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Du M, Liu J, Wang Q, Wang F, Bi L, Ma C, Song M, Jiang G. Immobilization of laccase on magnetic PEGDA-CS inverse opal hydrogel for enhancement of bisphenol A degradation in aqueous solution. J Environ Sci (China) 2025; 147:74-82. [PMID: 39003085 DOI: 10.1016/j.jes.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 07/15/2024]
Abstract
Endocrine disruptors such as bisphenol A (BPA) adversely affect the environment and human health. Laccases are used for the efficient biodegradation of various persistent organic pollutants in an environmentally safe manner. However, the direct application of free laccases is generally hindered by short enzyme lifetimes, non-reusability, and the high cost of a single use. In this study, laccases were immobilized on a novel magnetic three-dimensional poly(ethylene glycol) diacrylate (PEGDA)-chitosan (CS) inverse opal hydrogel (LAC@MPEGDA@CS@IOH). The immobilized laccase showed significant improvement in the BPA degradation performance and superior storage stability compared with the free laccase. 91.1% of 100 mg/L BPA was removed by the LAC@MPEGDA@CS@IOH in 3 hr, whereas only 50.6% of BPA was removed by the same amount of the free laccase. Compared with the laccase, the outstanding BPA degradation efficiency of the LAC@MPEGDA@CS@IOH was maintained over a wider range of pH values and temperatures. Moreover, its relative activity of was maintained at 70.4% after 10 cycles, and the system performed well in actual water matrices. This efficient method for preparing immobilized laccases is simple and green, and it can be used to further develop ecofriendly biocatalysts to remove organic pollutants from wastewater.
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Affiliation(s)
- Mei Du
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingzhang Liu
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiong Wang
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengbang Wang
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Bi
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyan Ma
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoyong Song
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guibin Jiang
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Zhang F, Liu L, Chen Y, Liu G, Eric Hu X, Wang N, Long B, Deng GJ, Song T. Photoselectively modulating main products by changing the wavelength of visible light over D-π-A-D conjugated polymers. J Colloid Interface Sci 2024; 670:676-686. [PMID: 38781656 DOI: 10.1016/j.jcis.2024.05.116] [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: 01/12/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
The diversity of catalytic products determines the difficulty of selective product modulation, which usually relies on adjusting the catalyst and reaction conditions to obtain different main products selectively. Herein, we synthesized D-π-A-D conjugated organic polymers (TH-COP) using cyclotriphosphonitrile, alkyne, 2H-benzimidazole, and sulfur units as electron donors, π bridges, electron acceptors, and electron donors, respectively. TH-COP exhibited excellent photoinduced carrier separation and redox ability under different visible light wavelengths, and the main products of its CO2 reduction are CH4 (1000.0 μmol g-1) and CO (837.0 μmol g-1) under 400-420 nm and 420-560 nm, respectively. In addition, TH-COP could completely convert phenylmethyl sulfide to methyl phenyl sulfone at 400-420 nm and diphenyl disulfide at 480-485 nm in yields up to 95 %. This study presents a novel strategy for the targeted fabrication of various main products using conjugated polymers by simply changing the wavelength range of visible light.
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Affiliation(s)
- Fengxuan Zhang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Linyi Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Yizheng Chen
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, PR China
| | - Guanhui Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Xiayi Eric Hu
- College of Chemical Engineering, Xiangtan University, Xiangtan, 411105, PR China
| | - Nailiang Wang
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan, Ningxia 750021, PR China
| | - Bei Long
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Guo-Jun Deng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, PR China; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, PR China
| | - Ting Song
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, PR China.
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3
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Li Z, Wang Q, Wang Y, Chen J, Lei X, Jiu R, Liu H, Bai T, Liu J. Degradation of Di (2-ethylhexyl) phthalic acid plasticizer in baijiu by a foam titanium flow reactor attached with hairpin-like structured peptide enzyme mimics. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134596. [PMID: 38820744 DOI: 10.1016/j.jhazmat.2024.134596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/02/2024]
Abstract
Because of the significant environmental and health hazards imposed by di(2-ethylhexyl) phthalate (DEHP), a common plasticizer, developing safe and green techniques to degrade DEHP plasticizer is of huge scientific significance. It has been observed that environmental contamination of DEHP may also induce serious food safety problems because crops raised in plasticizers contaminated soils would transfer the plasticizer into foods, such as Baijiu. Additionally, when plastic packaging or vessels are used during Baijiu fermentation and processing, plasticizer compounds frequently migrate and contaminate the product. In this study, hairpin-like structured peptides with catalytically active sites containing serine, histidine and aspartic acid were found to degrade DEHP. Furthermore, after incorporating caffeic acid molecules at the N-terminus, the peptides could be attached onto foam titanium (Ti) surfaces via enediol-metal interactions to create an enzyme-mimicking flow reactor for the degradation of DEHP in Baijiu. The structure and catalytic activity of peptides, their interaction with DEHP substrate and the hydrolysis mechanism of DEHP were discussed in this work. The stability and reusability of the peptide-modified foam Ti flow reactor were also investigated. This approach provides an effective technique for the degradation of plasticizer compounds.
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Affiliation(s)
- Zongda Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Qiuying Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yunyao Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jianan Chen
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xiangmin Lei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Ruiqing Jiu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Haochi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Tianhou Bai
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jifeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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4
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Korica M, Mihajlovski K, Mohan T, Kostić M. Films based on TEMPO-oxidized chitosan nanoparticles: Obtaining and potential application as wound dressings. Carbohydr Res 2024; 542:109203. [PMID: 38964016 DOI: 10.1016/j.carres.2024.109203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/27/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
A series of novel films based on TEMPO-oxidized chitosan nanoparticles were prepared by casting method. Fourier transform infrared spectroscopy (FTIR) was employed to ascertain the chemical structure of TEMPO-oxidized chitosan. The surface morphology of the TEMPO-oxidized chitosan nanoparticles was analyzed by atomic force microscopy (AFM). The physicochemical (area density, thickness, iodine sorption, roughness), functional (moisture sorption, liquid absorption capacity, weight loss upon contact with the liquid, and water vapor transmission rate), antibacterial, and antioxidant properties of films based on TEMPO-oxidized chitosan nanoparticles were also investigated. The physicochemical properties of the films varied widely: area density ranged from 77.83 ± 0.06 to184.46 ± 0.05 mg/cm2, thickness varied between 80.5 ± 1.6 and 200.5 ± 1.6 μm, iodine sorption spanned from 333.7 ± 2.1 to166.4 ± 2.2 mg I2/g, and roughness ranged from 4.1 ± 0.2 to 5.6 ± 0.3 nm. Similarly, the functional properties also varied significantly: moisture sorption ranged from 4.76 ± 0.03 to 9.62 ± 0.11 %, liquid absorption capacity was between 129.04 ± 0.24 and 159.33 ± 0.73 % after 24 h, weight loss upon contact with the liquid varied between 31.06 ± 0.35 and 45.88 ± 0.58 % after 24 h and water vapor transmission rate ranged from 1220.10 ± 2.91to1407.77 ± 5.22 g/m2 day. Despite the wide variations in physicochemical and functional properties, all films showed maximum bacterial reduction of Staphylococcus aureus and Escherichia coli, although they exhibited low antioxidant activity. The results suggest that the films could be effectively utilized as antibacterial wound dressings.
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Affiliation(s)
- Matea Korica
- Innovation Center of Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11000, Belgrade, Serbia.
| | - Katarina Mihajlovski
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11000, Belgrade, Serbia.
| | - Tamilselvan Mohan
- Institute for Chemistry and Technology of Biobased System (IBioSys), Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria; Laboratory for Characterisation and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova ulica17, 2000, Maribor, Slovenia.
| | - Mirjana Kostić
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11000, Belgrade, Serbia.
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5
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Alishah Aratboni H, Martinez M, Olvera C, Ayala M. Thermostabilization of a fungal laccase by entrapment in enzymatically synthesized levan nanoparticles. PLoS One 2024; 19:e0304242. [PMID: 39024280 DOI: 10.1371/journal.pone.0304242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024] Open
Abstract
In this work, we present a comprehensive investigation of the entrapment of laccase, a biotechnologically relevant enzyme, into levan-based nanoparticles (LNPs). The entrapment of laccase was achieved concomitantly with the synthesis of LNP, catalyzed by a truncated version of a levansucrase from Leuconostoc mesenteroides. The study aimed to obtain a biocompatible nanomaterial, able to entrap functional laccase, and characterize its physicochemical, kinetic and thermal stability properties. The experimental findings demonstrated that a colloidal stable solution of spherically shaped LNP, with an average diameter of 68 nm, was obtained. An uniform particle size distribution was observed, according to the polydispersity index determined by DLS. When the LNPs synthesis was performed in the presence of laccase, biocatalytically active nanoparticles with a 1.25-fold larger diameter (85 nm) were obtained, and a maximum load of 243 μg laccase per g of nanoparticle was achieved. The catalytic efficiency was 972 and 103 (μM·min)-1, respectively, for free and entrapped laccase. A decrease in kcat values (from 7050 min-1 to 1823 min-1) and an increase in apparent Km (from 7.25 μM to 17.73 μM) was observed for entrapped laccase, compared to the free enzyme. The entrapped laccase exhibited improved thermal stability, retaining 40% activity after 1 h-incubation at 70°C, compared to complete inactivation of free laccase under the same conditions, thereby highlighting the potential of LNPs in preserving enzyme activity under elevated temperatures. The outcomes of this investigation significantly contribute to the field of nanobiotechnology by expanding the applications of laccase and presenting an innovative strategy for enhancing enzyme stability through the utilization of fructan-based nanoparticle entrapments.
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Affiliation(s)
- Hossein Alishah Aratboni
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico
| | - Maura Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico
| | - Clarita Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico
| | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico
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6
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Fansher DJ, Besna JN, Pelletier JN. Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation. Faraday Discuss 2024. [PMID: 38993060 DOI: 10.1039/d4fd00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified via their blue phenotype. Indigo (+) single variants, indigo (-) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified via colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.
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Affiliation(s)
- Douglas J Fansher
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
| | - Jonathan N Besna
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Joelle N Pelletier
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
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7
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Li Z, Lou M, Sun C, Li Z. Engineering a Robust UDP-Glucose Pyrophosphorylase for Enhanced Biocatalytic Synthesis via ProteinMPNN and Ancestral Sequence Reconstruction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15284-15292. [PMID: 38918953 DOI: 10.1021/acs.jafc.4c03126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
UDP-glucose is a key metabolite in carbohydrate metabolism and plays a vital role in glycosyl transfer reactions. Its significance spans across the food and agricultural industries. This study focuses on UDP-glucose synthesis via multienzyme catalysis using dextrin, incorporating UTP production and ATP regeneration modules to reduce costs. To address thermal stability limitations of the key UDP-glucose pyrophosphorylase (UGP), a deep learning-based protein sequence design approach and ancestral sequence reconstruction are employed to engineer a thermally stable UGP variant. The engineered UGP variant is significantly 500-fold more thermally stable at 60 °C and has a half-life of 49.8 h compared to the wild-type enzyme. MD simulations and umbrella sampling calculations provide insights into the mechanism behind the enhanced thermal stability. Experimental validation demonstrates that the engineered UGP variant can produce 52.6 mM UDP-glucose within 6 h in an in vitro cascade reaction. This study offers practical insights for efficient UDP-glucose synthesis methods.
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Affiliation(s)
- Zonglin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Miaozi Lou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chuanqi Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
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8
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Breausche F, Somerlot A, Walder J, Osei K, Okyem S, Driskell JD. Immobilization of Thiol-Modified Horseradish Peroxidase on Gold Nanoparticles Enhances Enzyme Stability and Prevents Proteolytic Digestion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:13957-13967. [PMID: 38919992 PMCID: PMC11238584 DOI: 10.1021/acs.langmuir.4c01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
The specificity and efficiency of enzyme-mediated reactions have the potential to positively impact many biotechnologies; however, many enzymes are easily degraded. Immobilization on a solid support has recently been explored to improve enzyme stability. This study aims to gain insights and facilitate enzyme adsorption onto gold nanoparticles (AuNPs) to form a stable bioconjugate through the installation of thiol functional groups that alter the protein chemistry. In specific, the model enzyme, horseradish peroxidase (HRP), is thiolated via Traut's reagent to increase the robustness and enzymatic activity of the bioconjugate. This study compares HRP and its thiolated analog (THRP) to deduce the impact of thiolation and AuNP-immobilization on the enzyme activity and stability. HRP, THRP, and their corresponding bioconjugates, HRP-AuNP and THRP-AuNP, were analyzed via UV-vis spectrophotometry, circular dichroism, zeta potential, and enzyme-substrate kinetics assays. Our data show a 5-fold greater adsorption for THRP on the AuNP, in comparison to HRP, that translated to a 5-fold increase in the THRP-AuNP bioconjugate activity. The thiolated and immobilized HRP exhibited a substantial improvement in stability at elevated temperatures (50 °C) and storage times (1 month) relative to the native enzyme in solution. Moreover, HRP, THRP, and their bioconjugates were incubated with trypsin to assess the susceptibility to proteolytic digestion. Our results demonstrate that THRP-AuNP bioconjugates maintain full enzymatic activity after 18 h of incubation with trypsin, whereas free HRP, free THRP, and HRP-AuNP conjugates are rendered inactive by trypsin treatment. These results highlight the potential for protein modification and immobilization to substantially extend enzyme shelf life, resist protease digestion, and enhance biological function to realize enzyme-enabled biotechnologies.
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Affiliation(s)
- Faith
E. Breausche
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790, United States
| | - Annelise Somerlot
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790, United States
| | - Jason Walder
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790, United States
| | - Kwame Osei
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790, United States
| | - Samuel Okyem
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jeremy D. Driskell
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790, United States
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9
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Tataruch M, Illeová V, Kluza A, Cabadaj P, Polakovič M. Catalytic Stability of S-1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from Aromatoleum aromaticum. Int J Mol Sci 2024; 25:7385. [PMID: 39000491 PMCID: PMC11242144 DOI: 10.3390/ijms25137385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Derived from the denitrifying bacterium Aromatoleum aromaticum EbN1 (Azoarcus sp.), the enzyme S-1-(4-hydroxyphenyl)-ethanol dehydrogenase (S-HPED) belongs to the short-chain dehydrogenase/reductase family. Using research techniques like UV-Vis spectroscopy, dynamic light scattering, thermal-shift assay and HPLC, we investigated the catalytic and structural stability of S-HPED over a wide temperature range and within the pH range of 5.5 to 9.0 under storage and reaction conditions. The relationship between aggregation and inactivation of the enzyme in various pH environments was also examined and interpreted. At pH 9.0, where the enzyme exhibited no aggregation, we characterized thermally induced enzyme inactivation. Through isothermal and multitemperature analysis of inactivation data, we identified and confirmed the first-order inactivation mechanism under these pH conditions and determined the kinetic parameters of the inactivation process. Additionally, we report the positive impact of glucose as an enzyme stabilizer, which slows down the dynamics of S-HPED inactivation over a wide range of pH and temperature and limits enzyme aggregation. Besides characterizing the stability of S-HPED, the enzyme's catalytic activity and high stereospecificity for 10 prochiral carbonyl compounds were positively verified, thus expanding the spectrum of substrates reduced by S-HPED. Our research contributes to advancing knowledge about the biocatalytic potential of this catalyst.
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Affiliation(s)
- Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland; (M.T.); (A.K.)
| | - Viera Illeová
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; (V.I.); (P.C.)
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland; (M.T.); (A.K.)
| | - Patrik Cabadaj
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; (V.I.); (P.C.)
| | - Milan Polakovič
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; (V.I.); (P.C.)
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10
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Bornscheuer UT. Concluding remarks: biocatalysis. Faraday Discuss 2024. [PMID: 38958033 DOI: 10.1039/d4fd00127c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Biocatalysis is a rapidly evolving field with increasing impact in organic synthesis, chemical manufacturing and medicine. The Faraday Discussion reflected the current state of biocatalysis, covering the design of de novo enzymatic activities, but especially methods for the improvement of enzymes targeting a broad range of applications (i.e., hydroxylations by P450 monooxygenases, enzymatic deprotection of organic compounds under mild conditions, synthesis of chiral intermediates, plastic degradation, silicone polymer synthesis, and peptide synthesis). Central themes have been how to improve an enzyme using methods of rational design and directed evolution, informed by computer modelling and machine learning, and the incorporation of new catalytic functionalities to create hybrid and artificial enzymes.
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Affiliation(s)
- Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany.
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11
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Zhou Z, Zhang L, Yu Y, Wu B, Li M, Hong L, Tan P. Enhancing efficiency of protein language models with minimal wet-lab data through few-shot learning. Nat Commun 2024; 15:5566. [PMID: 38956442 PMCID: PMC11219809 DOI: 10.1038/s41467-024-49798-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/11/2024] [Indexed: 07/04/2024] Open
Abstract
Accurately modeling the protein fitness landscapes holds great importance for protein engineering. Pre-trained protein language models have achieved state-of-the-art performance in predicting protein fitness without wet-lab experimental data, but their accuracy and interpretability remain limited. On the other hand, traditional supervised deep learning models require abundant labeled training examples for performance improvements, posing a practical barrier. In this work, we introduce FSFP, a training strategy that can effectively optimize protein language models under extreme data scarcity for fitness prediction. By combining meta-transfer learning, learning to rank, and parameter-efficient fine-tuning, FSFP can significantly boost the performance of various protein language models using merely tens of labeled single-site mutants from the target protein. In silico benchmarks across 87 deep mutational scanning datasets demonstrate FSFP's superiority over both unsupervised and supervised baselines. Furthermore, we successfully apply FSFP to engineer the Phi29 DNA polymerase through wet-lab experiments, achieving a 25% increase in the positive rate. These results underscore the potential of our approach in aiding AI-guided protein engineering.
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Affiliation(s)
- Ziyi Zhou
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center) & Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liang Zhang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuanxi Yu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Banghao Wu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingchen Li
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai National Center for Applied Mathematics (SJTU Center) & Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China.
- Zhang Jiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 201203, China.
| | - Pan Tan
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai National Center for Applied Mathematics (SJTU Center) & Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China.
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12
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Fong JK, Mathieu Y, Vo MT, Bellemare A, Tsang A, Brumer H. Expansion of Auxiliary Activity Family 5 sequence space via biochemical characterization of six new copper radical oxidases. Appl Environ Microbiol 2024:e0101424. [PMID: 38953370 DOI: 10.1128/aem.01014-24] [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: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
Bacterial and fungal copper radical oxidases (CROs) from Auxiliary Activity Family 5 (AA5) are implicated in morphogenesis and pathogenesis. The unique catalytic properties of CROs also make these enzymes attractive biocatalysts for the transformation of small molecules and biopolymers. Despite a recent increase in the number of characterized AA5 members, especially from subfamily 2 (AA5_2), the catalytic diversity of the family as a whole remains underexplored. In the present study, phylogenetic analysis guided the selection of six AA5_2 members from diverse fungi for recombinant expression in Komagataella pfaffii (syn. Pichia pastoris) and biochemical characterization in vitro. Five of the targets displayed predominant galactose 6-oxidase activity (EC 1.1.3.9), and one was a broad-specificity aryl alcohol oxidase (EC 1.1.3.7) with maximum activity on the platform chemical 5-hydroxymethyl furfural (EC 1.1.3.47). Sequence alignment comparing previously characterized AA5_2 members to those from this study indicated various amino acid substitutions at active site positions implicated in the modulation of specificity.IMPORTANCEEnzyme discovery and characterization underpin advances in microbial biology and the application of biocatalysts in industrial processes. On one hand, oxidative processes are central to fungal saprotrophy and pathogenesis. On the other hand, controlled oxidation of small molecules and (bio)polymers valorizes these compounds and introduces versatile functional groups for further modification. The biochemical characterization of six new copper radical oxidases further illuminates the catalytic diversity of these enzymes, which will inform future biological studies and biotechnological applications.
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Affiliation(s)
- Jessica K Fong
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Minh Tri Vo
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Annie Bellemare
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
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Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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14
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Šketa B, Galman JL, Turner NJ, Žnidaršič-Plazl P. Immobilization of His 6-tagged amine transaminases in microreactors using functionalized nonwoven nanofiber membranes. N Biotechnol 2024; 83:46-55. [PMID: 38960020 DOI: 10.1016/j.nbt.2024.06.005] [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: 04/15/2024] [Revised: 06/14/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Process intensification is crucial for industrial implementation of biocatalysis and can be achieved by continuous process operation in miniaturized reactors with efficiently immobilized biocatalysts, enabling their long-term use. Due to their extremely large surface-to-volume ratio, nanomaterials are promising supports for enzyme immobilization. In this work, different functionalized nanofibrous nonwoven membranes were embedded in a two-plate microreactor to enable immobilization of hexahistidine (His6)-tagged amine transaminases (ATAs) in flow. A membrane coated with Cu2+ ions gave the best results regarding His6-tagged ATAs immobilization among the membranes tested yielding an immobilization yield of up to 95.3 % for the purified N-His6-ATA-wt enzyme. Moreover, an efficient one-step enzyme immobilization process from overproduced enzyme in Escherichia coli cell lysate was developed and yielded enzyme loads up to 1088 U mL-1. High enzyme loads resulted in up to 80 % yields of acetophenone produced from 40 mM (S)-α-methylbenzylamine in less than 4 min using a continuously operated microreactor. Up to 81 % of the initial activity was maintained in a 5-day continuous microreactor operation with immobilized His6-tagged ATA constructs. The highest turnover number within the indicated time was 7.23·106, which indicates that this immobilization approach using advanced material and reactor system is highly relevant for industrial implementation.
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Affiliation(s)
- Borut Šketa
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; Chair of Micro Process Engineering and Technology - COMPETE, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - James L Galman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Polona Žnidaršič-Plazl
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; Chair of Micro Process Engineering and Technology - COMPETE, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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15
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Li X, Kuchinski LM, Park A, Murphy GS, Soto KC, Schuster BS. Enzyme purification and sustained enzyme activity for pharmaceutical biocatalysis by fusion with phase-separating intrinsically disordered protein. Biotechnol Bioeng 2024. [PMID: 38951956 DOI: 10.1002/bit.28787] [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: 12/06/2023] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
In recent decades, biocatalysis has emerged as an important alternative to chemical catalysis in pharmaceutical manufacturing. Biocatalysis is attractive because enzymatic cascades can synthesize complex molecules with incredible selectivity, yield, and in an environmentally benign manner. Enzymes for pharmaceutical biocatalysis are typically used in their unpurified state, since it is time-consuming and cost-prohibitive to purify enzymes using conventional chromatographic processes at scale. However, impurities present in crude enzyme preparations can consume substrate, generate unwanted byproducts, as well as make the isolation of desired products more cumbersome. Hence, a facile, nonchromatographic purification method would greatly benefit pharmaceutical biocatalysis. To address this issue, here we have captured enzymes into membraneless compartments by fusing enzymes with an intrinsically disordered protein region, the RGG domain from LAF-1. The RGG domain can undergo liquid-liquid phase separation, forming liquid condensates triggered by changes in temperature or salt concentration. By centrifuging these liquid condensates, we have successfully purified enzyme-RGG fusions, resulting in significantly enhanced purity compared to cell lysate. Furthermore, we performed enzymatic reactions utilizing purified fusion proteins to assay enzyme activity. Results from the enzyme assays indicate that enzyme-RGG fusions purified by the centrifugation method retain enzymatic activity, with greatly reduced background activity compared to crude enzyme preparations. Our work focused on three different enzymes-a kinase, a phosphorylase, and an ATP-dependent ligase. The kinase and phosphorylase are components of the biocatalytic cascade for manufacturing molnupiravir, and we demonstrated facile co-purification of these two enzymes by co-phase separation. To conclude, enzyme capture by RGG tagging promises to overcome difficulties in bioseparations and biocatalysis for pharmaceutical synthesis.
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Affiliation(s)
- Xinyi Li
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Liam M Kuchinski
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Augene Park
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Grant S Murphy
- Department of Process Research and Development, Process Research and Development, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Karla Camacho Soto
- Department of Process Research and Development, Process Research and Development, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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16
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Baby EK, Savitha R, Kinsella GK, Nolan K, Ryan BJ, Henehan GT. Influence of deep eutectic solvents on redox biocatalysis involving alcohol dehydrogenases. Heliyon 2024; 10:e32550. [PMID: 38948051 PMCID: PMC11209023 DOI: 10.1016/j.heliyon.2024.e32550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 07/02/2024] Open
Abstract
Redox biocatalysis plays an increasingly important role in modern organic synthesis. The recent integration of novel media such as deep eutectic solvents (DESs) has significantly impacted this field of chemical biology. Alcohol dehydrogenases (ADHs) are important biocatalysts where their unique specificity is used for enantioselective synthesis. This review explores aspects of redox biocatalysis in the presence of DES both with whole cells and with isolated ADHs. In both cases, the presence of DES has a significant influence on the outcome of reactions albeit via different mechanisms. For whole cells, DES was shown to be a useful tool to direct product formation or configuration - a process of solvent engineering. Whole cells can tolerate DES as media components for the solubilization of hydrophobic substrates. In some cases, DES in the growth medium altered the enantioselectivity of whole cell transformations by solvent control. For isolated enzymes, on the other hand, the presence of DES promotes substrate solubility as well as enhancing enzyme stability and activity. DES can be employed as a smart solvent or smart cosubstrate particularly for cofactor regeneration purposes. From the literatures examined, it is suggested that DES based on choline chloride (ChCl) such as ChCl:Glycerol (Gly), ChCl:Glucose (Glu), and ChCl:1,4-butanediol (1,4-BD) are useful starting points for ADH-based redox biocatalysis. However, each specific reaction will require optimisation due to the influence of several factors on biocatalysis in DES. These include solvent composition, enzyme source, temperature, pH and ionic strength as well as the substrates and products under investigation.
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Affiliation(s)
- Ebin K. Baby
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman Lower, Dublin 7, D07 E244, Ireland
| | - Rangasamy Savitha
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman Lower, Dublin 7, D07 E244, Ireland
| | - Gemma K. Kinsella
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman Lower, Dublin 7, D07 E244, Ireland
| | - Kieran Nolan
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, D09 V209, Ireland
| | - Barry J. Ryan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman Lower, Dublin 7, D07 E244, Ireland
| | - Gary T.M. Henehan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman Lower, Dublin 7, D07 E244, Ireland
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17
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Sudar M, Milčić N, Česnik Katulić M, Szekrenyi A, Hernández K, Fekete M, Wardenga R, Majerić Elenkov M, Qi Y, Charnock S, Vasić-Rački Đ, Fessner WD, Clapés P, Findrik Blažević Z. Cascade enzymatic synthesis of a statin side chain precursor - the role of reaction engineering in process optimization. RSC Adv 2024; 14:21158-21173. [PMID: 38966813 PMCID: PMC11223575 DOI: 10.1039/d4ra01633e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
Statins are an important class of drugs used to lower blood cholesterol levels and are often used to combat cardiovascular disease. In view of the importance of safe and reliable supply and production of statins in modern medicine and the global need for sustainable processes, various biocatalytic strategies for their synthesis have been investigated. In this work, a novel biocatalytic route to a statin side chain precursor was investigated in a one-pot cascade reaction starting from the protected alcohol N-(3-hydroxypropyl)-2-phenylacetamide, which is oxidized to the corresponding aldehyde in the first reaction step, and then reacts with two equivalents of acetaldehyde to form the final product N-(2-((2S,4S,6S)-4,6-dihydroxytetrahydro-2H-pyran-2-yl)ethyl)-2-phenylacetamide (phenylacetamide-lactol). To study this complex reaction, an enzyme reaction engineering approach was used, i.e. the kinetics of all reactions occurring in the cascade (including side reactions) were determined. The obtained kinetic model together with the simulations gave an insight into the system and indicated the best reactor mode for the studied reaction, which was fed-batch with acetaldehyde feed to minimize its negative effect on the enzyme activity during the reaction. The mathematical model of the process was developed and used to simulate different scenarios and to find the reaction conditions (enzyme and coenzyme concentration, substrate feed concentration and flow rate) at which the highest yield of phenylacetamide-lactol (75%) can be obtained. In the end, our goal was to show that this novel cascade route is an interesting alternative for the synthesis of the statin side chain precursor and that is why we also calculated an initial estimate of the potential value addition.
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Affiliation(s)
- Martina Sudar
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia +385 1 4597 133 +385 1 4597 157 +385 1 4597 101
| | - Nevena Milčić
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia +385 1 4597 133 +385 1 4597 157 +385 1 4597 101
| | - Morana Česnik Katulić
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia +385 1 4597 133 +385 1 4597 157 +385 1 4597 101
| | - Anna Szekrenyi
- Technische Universität Darmstadt Peter-Grünberg-Straße 4 64287 Darmstadt Germany
| | - Karel Hernández
- Institute of Advanced Chemistry of Catalonia, Biotransformation and Bioactive Molecules Group, IQAC-CSIC Jordi Girona 18-26 08034 Barcelona Spain
| | - Melinda Fekete
- Enzymicals AG Walther-Rathenau-Straße 49b 17489 Greifswald Germany
- piCHEM Forschungs-und Entwicklungs GmbH Parkring 3 8074 Raaba-Grambach Austria
| | - Rainer Wardenga
- Enzymicals AG Walther-Rathenau-Straße 49b 17489 Greifswald Germany
| | | | - Yuyin Qi
- Prozomix Ltd Haltwhistle Northumberland NE49 9HA UK
| | | | - Đurđa Vasić-Rački
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia +385 1 4597 133 +385 1 4597 157 +385 1 4597 101
| | - Wolf-Dieter Fessner
- Technische Universität Darmstadt Peter-Grünberg-Straße 4 64287 Darmstadt Germany
| | - Pere Clapés
- Institute of Advanced Chemistry of Catalonia, Biotransformation and Bioactive Molecules Group, IQAC-CSIC Jordi Girona 18-26 08034 Barcelona Spain
| | - Zvjezdana Findrik Blažević
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia +385 1 4597 133 +385 1 4597 157 +385 1 4597 101
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18
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Wu Z, Ye Y, Guo Z, Wu X, Zhang L, Huang Z, Chen F. Stereoselective reduction of diarylmethanones via a ketoreductase@metal-organic framework. Org Biomol Chem 2024; 22:5198-5204. [PMID: 38864364 DOI: 10.1039/d4ob00744a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Mainly owing to their well-defined pore structures and high surface areas, metal-organic frameworks (MOFs) have recently become a versatile class of materials for enzyme immobilization. Nevertheless, most previous studies were focused on model enzymes such as cytochrome c, catalase, and glucose oxidase, with the application of MOF-derived biocomposites for (asymmetric) organic synthesis being rare. In the present work, the immobilization of the ketoreductase KmCR2 onto the zeolitic imidazolate framework (ZIF), a prominent type of MOF, was pursued using the controlled co-precipitation strategy, with a low 2-methylimidazole (2-mIM)/Zn molar ratio of 8 : 1 being employed. Such fabricated biocomposites denoted as KmCR2@ZIF were found to exist mainly in an amorphous phase, as suggested by the scanning electron microscopy (SEM) and powder X-ray diffraction (PXRD) data. Improved thermal and storage stabilities were observed for KmCR2@ZIF compared with the free enzyme. Stereoselective reduction of nine diarylmethanones 1 catalyzed by KmCR2@ZIF was performed, and the corresponding enantioenriched diarylmethanols 2 were afforded in 40-92% conversions with good to excellent optical purities (up to >99% ee). Critically, the current work demonstrated that the unique characteristic of KmCR2, namely the substituent position-controlled stereospecificity (meta versus para or ortho), was not altered upon the enzyme immobilization onto the ZIF.
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Affiliation(s)
- Zexin Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, P. R. China.
| | - Yangtian Ye
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, 220 Handan Road, Shanghai, 200433, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Zijun Guo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, P. R. China.
| | - Xiaofan Wu
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, 220 Handan Road, Shanghai, 200433, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Li Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Zedu Huang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, 220 Handan Road, Shanghai, 200433, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Fener Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, P. R. China.
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, 220 Handan Road, Shanghai, 200433, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, P. R. China
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P. R. China
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19
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Kattula B, Munakala A, Kashyap R, Nallamilli T, Nagendla NK, Naza S, Mudiam MKR, Chegondi R, Addlagatta A. Strategic enzymatic enantioselective desymmetrization of prochiral cyclohexa-2,5-dienones. Chem Commun (Camb) 2024; 60:6647-6650. [PMID: 38856301 DOI: 10.1039/d4cc02181a] [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: 06/11/2024]
Abstract
Asymmetric desymmetrization through the selective reduction of one double bond of prochiral 2,5-cyclohexadienones is highly challenging. A novel method has been developed for synthesizing chiral cyclohexenones by employing an ene-reductase (Bacillus subtilis YqjM) enzyme that belongs to the OYE family. Our strategy demonstrates high substrate scope and enantioselectivity towards substrates containing all-carbon as well as heteroatom (O, N)-containing quaternary centers. The mechanistic studies (kH/D = ∼1.8) indicate that hydride transfer is probably the rate-limiting step. Mutation of several active site residues did not affect the stereochemical outcomes. This work provides a convenient way of synthesizing various enantioselective γ,γ-disubstituted cyclohexanones using enzymes.
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Affiliation(s)
- Bhavita Kattula
- Department of Applied Biology, Hyderabad, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Anandarao Munakala
- Department of Organic Synthesis and Process Chemistry, Hyderabad, Telangana, India.
| | | | - Tarun Nallamilli
- Department of Organic Synthesis and Process Chemistry, Hyderabad, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Narendra Kumar Nagendla
- Department of Analytical and Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Surabhi Naza
- Department of Applied Biology, Hyderabad, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Mohana Krishna Reddy Mudiam
- Department of Analytical and Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rambabu Chegondi
- Department of Organic Synthesis and Process Chemistry, Hyderabad, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Anthony Addlagatta
- Department of Applied Biology, Hyderabad, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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20
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Branson Y, Schnell B, Zurr C, Bayer T, Badenhorst CPS, Wei R, Bornscheuer UT. An Extremely Sensitive Ultra-High Throughput Growth Selection Assay for the Identification of Amidase Activity. Appl Microbiol Biotechnol 2024; 108:392. [PMID: 38910173 PMCID: PMC11194204 DOI: 10.1007/s00253-024-13233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
In the last decades, biocatalysis has offered new perspectives for the synthesis of (chiral) amines, which are essential building blocks for pharmaceuticals, fine and bulk chemicals. In this regard, amidases have been employed due to their broad substrate scope and their independence from expensive cofactors. To expand the repertoire of amidases, tools for their rapid identification and characterization are greatly demanded. In this work an ultra-high throughput growth selection assay based on the production of the folate precursor p-aminobenzoic acid (PABA) is introduced to identify amidase activity. PABA-derived amides structurally mimic the broad class of commonly used chromogenic substrates derived from p-nitroaniline. This suggests that the assay should be broadly applicable for the identification of amidases. Unlike conventional growth selection assays that rely on substrates as nitrogen or carbon source, our approach requires PABA in sub-nanomolar concentrations, making it exceptionally sensitive and ideal for engineering campaigns that aim at enhancing amidase activities from minimally active starting points, for example. The presented assay offers flexibility in the adjustment of sensitivity to suit project-specific needs using different expression systems and fine-tuning with the antimetabolite sulfathiazole. Application of this PABA-based assay facilitates the screening of millions of enzyme variants on a single agar plate within two days, without the need for laborious sample preparation or expensive instruments, with transformation efficiency being the only limiting factor. KEY POINTS: • Ultra-high throughput assay (tens of millions on one agar plate) for amidase screening • High sensitivity by coupling selection to folate instead of carbon or nitrogen source • Highly adjustable in terms of sensitivity and expression of the engineering target.
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Affiliation(s)
- Yannick Branson
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Bjarne Schnell
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Celine Zurr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Christoffel P S Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Ren Wei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany.
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21
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Jain S, Ospina F, Hammer SC. A New Age of Biocatalysis Enabled by Generic Activation Modes. JACS AU 2024; 4:2068-2080. [PMID: 38938808 PMCID: PMC11200230 DOI: 10.1021/jacsau.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to a discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic activation modes enable a wide range of reaction types and played a pivotal role in advancing the fields of organo- and photocatalysis. This perspective aims to summarize the principal activation modes harnessed in enzymes to develop new biocatalysts. Although extensively researched in the past, the highlighted activation modes, when applied within enzyme active sites, facilitate chemical transformations that have largely eluded efficient and selective catalysis. This advance is attributed to multiple tunable interactions in the substrate binding pocket that precisely control competing reaction pathways and transition states. We will highlight cases of new synthetic methodologies achieved by engineered enzymes and will provide insights into potential future developments in this rapidly evolving field.
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Affiliation(s)
| | | | - Stephan C. Hammer
- Research Group for Organic Chemistry
and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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22
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Koomson DA, Nicholson JH, Brogan APS, Aldous L. Re-assessing viologens for modern bio-electrocatalysis. Chem Sci 2024; 15:9325-9332. [PMID: 38903224 PMCID: PMC11186337 DOI: 10.1039/d4sc02431a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Viologens, 1,1'-disubstituted-4,4'-bipyridinium salts, are organic redox species that can be used in place of NADPH as mediators for redox enzymes. In this study, using the reduction of oxidized glutathione by glutathione reductase as a model system, a rationally designed library of viologens covering a range of polarities and functional groups were explored as electron transfer mediators for bio-electrocatalysis. Through a series of electrochemical investigations, the reduction potential was found to be the primary determining factor for electron transfer between the viologen and enzyme. Through enhancing the solubility of viologen such that the fully reduced state remained soluble, we demonstrate a much-widened window of useable viologen potentials. In doing so, we describe for the first time a highly efficient electron transfer to a flavoenzyme promoting the catalytic reaction in the absence of co-factors. As such, our study provides a platform for broadening the scope for using viologens as mediating agents for electrochemically-driven enzymatic processes.
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Affiliation(s)
- Desmond Ato Koomson
- Department of Chemistry, King's College London Britannia House London SE1 1DB UK
| | - Jake H Nicholson
- Department of Chemistry, King's College London Britannia House London SE1 1DB UK
| | - Alex P S Brogan
- Department of Chemistry, King's College London Britannia House London SE1 1DB UK
| | - Leigh Aldous
- Department of Chemistry, King's College London Britannia House London SE1 1DB UK
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23
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Cai X, Huang Y, Zhu C. Immobilized Multi-Enzyme/Nanozyme Biomimetic Cascade Catalysis for Biosensing Applications. Adv Healthc Mater 2024:e2401834. [PMID: 38889805 DOI: 10.1002/adhm.202401834] [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: 05/17/2024] [Revised: 06/17/2024] [Indexed: 06/20/2024]
Abstract
Multiple enzyme-induced cascade catalysis has an indispensable role in the process of complex life activities, and is widely used to construct robust biosensors for analyzing various targets. The immobilized multi-enzyme cascade catalysis system is a novel biomimetic catalysis strategy that immobilizes various enzymes with different functions in stable carriers to simulate the synergistic catalysis of multiple enzymes in biological systems, which enables high stability of enzymes and efficiency enzymatic cascade catalysis. Nanozymes, a type of nanomaterial with intrinsic enzyme-like characteristics and excellent stabilities, are also widely applied instead of enzymes to construct immobilized cascade systems, achieving better catalytic performance and reaction stability. Due to good stability, reusability, and remarkably high efficiency, the immobilized multi-enzyme/nanozyme biomimetic cascade catalysis systems show distinct advantages in promoting signal transduction and amplification, thereby attracting vast research interest in biosensing applications. This review focuses on the research progress of the immobilized multi-enzyme/nanozyme biomimetic cascade catalysis systems in recent years. The construction approaches, factors affecting the efficiency, and applications for sensitive biosensing are discussed in detail. Further, their challenges and outlooks for future study are also provided.
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Affiliation(s)
- Xiaoli Cai
- Academy of Nutrition and Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, P.R. China
| | - Yuteng Huang
- Academy of Nutrition and Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, P.R. China
| | - Chengzhou Zhu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
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24
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Ran L, Lin Y, Su G, Yang Z, Teng H. Co-Immobilization of ADH and GDH on Metal-Organic-Framework: An Effective Biocatalyst for Asymmetric Reduction of Ketones. Chembiochem 2024; 25:e202400147. [PMID: 38629211 DOI: 10.1002/cbic.202400147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/14/2024] [Indexed: 05/22/2024]
Abstract
Chiral alcohols are not only important building blocks of various bioactive natural compounds and pharmaceuticals, but can serve as synthetic precursors for other valuable organic chemicals, thus the synthesis of these products is of great importance. Bio-catalysis represents one effective way to obtain these molecules, however, the weak stability and high cost of enzymes often hinder its broad application. In this work, we designed a biological nanoreactor by embedding alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) in metal-organic-framework ZIF-8. The biocatalyst ADH&GDH@ZIF-8 could be applied to the asymmetric reduction of a series of ketones to give chiral alcohols in high yields (up to 99 %) and with excellent enantioselectivities (>99 %). In addition, the heterogeneous biocatalyst could be recycled and reused at least four times with slight activity decline. Moreover, E. coli containing ADH and GDH was immobilized by ZIF-8 to form biocatalyst E. coli@ZIF-8, which also exhibits good catalytic behaviours. Finally, the chiral alcohols are further converted to marketed drugs (R)-Fendiline, (S)-Rivastigmine and NPS R-568 respectively.
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Affiliation(s)
- Lu Ran
- College of Chemistry, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yu Lin
- College of Chemistry, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Guorong Su
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhenyan Yang
- College of Chemistry, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Huailong Teng
- College of Chemistry, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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25
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Gao CY, Yang GY, Ding XW, Xu JH, Cheng X, Zheng GW, Chen Q. Engineering of Halide Methyltransferase BxHMT through Dynamic Cross-Correlation Network Analysis. Angew Chem Int Ed Engl 2024; 63:e202401235. [PMID: 38623716 DOI: 10.1002/anie.202401235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/18/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Halide methyltransferases (HMTs) provide an effective way to regenerate S-adenosyl methionine (SAM) from S-adenosyl homocysteine and reactive electrophiles, such as methyl iodide (MeI) and methyl toluene sulfonate (MeOTs). As compared with MeI, the cost-effective unnatural substrate MeOTs can be accessed directly from cheap and abundant alcohols, but shows only limited reactivity in SAM production. In this study, we developed a dynamic cross-correlation network analysis (DCCNA) strategy for quickly identifying hot spots influencing the catalytic efficiency of the enzyme, and applied it to the evolution of HMT from Paraburkholderia xenovorans. Finally, the optimal mutant, M4 (V55T/C125S/L127T/L129P), exhibited remarkable improvement, with a specific activity of 4.08 U/mg towards MeOTs, representing an 82-fold increase as compared to the wild-type (WT) enzyme. Notably, M4 also demonstrated a positive impact on the catalytic ability with other methyl donors. The structural mechanism behind the enhanced enzyme activity was uncovered by molecular dynamics simulations. Our work not only contributes a promising biocatalyst for the regeneration of SAM, but also offers a strategy for efficient enzyme engineering.
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Affiliation(s)
- Chun-Yu Gao
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Gui-Ying Yang
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Xu-Wei Ding
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
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26
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Ndochinwa OG, Wang QY, Amadi OC, Nwagu TN, Nnamchi CI, Okeke ES, Moneke AN. Current status and emerging frontiers in enzyme engineering: An industrial perspective. Heliyon 2024; 10:e32673. [PMID: 38912509 PMCID: PMC11193041 DOI: 10.1016/j.heliyon.2024.e32673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.
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Affiliation(s)
- Obinna Giles Ndochinwa
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Qing-Yan Wang
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Oyetugo Chioma Amadi
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Tochukwu Nwamaka Nwagu
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., 212013, Zhenjiang, Jiangsu, China
| | - Anene Nwabu Moneke
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
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27
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Liu H, Sun R, Yang Y, Zhang C, Zhao G, Zhang K, Liang L, Huang X. Review on Microreactors for Photo-Electrocatalysis Artificial Photosynthesis Regeneration of Coenzymes. MICROMACHINES 2024; 15:789. [PMID: 38930759 PMCID: PMC11205774 DOI: 10.3390/mi15060789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
In recent years, with the outbreak of the global energy crisis, renewable solar energy has become a focal point of research. However, the utilization efficiency of natural photosynthesis (NPS) is only about 1%. Inspired by NPS, artificial photosynthesis (APS) was developed and utilized in applications such as the regeneration of coenzymes. APS for coenzyme regeneration can overcome the problem of high energy consumption in comparison to electrocatalytic methods. Microreactors represent a promising technology. Compared with the conventional system, it has the advantages of a large specific surface area, the fast diffusion of small molecules, and high efficiency. Introducing microreactors can lead to more efficient, economical, and environmentally friendly coenzyme regeneration in artificial photosynthesis. This review begins with a brief introduction of APS and microreactors, and then summarizes research on traditional electrocatalytic coenzyme regeneration, as well as photocatalytic and photo-electrocatalysis coenzyme regeneration by APS, all based on microreactors, and compares them with the corresponding conventional system. Finally, it looks forward to the promising prospects of this technology.
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Affiliation(s)
- Haixia Liu
- Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (H.L.); (Y.Y.); (C.Z.); (G.Z.)
| | - Rui Sun
- Jiaxing Key Laboratory of Biosemiconductors, Xiangfu Laboratory, Jiashan 314102, China;
| | - Yujing Yang
- Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (H.L.); (Y.Y.); (C.Z.); (G.Z.)
| | - Chuanhao Zhang
- Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (H.L.); (Y.Y.); (C.Z.); (G.Z.)
| | - Gaozhen Zhao
- Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (H.L.); (Y.Y.); (C.Z.); (G.Z.)
| | - Kaihuan Zhang
- 2020 X-Lab, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China;
| | - Lijuan Liang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaowen Huang
- Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (H.L.); (Y.Y.); (C.Z.); (G.Z.)
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28
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Li Q, Zhang S, Liu F, Su H, Sheng X. Quantum chemical modeling of enantioselective sulfoxidation and epoxidation reactions by indole monooxygenase VpIndA1. Phys Chem Chem Phys 2024; 26:16521-16528. [PMID: 38809594 DOI: 10.1039/d4cp00552j] [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: 05/30/2024]
Abstract
Indole monooxygenases (IMOs) are enzymes from the family of Group E monooxygenases, requiring flavin adenine dinucleotide (FAD) for their activities. IMOs play important roles in both sulfoxidation and epoxidation reactions. The broad substrate range and high selectivity of IMOs make them promising biocatalytic tools for synthesizing chiral compounds. In the present study, quantum chemical calculations using the cluster approach were performed to investigate the reaction mechanism and the enantioselectivity of the IMO from Variovorax paradoxus EPS (VpIndA1). The sulfoxidation of methyl phenyl sulfide (MPS) and the epoxidation of indene were chosen as the representative reactions. The calculations confirmed that the FADOOH intermediate is the catalytic species in the VpIndA1 reactions. The oxidation of MPS adopts a one-step mechanism involving the direct oxygen-transfer from FADOOH to the substrate and the proton transfer from the -OH group back to FAD, while the oxidation of indene follows a stepwise mechanism involving a carbocation intermediate. It was computationally predicted that VpIndA1 prefers the formation of (S)-product for the MPS sulfoxidation and (1S,2R)-product for the indene epoxidation, consistent with the experimental observations. Importantly, the factors controlling the stereo-preference of the two reactions are identified. The findings in the present study provide valuable insights into the VpIndA1-catalyzed reactions, which are essential for the rational design of this enzyme and other IMOs for industrial applications. It is also worth emphasizing that the quantum chemical cluster approach is again demonstrated to be powerful in studying the enantioselectivity of enzymatic reactions.
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Affiliation(s)
- Qinrou Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
| | - Shiqing Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, P. R. China
| | - Fufeng Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Hao Su
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, P. R. China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, P. R. China
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29
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Liu S, Yang Q, Zhang L, Luo S. Accurate Protein p Ka Prediction with Physical Organic Chemistry Guided 3D Protein Representation. J Chem Inf Model 2024; 64:4410-4418. [PMID: 38780156 DOI: 10.1021/acs.jcim.4c00354] [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
Protein pKa is a fundamental physicochemical parameter that dictates protein structure and function. However, accurately determining protein site-pKa values remains a substantial challenge, both experimentally and theoretically. In this study, we introduce a physical organic approach, leveraging a protein structural and physical-organic-parameter-based representation (P-SPOC), to develop a rapid and intuitive model for protein pKa prediction. Our P-SPOC model achieves state-of-the-art predictive accuracy, with a mean absolute error (MAE) of 0.33 pKa units. Furthermore, we have incorporated advanced protein structure prediction models, like AlphaFold2, to approximate structures for proteins lacking three-dimensional representations, which enhances the applicability of our model in the context of structure-undetermined protein research. To promote broader accessibility within the research community, an online prediction interface was also established at isyn.luoszgroup.com.
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Affiliation(s)
- Siyuan Liu
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qi Yang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Long Zhang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sanzhong Luo
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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30
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Elisée E, Ducrot L, Méheust R, Bastard K, Fossey-Jouenne A, Grogan G, Pelletier E, Petit JL, Stam M, de Berardinis V, Zaparucha A, Vallenet D, Vergne-Vaxelaire C. A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening. Nat Commun 2024; 15:4933. [PMID: 38858403 PMCID: PMC11164908 DOI: 10.1038/s41467-024-49009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/20/2024] [Indexed: 06/12/2024] Open
Abstract
Native amine dehydrogenases offer sustainable access to chiral amines, so the search for scaffolds capable of converting more diverse carbonyl compounds is required to reach the full potential of this alternative to conventional synthetic reductive aminations. Here we report a multidisciplinary strategy combining bioinformatics, chemoinformatics and biocatalysis to extensively screen billions of sequences in silico and to efficiently find native amine dehydrogenases features using computational approaches. In this way, we achieve a comprehensive overview of the initial native amine dehydrogenase family, extending it from 2,011 to 17,959 sequences, and identify native amine dehydrogenases with non-reported substrate spectra, including hindered carbonyls and ethyl ketones, and accepting methylamine and cyclopropylamine as amine donor. We also present preliminary model-based structural information to inform the design of potential (R)-selective amine dehydrogenases, as native amine dehydrogenases are mostly (S)-selective. This integrated strategy paves the way for expanding the resource of other enzyme families and in highlighting enzymes with original features.
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Affiliation(s)
- Eddy Elisée
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Laurine Ducrot
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Raphaël Méheust
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Bastard
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Aurélie Fossey-Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Mark Stam
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - David Vallenet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Carine Vergne-Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
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31
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Zukic E, Mokos D, Weber M, Stix N, Ditrich K, Ferrario V, Müller H, Willrodt C, Gruber K, Daniel B, Kroutil W. Biocatalytic Heteroaromatic Amide Formation in Water Enabled by a Catalytic Tetrad and Two Access Tunnels. ACS Catal 2024; 14:8913-8921. [PMID: 38868102 PMCID: PMC11165448 DOI: 10.1021/acscatal.4c01268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024]
Abstract
The amide moiety belongs to the most common motives in pharmaceutical chemistry, present in many prescribed small-molecule pharmaceuticals. Methods for its manufacture are still in high demand, especially using water/buffer as a solvent and avoiding stoichiometric amounts of activation reagents. Herein, we identified from a library of lipases/esterases/acyltransferases and variants thereof a lipase originating from Sphingomonas sp. HXN-200 (SpL) able to form amides in aqueous solution starting from a broad scope of sterically demanding heteroaromatic ethyl esters as well as aliphatic amines, reaching isolated yields up to 99% on preparative scale and space time yields of up to 864 g L-1 d-1; thus, in selected cases, the amide was formed within minutes. The enzyme features an aspartate next to the canonical serine of the catalytic triad, which was essential for amide formation. Furthermore, the enzyme structure revealed two tunnels to the active site, presumably one for the ester and one for the amine, which permit the bringing together of the sterically demanding heteroaromatic esters and the amine in the active site. This work shows that biocatalytic amide formation starting from various five- and six-membered heteroaromatic ethyl esters in the buffer can serve as a platform for preparative amide synthesis.
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Affiliation(s)
- Erna Zukic
- Austrian
Centre of Industrial Biotechnology Acib GmbH c/o University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Daniel Mokos
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße
50, 8010 Graz, Austria
| | - Melanie Weber
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Niklas Stix
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Klaus Ditrich
- Group
Research BASF SE, A030, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Valerio Ferrario
- Group
Research BASF SE, A030, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Henrik Müller
- Group
Research BASF SE, A030, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Christian Willrodt
- Group
Research BASF SE, A030, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Karl Gruber
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße
50, 8010 Graz, Austria
- Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed
Graz, 8010 Graz, Austria
| | - Bastian Daniel
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße
50, 8010 Graz, Austria
- BioTechMed
Graz, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße
50, 8010 Graz, Austria
- Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed
Graz, 8010 Graz, Austria
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32
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Casilli F, Canyelles-Niño M, Roelfes G, Alonso-Cotchico L. Computation-guided engineering of distal mutations in an artificial enzyme. Faraday Discuss 2024. [PMID: 38836699 DOI: 10.1039/d4fd00069b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Artificial enzymes are valuable biocatalysts able to perform new-to-nature transformations with the precision and (enantio-)selectivity of natural enzymes. Although they are highly engineered biocatalysts, they often cannot reach catalytic rates akin those of their natural counterparts, slowing down their application in real-world industrial processes. Typically, their designs only optimise the chemistry inside the active site, while overlooking the role of protein dynamics on catalysis. In this work, we show how the catalytic performance of an already engineered artificial enzyme can be further improved by distal mutations that affect the conformational equilibrium of the protein. To this end, we subjected a specialised artificial enzyme based on the lactococcal multidrug resistance regulator (LmrR) to an innovative algorithm that quickly inspects the whole protein sequence space for hotpots which affect the protein dynamics. From an initial predicted selection of 73 variants, two variants with mutations distant by more than 11 Å from the catalytic pAF residue showed increased catalytic activity towards the new-to-nature hydrazone formation reaction. Their recombination displayed a 66% higher turnover number and 14 °C higher thermostability. Microsecond time scale molecular dynamics simulations evidenced a shift in the distribution of productive enzyme conformations, which are the result of a cascade of interactions initiated by the introduced mutations.
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Affiliation(s)
- Fabrizio Casilli
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands.
| | | | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands.
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33
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Tripathi A, Dubey KD. The mechanistic insights into different aspects of promiscuity in metalloenzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:23-66. [PMID: 38960476 DOI: 10.1016/bs.apcsb.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity. Depending on the metal and its coordination environment, the metal ion or cofactor may function as a Lewis acid or base and a redox center and thus can catalyze a plethora of natural reactions. In fact, the versatility in the oxidation state of the metal ions provides metalloenzymes with a high level of catalytic adaptability and promiscuity. In this chapter, we discuss different aspects of promiscuity in metalloenzymes by using several recent experimental and theoretical works as case studies. We start our discussion by introducing the concept of promiscuity and then we delve into the mechanistic insight into promiscuity at the molecular level.
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Affiliation(s)
- Ankita Tripathi
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India.
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34
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Zhang F, Naeem M, Yu B, Liu F, Ju J. Improving the enzymatic activity and stability of N-carbamoyl hydrolase using deep learning approach. Microb Cell Fact 2024; 23:164. [PMID: 38834993 PMCID: PMC11151596 DOI: 10.1186/s12934-024-02439-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Optically active D-amino acids are widely used as intermediates in the synthesis of antibiotics, insecticides, and peptide hormones. Currently, the two-enzyme cascade reaction is the most efficient way to produce D-amino acids using enzymes DHdt and DCase, but DCase is susceptible to heat inactivation. Here, to enhance the enzymatic activity and thermal stability of DCase, a rational design software "Feitian" was developed based on kcat prediction using the deep learning approach. RESULTS According to empirical design and prediction of "Feitian" software, six single-point mutants with high kcat value were selected and successfully constructed by site-directed mutagenesis. Out of six, three mutants (Q4C, T212S, and A302C) showed higher enzymatic activity than the wild-type. Furthermore, the combined triple-point mutant DCase-M3 (Q4C/T212S/A302C) exhibited a 4.25-fold increase in activity (29.77 ± 4.52 U) and a 2.25-fold increase in thermal stability as compared to the wild-type, respectively. Through the whole-cell reaction, the high titer of D-HPG (2.57 ± 0.43 mM) was produced by the mutant Q4C/T212S/A302C, which was about 2.04-fold of the wild-type. Molecular dynamics simulation results showed that DCase-M3 significantly enhances the rigidity of the catalytic site and thus increases the activity of DCase-M3. CONCLUSIONS In this study, an efficient rational design software "Feitian" was successfully developed with a prediction accuracy of about 50% in enzymatic activity. A triple-point mutant DCase-M3 (Q4C/T212S/A302C) with enhanced enzymatic activity and thermostability was successfully obtained, which could be applied to the development of a fully enzymatic process for the industrial production of D-HPG.
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Affiliation(s)
- Fa Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Bo Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feixia Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
- Hebei Collaborative Innovation Center for Eco-Environment, Shijiazhuang, 050024, China.
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35
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Eggerichs D, Weindorf N, Weddeling HG, Van der Linden IM, Tischler D. Substrate scope expansion of 4-phenol oxidases by rational enzyme selection and sequence-function relations. Commun Chem 2024; 7:123. [PMID: 38831005 PMCID: PMC11148156 DOI: 10.1038/s42004-024-01207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
Enzymes are natures' catalysts and will have a lasting impact on (organic) synthesis as they possess unchallenged regio- and stereo selectivity. On the downside, this high selectivity limits enzymes' substrate range and hampers their universal application. Therefore, substrate scope expansion of enzyme families by either modification of known biocatalysts or identification of new members is a key challenge in enzyme-driven catalysis. Here, we present a streamlined approach to rationally select enzymes with proposed functionalities from the ever-increasing amount of available sequence data. In a case study on 4-phenol oxidoreductases, eight enzymes of the oxidase branch were selected from 292 sequences on basis of the properties of first shell residues of the catalytic pocket, guided by the computational tool A2CA. Correlations between these residues and enzyme activity yielded robust sequence-function relations, which were exploited by site-saturation mutagenesis. Application of a peroxidase-independent oxidase screening resulted in 16 active enzyme variants which were up to 90-times more active than respective wildtype enzymes and up to 6-times more active than the best performing natural variants. The results were supported by kinetic experiments and structural models. The newly introduced amino acids confirmed the correlation studies which overall highlights the successful logic of the presented approach.
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Affiliation(s)
- Daniel Eggerichs
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Nils Weindorf
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Heiner G Weddeling
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Inja M Van der Linden
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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36
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Bakunova AK, Matyuta IO, Minyaev ME, Isaikina TY, Boyko KM, Popov VO, Bezsudnova EY. Multifunctionality of arginine residues in the active sites of non-canonical d-amino acid transaminases. Arch Biochem Biophys 2024; 756:110011. [PMID: 38649133 DOI: 10.1016/j.abb.2024.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Structure-function relationships are key to understanding enzyme mechanisms, controlling enzyme activities, and designing biocatalysts. Here, we investigate the functions of arginine residues in the active sites of pyridoxal-5'-phosphate (PLP)-dependent non-canonical d-amino acid transaminases, focusing on the analysis of a transaminase from Haliscomenobacter hydrossis. Our results show that the tandem of arginine residues R28* and R90, which form the conserved R-[RK] motif in non-canonical d-amino acid transaminases, not only facilitates effective substrate binding but also regulates the catalytic properties of PLP. Non-covalent interactions between residues R28*, R90, and Y147 strengthen the hydrogen bond between Y147 and PLP, thereby maintaining the reactivity of the cofactor. Next, the R90 residue contributes to the stability of the holoenzyme. Finally, the R90I substitution induces structural changes that lead to substrate promiscuity, as evidenced by the effective binding of substrates with and without the α-carboxylate group. This study sheds light on the structural determinants of the activity of non-canonical d-amino acid transaminases. Understanding the structural basis of the active site plasticity in the non-canonical transaminase from H. hydrossis, which is characterized by effective conversion of d-amino acids and α-keto acids, may help to tailor it for industrial applications.
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Affiliation(s)
- Alina K Bakunova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia.
| | - Ilya O Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia
| | - Mikhail E Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Ave. 47, 119334, Moscow, Russia
| | - Tatiana Y Isaikina
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia; Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119991, Moscow, Russia
| | - Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia
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37
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Zhao J, Xu Y, Ding Z, Wu Q, Li W, Sun B, Li X. Discovery and mechanism explanation of a novel green biocatalyst esterase Bur01 from Burkholderia ambifaria for ester synthesis under aqueous phase. Int J Biol Macromol 2024; 272:132630. [PMID: 38810853 DOI: 10.1016/j.ijbiomac.2024.132630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Biocatalyst catalyzing the synthesis of esters under aqueous phase is an alternative with green and sustainable characteristics. Here, a biocatalyst esterase Bur01 was identified through genome sequencing and gene library construction from a Burkholderia ambifaria BJQ0010 with efficient ester synthesis property under aqueous phase for the first time. Bur01 was soluble expressed and the purified enzyme showed the highest activity at pH 4.0 and 40 °C. It had a broad substrate spectrum, especially for ethyl esters. The structure of Bur01 was categorized as a member of α/β fold hydrolase superfamily. The easier opening of lid under aqueous phase and the hydrophobicity of substrate channel contribute to easier access to the active center for substrate. Molecular docking and site-directed mutation demonstrated that the oxyanion hole Ala22, Met112 and π-bond stacking between His24 and Phe217 played essential roles in catalytic function. The mutants V149A, V149I, L159I and F137I enhanced enzyme activity to 1.42, 1.14, 1.32 and 2.19 folds due to reduced spatial resistance and increased hydrophobicity of channel and ethyl octanoate with the highest conversion ratio of 68.28 % was obtained for F137I. These results provided new ideas for developing green catalysts and catalytic basis of mechanistic studies for ester synthetase under aqueous phase.
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Affiliation(s)
- Jingrong Zhao
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
| | - Ze Ding
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qiuhua Wu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
| | - Baoguo Sun
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Xiuting Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China; China Bio-Specialty Food Enzyme Technology Research Development and Promotion Center, Beijing 100048, China.
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38
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Lin X, Li Y, Xu Z, Yu S, Feng J, Diao A, Yao P, Wu Q, Zhu D. Engineered Imine Reductase for Asymmetric Synthesis of Dextromethorphan Key Intermediate. Org Lett 2024; 26:4463-4468. [PMID: 38747552 DOI: 10.1021/acs.orglett.4c01079] [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: 06/01/2024]
Abstract
(S)-1-(4-Methoxybenzyl)-1,2,3,4,5,6,7,8-octahydroisoquinoline ((S)-1-(4-methoxybenzyl)-OHIQ) is the key intermediate of the nonopioid antitussive dextromethorphan. In this study, (S)-IR61-V69Y/P123A/W179G/F182I/L212V (M4) was identified with a 766-fold improvement in catalytic efficiency compared with wide-type IR61 through enzyme engineering. M4 could completely convert 200 mM of 1-(4-methoxybenzyl)-3,4,5,6,7,8-hexahydroisoquinoline into (S)-1-(4-methoxybenzyl)-OHIQ in 77% isolated yield, with >99% enantiomeric excess and a high space-time yield of 542 g L-1 day-1, demonstrating a great potential for the synthesis of dextromethorphan intermediate in industrial applications.
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Affiliation(s)
- Xiaofeng Lin
- School of Biotechnology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yixuan Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zefei Xu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shanshan Yu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aipo Diao
- School of Biotechnology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Peiyuan Yao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaqing Wu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dunming Zhu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Engineering Research Center of Industrial Enzymes, National Center of Technology Innovation for Synthetic Biology, Tianjin Engineering Research Center of Biocatalytic Technology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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39
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Luo Z, Qiao L, Chen H, Mao Z, Wu S, Ma B, Xie T, Wang A, Pei X, Sheldon RA. Precision Engineering of the Co-immobilization of Enzymes for Cascade Biocatalysis. Angew Chem Int Ed Engl 2024; 63:e202403539. [PMID: 38556813 DOI: 10.1002/anie.202403539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
The design and orderly layered co-immobilization of multiple enzymes on resin particles remain challenging. In this study, the SpyTag/SpyCatcher binding pair was fused to the N-terminus of an alcohol dehydrogenase (ADH) and an aldo-keto reductase (AKR), respectively. A non-canonical amino acid (ncAA), p-azido-L-phenylalanine (p-AzF), as the anchor for covalent bonding enzymes, was genetically inserted into preselected sites in the AKR and ADH. Employing the two bioorthogonal counterparts of SpyTag/SpyCatcher and azide-alkyne cycloaddition for the immobilization of AKR and ADH enabled sequential dual-enzyme coating on porous microspheres. The ordered dual-enzyme reactor was subsequently used to synthesize (S)-1-(2-chlorophenyl)ethanol asymmetrically from the corresponding prochiral ketone, enabling the in situ regeneration of NADPH. The reactor exhibited a high catalytic conversion of 74 % and good reproducibility, retaining 80 % of its initial activity after six cycles. The product had 99.9 % ee, which that was maintained in each cycle. Additionally, the double-layer immobilization method significantly increased the enzyme loading capacity, which was approximately 1.7 times greater than that of traditional single-layer immobilization. More importantly, it simultaneously enabled both the purification and immobilization of multiple enzymes on carriers, thus providing a convenient approach to facilitate cascade biocatalysis.
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Affiliation(s)
- Zhiyuan Luo
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Li Qiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Haomin Chen
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Zhili Mao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Shujiao Wu
- School of Pharmacy, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Bianqin Ma
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand PO Wits., 2050, Johannesburg, South Africa
- Department of Biotechnology, Section BOC, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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40
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Luo P, Huang JH, Lv JM, Wang GQ, Hu D, Gao H. Biosynthesis of fungal terpenoids. Nat Prod Rep 2024; 41:748-783. [PMID: 38265076 DOI: 10.1039/d3np00052d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Covering: up to August 2023Terpenoids, which are widely distributed in animals, plants, and microorganisms, are a large group of natural products with diverse structures and various biological activities. They have made great contributions to human health as therapeutic agents, such as the anti-cancer drug paclitaxel and anti-malarial agent artemisinin. Accordingly, the biosynthesis of this important class of natural products has been extensively studied, which generally involves two major steps: hydrocarbon skeleton construction by terpenoid cyclases and skeleton modification by tailoring enzymes. Additionally, fungi (Ascomycota and Basidiomycota) serve as an important source for the discovery of terpenoids. With the rapid development of sequencing technology and bioinformatics approaches, genome mining has emerged as one of the most effective strategies to discover novel terpenoids from fungi. To date, numerous terpenoid cyclases, including typical class I and class II terpenoid cyclases as well as emerging UbiA-type terpenoid cyclases, have been identified, together with a variety of tailoring enzymes, including cytochrome P450 enzymes, flavin-dependent monooxygenases, and acyltransferases. In this review, our aim is to comprehensively present all fungal terpenoid cyclases identified up to August 2023, with a focus on newly discovered terpenoid cyclases, especially the emerging UbiA-type terpenoid cyclases, and their related tailoring enzymes from 2015 to August 2023.
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Affiliation(s)
- Pan Luo
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
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41
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Shen Q, Yan J, Han Y, Zhang Z, Li H, Kong D, Shi J, Cui C, Zhang W. Peroxygenase-Enabled Reductive Kinetic Resolution for the Enantioenrichment of Organoperoxides. Angew Chem Int Ed Engl 2024; 63:e202401590. [PMID: 38477082 DOI: 10.1002/anie.202401590] [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: 01/23/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Enantiomerically pure organoperoxides serve as valuable precursors in organic transformations. Herein, we present the first examples of unspecific peroxygenase catalyzed kinetic resolution of racemic organoperoxides through asymmetric reduction. Through meticulous investigation of the reaction conditions, it is shown that the unspecific peroxygenase from Agrocybe aegerita (AaeUPO) exhibits robust catalytic activity in the kinetic resolution reactions of the model substrate with turnover numbers up to 60000 and turnover frequency of 5.6 s-1. Various aralkyl organoperoxides were successfully resolved by AaeUPO, achieving excellent enantioselectivities (e.g., up to 99 % ee for the (S)-organoperoxide products). Additionally, we screened commercial peroxygenase variants to obtain the organoperoxides with complementary chirality, with one mutant yielding the (R)-products. While unspecific peroxygenases have been extensively demonstrated as a powerful oxidative catalysts, this study highlights their usefulness in catalyzing the reduction of organoperoxides and providing versatile chiral synthons.
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Affiliation(s)
- Qianqian Shen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Juzhang Yan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Yuchen Han
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Zaoxiao Zhang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Huanhuan Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Dulin Kong
- School of Pharmacy, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Jianjun Shi
- College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Chengsen Cui
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Wuyuan Zhang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
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42
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Ghosh A, Sagadevan A, Murugesan K, Nastase SAF, Maity B, Bodiuzzaman M, Shkurenko A, Hedhili MN, Yin J, Mohammed OF, Eddaoudi M, Cavallo L, Rueping M, Bakr OM. Multiple neighboring active sites of an atomically precise copper nanocluster catalyst for efficient bond-forming reactions. MATERIALS HORIZONS 2024; 11:2494-2505. [PMID: 38477151 DOI: 10.1039/d4mh00098f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Atomically precise copper nanoclusters (NCs) are an emerging class of nanomaterials for catalysis. Their versatile core-shell architecture opens the possibility of tailoring their catalytically active sites. Here, we introduce a core-shell copper nanocluster (CuNC), [Cu29(StBu)13Cl5(PPh3)4H10]tBuSO3 (StBu: tert-butylthiol; PPh3: triphenylphosphine), Cu29NC, with multiple accessible active sites on its shell. We show that this nanocluster is a versatile catalyst for C-heteroatom bond formation (C-O, C-N, and C-S) with several advantages over previous Cu systems. When supported, the cluster can also be reused as a heterogeneous catalyst without losing its efficiency, making it a hybrid homogeneous and heterogeneous catalyst. We elucidated the atomic-level mechanism of the catalysis using density functional theory (DFT) calculations based on the single crystal structure. We found that the cooperative action of multiple neighboring active sites is essential for the catalyst's efficiency. The calculations also revealed that oxidative addition is the rate-limiting step that is facilitated by the neighboring active sites of the Cu29NC, which highlights a unique advantage of nanoclusters over traditional copper catalysts. Our results demonstrate the potential of nanoclusters for enabling the rational atomically precise design and investigation of multi-site catalysts.
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Affiliation(s)
- Atanu Ghosh
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Arunachalam Sagadevan
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Kathiravan Murugesan
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Stefan Adrian F Nastase
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Bholanath Maity
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Mohammad Bodiuzzaman
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Aleksander Shkurenko
- Advanced Membranes and Porous Materials Center (AMPMC), Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed Nejib Hedhili
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jun Yin
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, 999077, Hong Kong, China
| | - Omar F Mohammed
- Advanced Membranes and Porous Materials Center (AMPMC), Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed Eddaoudi
- Advanced Membranes and Porous Materials Center (AMPMC), Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Osman M Bakr
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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43
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Saha B, Lee JH, Kwon I, Chung H. Site-Specific Conjugation of Bottlebrush Polymers to Therapeutic Protein via Bioorthogonal Chemistry. Biomacromolecules 2024; 25:3200-3211. [PMID: 38591457 DOI: 10.1021/acs.biomac.4c00359] [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: 04/10/2024]
Abstract
Achieving efficient and site-specific conjugation of therapeutic protein to polymer is crucial to augment their applicability in the realms of biomedicine by improving their stability and enzymatic activity. In this study, we exploited tetrazine bioorthogonal chemistry to achieve the site-specific conjugation of bottlebrush polymers to urate oxidase (UOX), a therapeutic protein for gout treatment. An azido-functionalized zwitterionic bottlebrush polymer (N3-ZBP) using a "grafting-from" strategy involving RAFT and ATRP methods was synthesized, and a trans-cyclooctene (TCO) moiety was introduced at the polymer end through the strain-promoted azide-alkyne click (SPAAC) reaction. The subsequent coupling between TCO-incorporated bottlebrush polymer and tetrazine-labeled UOX using a fast and safe bioorthogonal reaction, inverse electron demand Diels-Alder (IEDDA), led to the formation of UOX-ZBP conjugates with a 52% yield. Importantly, the enzymatic activity of UOX remained unaffected following polymer conjugation, suggesting a minimal change in the folded structure of UOX. Moreover, UOX-ZBP conjugates exhibited enhanced proteolytic resistance and reduced antibody binding, compared to UOX-wild type. Overall, the present findings reveal an efficient and straightforward route for synthesizing protein-bottlebrush polymer conjugates without compromising the enzymatic activity while substantially reducing proteolytic degradation and antibody binding.
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Affiliation(s)
- Biswajit Saha
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Tallahassee, Florida 32310, United States
| | - Jae Hun Lee
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Hoyong Chung
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Tallahassee, Florida 32310, United States
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44
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Diamanti E, López-Gallego F. Single-Particle and Single-Molecule Characterization of Immobilized Enzymes: A Multiscale Path toward Optimizing Heterogeneous Biocatalysts. Angew Chem Int Ed Engl 2024; 63:e202319248. [PMID: 38476019 DOI: 10.1002/anie.202319248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Heterogeneous biocatalysis is highly relevant in biotechnology as it offers several benefits and practical uses. To leverage the full potential of heterogeneous biocatalysts, the establishment of well-crafted protocols, and a deeper comprehension of enzyme immobilization on solid substrates are essential. These endeavors seek to optimize immobilized biocatalysts, ensuring maximal enzyme performance within confined spaces. For this aim, multidimensional characterization of heterogeneous biocatalysts is required. In this context, spectroscopic and microscopic methodologies conducted at different space and temporal scales can inform about the intraparticle enzyme kinetics, the enzyme spatial distribution, and the mass transport issues. In this Minireview, we identify enzyme immobilization, enzyme catalysis, and enzyme inactivation as the three main processes for which advanced characterization tools unveil fundamental information. Recent advances in operando characterization of immobilized enzymes at the single-particle (SP) and single-molecule (SM) levels inform about their functional properties, unlocking the full potential of heterogeneous biocatalysis toward biotechnological applications.
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Affiliation(s)
- Eleftheria Diamanti
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-, Basque Research and Technology Alliance (BRTA), Paseo Miramón, 194, 20014, Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-, Basque Research and Technology Alliance (BRTA), Paseo Miramón, 194, 20014, Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain
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45
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Liga S, Paul C. Puerarin-A Promising Flavonoid: Biosynthesis, Extraction Methods, Analytical Techniques, and Biological Effects. Int J Mol Sci 2024; 25:5222. [PMID: 38791264 PMCID: PMC11121215 DOI: 10.3390/ijms25105222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Flavonoids, a variety of plant secondary metabolites, are known for their diverse biological activities. Isoflavones are a subgroup of flavonoids that have gained attention for their potential health benefits. Puerarin is one of the bioactive isoflavones found in the Kudzu root and Pueraria genus, which is widely used in alternative Chinese medicine, and has been found to be effective in treating chronic conditions like cardiovascular diseases, liver diseases, gastric diseases, respiratory diseases, diabetes, Alzheimer's disease, and cancer. Puerarin has been extensively researched and used in both scientific and clinical studies over the past few years. The purpose of this review is to provide an up-to-date exploration of puerarin biosynthesis, the most common extraction methods, analytical techniques, and biological effects, which have the potential to provide a new perspective for medical and pharmaceutical research and development.
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Affiliation(s)
| | - Cristina Paul
- Biocatalysis Group, Department of Applied Chemistry and Engineering of Organic and Natural Compounds, Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University Timisoara, Vasile Pârvan No. 6, 300223 Timisoara, Romania;
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46
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Weiz G, González AL, Mansilla IS, Fernandez-Zapico ME, Molejón MI, Breccia JD. Rutinosides-derived from Sarocladium strictum 6-O-α-rhamnosyl-β-glucosidase show enhanced anti-tumoral activity in pancreatic cancer cells. Microb Cell Fact 2024; 23:133. [PMID: 38720294 PMCID: PMC11077868 DOI: 10.1186/s12934-024-02395-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Low targeting efficacy and high toxicity continue to be challenges in Oncology. A promising strategy is the glycosylation of chemotherapeutic agents to improve their pharmacodynamics and anti-tumoral activity. Herein, we provide evidence of a novel approach using diglycosidases from fungi of the Hypocreales order to obtain novel rutinose-conjugates therapeutic agents with enhanced anti-tumoral capacity. RESULTS Screening for diglycosidase activity in twenty-eight strains of the genetically related genera Acremonium and Sarocladium identified 6-O-α-rhamnosyl-β-glucosidase (αRβG) of Sarocladium strictum DMic 093557 as candidate enzyme for our studies. Biochemically characterization shows that αRβG has the ability to transglycosylate bulky OH-acceptors, including bioactive compounds. Interestingly, rutinoside-derivatives of phloroglucinol (PR) resorcinol (RR) and 4-methylumbelliferone (4MUR) displayed higher growth inhibitory activity on pancreatic cancer cells than the respective aglycones without significant affecting normal pancreatic epithelial cells. PR exhibited the highest efficacy with an IC50 of 0.89 mM, followed by RR with an IC50 of 1.67 mM, and 4MUR with an IC50 of 2.4 mM, whereas the respective aglycones displayed higher IC50 values: 4.69 mM for phloroglucinol, 5.90 mM for resorcinol, and 4.8 mM for 4-methylumbelliferone. Further, glycoconjugates significantly sensitized pancreatic cancer cells to the standard of care chemotherapy agent gemcitabine. CONCLUSIONS αRβG from S. strictum transglycosylate-based approach to synthesize rutinosides represents a suitable option to enhance the anti-proliferative effect of bioactive compounds. This finding opens up new possibilities for developing more effective therapies for pancreatic cancer and other solid malignancies.
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Affiliation(s)
- Gisela Weiz
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa-Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina.
| | - Alina L González
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa-Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Iara S Mansilla
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa-Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Martín E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - María I Molejón
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa-Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Javier D Breccia
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa-Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
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47
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Wang H, Abe I. Recent developments in the enzymatic modifications of steroid scaffolds. Org Biomol Chem 2024; 22:3559-3583. [PMID: 38639195 DOI: 10.1039/d4ob00327f] [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: 04/20/2024]
Abstract
Steroids are an important family of bioactive compounds. Steroid drugs are renowned for their multifaceted pharmacological activities and are the second-largest category in the global pharmaceutical market. Recent developments in biocatalysis and biosynthesis have led to the increased use of enzymes to enhance the selectivity, efficiency, and sustainability for diverse modifications of steroids. This review discusses the advancements achieved over the past five years in the enzymatic modifications of steroid scaffolds, focusing on enzymatic hydroxylation, reduction, dehydrogenation, cascade reactions, and other modifications for future research on the synthesis of novel steroid compounds and related drugs, and new therapeutic possibilities.
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Affiliation(s)
- Huibin Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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48
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Fu H, Hyster TK. From Ground-State to Excited-State Activation Modes: Flavin-Dependent "Ene"-Reductases Catalyzed Non-natural Radical Reactions. Acc Chem Res 2024; 57:1446-1457. [PMID: 38603772 DOI: 10.1021/acs.accounts.4c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Enzymes are desired catalysts for chemical synthesis, because they can be engineered to provide unparalleled levels of efficiency and selectivity. Yet, despite the astonishing array of reactions catalyzed by natural enzymes, many reactivity patterns found in small molecule catalysts have no counterpart in the living world. With a detailed understanding of the mechanisms utilized by small molecule catalysts, we can identify existing enzymes with the potential to catalyze reactions that are currently unknown in nature. Over the past eight years, our group has demonstrated that flavin-dependent "ene"-reductases (EREDs) can catalyze various radical-mediated reactions with unparalleled levels of selectivity, solving long-standing challenges in asymmetric synthesis.This Account presents our development of EREDs as general catalysts for asymmetric radical reactions. While we have developed multiple mechanisms for generating radicals within protein active sites, this account will focus on examples where flavin mononucleotide hydroquinone (FMNhq) serves as an electron transfer radical initiator. While our initial mechanistic hypotheses were rooted in electron-transfer-based radical initiation mechanisms commonly used by synthetic organic chemists, we ultimately uncovered emergent mechanisms of radical initiation that are unique to the protein active site. We will begin by covering intramolecular reactions and discussing how the protein activates the substrate for reduction by altering the redox-potential of alkyl halides and templating the charge transfer complex between the substrate and flavin-cofactor. Protein engineering has been used to modify the fundamental photophysics of these reactions, highlighting the opportunity to tune these systems further by using directed evolution. This section highlights the range of coupling partners and radical termination mechanisms available to intramolecular reactions.The next section will focus on intermolecular reactions and the role of enzyme-templated ternary charge transfer complexes among the cofactor, alkyl halide, and coupling partner in gating electron transfer to ensure that it only occurs when both substrates are bound within the protein active site. We will highlight the synthetic applications available to this activation mode, including olefin hydroalkylation, carbohydroxylation, arene functionalization, and nitronate alkylation. This section also discusses how the protein can favor mechanistic steps that are elusive in solution for the asymmetric reductive coupling of alkyl halides and nitroalkanes. We are aware of several recent EREDs-catalyzed photoenzymatic transformations from other groups. We will discuss results from these papers in the context of understanding the nuances of radical initiation with various substrates.These biocatalytic asymmetric radical reactions often complement the state-of-the-art small-molecule-catalyzed reactions, making EREDs a valuable addition to a chemist's synthetic toolbox. Moreover, the underlying principles studied with these systems are potentially operative with other cofactor-dependent proteins, opening the door to different types of enzyme-catalyzed radical reactions. We anticipate that this Account will serve as a guide and inspire broad interest in repurposing existing enzymes to access new transformations.
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Affiliation(s)
- Haigen Fu
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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49
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Li Y, Yin D, Lee SY, Lv Y. Engineered polymer nanoparticles as artificial chaperones facilitating the selective refolding of denatured enzymes. Proc Natl Acad Sci U S A 2024; 121:e2403049121. [PMID: 38691587 PMCID: PMC11087784 DOI: 10.1073/pnas.2403049121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/28/2024] [Indexed: 05/03/2024] Open
Abstract
Molecular chaperones assist in protein refolding by selectively binding to proteins in their nonnative states. Despite progress in creating artificial chaperones, these designs often have a limited range of substrates they can work with. In this paper, we present molecularly imprinted flexible polymer nanoparticles (nanoMIPs) designed as customizable biomimetic chaperones. We used model proteins such as cytochrome c, laccase, and lipase to screen polymeric monomers and identify the most effective formulations, offering tunable charge and hydrophobic properties. Utilizing a dispersed phase imprinting approach, we employed magnetic beads modified with destabilized whole-protein as solid-phase templates. This process involves medium exchange facilitated by magnetic pulldowns, resulting in the synthesis of nanoMIPs featuring imprinted sites that effectively mimic chaperone cavities. These nanoMIPs were able to selectively refold denatured enzymes, achieving up to 86.7% recovery of their activity, significantly outperforming control samples. Mechanistic studies confirmed that nanoMIPs preferentially bind denatured rather than native enzymes, mimicking natural chaperone interactions. Multifaceted analyses support the functionality of nanoMIPs, which emulate the protective roles of chaperones by selectively engaging with denatured proteins to inhibit aggregation and facilitate refolding. This approach shows promise for widespread use in protein recovery within biocatalysis and biomedicine.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Deping Yin
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
- KAIST Institute for the BioCentury, KAIST Institute for AI, BioProcess Engineering Research Center, BioInformatics Research Center, and Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Yongqin Lv
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
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50
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Syrén PO. Ancestral terpene cyclases: From fundamental science to applications in biosynthesis. Methods Enzymol 2024; 699:311-341. [PMID: 38942509 DOI: 10.1016/bs.mie.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpenes constitute one of the largest family of natural products with potent applications as renewable platform chemicals and medicines. The low activity, selectivity and stability displayed by terpene biosynthetic machineries can constitute an obstacle towards achieving expedient biosynthesis of terpenoids in processes that adhere to the 12 principles of green chemistry. Accordingly, engineering of terpene synthase enzymes is a prerequisite for industrial biotechnology applications, but obstructed by their complex catalysis that depend on reactive carbocationic intermediates that are prone to undergo bifurcation mechanisms. Rational redesign of terpene synthases can be tedious and requires high-resolution structural information, which is not always available. Furthermore, it has proven difficult to link sequence space of terpene synthase enzymes to specific product profiles. Herein, the author shows how ancestral sequence reconstruction (ASR) can favorably be used as a protein engineering tool in the redesign of terpene synthases without the need of a structure, and without excessive screening. A detailed workflow of ASR is presented along with associated limitations, with a focus on applying this methodology on terpene synthases. From selected examples of both class I and II enzymes, the author advocates that ancestral terpene cyclases constitute valuable assets to shed light on terpene-synthase catalysis and in enabling accelerated biosynthesis.
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Affiliation(s)
- Per-Olof Syrén
- School of Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden; School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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