [Indexed: 11/30/2022] Open
Abstract
D-amino acid oxidases (DAAO) are stereospecific enzymes which are generally almost inactive towards L-enantiomer in neutral solution when L-, D-amino acids are supplied as substrates. In this paper, the D-amino acid oxidase can catalytic oxidize L-amino acids by modulating pH of aqueous solution. With L-Pro as substrate, the catalytic rate (kcat) and the affinity (Km) of DAAO were 6.71 s−1 and 33 mM at pH 8.0, respectively, suggesting that optimal pH condition enhanced the activity of DAAO towards L-Pro. Similar results were obtained when L-Ala (pH 9.8), L-Arg (pH 6.5), L-Phe (pH 9.0), L-Thr (pH 9.4), and L-Val (pH 8.5) were catalyzed by DAAO at various pH values. The racemization of the L-amino acids was not found by capillary electrophoresis analysis during oxidation, and quantification analysis of L-amino acids before and after catalytic reaction was performed, which confirmed that the modulation of enantioselectivity of DAAO resulted from the oxidation of L-amino acids rather than D-amino acids by changing pH. A mechanistic model was proposed to explain enhanced activity of DAAO towards L-amino acids under optimal pH condition.
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37
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Aleku GA, France SP, Man H, Mangas-Sanchez J, Montgomery SL, Sharma M, Leipold F, Hussain S, Grogan G, Turner NJ. A reductive aminase from Aspergillus oryzae. Nat Chem 2017; 9:961-969. [PMID: 28937665 DOI: 10.1038/nchem.2782] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 04/13/2017] [Indexed: 12/24/2022]
Abstract
Reductive amination is one of the most important methods for the synthesis of chiral amines. Here we report the discovery of an NADP(H)-dependent reductive aminase from Aspergillus oryzae (AspRedAm, Uniprot code Q2TW47) that can catalyse the reductive coupling of a broad set of carbonyl compounds with a variety of primary and secondary amines with up to >98% conversion and with up to >98% enantiomeric excess. In cases where both carbonyl and amine show high reactivity, it is possible to employ a 1:1 ratio of the substrates, forming amine products with up to 94% conversion. Steady-state kinetic studies establish that the enzyme is capable of catalysing imine formation as well as reduction. Crystal structures of AspRedAm in complex with NADP(H) and also with both NADP(H) and the pharmaceutical ingredient (R)-rasagiline are reported. We also demonstrate preparative scale reductive aminations with wild-type and Q240A variant biocatalysts displaying total turnover numbers of up to 32,000 and space time yields up to 3.73 g l-1 d-1.
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Affiliation(s)
- Godwin A Aleku
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Scott P France
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Henry Man
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Juan Mangas-Sanchez
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Sarah L Montgomery
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Friedemann Leipold
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Shahed Hussain
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Nicholas J Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
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38
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Li G, Yao P, Gong R, Li J, Liu P, Lonsdale R, Wu Q, Lin J, Zhu D, Reetz MT. Simultaneous engineering of an enzyme's entrance tunnel and active site: the case of monoamine oxidase MAO-N. Chem Sci 2017; 8:4093-4099. [PMID: 30155214 PMCID: PMC6099926 DOI: 10.1039/c6sc05381e] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
A new directed evolution approach is presented to enhance the activity of an enzyme and to manipulate stereoselectivity by focusing iterative saturation mutagenesis (ISM) simultaneously on residues lining the entrance tunnel and the binding pocket. This combined mutagenesis strategy was applied successfully to the monoamine oxidase from Aspergillus niger (MAO-N) in the reaction of sterically demanding substrates which are of interest in the synthesis of chiral pharmaceuticals based on the benzo-piperidine scaffold. Reversal of enantioselectivity of Turner-type deracemization was achieved in the synthesis of (S)-1,2,3,4-tetrahydro-1-methyl-isoquinoline, (S)-1,2,3,4-tetrahydro-1-ethylisoquinoline and (S)-1,2,3,4-tetrahydro-1-isopropylisoquinoline. Extensive molecular dynamics simulations indicate that the altered catalytic profile is due to increased hydrophobicity of the entrance tunnel acting in concert with the altered shape of the binding pocket.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Rui Gong
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Jinlong Li
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Pi Liu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Jianping Lin
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
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39
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Trimmer EE, Wanninayake US, Fitzpatrick PF. Mechanistic Studies of an Amine Oxidase Derived from d-Amino Acid Oxidase. Biochemistry 2017; 56:2024-2030. [PMID: 28355481 DOI: 10.1021/acs.biochem.7b00161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The flavoprotein d-amino acid oxidase has long served as a paradigm for understanding the mechanism of oxidation of amino acids by flavoproteins. Recently, a mutant d-amino acid oxidase (Y228L/R283G) that catalyzed the oxidation of amines rather than amino acids was described [Yasukawa, K., et al. (2014) Angew. Chem., Int. Ed. 53, 4428-4431]. We describe here the use of pH and kinetic isotope effects with (R)-α-methylbenzylamine as a substrate to determine whether the mutant enzyme utilizes the same catalytic mechanism as the wild-type enzyme. The effects of pH on the steady-state and rapid-reaction kinetics establish that the neutral amine is the substrate, while an active-site residue, likely Tyr224, must be uncharged for productive binding. There is no solvent isotope effect on the kcat/Km value for the amine, consistent with the neutral amine being the substrate. The deuterium isotope effect on the kcat/Km value is pH-independent, with an average value of 5.3, similar to values found with amino acids as substrates for the wild-type enzyme and establishing that there is no commitment to catalysis with this substrate. The kcat/KO2 value is similar to that seen with amino acids as the substrate, consistent with the oxidative half-reaction being unperturbed by the mutation and with flavin oxidation preceding product release. All of the data are consistent with the mutant enzyme utilizing the same mechanism as the wild-type enzyme, transfer of hydride from the neutral amine to the flavin.
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Affiliation(s)
- Elizabeth E Trimmer
- Department of Chemistry, Grinnell College , Grinnell, Iowa 50112, United States
| | - Udayanga S Wanninayake
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center , San Antonio, Texas 78229, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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40
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41
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Complementary transcriptomic and proteomic analyses reveal regulatory mechanisms of milk protein production in dairy cows consuming different forages. Sci Rep 2017; 7:44234. [PMID: 28290485 PMCID: PMC5349593 DOI: 10.1038/srep44234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 11/19/2022] Open
Abstract
Forage plays a critical role in the milk production of dairy cows; however, the mechanisms regulating bovine milk synthesis in dairy cows fed high forage rations with different basal forage types are not well-understood. In the study, rice straw (RS, low-quality) and alfalfa hay (AH, high-quality) diets were fed to lactating cows to explore how forage quality affected the molecular mechanisms regulating milk production using RNA-seq transcriptomic method with iTRAQ proteomic technique. A total of 554 transcripts (423 increased and 131 decreased) and 517 proteins (231 up-regulated and 286 down-regulated) were differentially expressed in the mammary glands of the two groups. The correlation analysis demonstrated seven proteins (six up-regulated and one down-regulated) had consistent mRNA expression. Functional analysis of the differentially expressed transcripts/proteins suggested that enhanced capacity for energy and fatty acid metabolism, increased protein degradation, reduced protein synthesis, decreased amino acid metabolism and depressed cell growth were related to RS consumption. The results indicated cows consuming RS diets may have had depressed milk protein synthesis because these animals had decreased capacity for protein synthesis, enhanced proteolysis, inefficient energy generation and reduced cell growth. Additional work evaluating RS- and AH-based rations may help better isolate molecular adaptations to low nutrient availability during lactation.
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42
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Nakano S, Yasukawa K, Tokiwa T, Ishikawa T, Ishitsubo E, Matsuo N, Ito S, Tokiwa H, Asano Y. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase. J Phys Chem B 2016; 120:10736-10743. [DOI: 10.1021/acs.jpcb.6b09328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Nakano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuyuki Yasukawa
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takaki Tokiwa
- Department
of Chemistry, Graduate School of Science, Tohoku University, Aramaki,
Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeshi Ishikawa
- Department
of Molecular Microbiology and Immunology, Graduate School of Biomedical
Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Erika Ishitsubo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Naoya Matsuo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Sohei Ito
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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43
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Miki Y, Okazaki S, Asano Y. Engineering an ATP-dependent D-Ala:D-Ala ligase for synthesizing amino acid amides from amino acids. J Ind Microbiol Biotechnol 2016; 44:667-675. [PMID: 27585794 DOI: 10.1007/s10295-016-1833-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/21/2016] [Indexed: 12/01/2022]
Abstract
We successfully engineered a new enzyme that catalyzes the formation of D-Ala amide (D-AlaNH2) from D-Ala by modifying ATP-dependent D-Ala:D-Ala ligase (EC 6.3.2.4) from Thermus thermophilus, which catalyzes the formation of D-Ala-D-Ala from two molecules of D-Ala. The new enzyme was created by the replacement of the Ser293 residue with acidic amino acids, as it was speculated to bind to the second D-Ala of D-Ala-D-Ala. In addition, a replacement of the position with Glu performed better than that with Asp with regards to specificity for D-AlaNH2 production. The S293E variant, which was selected as the best enzyme for D-AlaNH2 production, exhibited an optimal activity at pH 9.0 and 40 °C for D-AlaNH2 production. The apparent K m values of this variant for D-Ala and NH3 were 7.35 mM and 1.58 M, respectively. The S293E variant could catalyze the synthesis of 9.3 and 35.7 mM of D-AlaNH2 from 10 and 50 mM D-Ala and 3 M NH4Cl with conversion yields of 93 and 71.4 %, respectively. This is the first report showing the enzymatic formation of amino acid amides from amino acids.
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Affiliation(s)
- Yuta Miki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,MicroBiopharm Japan Co.Ltd., 1-3-1 Kyobashi, Chuo-ku, Tokyo, 104-0031, Japan
| | - Seiji Okazaki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 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. .,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
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44
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Schmidt-Dannert C, Lopez-Gallego F. A roadmap for biocatalysis - functional and spatial orchestration of enzyme cascades. Microb Biotechnol 2016; 9:601-9. [PMID: 27418373 PMCID: PMC4993178 DOI: 10.1111/1751-7915.12386] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/25/2016] [Indexed: 12/23/2022] Open
Abstract
Advances in biological engineering and systems biology have provided new approaches and tools for the industrialization of biology. In the next decade, advanced biocatalytic systems will increasingly be used for the production of chemicals that cannot be made by current processes and/or where the use of enzyme catalysts is more resource efficient with a much reduced environmental impact. We expect that in the future, manufacture of chemicals and materials will utilize both biocatalytic and chemical synthesis synergistically. The realization of such advanced biomanufacturing processes currently faces a number of major challenges. Ready‐to‐deploy portfolios of biocatalysts for design to production must be created from biological diverse sources and through protein engineering. Robust and efficient multi‐step enzymatic reaction cascades must be developed that can operate simultaneously in one‐pot. For this to happen, bio‐orthogonal strategies for spatial and temporal control of biocatalyst activities must be developed. Promising approaches and technologies are emerging that will eventually lead to the design of in vitro biocatalytic systems that mimic the metabolic pathways and networks of cellular systems which will be discussed in this roadmap.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Fernando Lopez-Gallego
- Heterogeneous Biocatalysis Group, CIC BiomaGUNE, Pase Miramon 182, San Sebastian-Donostia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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45
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Immobilization of Genetically-Modified d-Amino Acid Oxidase and Catalase on Carbon Nanotubes to Improve the Catalytic Efficiency. Catalysts 2016. [DOI: 10.3390/catal6050066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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46
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Combined Imine Reductase and Amine Oxidase Catalyzed Deracemization of Nitrogen Heterocycles. ChemCatChem 2015. [DOI: 10.1002/cctc.201500822] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ji Y, Shi L, Chen MW, Feng GS, Zhou YG. Concise Redox Deracemization of Secondary and Tertiary Amines with a Tetrahydroisoquinoline Core via a Nonenzymatic Process. J Am Chem Soc 2015; 137:10496-9. [PMID: 26274896 DOI: 10.1021/jacs.5b06659] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A concise deracemization of racemic secondary and tertiary amines with a tetrahydroisoquinoline core has been successfully realized by orchestrating a redox process consisted of N-bromosuccinimide oxidation and iridum-catalyzed asymmetric hydrogenation. This compatible redox combination enables one-pot, single-operation deracemization to generate chiral 1-substituted 1,2,3,4-tetrahydroisoquinolines with up to 98% ee in 93% yield, offering a simple and scalable synthetic technique for chiral amines directly from racemic starting materials.
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Affiliation(s)
- Yue Ji
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, P. R. China
| | - Lei Shi
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, P. R. China.,State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116024, P. R. China
| | - Mu-Wang Chen
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, P. R. China
| | - Guang-Shou Feng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, P. R. China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, P. R. China
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Denard CA, Ren H, Zhao H. Improving and repurposing biocatalysts via directed evolution. Curr Opin Chem Biol 2015; 25:55-64. [DOI: 10.1016/j.cbpa.2014.12.036] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 11/27/2022]
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Köhler V, Turner NJ. Artificial concurrent catalytic processes involving enzymes. Chem Commun (Camb) 2014; 51:450-64. [PMID: 25350691 DOI: 10.1039/c4cc07277d] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The concurrent operation of multiple catalysts can lead to enhanced reaction features including (i) simultaneous linear multi-step transformations in a single reaction flask (ii) the control of intermediate equilibria (iii) stereoconvergent transformations (iv) rapid processing of labile reaction products. Enzymes occupy a prominent position for the development of such processes, due to their high potential compatibility with other biocatalysts. Genes for different enzymes can be co-expressed to reconstruct natural or construct artificial pathways and applied in the form of engineered whole cell biocatalysts to carry out complex transformations or, alternatively, the enzymes can be combined in vitro after isolation. Moreover, enzyme variants provide a wider substrate scope for a given reaction and often display altered selectivities and specificities. Man-made transition metal catalysts and engineered or artificial metalloenzymes also widen the range of reactivities and catalysed reactions that are potentially employable. Cascades for simultaneous cofactor or co-substrate regeneration or co-product removal are now firmly established. Many applications of more ambitious concurrent cascade catalysis are only just beginning to appear in the literature. The current review presents some of the most recent examples, with an emphasis on the combination of transition metal with enzymatic catalysis and aims to encourage researchers to contribute to this emerging field.
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Affiliation(s)
- Valentin Köhler
- Department of Chemistry, University of Basel, Spitalststrasse 51, CH-4056 Basel, Switzerland.
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