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Salvatti BA, Chagas MA, Fernandes PO, Ladeira YFX, Bozzi AS, Valadares VS, Valente AP, de Miranda AS, Rocha WR, Maltarollo VG, Moraes AH. Understanding the Enzyme ( S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. J Chem Inf Model 2024; 64:4462-4474. [PMID: 38776464 DOI: 10.1021/acs.jcim.3c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.
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Affiliation(s)
- Brunno A Salvatti
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Marcelo A Chagas
- Departamento de Ciências Exatas, Universidade do Estado de Minas Gerais, João Monlevade, Minas Gerais 35930-314, Brazil
| | - Phillipe O Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Yan F X Ladeira
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Aline S Bozzi
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Veronica S Valadares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Amanda S de Miranda
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Willian R Rocha
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinicius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
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Boukid F, Ganeshan S, Wang Y, Tülbek MÇ, Nickerson MT. Bioengineered Enzymes and Precision Fermentation in the Food Industry. Int J Mol Sci 2023; 24:10156. [PMID: 37373305 DOI: 10.3390/ijms241210156] [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: 05/20/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.
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Affiliation(s)
- Fatma Boukid
- ClonBio Group Ltd., 6 Fitzwilliam Pl, D02 XE61 Dublin, Ireland
| | | | - Yingxin Wang
- Saskatchewan Food Industry Development Centre, Saskatoon, SK S7M 5V1, Canada
| | | | - Michael T Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Li H, Qin F, Huang L, Jia W, Zhang M, Li X, Shu Z. Enzymatic synthesis of 2-phenethyl acetate in water catalyzed by an immobilized acyltransferase from Mycobacterium smegmatis. RSC Adv 2022; 12:2310-2318. [PMID: 35425272 PMCID: PMC8979223 DOI: 10.1039/d1ra07946h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/07/2022] [Indexed: 11/30/2022] Open
Abstract
Although water is an ideal green solvent for organic synthesis, it is difficult for most biocatalysts to carry out transesterification reactions in water because of the reversible hydrolysis reaction. 3D structural characteristics and the microenvironment of an enzyme has an important effect on its selectivity for the transesterification reaction over the hydrolysis reaction. A novel 2-phenethyl acetate synthesis technology was developed using acyltransferase (EC 3.1.1.2) from Mycobacterium smegmatis (MsAcT) in water. Firstly, MsAcT was entrapped in a tetramethoxysilane gel network and the immobilization process of MsAcT increased its selectivity for the transesterification reaction over the hydrolysis reaction by 6.33-fold. Then, the synthesis technology of 2-phenethyl acetate using the immobilized MsAcT in water was optimized as follows: vinyl acetate was used as acyl donor, the molar ratio of vinyl acetate to 2-phenylethyl alcohol was 2 : 1, and the water content was 80% (w/w). The reaction was carried out at 40 °C for 30 min and conversion rate reached 99.17%. The immobilized MsAcT could be recycled for 10 batches. The synthesis method of 2-phenethyl acetate using MsAcT as a biocatalyst in water is a prospective green process technology.
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Affiliation(s)
- Huan Li
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University Fuzhou 350117 China
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
| | - Feng Qin
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University Fuzhou 350117 China
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
| | - Lijuan Huang
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
| | - Wenjing Jia
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University Fuzhou 350117 China
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
| | - Mingliang Zhang
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University Fuzhou 350117 China
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
| | - Xin Li
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University Fuzhou 350117 China
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
| | - Zhengyu Shu
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University Fuzhou 350117 China
- College of Life Sciences, Fujian Normal University (Qishan Campus) Fuzhou 350117 China
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Ebensperger P, Jessen-Trefzer C. Artificial metalloenzymes in a nutshell: the quartet for efficient catalysis. Biol Chem 2021; 403:403-412. [PMID: 34653321 DOI: 10.1515/hsz-2021-0329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
Artificial metalloenzymes combine the inherent reactivity of transition metal catalysis with the sophisticated reaction control of natural enzymes. By providing new opportunities in bioorthogonal chemistry and biocatalysis, artificial metalloenzymes have the potential to overcome certain limitations in both drug discovery and green chemistry or related research fields. Ongoing advances in organometallic catalysis, directed evolution, and bioinformatics are enabling the design of increasingly powerful systems that outperform conventional catalysis in a growing number of cases. Therefore, this review article collects challenges and opportunities in designing artificial metalloenzymes described in recent review articles. This will provide an equitable insight for those new to and interested in the field.
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Affiliation(s)
- Paul Ebensperger
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
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Magnetically Agitated Nanoparticle-Based Batch Reactors for Biocatalysis with Immobilized Aspartate Ammonia-Lyase. Catalysts 2021. [DOI: 10.3390/catal11040483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this study, we investigated the influence of different modes of magnetic mixing on effective enzyme activity of aspartate ammonia-lyase from Pseudomonas fluorescens immobilized onto epoxy-functionalized magnetic nanoparticles by covalent binding (AAL-MNP). The effective specific enzyme activity of AAL-MNPs in traditional shake vial method was compared to the specific activity of the MNP-based biocatalyst in two devices designed for magnetic agitation. The first device agitated the AAL-MNPs by moving two permanent magnets at two opposite sides of a vial in x-axis direction (being perpendicular to the y-axis of the vial); the second device unsettled the MNP biocatalyst by rotating the two permanent magnets around the y-axis of the vial. In a traditional shake vial, the substrate and biocatalyst move in the same direction with the same pattern. In magnetic agitation modes, the MNPs responded differently to the external magnetic field of two permanent magnets. In the axial agitation mode, MNPs formed a moving cloud inside the vial, whereas in the rotating agitation mode, they formed a ring. Especially, the rotating agitation of the MNPs generated small fluid flow inside the vial enabling the mixing of the reaction mixture, leading to enhanced effective activity of AAL-MNPs compared to shake vial agitation.
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Sánta-Bell E, Molnár Z, Varga A, Nagy F, Hornyánszky G, Paizs C, Balogh-Weiser D, Poppe L. "Fishing and Hunting"-Selective Immobilization of a Recombinant Phenylalanine Ammonia-Lyase from Fermentation Media. Molecules 2019; 24:E4146. [PMID: 31731791 PMCID: PMC6891789 DOI: 10.3390/molecules24224146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
This article overviews the numerous immobilization methods available for various biocatalysts such as whole-cells, cell fragments, lysates or enzymes which do not require preliminary enzyme purification and introduces an advanced approach avoiding the costly and time consuming downstream processes required by immobilization of purified enzyme-based biocatalysts (such as enzyme purification by chromatographic methods and dialysis). Our approach is based on silica shell coated magnetic nanoparticles as solid carriers decorated with mixed functions having either coordinative binding ability (a metal ion complexed by a chelator anchored to the surface) or covalent bond-forming ability (an epoxide attached to the surface via a proper linker) enabling a single operation enrichment and immobilization of a recombinant phenylalanine ammonia-lyase from parsley fused to a polyhistidine affinity tag.
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Affiliation(s)
- Evelin Sánta-Bell
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1111 Budapest, Hungary; (E.S.-B.); (Z.M.); (F.N.); (G.H.)
| | - Zsófia Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1111 Budapest, Hungary; (E.S.-B.); (Z.M.); (F.N.); (G.H.)
- Fermentia Microbiological Ltd., 1405 Budapest, Hungary
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Science, 1117 Budapest, Hungary
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, 400028 Cluj-Napoca, Romania; (A.V.); (C.P.)
| | - Flóra Nagy
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1111 Budapest, Hungary; (E.S.-B.); (Z.M.); (F.N.); (G.H.)
| | - Gábor Hornyánszky
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1111 Budapest, Hungary; (E.S.-B.); (Z.M.); (F.N.); (G.H.)
- SynBiocat Ltd., 1172 Budapest, Hungary
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, 400028 Cluj-Napoca, Romania; (A.V.); (C.P.)
| | - Diána Balogh-Weiser
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1111 Budapest, Hungary; (E.S.-B.); (Z.M.); (F.N.); (G.H.)
- SynBiocat Ltd., 1172 Budapest, Hungary
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1111 Budapest, Hungary; (E.S.-B.); (Z.M.); (F.N.); (G.H.)
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, 400028 Cluj-Napoca, Romania; (A.V.); (C.P.)
- SynBiocat Ltd., 1172 Budapest, Hungary
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Abstract
Biocatalysis is the term used to describe the application of any type of biocatalyst (enzymes, as isolated preparations of wild-type or genetically modified variants, or whole cells, either as native cells or as recombinant expressed proteins inside host cells) in a given synthetic schedule [...]
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Petroll K, Kopp D, Care A, Bergquist PL, Sunna A. Tools and strategies for constructing cell-free enzyme pathways. Biotechnol Adv 2018; 37:91-108. [PMID: 30521853 DOI: 10.1016/j.biotechadv.2018.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/22/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Abstract
Single enzyme systems or engineered microbial hosts have been used for decades but the notion of assembling multiple enzymes into cell-free synthetic pathways is a relatively new development. The extensive possibilities that stem from this synthetic concept makes it a fast growing and potentially high impact field for biomanufacturing fine and platform chemicals, pharmaceuticals and biofuels. However, the translation of individual single enzymatic reactions into cell-free multi-enzyme pathways is not trivial. In reality, the kinetics of an enzyme pathway can be very inadequate and the production of multiple enzymes can impose a great burden on the economics of the process. We examine here strategies for designing synthetic pathways and draw attention to the requirements of substrates, enzymes and cofactor regeneration systems for improving the effectiveness and sustainability of cell-free biocatalysis. In addition, we comment on methods for the immobilisation of members of a multi-enzyme pathway to enhance the viability of the system. Finally, we focus on the recent development of integrative tools such as in silico pathway modelling and high throughput flux analysis with the aim of reinforcing their indispensable role in the future of cell-free biocatalytic pathways for biomanufacturing.
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Affiliation(s)
- Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Peter L Bergquist
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Department of Molecular Medicine & Pathology, University of Auckland, Auckland, New Zealand
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia.
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