1
|
Qian W, Wang X, Kang Y, Pan P, Hou T, Hsieh CY. A general model for predicting enzyme functions based on enzymatic reactions. J Cheminform 2024; 16:38. [PMID: 38556873 PMCID: PMC10983695 DOI: 10.1186/s13321-024-00827-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/16/2024] [Indexed: 04/02/2024] Open
Abstract
Accurate prediction of the enzyme comission (EC) numbers for chemical reactions is essential for the understanding and manipulation of enzyme functions, biocatalytic processes and biosynthetic planning. A number of machine leanring (ML)-based models have been developed to classify enzymatic reactions, showing great advantages over costly and long-winded experimental verifications. However, the prediction accuracy for most available models trained on the records of chemical reactions without specifying the enzymatic catalysts is rather limited. In this study, we introduced BEC-Pred, a BERT-based multiclassification model, for predicting EC numbers associated with reactions. Leveraging transfer learning, our approach achieves precise forecasting across a wide variety of Enzyme Commission (EC) numbers solely through analysis of the SMILES sequences of substrates and products. BEC-Pred model outperformed other sequence and graph-based ML methods, attaining a higher accuracy of 91.6%, surpassing them by 5.5%, and exhibiting superior F1 scores with improvements of 6.6% and 6.0%, respectively. The enhanced performance highlights the potential of BEC-Pred to serve as a reliable foundational tool to accelerate the cutting-edge research in synthetic biology and drug metabolism. Moreover, we discussed a few examples on how BEC-Pred could accurately predict the enzymatic classification for the Novozym 435-induced hydrolysis and lipase efficient catalytic synthesis. We anticipate that BEC-Pred will have a positive impact on the progression of enzymatic research.
Collapse
Affiliation(s)
- Wenjia Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xiaorui Wang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
- CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Chang-Yu Hsieh
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| |
Collapse
|
2
|
Kordesedehi R, Asadollahi MA, Shahpiri A, Biria D, Nikel PI. Optimized enantioselective (S)-2-hydroxypropiophenone synthesis by free- and encapsulated-resting cells of Pseudomonas putida. Microb Cell Fact 2023; 22:89. [PMID: 37131175 PMCID: PMC10155308 DOI: 10.1186/s12934-023-02073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/25/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Aromatic α-hydroxy ketones, such as S-2-hydroxypropiophenone (2-HPP), are highly valuable chiral building blocks useful for the synthesis of various pharmaceuticals and natural products. In the present study, enantioselective synthesis of 2-HPP was investigated by free and immobilized whole cells of Pseudomonas putida ATCC 12633 starting from readily-available aldehyde substrates. Whole resting cells of P. putida, previously grown in a culture medium containing ammonium mandelate, are a source of native benzoylformate decarboxylase (BFD) activity. BFD produced by induced P. putida resting cells is a highly active biocatalyst without any further treatment in comparison with partially purified enzyme preparations. These cells can convert benzaldehyde and acetaldehyde into the acyloin compound 2-HPP by BFD-catalyzed enantioselective cross-coupling reaction. RESULTS The reaction was carried out in the presence of exogenous benzaldehyde (20 mM) and acetaldehyde (600 mM) as substrates in 6 mL of 200 mM phosphate buffer (pH 7) for 3 h. The optimal biomass concentration was assessed to be 0.006 g dry cell weight (DCW) mL- 1. 2-HPP titer, yield and productivity using the free cells were 1.2 g L- 1, 0.56 g 2-HPP/g benzaldehyde (0.4 mol 2-HPP/mol benzaldehyde), 0.067 g 2-HPP g- 1 DCW h- 1, respectively, under optimized biotransformation conditions (30 °C, 200 rpm). Calcium alginate (CA)-polyvinyl alcohol (PVA)-boric acid (BA)-beads were used for cell entrapment. Encapsulated whole-cells were successfully employed in four consecutive cycles for 2-HPP production under aerobic conditions without any noticeable beads degradation. Moreover, there was no production of benzyl alcohol as an unwanted by-product. CONCLUSIONS Bioconversion by whole P. putida resting cells is an efficient strategy for the production of 2-HPP and other α-hydroxyketones.
Collapse
Affiliation(s)
- Reihaneh Kordesedehi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Davoud Biria
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
3
|
Gajdoš M, Wagner J, Ospina F, Köhler A, Engqvist MKM, Hammer SC. Chiral Alcohols from Alkenes and Water: Directed Evolution of a Styrene Hydratase. Angew Chem Int Ed Engl 2023; 62:e202215093. [PMID: 36511829 PMCID: PMC10107627 DOI: 10.1002/anie.202215093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Enantioselective synthesis of chiral alcohols through asymmetric addition of water across an unactivated alkene is a highly sought-after transformation and a big challenge in catalysis. Herein we report the identification and directed evolution of a fatty acid hydratase from Marinitoga hydrogenitolerans for the highly enantioselective hydration of styrenes to yield chiral 1-arylethanols. While directed evolution for styrene hydration was performed in the presence of heptanoic acid to mimic fatty acid binding, the engineered enzyme displayed remarkable asymmetric styrene hydration activity in the absence of the small molecule activator. The evolved styrene hydratase provided access to chiral alcohols from simple alkenes and water with high enantioselectivity (>99 : 1 e.r.) and could be applied on a preparative scale.
Collapse
Affiliation(s)
- Matúš Gajdoš
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Jendrik Wagner
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Felipe Ospina
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Antonia Köhler
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering., Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Stephan C Hammer
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| |
Collapse
|
4
|
Bellur A, Das S, Jayaraman V, Behera S, Suryavanshi A, Balasubramanian S, Balaram P, Jindal G, Balaram H. Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin. Biochemistry 2023; 62:476-493. [PMID: 36595439 DOI: 10.1021/acs.biochem.2c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fumarate hydratase (FH) is a remarkable catalyst that decreases the free energy of the catalyzed reaction by 30 kcal mol-1, much larger than most exceptional enzymes with extraordinary catalytic rates. Two classes of FH are observed in nature: class-I and class-II, which have different folds, yet catalyze the same reversible hydration/dehydration reaction of the dicarboxylic acids fumarate/malate, with equal efficiencies. Using class-I FH from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj) as a model along with comparative analysis with the only other available class-I FH structure from Leishmania major (Lm), we provide insights into the molecular mechanism of catalysis in this class of enzymes. The structure of MjFH apo-protein has been determined, revealing that large intersubunit rearrangements occur across apo- and holo-protein forms, with a largely preorganized active site for substrate binding. Site-directed mutagenesis of active site residues, kinetic analysis, and computational studies, including density functional theory (DFT) and natural population analysis, together show that residues interacting with the carboxylate group of the substrate play a pivotal role in catalysis. Our study establishes that an electrostatic network at the active site of class-I FH polarizes the substrate fumarate through interactions with its carboxylate groups, thereby permitting an easier addition of a water molecule across the olefinic bond. We propose a mechanism of catalysis in FH that occurs through transition-state stabilization involving the distortion of the electronic structure of the substrate olefinic bond mediated by the charge polarization of the bound substrate at the enzyme active site.
Collapse
Affiliation(s)
- Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Soumik Das
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Vijay Jayaraman
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Sudarshan Behera
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Arpitha Suryavanshi
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | | | - Garima Jindal
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| |
Collapse
|
5
|
Lin H, Meng Y, Li N, Tang Y, Dong S, Wu Z, Xu C, Kazlauskas R, Chen H. Enzymatic Enantioselective anti‐Markovnikov Hydration of Aryl Alkenes. Angew Chem Int Ed Engl 2022; 61:e202206472. [DOI: 10.1002/anie.202206472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Hui Lin
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Yinyin Meng
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Na Li
- College of Biological Engineering Henan University of Technology 100 Lianhua Street Zhengzhou 450001 China
| | - Yanhong Tang
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Shuang Dong
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Zhongliu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology & Environmental Microbiology Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Chengdu 610041 China
| | - Cuilian Xu
- College of Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Romas Kazlauskas
- Department of Biochemistry Molecular Biology and Biophysics and the BioTechnology Institute University of Minnesota St Paul MN 55108 USA
| | - Hongge Chen
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| |
Collapse
|
6
|
Lin H, Meng Y, Li N, Tang Y, Dong S, Wu Z, Xu C, Kazlauskas R, Chen H. Enzymatic Enantioselective anti‐Markovnikov Hydration of Aryl Alkenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hui Lin
- Henan Agricultural University College of Life Science 95 Wenhua Road 450002 Zhengzhou CHINA
| | - Yinyin Meng
- Henan Agricultural University College of Life Sciences CHINA
| | - Na Li
- Henan University of Technology College of Biological Engineering CHINA
| | - Yanhong Tang
- Henan Agricultural University College of Life Sciences CHINA
| | - Shuang Dong
- Henan Agricultural University College of Life Sciences CHINA
| | - Zhongliu Wu
- Chengdu Institute of Biology CAS Key Laboratory of Environmental and Applied Microbiology CHINA
| | - Cuilian Xu
- Henan Agricultural University College of Sciences CHINA
| | - Romas Kazlauskas
- University of Minnesota College of Biological Sciences Department of Biochemistry, Molecular Biology and Biophysics CHINA
| | - Hongge Chen
- Henan Agricultural University College of Life Sciences CHINA
| |
Collapse
|
7
|
Zhang Y, Eser BE, Guo Z. A Bi-Enzymatic Cascade Pathway towards Optically Pure FAHFAs*. Chembiochem 2021; 22:2146-2153. [PMID: 33792147 DOI: 10.1002/cbic.202100070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/31/2021] [Indexed: 01/28/2023]
Abstract
Recently discovered endogenous mammalian lipids, fatty acid esters of hydroxy fatty acids (FAHFAs), have been proved to have anti-inflammatory and anti-diabetic effects. Due to their extremely low abundancies in vivo, forging a feasible scenario for FAHFA synthesis is critical for their use in uncovering biological mechanisms or in clinical trials. Here, we showcase a fully enzymatic approach, a novel in vitro bi-enzymatic cascade system, enabling an effective conversion of nature-abundant fatty acids into FAHFAs. Two hydratases from Lactobacillus acidophilus were used for converting unsaturated fatty acids to various enantiomeric hydroxy fatty acids, followed by esterification with another fatty acid catalyzed by Candida antarctica lipase A (CALA). Various FAHFAs were synthesized in a semi-preparative scale using this bi-enzymatic approach in a one-pot two-step operation mode. In all, we demonstrate that the hydratase-CALA system offers a promising route for the synthesis of optically pure structure-diverse FAHFAs.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| |
Collapse
|
8
|
Quantification of Carbonic Contamination of Fused Silica Surfaces at Different Stages of Classical Optics Manufacturing. MATERIALS 2021; 14:ma14071620. [PMID: 33810409 PMCID: PMC8036488 DOI: 10.3390/ma14071620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022]
Abstract
The chemical composition of ground and polished fused silica glass surfaces plays a decisive role in different applications of optics. In particular, a high level of carbon impurities is often undesirable for further processing and especially for gluing or cementing where adhesion failure may be attributed to carbonic surface-adherent contaminants. In this study, the surface carbon content at different stages of classical optics manufacturing was thus investigated. Two different standard processes—grinding and lapping with two final polishing processes using both polyurethane and pitch pads—were considered. After each process step, the chemical composition and roughness of the surface were analysed using X-ray photoelectron spectroscopy and atomic force microscopy. An obvious correlation between surface roughness and effective surface area, respectively, and the proportion of carbon contamination was observed. The lowest carbon contamination was found in case of lapped and pitch polished surfaces.
Collapse
|
9
|
Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 540] [Impact Index Per Article: 180.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
Collapse
Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| |
Collapse
|
10
|
Sui X, Liu J, Xin Y, Qu M, Qiu Y, He T, Luo H, Wang W, Qiu Z. Highly regioselective biotransformation of ginsenoside Rg1 to 25-OH derivatives of 20(S/R)-Rh1 by Cordyceps Sinensis. Bioorg Med Chem Lett 2020; 30:127504. [PMID: 32827631 DOI: 10.1016/j.bmcl.2020.127504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 11/20/2022]
Abstract
25-OH ginsenosides are potent and rare prodrugs in natural sources. However current strategies for such modification always end up in undesirable side products and unsatisfied yield that hinders them from further applications. Herein, ginsenoside Rg1 was thoroughly converted into 20(S/R)-Rh1 and 25-OH-20(S/R)-Rh1 by Cordyceps Sinensis in an optimum medium. The chemical correctness of either 25-OH-20(S/R)-Rh1 epimers was validated by LC-IT-TOF-MSn and 13C NMR spectrometry. The biocatalytic pathway was established as Rg1 → 20(S/R)-Rh1 → 25-OH-20(S/R)-Rh1. The molar bioconversion rate for total 25-OH-20(S/R)-Rh1 was calculated to be 82.5%, of which S-configuration accounted for 43.2% while R-configuration 39.3%. These two 25-OH derivatives are direct hydration products from 20(S/R)-Rh1 without other side metabolites, suggesting this is a highly regioselective process. In conclusion, this biocatalytic system could be harnessed to facilitate the preparation of diversified 25-OH ginsenosides with high yields of the target compound and simple chemical background in the reaction mixture.
Collapse
Affiliation(s)
- Xin Sui
- Changchun University of Chinese Medicine, Changchun 130117, China; The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun 130117, China
| | - Jishuang Liu
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yu Xin
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Mo Qu
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Ye Qiu
- Changchun University of Chinese Medicine, Changchun 130117, China; National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130117, China
| | - Tianzhu He
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Haoming Luo
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Weinan Wang
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Zhidong Qiu
- Changchun University of Chinese Medicine, Changchun 130117, China
| |
Collapse
|
11
|
Cuetos A, Iglesias-Fernández J, Danesh-Azari HR, Zukic E, Dowle A, Osuna S, Grogan G. Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anibal Cuetos
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Erna Zukic
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD, York, U.K
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| |
Collapse
|
12
|
Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| |
Collapse
|
13
|
Zhang Y, Eser BE, Kristensen P, Guo Z. Fatty acid hydratase for value-added biotransformation: A review. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
14
|
Bismuth trichloride-catalyzed oxy-Michael addition of water and alcohol to α,β-unsaturated ketones. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
15
|
Knockout of secondary alcohol dehydrogenase in Nocardia cholesterolicum NRRL 5767 by CRISPR/Cas9 genome editing technology. PLoS One 2020; 15:e0230915. [PMID: 32218601 PMCID: PMC7101164 DOI: 10.1371/journal.pone.0230915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/11/2020] [Indexed: 11/19/2022] Open
Abstract
Nocardia cholesterolicum NRRL 5767 is well-known for its ability to convert oleic acid to 10-hydroxystearic acid (~88%, w/w) and 10-ketostearic acid (~11%, w/w). Conversion of oleic acid to 10-hydroxystearic acid and then to 10-ketostearic acid has been proposed to be catalyzed by oleate hydratase and secondary alcohol dehydrogenase, respectively. Hydroxy fatty acids are value-added with many industrial applications. The objective of this study was to improve the Nocardia cholesterolicum NRRL5767 strain by CRISPR/Cas9 genome editing technology to knockout the secondary alcohol dehydrogenase gene, thus blocking the conversion of 10-hydroxystearic acid to 10-ketostearic acid. The improved strain would produce 10-hydroxystearic acid solely from oleic acid. Such improvement would enhance the production of 10-hydroxystearic acid by eliminating downstream separation of 10-hydroxystearic acid from 10-ketostearic acid. Here, we report: (1) Molecular cloning and characterization of two functional recombinant oleate hydratase isozymes and a functional recombinant secondary alcohol dehydrogenase from Nocardia cholesterolicum NRRL5767. Existence of two oleate hydratase isozymes may explain the high conversion yield of 10-hydroxystearic acid from oleic acid. (2) Construction of a CRISPR/Cas9/sgRNA chimeric plasmid that specifically targeted the secondary alcohol dehydrogenase gene by Golden Gate Assembly. (3) Transformation of the chimeric plasmid into Nocardia cholesterolicum NRRL 5767 by electroporation and screening of secondary alcohol dehydrogenase knockout mutants. Two mutants were validated by their lack of secondary alcohol dehydrogenase activity at the protein level and mutation at the targeted 5’ coding region and the 5’ upstream at the DNA level. The knockout mutants offer improvements by converting added oleic acid to solely 10-hydroxystearic acid, thus eliminating downstream separation of 10-hydroxystearic acid from 10-ketostearic acid. To the best of our knowledge, we report the first successful knockout of a target gene in the Nocardia species using CRISPR/Cas9/sgRNA-mediated genome editing technology.
Collapse
|
16
|
Nomura T, Kato Y. Identification of tuliposide G, a novel glucoside ester-type tuliposide, and its distribution in tulip. ACTA ACUST UNITED AC 2020; 75:75-86. [PMID: 32092042 DOI: 10.1515/znc-2019-0176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/21/2020] [Indexed: 11/15/2022]
Abstract
Tuliposides (Pos) are major defensive secondary metabolites in tulip (genus Tulipa), having 4-hydroxy-2-methylenebutanoyl and/or (3S)-3,4-dihydroxy-2-methylenebutanoyl groups at the C-1 and/or C-6 positions of d-glucose. The acyl group at the C-6 position is converted to antimicrobial lactones, tulipalins, by tuliposide-converting enzymes (TCEs). In the course of a survey of tulip tissue extracts to identify novel Pos, we found a minute high-performance liquid chromatography peak that disappeared following the action of a TCE, and whose retention time differed from those of known Pos. Spectroscopic analyses of the purified compound, as well as its enzymatic degradation products, revealed its structure as 5″-O-(6-O-(4'-hydroxy-2'-methylenebutanoyl))-β-d-glucopyranosyl-(2″R)-2″-hydroxymethyl-4″-butyrolactone, which is a novel glucoside ester-type Pos. We gave this compound the trivial name 'tuliposide G' (PosG). PosG accumulated in bulbs, at markedly lower levels than 6-PosA (the major Pos in bulbs), but was not found in any other tissues. Quantification of PosG in bulbs of 52 types of tulip, including 30 cultivars (Tulipa gesneriana) and 22 wild Tulipa spp., resulted in the detection of PosG in 28 cultivars, while PosG was present only in three wild species belonging to the subgenus Tulipa, the same subgenus to which tulip cultivars belong, suggesting the potential usefulness of PosG as a chemotaxonomic marker in tulip.
Collapse
Affiliation(s)
- Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan, Tel.: +81-766-56-7500 (ex. 1516), Fax: +81-766-56-2498
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| |
Collapse
|
17
|
Wang W, Liu J, Xin Y, He T, Qiu Y, Qu M, Song Y, Qiu Z. Highly regioselective bioconversion of ginsenoside Re into 20(S/R)-Rf2 by an optimized culture of Cordyceps sinensis. NEW J CHEM 2020. [DOI: 10.1039/d0nj01828g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Highly regioselective hydration of the C24–C25 double bond is discovered during the bioconversion of ginsenoside Re by Cordyceps sinensis.
Collapse
Affiliation(s)
- Weinan Wang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Jishuang Liu
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Yu Xin
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Tianzhu He
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Ye Qiu
- National Engineering Laboratory for Druggable Gene and Protein Screening
- Northeast Normal University
- Changchun 130117
- China
| | - Mo Qu
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Yan Song
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Zhidong Qiu
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| |
Collapse
|
18
|
Wu L, Deng H. Defluorination of 4-fluorothreonine by threonine deaminase. Org Biomol Chem 2020; 18:6236-6240. [DOI: 10.1039/d0ob01358g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Threonine deaminase from E. coli catalyses defluorination on 4-fluorothreonine.
Collapse
Affiliation(s)
- Linrui Wu
- Department of Chemistry
- University of Aberdeen
- Aberdeen AB24 3UE
- UK
| | - Hai Deng
- Department of Chemistry
- University of Aberdeen
- Aberdeen AB24 3UE
- UK
| |
Collapse
|
19
|
Engleder M, Strohmeier GA, Weber H, Steinkellner G, Leitner E, Müller M, Mink D, Schürmann M, Gruber K, Pichler H. Weiterentwicklung der Substrattoleranz von
Elizabethkingia meningoseptica
Oleathydratase zur regio‐ und stereoselektiven Hydratisierung von Ölsäurederivaten. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthias Engleder
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
| | - Gernot A. Strohmeier
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
- Institut für Organische ChemieTechnische Universität Graz, NAWI Graz Stremayrgasse 9 8010 Graz Österreich
| | - Hansjörg Weber
- Institut für Organische ChemieTechnische Universität Graz, NAWI Graz Stremayrgasse 9 8010 Graz Österreich
| | - Georg Steinkellner
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
- Innophore GmbH Am Eisernen Tor 3 8010 Graz Österreich
| | - Erich Leitner
- Institut für Analytische Chemie und LebensmittelchemieTechnische Universität Graz, NAWI Graz Stremayrgasse 9 8010 Graz Österreich
| | - Monika Müller
- InnoSyn B.V. Urmonderbaan 22 6167 RD Geleen Niederlande
| | - Daniel Mink
- InnoSyn B.V. Urmonderbaan 22 6167 RD Geleen Niederlande
| | | | - Karl Gruber
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
- Institut für Molekulare BiowissenschaftenUniversität Graz, NAWI Graz, BioTechMed Graz Humboldtstraße 50 8010 Graz Österreich
| | - Harald Pichler
- Institut für Molekulare BiotechnologieTechnische Universität Graz, NAWI Graz, BioTechMed Graz Petersgasse 14 8010 Graz Österreich
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
| |
Collapse
|
20
|
Engleder M, Strohmeier GA, Weber H, Steinkellner G, Leitner E, Müller M, Mink D, Schürmann M, Gruber K, Pichler H. Evolving the Promiscuity of Elizabethkingia meningoseptica Oleate Hydratase for the Regio- and Stereoselective Hydration of Oleic Acid Derivatives. Angew Chem Int Ed Engl 2019; 58:7480-7484. [PMID: 30848865 PMCID: PMC6563698 DOI: 10.1002/anie.201901462] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 12/15/2022]
Abstract
The addition of water to non-activated carbon-carbon double bonds catalyzed by fatty acid hydratases (FAHYs) allows for highly regio- and stereoselective oxyfunctionalization of renewable oil feedstock. So far, the applicability of FAHYs has been limited to free fatty acids, mainly owing to the requirement of a carboxylate function for substrate recognition and binding. Herein, we describe for the first time the hydration of oleic acid (OA) derivatives lacking this free carboxylate by the oleate hydratase from Elizabethkingia meningoseptica (OhyA). Molecular docking of OA to the OhyA 3D-structure and a sequence alignment uncovered conserved amino acid residues at the entrance of the substrate channel as target positions for enzyme engineering. Exchange of selected amino acids gave rise to OhyA variants which showed up to an 18-fold improved conversion of OA derivatives, while retaining the excellent regio- and stereoselectivity in the olefin hydration reaction.
Collapse
Affiliation(s)
- Matthias Engleder
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
| | - Gernot A. Strohmeier
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Institute of Organic ChemistryGraz University of Technology, NAWI GrazStremayrgasse 98010GrazAustria
| | - Hansjörg Weber
- Institute of Organic ChemistryGraz University of Technology, NAWI GrazStremayrgasse 98010GrazAustria
| | - Georg Steinkellner
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Innophore GmbHAm Eisernen Tor 38010GrazAustria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food ChemistryGraz University of Technology, NAWI GrazStremayrgasse 98010GrazAustria
| | - Monika Müller
- InnoSyn B.V.Urmonderbaan 226167 RDGeleenThe Netherlands
| | - Daniel Mink
- InnoSyn B.V.Urmonderbaan 226167 RDGeleenThe Netherlands
| | | | - Karl Gruber
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Institute of Molecular BiosciencesUniversity of Graz, NAWI Graz, BioTechMed GrazHumboldtstrasse 508010GrazAustria
| | - Harald Pichler
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI Graz, BioTechMed GrazPetersgasse 148010GrazAustria
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
| |
Collapse
|
21
|
Alonso-Cotchico L, Sciortino G, Vidossich P, Rodríguez-Guerra Pedregal J, Drienovská I, Roelfes G, Lledós A, Maréchal JD. Integrated Computational Study of the Cu-Catalyzed Hydration of Alkenes in Water Solvent and into the Context of an Artificial Metallohydratase. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Pietro Vidossich
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
- COBO Computational Bio-Organic Chemistry Bogotá, Department of Chemistry, Universidad de los Andes, Carrera 1 N° 18A 10, Bogotá 111711, Colombia
| | | | - Ivana Drienovská
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Agusti Lledós
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
| |
Collapse
|
22
|
Yum JH, Park S, Hiraga R, Okamura I, Notsu S, Sugiyama H. Modular DNA-based hybrid catalysts as a toolbox for enantioselective hydration of α,β-unsaturated ketones. Org Biomol Chem 2019; 17:2548-2553. [PMID: 30762058 DOI: 10.1039/c9ob00196d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The direct addition of water to a carbon-carbon double bond remains a challenge, but such a reaction is essential for the development of efficient catalysts that enable direct access to chiral alcohols. We now report on the enantioselective hydration of α,β-unsaturated ketones, catalyzed by modular DNA-based hybrid catalysts, affording β-hydroxy ketones with up to 87% enantiomeric excess. Oligonucleotides containing an intrastrand bipyridine ligand were readily synthesized by a straightforward process using an automated solid-phase synthesis. A library of DNA-based hybrid catalysts could be systematically generated based on the composition of nucleobases, and the incorporation of a binding ligand and a nonbinding steric moiety. This study demonstrates the potential of modular DNA-based hybrid catalysts as a toolbox to accomplish the challenging enantioselective hydration reaction.
Collapse
Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | | | | | | | | | | |
Collapse
|
23
|
Abstract
![]()
The biotechnological revolution has made it
possible to create
enzymes for many reactions by directed evolution. However, because
of the immense number of possibilities, the availability of enzymes
that possess a basal level of the desired catalytic activity is a
prerequisite for success. For new-to-nature reactions, artificial
metalloenzymes (ARMs), which are rationally designed hybrids of proteins
and catalytically active transition-metal complexes, can be such a
starting point. This Account details our efforts toward the
creation of ARMs for
the catalysis of new-to-nature reactions. Key to our approach is the
notion that the binding of substrates, that is, effective molarity,
is a key component to achieving large accelerations in catalysis.
For this reason, our designs are based on the multidrug resistance
regulator LmrR, a dimeric transcription factor with a large, hydrophobic
binding pocket at its dimer interface. In this pocket, there are two
tryptophan moieties, which are important for promiscuous binding of
planar hydrophobic conjugated compounds by π-stacking. The catalytic
machinery is introduced either by the covalent linkage of a catalytically
active metal complex or via the ligand or supramolecular assembly,
taking advantage of the two central tryptophan moieties for noncovalent
binding of transition-metal complexes. Designs based on the
chemical modification of LmrR were successful
in catalysis, but this approach proved too laborious to be practical.
Therefore, expanded genetic code methodologies were used to introduce
metal binding unnatural amino acids during LmrR biosynthesis in vivo.
These ARMs have been successfully applied in Cu(II) catalyzed Friedel–Crafts
alkylation of indoles. The extension to MDRs from the TetR family
resulted in ARMs capable of providing the opposite enantiomer of the
Friedel–Crafts product. We have employed a computationally
assisted redesign of these ARMs to create a more active and selective
artificial hydratase, introducing a glutamate as a general base at
a judicious position so it can activate and direct the incoming water
nucleophile. A supramolecularly assembled ARM from LmrR and
copper(II)–phenanthroline
was successful in Friedel–Crafts alkylation reactions, giving
rise to up to 94% ee. Also, hemin was bound, resulting in an artificial
heme enzyme for enantioselective cyclopropanation reactions. The importance
of structural dynamics of LmrR was suggested by computational studies,
which showed that the pore can open up to allow access of substrates
to the catalytic iron center, which, according to the crystal structure,
is deeply buried inside the protein. Finally, the assembly approaches
were combined to introduce both
a catalytic and a regulatory domain, resulting in an ARM that was
specifically activated in the presence of Fe(II) salts but not Zn(II)
salts. Our work demonstrates that LmrR is a privileged scaffold
for ARM
design: It allows for multiple assembly methods and even combinations
of these, it can be applied in a variety of different catalytic reactions,
and it shows significant structural dynamics that contribute to achieving
the desired catalytic activity. Moreover, both the creation via expanded
genetic code methods as well as the supramolecular assembly make LmrR-based
ARMs highly suitable for achieving the ultimate goal of the integration
of ARMs in biosynthetic pathways in vivo to create a hybrid metabolism.
Collapse
Affiliation(s)
- Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
24
|
Wu S, Zhou Y, Li Z. Biocatalytic selective functionalisation of alkenes via single-step and one-pot multi-step reactions. Chem Commun (Camb) 2019; 55:883-896. [PMID: 30566124 DOI: 10.1039/c8cc07828a] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alkenes are excellent starting materials for organic synthesis due to the versatile reactivity of C[double bond, length as m-dash]C bonds and the easy availability of many unfunctionalised alkenes. Direct regio- and/or enantioselective conversion of alkenes into functionalised (chiral) compounds has enormous potential for industrial applications, and thus has attracted the attention of researchers for extensive development using chemo-catalysis over the past few years. On the other hand, many enzymes have also been employed for conversion of alkenes in a highly selective and much greener manner to offer valuable products. Herein, we review recent advances in seven well-known types of biocatalytic conversion of alkenes. Remarkably, recent mechanism-guided directed evolution and enzyme cascades have enabled the development of seven novel types of single-step and one-pot multi-step functionalisation of alkenes, some of which are even unattainable via chemo-catalysis. These new reactions are particularly highlighted in this feature article. Overall, we present an ever-expanding enzyme toolbox for various alkene functionalisations inspiring further research in this fast-developing theme.
Collapse
Affiliation(s)
- Shuke Wu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585.
| | | | | |
Collapse
|
25
|
Chen BS, Ribeiro de Souza FZ. Enzymatic synthesis of enantiopure alcohols: current state and perspectives. RSC Adv 2019; 9:2102-2115. [PMID: 35516160 PMCID: PMC9059855 DOI: 10.1039/c8ra09004a] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Enantiomerically pure alcohols, as key intermediates, play an essential role in the pharmaceutical, agrochemical and chemical industries. Among the methods used for their production, biotechnological approaches are generally considered a green and effective alternative due to their mild reaction conditions and remarkable enantioselectivity. An increasing number of enzymatic strategies for the synthesis of these compounds has been developed over the years, among which seven primary methodologies can be distinguished as follows: (1) enantioselective water addition to alkenes, (2) enantioselective aldol addition, (3) enantioselective coupling of ketones with hydrogen cyanide, (4) asymmetric reduction of carbonyl compounds, (5) (dynamic) kinetic resolution of racemates, (6) enantioselective hydrolysis of epoxides, and (7) stereoselective hydroxylation of unactivated C-H bonds. Some recent reviews have examined these approaches separately; however, to date, no review has included all the above mentioned strategies. The aim of this mini-review is to provide an overview of all seven enzymatic strategies and draw conclusions on the effect of each approach.
Collapse
Affiliation(s)
- Bi-Shuang Chen
- School of Marine Sciences, Sun Yat-Sen University Guangzhou 510275 China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-Sen University Guangzhou 510275 China
| | | |
Collapse
|
26
|
Demming RM, Hammer SC, Nestl BM, Gergel S, Fademrecht S, Pleiss J, Hauer B. Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes. Angew Chem Int Ed Engl 2019; 58:173-177. [PMID: 30256501 PMCID: PMC6471033 DOI: 10.1002/anie.201810005] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Indexed: 11/30/2022]
Abstract
The direct enantioselective addition of water to unactivated alkenes could simplify the synthesis of chiral alcohols and solve a long-standing challenge in catalysis. Here we report that an engineered fatty acid hydratase can catalyze the asymmetric hydration of various terminal and internal alkenes. In the presence of a carboxylic acid decoy molecule for activation of the oleate hydratase from E. meningoseptica, asymmetric hydration of unactivated alkenes was achieved with up to 93 % conversion, excellent selectivity (>99 % ee, >95 % regioselectivity), and on a preparative scale.
Collapse
Affiliation(s)
- Rebecca M. Demming
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Stephan C. Hammer
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Bettina M. Nestl
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Sebastian Gergel
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| |
Collapse
|
27
|
Demming RM, Hammer SC, Nestl BM, Gergel S, Fademrecht S, Pleiss J, Hauer B. Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rebecca M. Demming
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Stephan C. Hammer
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bettina M. Nestl
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sebastian Gergel
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry; Department of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
28
|
Yun JJ, Liu XY, Deng W, Chu XQ, Shen ZL, Loh TP. Chromium(III)-Catalyzed Addition of Water and Alcohol to α,β-Unsaturated Ketones for the Synthesis of β-Hydroxyl and β-Alkoxyl Ketones in Aqueous Media. J Org Chem 2018; 83:10898-10907. [DOI: 10.1021/acs.joc.8b01584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jin-Jin Yun
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Xuan-Yu Liu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Wei Deng
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Xue-Qiang Chu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Zhi-Liang Shen
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Teck-Peng Loh
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| |
Collapse
|
29
|
Zheng K, Liu X, Feng X. Recent Advances in Metal-Catalyzed Asymmetric 1,4-Conjugate Addition (ACA) of Nonorganometallic Nucleophiles. Chem Rev 2018; 118:7586-7656. [PMID: 30047721 DOI: 10.1021/acs.chemrev.7b00692] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The metal-catalyzed asymmetric conjugate addition (ACA) reaction has emerged as a general and powerful approach for the construction of optically active compounds and is among the most significant and useful reactions in synthetic organic chemistry. In recent years, great progress has been made in this area with the use of various chiral metal complexes based on different chiral ligands. This review provides comprehensive and critical information on the enantioselective 1,4-conjugate addition of nonorganometallic (soft) nucleophiles and their importance in synthetic applications. The literature is covered from the last 10 years, and a number of examples from before 2007 are included as background information. The review is divided into multiple parts according to the type of nucleophile involved in the reaction (such as C-, B-, O-, N-, S-, P-, and Si-centered nucleophiles) and metal catalyst systems used.
Collapse
Affiliation(s)
- Ke Zheng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Xiaohua Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Xiaoming Feng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| |
Collapse
|
30
|
Engleder M, Pichler H. On the current role of hydratases in biocatalysis. Appl Microbiol Biotechnol 2018; 102:5841-5858. [PMID: 29785499 PMCID: PMC6013536 DOI: 10.1007/s00253-018-9065-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 11/06/2022]
Abstract
Water addition to carbon-carbon double bonds provides access to value-added products from inexpensive organic feedstock. This interesting but relatively little-studied reaction is catalysed by hydratases in a highly regio- and enantiospecific fashion with excellent atom economy. Considering that asymmetric hydration of (non-activated) carbon-carbon double bonds is virtually impossible with current organic chemistry, enzymatic hydration reactions are highly attractive for industrial applications. Hydratases have been known for several decades but their biocatalytic potential has only been explored over the past 15 years. As a result, a considerable amount of information on this enzyme group has become available, enabling their development for practical applications. This review focuses on hydratases catalysing water addition to non-activated carbon-carbon double bonds, and examines hydratases from a biochemical, structural and mechanistic angle. Current challenges and opportunities in hydration biocatalysis are discussed, and, ultimately, their potential for organic synthesis is highlighted.
Collapse
Affiliation(s)
- Matthias Engleder
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 8010, Graz, Austria.
| |
Collapse
|
31
|
Yun J, Zhi M, Shi W, Chu X, Shen Z, Loh T. Indium(III)‐Catalyzed Hydration and Hydroalkoxylation of α,β‐Unsaturated Ketones in Aqueous Media. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800301] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jin‐Jin Yun
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 People's Republic of China
| | - Man‐Ling Zhi
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 People's Republic of China
| | - Wen‐Xiao Shi
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 People's Republic of China
| | - Xue‐Qiang Chu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 People's Republic of China
| | - Zhi‐Liang Shen
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 People's Republic of China
| | - Teck‐Peng Loh
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 People's Republic of China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| |
Collapse
|
32
|
Engleder M, Horvat M, Emmerstorfer-Augustin A, Wriessnegger T, Gabriel S, Strohmeier G, Weber H, Müller M, Kaluzna I, Mink D, Schürmann M, Pichler H. Recombinant expression, purification and biochemical characterization of kievitone hydratase from Nectria haematococca. PLoS One 2018; 13:e0192653. [PMID: 29420618 PMCID: PMC5805349 DOI: 10.1371/journal.pone.0192653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/26/2018] [Indexed: 01/29/2023] Open
Abstract
Kievitone hydratase catalyzes the addition of water to the double bond of the prenyl moiety of plant isoflavonoid kievitone and, thereby, forms the tertiary alcohol hydroxy-kievitone. In nature, this conversion is associated with a defense mechanism of fungal pathogens against phytoalexins generated by host plants after infection. As of today, a gene sequence coding for kievitone hydratase activity has only been identified and characterized in Fusarium solani f. sp. phaseoli. Here, we report on the identification of a putative kievitone hydratase sequence in Nectria haematococca (NhKHS), the teleomorph state of F. solani, based on in silico sequence analyses. After heterologous expression of the enzyme in the methylotrophic yeast Pichia pastoris, we have confirmed its kievitone hydration activity and have assessed its biochemical properties and substrate specificity. Purified recombinant NhKHS is obviously a homodimeric glycoprotein. Due to its good activity for the readily available chalcone derivative xanthohumol (XN), this compound was selected as a model substrate for biochemical studies. The optimal pH and temperature for hydratase activity were 6.0 and 35°C, respectively, and apparent Vmax and Km values for hydration of XN were 7.16 μmol min-1 mg-1 and 0.98 ± 0.13 mM, respectively. Due to its catalytic properties and apparent substrate promiscuity, NhKHS is a promising enzyme for the biocatalytic production of tertiary alcohols.
Collapse
Affiliation(s)
- Matthias Engleder
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Graz, Austria
| | - Melissa Horvat
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Graz, Austria
| | | | | | - Stefanie Gabriel
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Graz, Austria
| | - Gernot Strohmeier
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Monika Müller
- DSM Ahead R&D—Innovative Synthesis, Geleen, The Netherlands
| | - Iwona Kaluzna
- DSM Ahead R&D—Innovative Synthesis, Geleen, The Netherlands
| | - Daniel Mink
- DSM Ahead R&D—Innovative Synthesis, Geleen, The Netherlands
| | | | - Harald Pichler
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Graz, Austria
- * E-mail:
| |
Collapse
|
33
|
Lorenzen J, Driller R, Waldow A, Qoura F, Loll B, Brück T. Rhodococcus erythropolis
Oleate Hydratase: a New Member in the Oleate Hydratase Family Tree-Biochemical and Structural Studies. ChemCatChem 2017. [DOI: 10.1002/cctc.201701350] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jan Lorenzen
- Professorship for Industrial Biocatalysis; Technical University Munich; Lichtenberg Str. 4 85748 Garching Germany
| | - Ronja Driller
- Institute of Chemistry and Biochemistry; Structural Biochemistry; Freie Universität Berlin; Takustr. 6 14195 Berlin Germany
| | - Ayk Waldow
- Institute of Chemistry and Biochemistry; Structural Biochemistry; Freie Universität Berlin; Takustr. 6 14195 Berlin Germany
| | - Farah Qoura
- Professorship for Industrial Biocatalysis; Technical University Munich; Lichtenberg Str. 4 85748 Garching Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry; Structural Biochemistry; Freie Universität Berlin; Takustr. 6 14195 Berlin Germany
- moloX GmbH; Takustr. 6 14195 Berlin Germany
| | - Thomas Brück
- Professorship for Industrial Biocatalysis; Technical University Munich; Lichtenberg Str. 4 85748 Garching Germany
| |
Collapse
|
34
|
Drienovská I, Alonso-Cotchico L, Vidossich P, Lledós A, Maréchal JD, Roelfes G. Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid. Chem Sci 2017; 8:7228-7235. [PMID: 29081955 PMCID: PMC5633786 DOI: 10.1039/c7sc03477f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023] Open
Abstract
The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the in vivo incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-defined metal-binding site. Here, we report a designed artificial metallohydratase, based on the transcriptional repressor lactococcal multidrug resistance regulator (LmrR), in which the non-canonical amino acid (2,2'-bipyridin-5yl)alanine is used to bind the catalytic Cu(ii) ion. Starting from a set of empirical pre-conditions, a combination of cluster model calculations (QM), protein-ligand docking and molecular dynamics simulations was used to propose metallohydratase variants, that were experimentally verified. The agreement observed between the computationally predicted and experimentally observed catalysis results demonstrates the power of the artificial metalloenzyme design approach presented here.
Collapse
Affiliation(s)
- Ivana Drienovská
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
| | - Lur Alonso-Cotchico
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Pietro Vidossich
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Agustí Lledós
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Jean-Didier Maréchal
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Gerard Roelfes
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
| |
Collapse
|
35
|
Wu S, Liu J, Li Z. Biocatalytic Formal Anti-Markovnikov Hydroamination and Hydration of Aryl Alkenes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01464] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Shuke Wu
- Department of Chemical
and
Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Ji Liu
- Department of Chemical
and
Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical
and
Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| |
Collapse
|
36
|
Payer SE, Sheng X, Pollak H, Wuensch C, Steinkellner G, Himo F, Glueck SM, Faber K. Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene. Adv Synth Catal 2017; 359:2066-2075. [PMID: 28713228 PMCID: PMC5488193 DOI: 10.1002/adsc.201700247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Indexed: 01/29/2023]
Abstract
The catalytic promiscuity of a ferulic acid decarboxylase from Enterobacter sp. (FDC_Es) and phenolic acid decarboxylases (PADs) for the asymmetric conjugate addition of water across the C=C bond of hydroxystyrenes was extended to the N‐, C‐ and S‐nucleophiles methoxyamine, cyanide and propanethiol to furnish the corresponding addition products in up to 91% ee. The products obtained from the biotransformation employing the most suitable enzyme/nucleophile pairs were isolated and characterized after optimizing the reaction conditions. Finally, a mechanistic rationale supported by quantum mechanical calculations for the highly (S)‐selective addition of cyanide is proposed. ![]()
Collapse
Affiliation(s)
- Stefan E Payer
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Xiang Sheng
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Hannah Pollak
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Christiane Wuensch
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Center for Molecular Biosciences University of Graz Humboldtstrasse 508010 Graz Austria
| | - Fahmi Himo
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Kurt Faber
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| |
Collapse
|
37
|
Ferro I, Chelysheva I, Ignatova Z. Competition for amino acid flux among translation, growth and detoxification in bacteria. RNA Biol 2017; 15:991-994. [PMID: 28296576 DOI: 10.1080/15476286.2017.1306174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Transfer-tRNAs (tRNAs) are central entities for translation that deliver amino acids to the ribosome to translate genetic information in an mRNA-template dependent manner. Recent discoveries from our laboratory show that in E. coli and B. licheniformis, some tRNAs are poorly charged despite the plentiful intracellular cognate amino acid. Specifically, tRNAs carrying amino acids that exert toxicity and inhibit bacterial growth when added separately to the growth medium are poorly charged. Here, we discuss various evolutionary strategies different bacterial cells have adopted to precisely hone the competition between amino acid utilization for translation and proliferation and combat the inhibitory effect toward maximizing bacterial fitness. These data add a new twist to the amino acid flux models and to our understanding of the complex intimate link between dynamics of translation and bacterial growth.
Collapse
Affiliation(s)
- Iolanda Ferro
- a Institute of Biochemistry and Molecular Biology, University of Hamburg , Germany
| | - Irina Chelysheva
- a Institute of Biochemistry and Molecular Biology, University of Hamburg , Germany
| | - Zoya Ignatova
- a Institute of Biochemistry and Molecular Biology, University of Hamburg , Germany
| |
Collapse
|
38
|
Otte KB, Maurer E, Kirtz M, Grabs D, Althoff E, Bartsch S, Vogel A, Nestl BM, Hauer B. Synthesis of Sebacic Acid Using a De Novo Designed Retro-Aldolase as a Key Catalyst. ChemCatChem 2017. [DOI: 10.1002/cctc.201601551] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Konrad B. Otte
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Elena Maurer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Marko Kirtz
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | | | | | | | - Andreas Vogel
- c-LEcta GmbH; Perlickstrasse 5 04103 Leipzig Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
39
|
Demming RM, Otte KB, Nestl BM, Hauer B. Optimized Reaction Conditions Enable the Hydration of Non-natural Substrates by the Oleate Hydratase fromElizabethkingia meningoseptica. ChemCatChem 2017. [DOI: 10.1002/cctc.201601329] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Rebecca M. Demming
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Konrad B. Otte
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
40
|
Structural and functional insights into asymmetric enzymatic dehydration of alkenols. Nat Chem Biol 2017; 13:275-281. [DOI: 10.1038/nchembio.2271] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 11/03/2016] [Indexed: 11/08/2022]
|
41
|
Schmid J, Steiner L, Fademrecht S, Pleiss J, Otte KB, Hauer B. Biocatalytic study of novel oleate hydratases. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
42
|
Wu S, Zhou Y, Wang T, Too HP, Wang DIC, Li Z. Highly regio- and enantioselective multiple oxy- and amino-functionalizations of alkenes by modular cascade biocatalysis. Nat Commun 2016; 7:11917. [PMID: 27297777 PMCID: PMC4911676 DOI: 10.1038/ncomms11917] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 05/12/2016] [Indexed: 12/24/2022] Open
Abstract
New types of asymmetric functionalizations of alkenes are highly desirable for chemical synthesis. Here, we develop three novel types of regio- and enantioselective multiple oxy- and amino-functionalizations of terminal alkenes via cascade biocatalysis to produce chiral α-hydroxy acids, 1,2-amino alcohols and α-amino acids, respectively. Basic enzyme modules 1–4 are developed to convert alkenes to (S)-1,2-diols, (S)-1,2-diols to (S)-α-hydroxyacids, (S)-1,2-diols to (S)-aminoalcohols and (S)-α-hydroxyacids to (S)-α-aminoacids, respectively. Engineering of enzyme modules 1 & 2, 1 & 3 and 1, 2 & 4 in Escherichia coli affords three biocatalysts over-expressing 4–8 enzymes for one-pot conversion of styrenes to the corresponding (S)-α-hydroxyacids, (S)-aminoalcohols and (S)-α-aminoacids in high e.e. and high yields, respectively. The new types of asymmetric alkene functionalizations provide green, safe and useful alternatives to the chemical syntheses of these compounds. The modular approach for engineering multi-step cascade biocatalysis is useful for developing other new types of one-pot biotransformations for chemical synthesis. Biocatalysis can perform highly selective multi-step synthesis in one pot, but with a limited range of non-natural reactions and products. Here, the authors report regio- and enantioselective bio-cascades, able to convert styrenes into a number of nitrogen and oxygen containing chiral molecules.
Collapse
Affiliation(s)
- Shuke Wu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.,Singapore-MIT Alliance, National University of Singapore, Singapore 117583, Singapore.,Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Yi Zhou
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Tianwen Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Heng-Phon Too
- Singapore-MIT Alliance, National University of Singapore, Singapore 117583, Singapore
| | - Daniel I C Wang
- Singapore-MIT Alliance, National University of Singapore, Singapore 117583, Singapore.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.,Singapore-MIT Alliance, National University of Singapore, Singapore 117583, Singapore.,Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| |
Collapse
|
43
|
Hiseni A, Otten LG, Arends IWCE. Identification of catalytically important residues of the carotenoid 1,2-hydratases from Rubrivivax gelatinosus and Thiocapsa roseopersicina. Appl Microbiol Biotechnol 2016; 100:1275-1284. [PMID: 26481619 PMCID: PMC4717167 DOI: 10.1007/s00253-015-6998-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/01/2015] [Accepted: 09/10/2015] [Indexed: 11/05/2022]
Abstract
Carotenoid 1,2-hydratases (CrtC) catalyze the selective addition of water to an isolated carbon-carbon double bond. Although their involvement in the carotenoid biosynthetic pathway is well understood, little is known about the mechanism by which these hydratases transform carotenoids such as lycopene into the corresponding hydroxyl compounds. Key residues were identified at positions His239, Trp241, Tyr266, and Asp268 in CrtC from Rubrivivax gelatinosus (and corresponding positions in Thiocapsa roseopersicina). Alanine mutants at these positions were found to be completely inactive, suggesting their direct involvement in the catalytic reaction. Our resulting mechanistic hypothesis is in analogy with the recently studied class of terpenoid cyclase enzymes containing a highly acidic aspartic residue in their active site. We propose that a similar aspartic acid residue, which is conserved through all putative CrtCs, is involved in initial protonation of the double bond in lycopene.
Collapse
Affiliation(s)
- Aida Hiseni
- Biocatalysis Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Linda G Otten
- Biocatalysis Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Isabel W C E Arends
- Biocatalysis Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
| |
Collapse
|
44
|
Khrimian A, Shirali S, Guzman F. Absolute Configurations of Zingiberenols Isolated from Ginger (Zingiber officinale) Rhizomes. JOURNAL OF NATURAL PRODUCTS 2015; 78:3071-4. [PMID: 26606508 DOI: 10.1021/acs.jnatprod.5b00638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Two stereoisomeric zingiberenols in ginger were identified as (3R,6R,7S)-1,10-bisaboladien-3-ol (2) and (3S,6R,7S)-1,10-bisaboladien-3-ol (5). Absolute configurations were assigned by utilizing 1,10-bisaboladien-3-ol stereoisomers and two gas-chromatography columns: a 25 m Hydrodex-β-6TBDM and 60 m DB-5MS. The C-6 and C-7 absolute configurations in both zingiberenols match those of zingiberene present abundantly in ginger rhizomes. Interestingly, zingiberenol 2 has recently been identified as a male-produced sex pheromone of the rice stink bug, Oebalus poecilus, thus indicating that ginger plants may be a potential source of the sex pheromone of this bug.
Collapse
Affiliation(s)
- Ashot Khrimian
- Invasive Insect Biocontrol and Behavior Laboratory, U.S. Department of Agriculture, Agricultural Research Service , Northeast Area, Bldg 007, Rm 301, BARC-West, 10300 Baltimore Avenue, Beltsville, Maryland 20705, United States
| | - Shyam Shirali
- Invasive Insect Biocontrol and Behavior Laboratory, U.S. Department of Agriculture, Agricultural Research Service , Northeast Area, Bldg 007, Rm 301, BARC-West, 10300 Baltimore Avenue, Beltsville, Maryland 20705, United States
| | - Filadelfo Guzman
- Invasive Insect Biocontrol and Behavior Laboratory, U.S. Department of Agriculture, Agricultural Research Service , Northeast Area, Bldg 007, Rm 301, BARC-West, 10300 Baltimore Avenue, Beltsville, Maryland 20705, United States
| |
Collapse
|
45
|
Sato H, Hummel W, Gröger H. Cooperative Catalysis of Noncompatible Catalysts through Compartmentalization: Wacker Oxidation and Enzymatic Reduction in a One-Pot Process in Aqueous Media. Angew Chem Int Ed Engl 2015; 54:4488-92. [DOI: 10.1002/anie.201409590] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Indexed: 01/22/2023]
|
46
|
Sato H, Hummel W, Gröger H. Kooperative Katalyse nicht-kompatibler Katalysatoren durch Kompartimentierung: Wacker-Oxidation und enzymatische Reduktion in einem Eintopf-Verfahren im wässrigen Medium. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409590] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
47
|
Abstract
The enantioselective Michael addition using water as both nucleophile and solvent has to date proved beyond the ability of synthetic chemists. Herein, the direct, enantioselective Michael addition of water in water to prepare important β-hydroxy carbonyl compounds using whole cells of Rhodococcus strains is described. Good yields and excellent enantioselectivities were achieved with this method. Deuterium labeling studies demonstrate that a Michael hydratase catalyzes the water addition exclusively with anti-stereochemistry.
Collapse
Affiliation(s)
- Bi-Shuang Chen
- Technische Universiteit Delft, Gebouw voor Scheikunde, Afdeling BiotechnologieJulianalaan 136, 2628 BL Delft (Netherlands)
| | - Verena Resch
- Technische Universiteit Delft, Gebouw voor Scheikunde, Afdeling BiotechnologieJulianalaan 136, 2628 BL Delft (Netherlands)
- University of Graz, Organic and Bioorganic Chemistry, Institute of ChemistryHeinrichstrasse 28, 8010 Graz (Austria)
| | - Linda G Otten
- Technische Universiteit Delft, Gebouw voor Scheikunde, Afdeling BiotechnologieJulianalaan 136, 2628 BL Delft (Netherlands)
| | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Afdeling BiotechnologieJulianalaan 136, 2628 BL Delft (Netherlands)
| |
Collapse
|
48
|
Chen BS, Otten LG, Hanefeld U. Stereochemistry of enzymatic water addition to C=C bonds. Biotechnol Adv 2015; 33:526-46. [PMID: 25640045 DOI: 10.1016/j.biotechadv.2015.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 12/20/2022]
Abstract
Water addition to carbon-carbon double bonds using hydratases is attracting great interest in biochemistry. Most of the known hydratases are involved in primary metabolism and to a lesser extent in secondary metabolism. New hydratases have recently been added to the toolbox, both from natural sources or artificial metalloenzymes. In order to comprehensively understand how the hydratases are able to catalyse the water addition to carbon-carbon double bonds, this review will highlight the mechanistic and stereochemical studies of the enzymatic water addition to carbon-carbon double bonds, focusing on the syn/anti-addition and stereochemistry of the reaction.
Collapse
Affiliation(s)
- Bi-Shuang Chen
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Linda G Otten
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands.
| |
Collapse
|
49
|
Zhao Y, Yang Z, Yu B, Zhang H, Xu H, Hao L, Han B, Liu Z. Task-specific ionic liquid and CO 2-cocatalysed efficient hydration of propargylic alcohols to α-hydroxy ketones. Chem Sci 2015; 6:2297-2301. [PMID: 29308143 PMCID: PMC5645775 DOI: 10.1039/c5sc00040h] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/15/2015] [Indexed: 11/21/2022] Open
Abstract
The hydration of propargylic alcohols is a green route to synthesize α-hydroxy ketones. Herein a CO2-reactive ionic liquid (IL), [Bu4P][Im], was found to display high performance for catalyzing the hydration of propargylic alcohols in the presence of atmospheric CO2, and a series of propargylic alcohols could be converted into the corresponding α-hydroxy ketones in good to excellent yields. In the IL/CO2 reaction system, CO2 served as a cocatalyst by forming α-alkylidene cyclic carbonates with propargylic alcohols, and was released via the rapid hydrolysis of the carbonates catalysed by the IL. This is the first example of the efficient hydration of propargylic alcohols under metal-free conditions.
Collapse
Affiliation(s)
- Yanfei Zhao
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Zhenzhen Yang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Bo Yu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Hongye Zhang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Huanjun Xu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Leiduan Hao
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| | - Zhimin Liu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Colloid, Interface and Thermodynamics , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China .
| |
Collapse
|
50
|
Abstract
Water is omnipresent and unreactive. How to speed up water addition and even make it selective are highlighted in this perspective.
Collapse
Affiliation(s)
- Verena Resch
- Gebouw voor Scheikunde
- Biokatalyse
- Afdeling Biotechnologie
- Technische Universiteit Delft
- 2628BL Delft
| | - Ulf Hanefeld
- Gebouw voor Scheikunde
- Biokatalyse
- Afdeling Biotechnologie
- Technische Universiteit Delft
- 2628BL Delft
| |
Collapse
|