201
|
Tasnim T, Ayodele MJ, Pitre SP. Recent Advances in Employing Catalytic Donors and Acceptors in Electron Donor-Acceptor Complex Photochemistry. J Org Chem 2022; 87:10555-10563. [PMID: 35904501 DOI: 10.1021/acs.joc.2c01013] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Electron donor-acceptor (EDA) complexes provide a means to initiate radical reactions under visible light irradiation using substrates that do not absorb visible light individually. Catalytic approaches to complex formation are vital for advancing this synthetic strategy as it decouples the complexation and photogeneration of radicals from substrate functionalization, a limitation inherent to stoichiometric approaches that restricts structural diversity. This Synopsis highlights recent developments in EDA complex photochemistry in which either the donor or acceptor are employed catalytically.
Collapse
Affiliation(s)
- Tarannum Tasnim
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| | - Mayokun J Ayodele
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| | - Spencer P Pitre
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| |
Collapse
|
202
|
Zhu J, Yang L, Wu J, Deng Z, Qu X. Engineering Imine Reductase for Efficient Biosynthesis of 1-Aryl-Tetrahydro-β-Carbolines and Their N-Methylation Products. ACS Catal 2022. [DOI: 10.1021/acscatal.1c06012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jinmei Zhu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Lu Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Jiequn Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| |
Collapse
|
203
|
Wu Y, Xu W, Jiao L, Gu W, Du D, Hu L, Lin Y, Zhu C. Nanobiocatalysis: a materials science road to biocatalysis. Chem Soc Rev 2022; 51:6948-6964. [PMID: 35894547 DOI: 10.1039/d1cs01106e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With high activity and specificity to conduct catalysis under mild conditions, enzymes show great promise in many fields. However, they are not acclimatized to environments in practice after leaving the familiar biological conditions. Aiming at this issue, nanobiocatalysis, a fresh area integrating nanotechnology and enzymatic catalysis, is expected to design biocatalysis based on materials science. Specifically, nano-integrated biocatalysis and bio-inspired nanocatalysis are considered as two effective nanobiocatalytic systems to meet different design needs. Notably, both systems are not entirely separated, and the combination of both further sparks more possibilities. This review summarizes the type, construction, and function of nanobiocatalytic systems, analyzing the pros and cons of different strategies. Moreover, the corresponding applications in bioassay, biotherapy, and environmental remediation are highlighted. We hope that the advent of nanobiocatalysis will help in grasping the inherence of biocatalysis and propel biocatalytic applications.
Collapse
Affiliation(s)
- Yu Wu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Weiqing Xu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Lei Jiao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Wenling Gu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Dan Du
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA.
| | - Liuyong Hu
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Hubei Engineering Technology Research Center of Optoelectronic and New Energy Materials, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA.
| | - Chengzhou Zhu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| |
Collapse
|
204
|
Fu Y, Chen H, Fu W, Garcia-Borràs M, Yang Y, Liu P. Engineered P450 Atom-Transfer Radical Cyclases are Bifunctional Biocatalysts: Reaction Mechanism and Origin of Enantioselectivity. J Am Chem Soc 2022; 144:13344-13355. [PMID: 35830682 PMCID: PMC9339536 DOI: 10.1021/jacs.2c04937] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New-to-nature radical biocatalysis has recently emerged as a powerful strategy to tame fleeting open-shell intermediates for stereoselective transformations. In 2021, we introduced a novel metalloredox biocatalysis strategy that leverages the innate redox properties of the heme cofactor of P450 enzymes, furnishing new-to-nature atom-transfer radical cyclases (ATRCases) with excellent activity and stereoselectivity. Herein, we report a combined computational and experimental study to shed light on the mechanism and origins of enantioselectivity for this system. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) calculations revealed an unexpected role of the key beneficial mutation I263Q. The glutamine residue serves as an essential hydrogen bond donor that engages with the carbonyl moiety of the substrate to promote bromine atom abstraction and enhance the enantioselectivity of radical cyclization. Therefore, the evolved ATRCase is a bifunctional biocatalyst, wherein the heme cofactor enables atom-transfer radical biocatalysis, while the hydrogen bond donor residue further enhances the activity and enantioselectivity. Unlike many enzymatic stereocontrol rationales based on a rigid substrate binding model, our computations demonstrate a high degree of rotational flexibility of the allyl moiety in an enzyme-substrate complex and succeeding intermediates. Therefore, the enantioselectivity is controlled by the radical cyclization transition states rather than the substrate orientation in ground-state complexes in the preceding steps. During radical cyclization, anchoring effects of the Q263 residue and steric interactions with the heme cofactor concurrently control the π-facial selectivity, allowing for highly enantioselective C-C bond formation. Our computational findings are corroborated by experiments with ATRCase mutants generated from site-directed mutagenesis.
Collapse
Affiliation(s)
- Yue Fu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Heyu Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Wenzhen Fu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catalisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
205
|
Abstract
The application of biocatalysis in conquering challenging synthesis requires the constant input of new enzymes. Developing novel biocatalysts by absorbing catalysis modes from synthetic chemistry has yielded fruitful new-to-nature enzymes. Organocatalysis was originally bio-inspired and has become the third pillar of asymmetric catalysis. Transferring organocatalytic reactions back to enzyme platforms is a promising approach for biocatalyst creation. Herein, we summarize recent developments in the design of novel biocatalysts that adopt iminium catalysis, a fundamental branch in organocatalysis. By repurposing existing enzymes or constructing artificial enzymes, various biocatalysts for iminium catalysis have been created and optimized via protein engineering to promote valuable abiological transformations. Recent advances in iminium biocatalysis illustrate the power of combining chemomimetic biocatalyst design and directed evolution to generate useful new-to-nature enzymes.
Collapse
Affiliation(s)
- Guangcai Xu
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713AV GroningenThe Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713AV GroningenThe Netherlands
| |
Collapse
|
206
|
A phosphite-based screening platform for identification of enzymes favoring nonnatural cofactors. Sci Rep 2022; 12:12484. [PMID: 35864126 PMCID: PMC9304416 DOI: 10.1038/s41598-022-16599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Enzymes with dedicated cofactor preference are essential for advanced biocatalysis and biomanufacturing, especially when employing nonnatural nicotinamide cofactors in redox reactions. However, directed evolution of an enzyme to switch its cofactor preference is often hindered by the lack of efficient and affordable method for screening as the cofactor per se or the substrate can be prohibitively expensive. Here, we developed a growth-based selection platform to identify nonnatural cofactor-dependent oxidoreductase mutants. The growth of bacteria depended on the nicotinamide cytosine dinucleotide (NCD) mediated conversion of non-metabolizable phosphite into phosphate. The strain BW14329 lacking the ability to oxidize phosphite was suitable as host, and NCD-dependent phosphite dehydrogenase (Pdh*) is essential to the selection platform. Previously confirmed NCD synthetase with NCD synthesis capacity and NCD-dependent malic enzyme were successfully identified by using the platform. The feasibility of this strategy was successfully demonstrated using derived NCD-active malic enzyme as well as for the directed evolution of NCD synthetase in Escherichia coli. A phosphite-based screening platform was built for identification of enzymes favoring nonnatural cofactor NCD. In the future, once Pdh variants favoring other biomimetic or nonnatural cofactors are available this selection platform may be readily redesigned to attain new enzyme variants with anticipated cofactor preference, providing opportunities to further expand the chemical space of redox cofactors in chemical biology and synthetic biology.
Collapse
|
207
|
Zhang Q, Azarin SM, Sarkar CA. Model-guided engineering of DNA sequences with predictable site-specific recombination rates. Nat Commun 2022; 13:4152. [PMID: 35858965 PMCID: PMC9300676 DOI: 10.1038/s41467-022-31538-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Site-specific recombination (SSR) is an important tool in synthetic biology, but its applications are limited by the inability to predictably tune SSR reaction rates. Facile rate manipulation could be achieved by modifying the DNA substrate sequence; however, this approach lacks rational design principles. Here, we develop an integrated experimental and computational method to engineer the DNA attachment sequence attP for predictably modulating the inversion reaction mediated by the recombinase Bxb1. After developing a qPCR method to measure SSR reaction rate, we design, select, and sequence attP libraries to inform a machine-learning model that computes Bxb1 inversion rate as a function of attP sequence. We use this model to predict reaction rates of attP variants in vitro and demonstrate their utility in gene circuit design in Escherichia coli. Our high-throughput, model-guided approach for rationally tuning SSR reaction rates enhances our understanding of recombinase function and expands the synthetic biology toolbox.
Collapse
Affiliation(s)
- Qiuge Zhang
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Samira M. Azarin
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Casim A. Sarkar
- grid.17635.360000000419368657Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| |
Collapse
|
208
|
Lee HS, Park J, Yeon YJ. Biocatalytic valorization of lignin subunit: Screening a carboxylic acid reductase with high substrate preference to syringyl functional group. Enzyme Microb Technol 2022; 161:110099. [PMID: 35905638 DOI: 10.1016/j.enzmictec.2022.110099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Lignin is inexpensive and the most abundant source of biological aromatics. It can be decomposed to three types of subunits, 4-hydroxybenzoic, vanillic and syringic acids, each of which can be valorized to value added compounds. Syringaldehyde is a versatile phenolic aldehyde implicated with multiple bioactive properties as well as intermediates for biofuels. Herein, fourteen microbial carboxylic acid reductases (CARs) were screened for the biocatalysis of the energetically unfavorable reduction of syringic acid to syringaldehyde. Nine CARs were positive to syringic acid reduction, among which Mycobacterium abscessus CAR exhibited the highest analytical yield of the product. By the optimization of the reaction condition, the whole-cell biocatalyst (i.e., recombinant Escherichia coli expressing the gene) successfully converted syringic acid to syringaldehyde with a yield of 90%. Furthermore, structural features of the screened CAR responsible for the specificity toward the syringyl subunit were analyzed that helps to further engineer the biocatalyst for improved performances.
Collapse
Affiliation(s)
- Hoe-Suk Lee
- Department of Biochemical Engineering, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do 25457, Republic of Korea
| | - Jisu Park
- Department of Biochemical Engineering, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do 25457, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do 25457, Republic of Korea.
| |
Collapse
|
209
|
Wang X, Lewis DA, Wang G, Meng T, Zhou S, Zhu Y, Hu D, Gao S, Zhang G. Covalent Organic Frameworks as a Biomacromolecule Immobilization Platform for Biomedical and Related Applications. ADVANCED THERAPEUTICS 2022. [DOI: 10.1002/adtp.202200053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xinyue Wang
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Damani A. Lewis
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Gang Wang
- Department of Respiratory and Critical Care Medicine The First Affiliated Hospital of Anhui Medical University Hefei 230022 China
| | - Tao Meng
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Shengnan Zhou
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Yuheng Zhu
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Danyou Hu
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Shan Gao
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| | - Guiyang Zhang
- Department of Pharmacology, School of Basic Medical Sciences Anhui Medical University Hefei 230032 China
| |
Collapse
|
210
|
Lu Y, Zhang X, Huang Y. Tuning nanozyme property of Co@NC via V doping to construct colorimetric sensor array for quantifying and discriminating antioxidant phenolic compounds. Biosens Bioelectron 2022; 215:114567. [PMID: 35853326 DOI: 10.1016/j.bios.2022.114567] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
Abstract
Through V2O5 etching of ZIF-67 and subsequent pyrolysis in an argon flow, the V doped Co@NC (V/Co@NC) with mixed-valence Co(II)/Co(III) and V(III)/V(IV) was successfully obtained. V doping plays an important role in regulating the enzyme-like activity of Co@NC. Specifically, the Co@NC has both oxidase-like activity and peroxidase-mimic activity, while the V/Co@NC possesses the specific oxidase-like activity. Benefiting from the elevated Co2+ level due to electrons transfer from the reduced V(III) to Co3+ and recyclable redox reactions between the Co(III)/Co(II) and V(IV)/V(III) couples, the V/Co@NC displays 4-fold increase in the oxidase-like activity, smaller Km (0.18 mM) and larger Vmax (4.01 × 10-8 M s-1) toward TMB relative to Co@NC. The origin of V/Co@NC as oxidase mimic is likely attributed to the generation of 1O2 and •OH. Different phenolic compounds (PC), like gallic acid, kaempferol, caffeic acid, quercetin, and catechin, have distinct antioxidant capacity, showing a differential inhibiting effect on the V/Co@NC-TMB system. The different PC antioxidants in the V/Co@NC-TMB system lead to unique decrease in the absorbance at 652 nm (A652), resulting in a unique absorbance signal response mode. By choosing different combinations of A652 signals at various time points, multichannel information can be extracted from a single nanozyme for pattern recognition. Based on this, a colorimetric array sensing platform for the identification of PC is established successfully. Furthermore, the constructed sensor array can be used for quantifying and discriminating multiple PC antioxidants.
Collapse
Affiliation(s)
- Yuwan Lu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Xiaodan Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yuming Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
211
|
Can deep eutectic solvents be the best alternatives to ionic liquids and organic solvents: A perspective in enzyme catalytic reactions. Int J Biol Macromol 2022; 217:255-269. [PMID: 35835302 DOI: 10.1016/j.ijbiomac.2022.07.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/23/2022] [Accepted: 07/07/2022] [Indexed: 01/17/2023]
Abstract
As a new generation of green solvents, deep eutectic solvents (DESs) have been considered as a promising alternative to classical organic solvents and ionic liquids (ILs). DESs are normally formed by two or more components via various h-bonds interactions. Up to date, four types of DESs are found, namely, type I DESs (formed by MClx, namely FeCl2, AlCl3, ZnCl2, CuCl2 and AgCl et al., and quaternary ammonium salts); type II DESs (formed by metal chloride hydrates and quaternary ammonium salts); type III DESs (formed by choline chlorides and different kinds of HBDs) and type IV DESs (formed by salts of transition metals and urea). DESs share many advantages, such as low vapor pressure, good substrate solubility and thermal stability, with ILs, and offering a high potential to be the medium of biocatalysis reactions. In this case, this paper reviews the applications of DESs in enzymatic reactions. Lipases are the most widely used enzyme in DESs systems as their versatile applications in various reactions and robustness. Interestingly, DESs can improve the efficiency of these reactions via enhancing the substrates solubility and the activity and stability of enzymes. Therefore, the directed engineering of DESs for special reactions such as degradation of polymers in high temperature or strong acid-base conditions will be one of the future perspectives of the investigation DESs.
Collapse
|
212
|
Huang C, Liu J, Fang J, Jia X, Zheng Z, You S, Qin B. Ketoreductase Catalyzed (Dynamic) Kinetic Resolution for Biomanufacturing of Chiral Chemicals. Front Bioeng Biotechnol 2022; 10:929784. [PMID: 35845398 PMCID: PMC9280296 DOI: 10.3389/fbioe.2022.929784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/16/2022] [Indexed: 11/25/2022] Open
Abstract
Biocatalyzed asymmetric reduction of ketones is an environmentally friendly approach and one of the most cost-effective routes for producing chiral alcohols. In comparison with the well-studied reduction of prochiral ketones to generate chiral alcohols with one chiral center, resolution of racemates by ketoreductases (KREDs) to produce chiral compounds with at least two chiral centers is also an important strategy in asymmetric synthesis. The development of protein engineering and the combination with chemo-catalysts further enhanced the application of KREDs in the efficient production of chiral alcohols with high stereoselectivity. This review discusses the advances in the research area of KRED catalyzed asymmetric synthesis for biomanufacturing of chiral chemicals with at least two chiral centers through the kinetic resolution (KR) approach and the dynamic kinetic resolution (DKR) approach.
Collapse
Affiliation(s)
- Chenming Huang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Junling Liu
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jiali Fang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Xian Jia
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Zhendong Zheng
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Song You
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang, China
| | - Bin Qin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| |
Collapse
|
213
|
Jin C, Li N, Lin E, Chen X, Wang T, Wang Y, Yang M, Liu W, Yu J, Zhang Z, Chen Y. Enzyme Immobilization in Porphyrinic Covalent Organic Frameworks for Photoenzymatic Asymmetric Catalysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chaonan Jin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - En Lin
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuepeng Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Ting Wang
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Mingfang Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Wansheng Liu
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiangyue Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Zhenjie Zhang
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yao Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
- National Institute for Advanced Materials, Nankai University, Tianjin 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300071, China
| |
Collapse
|
214
|
Li W, Bilal M, Singh AK, Sher F, Ashraf SS, Franco M, Américo-Pinheiro JHP, Iqbal HMN. Broadening the Scope of Biocatalysis Engineering by Tailoring Enzyme Microenvironment: A Review. Catal Letters 2022. [DOI: 10.1007/s10562-022-04065-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
215
|
Bipyridines mediate electron transfer from an electrode to nicotinamide adenine dinucleotide phosphate. PLoS One 2022; 17:e0269693. [PMID: 35709186 PMCID: PMC9202866 DOI: 10.1371/journal.pone.0269693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/25/2022] [Indexed: 11/30/2022] Open
Abstract
Biocatalysts are widely used in industry, but few examples of the use of oxidoreductases, in which enzymatic function often requires electrons, have been reported. NADPH is a cofactor that supplies an electron to oxidoreductases, but is consequently inactivated and no longer able to act as an electron donor. NADP+ can not receive electrons from electrodes through straightforward electrochemistry owing to its complicated three-dimensional structure. This study reports that bipyridines effectively mediate electron transfer between an electrode and NADP+, allowing them to serve as electron mediators for NADPH production. Using bipyridines, quinones, and anilines, which have negative oxidation–reduction potentials, an electrochemical investigation was conducted into whether electrons were transferred to NADP+. Only bipyridines with a reduction potential near -1.0 V exhibited electron transfer. Furthermore, the NADPH production level was measured using spectroscopy. NADPH was efficiently produced using bipyridines, such as methyl viologen and ethyl viologen, in which the bipyridyl 1- and 1’-positions bear small substituents. However, methyl viologen caused a dehydrogenation reaction of NADPH, making it unsuitable as an electron mediator for NADPH production. The dehydrogenation reaction did not occur using ethyl viologen. These results indicated that NADP+ can be reduced more effectively using substituents that prevent a dehydrogenation reaction at the bipyridyl 1- and 1’-positions while maintaining the reducing power.
Collapse
|
216
|
Shin KC, Seo MJ, Kim YS, Yeom SJ. Molecular Properties of β-Carotene Oxygenases and Their Potential in Industrial Production of Vitamin A and Its Derivatives. Antioxidants (Basel) 2022; 11:1180. [PMID: 35740077 PMCID: PMC9227343 DOI: 10.3390/antiox11061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
β-Carotene 15,15'-oxygenase (BCO1) and β-carotene 9',10'-oxygenase (BCO2) are potential producers of vitamin A derivatives, since they can catalyze the oxidative cleavage of dietary provitamin A carotenoids to retinoids and derivative such as apocarotenal. Retinoids are a class of chemical compounds that are vitamers of vitamin A or are chemically related to it, and are essential nutrients for humans and highly valuable in the food and cosmetics industries. β-carotene oxygenases (BCOs) from various organisms have been overexpressed in heterogeneous bacteria, such as Escherichia coli, and their biochemical properties have been studied. For the industrial production of retinal, there is a need for increased production of a retinal producer and biosynthesis of retinal using biocatalyst systems improved by enzyme engineering. The current review aims to discuss BCOs from animal, plants, and bacteria, and to elaborate on the recent progress in our understanding of their functions, biochemical properties, substrate specificity, and enzyme activities with respect to the production of retinoids in whole-cell conditions. Moreover, we specifically propose ways to integrate BCOs into retinal biosynthetic bacterial systems to improve the performance of retinal production.
Collapse
Affiliation(s)
- Kyung-Chul Shin
- Department of Integrative Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea;
| | - Min-Ju Seo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Yeong-Su Kim
- Wild Plants Industrialization Research Division, Baekdudaegan National Arboretum, Bonghwa 36209, Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| |
Collapse
|
217
|
Han K, Na Y, Zhang L, Tezcan FA. Dynamic, Polymer-Integrated Crystals for Efficient, Reversible Protein Encapsulation. J Am Chem Soc 2022; 144:10139-10144. [PMID: 35666988 DOI: 10.1021/jacs.2c02584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystalline materials are increasingly being used as platforms for encapsulating proteins to create stable, functional materials. However, the uptake efficiencies and stimuli-responsiveness of crystalline frameworks are limited by their rigidities. We have recently reported a new form of materials, polymer-integrated crystals (PIX), which combine the structural order of protein crystals with the dynamic, stimuli-responsive properties of synthetic polymers. Here we show that the crystallinity, flexibility, and chemical tunability of PIX can be exploited to encapsulate guest proteins with high loading efficiencies (up to 46% w/w). The electrostatic host-guest interactions enable reversible, pH-controlled uptake/release of guest proteins as well as the mutual stabilization of the host and the guest, thus creating a uniquely synergistic platform toward the development of functional biomaterials and the controlled delivery of biological macromolecules.
Collapse
Affiliation(s)
- Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ling Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
218
|
Abstract
The ability to design efficient enzymes from scratch would have a profound effect on chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past decade makes us optimistic that this ambition is within reach. The development of artificial enzymes containing metal cofactors and noncanonical organocatalytic groups shows how protein structure can be optimized to harness the reactivity of nonproteinogenic elements. In parallel, computational methods have been used to design protein catalysts for diverse reactions on the basis of fundamental principles of transition state stabilization. Although the activities of designed catalysts have been quite low, extensive laboratory evolution has been used to generate efficient enzymes. Structural analysis of these systems has revealed the high degree of precision that will be needed to design catalysts with greater activity. To this end, emerging protein design methods, including deep learning, hold particular promise for improving model accuracy. Here we take stock of key developments in the field and highlight new opportunities for innovation that should allow us to transition beyond the current state of the art and enable the robust design of biocatalysts to address societal needs.
Collapse
|
219
|
Chelating Metal Ions in a Metal-Organic Framework for Constructing a Biomimetic Catalyst Through Post-modification. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2125-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
220
|
Iannuzzelli J, Bacik JP, Moore EJ, Shen Z, Irving EM, Vargas DA, Khare SD, Ando N, Fasan R. Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Biochemistry 2022; 61:1041-1054. [PMID: 35612958 PMCID: PMC9178789 DOI: 10.1021/acs.biochem.2c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/04/2022] [Indexed: 11/30/2022]
Abstract
Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether "staples" into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with p-chloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔTm' = +27 °C) and temperature-induced heme loss (ΔT50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.
Collapse
Affiliation(s)
- Jacob
A. Iannuzzelli
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - John-Paul Bacik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Eric J. Moore
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Zhuofan Shen
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Ellen M. Irving
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sagar D. Khare
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Nozomi Ando
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| |
Collapse
|
221
|
Wang Y, Jin Y, Wang Z, Xiao G, Su H. A Light‐Dark Cascade Procedure for the Regeneration of NADH using Graphitic Carbon Nitride Nanosheets. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yaoqiang Wang
- Beijing University of Chemical Technology College of Life Science and Technology CHINA
| | - Yu Jin
- Beijing University of Chemical Technology College of Life Science and Technology CHINA
| | - Zishuai Wang
- Beijing University of Chemical Technology College of Life Science and Technology CHINA
| | - Gang Xiao
- Beijing University of Chemical Technology College of Life Science and Technology CHINA
| | - Haijia Su
- Beijing University of Chemical Technology College of Life Science and Technology No. 15 North 3rd Ring, RD East, Chaoyang District 100029 Beijing CHINA
| |
Collapse
|
222
|
Burnett JWH, Chen H, Li J, Li Y, Huang S, Shi J, McCue AJ, Howe RF, Minteer SD, Wang X. Supported Pt Enabled Proton-Driven NAD(P) + Regeneration for Biocatalytic Oxidation. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20943-20952. [PMID: 35482431 DOI: 10.1021/acsami.2c01743] [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: 06/14/2023]
Abstract
The utilization of biocatalytic oxidations has evolved from the niche applications of the early 21st century to a widely recognized tool for general chemical synthesis. One of the major drawbacks that hinders commercialization is the dependence on expensive nicotinamide adenine dinucleotide (NAD(P)+) cofactors, and so, their regeneration is essential. Here, we report the design of carbon-supported Pt catalysts that can regenerate NAD(P)+ by proton-driven NAD(P)H oxidation with concurrent hydrogen formation. The carbon support was modified to tune the electronic nature of the Pt nanoparticles, and it was found that the best catalyst for NAD(P)+ regeneration (TOF = 581 h-1) was electron-rich Pt on carbon. Finally, the heterogeneous Pt catalyst was applied in the biocatalytic oxidation of a variety of alcohols catalyzed by different alcohol dehydrogenases. The Pt catalyst exhibited good compatibility with the biocatalytic system. Its NAD(P)+ regeneration function successfully supported biocatalytic conversion from alcohols to corresponding ketone or lactone products. This work provides a promising strategy for chemical synthesis via NAD(P)+-dependent pathways utilizing a cooperative inorganic-enzymatic catalytic system.
Collapse
Affiliation(s)
- Joseph W H Burnett
- Chemical Engineering, Department of Engineering, Lancaster University, Lancaster LA1 4YW, United Kingdom
- Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Hui Chen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jianwei Li
- Chemical Engineering, Department of Engineering, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Ying Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 30072, China
| | - Shouying Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 30072, China
| | - Jiafu Shi
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Alan J McCue
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Russell F Howe
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Xiaodong Wang
- Chemical Engineering, Department of Engineering, Lancaster University, Lancaster LA1 4YW, United Kingdom
| |
Collapse
|
223
|
Zhou Z, He W, Chao H, Wang H, Su P, Song J, Yang Y. Insertion of Hemin into Metal-Organic Frameworks: Mimicking Natural Peroxidase Microenvironment for the Rapid Ultrasensitive Detection of Uranium. Anal Chem 2022; 94:6833-6841. [PMID: 35482423 DOI: 10.1021/acs.analchem.2c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Constructing enzyme-like active sites in mimic enzyme systems is critical for achieving catalytic performances comparable to natural enzymes and can shed light on the natural development of enzymes. In this study, we described a specific hemin-based mimetic enzyme, which was facilely synthesized by the assembly of zeolitic imidazolate framework-l (ZIF-l) and hemin. The obtained hemin-based mimetic enzyme (denoted as ZIF-l-hemin) displayed enhanced peroxidase activity compared to free hemin in solution. Such excellent activity originated from the ZIF-l framework mimicking the active site cavity microenvironment of horseradish peroxidase in terms of axially coordinated histidine and distal histidine. Additionally, the constructed peroxidase mimetic was extremely resistant to a variety of severe circumstances that would normally denature natural enzymes. These characteristics made ZIF-l-hemin a potential platform for the colorimetric sensor of uranium (UO22+) with wide linear ranges (0.25-40 μM) and low limits of detection (0.079 μM). Moreover, the detection mechanism demonstrated that the coordination of uranyl ion with imidazole of ZIF-l-hemin reduced the catalytic efficiency of ZIF-l-hemin. The current work not only proposed a novel approach for fabricating artificial peroxidase but also offered facile colorimetric methods for selective radionuclide detection.
Collapse
Affiliation(s)
- Zixin Zhou
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Wenting He
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hao Chao
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Han Wang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| |
Collapse
|
224
|
Xu G, Poelarends GJ. Unlocking New Reactivities in Enzymes by Iminium Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guangcai Xu
- University of Groningen: Rijksuniversiteit Groningen Chemical and Pharmaceutical Biology NETHERLANDS
| | - Gerrit J. Poelarends
- University of Groningen Chemical and Pharmaceutical Biology Antonius Deusinglaan 1 9713 AV Groningen NETHERLANDS
| |
Collapse
|
225
|
Woodley JM. Ensuring the Sustainability of Biocatalysis. CHEMSUSCHEM 2022; 15:e202102683. [PMID: 35084801 DOI: 10.1002/cssc.202102683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Biocatalysis offers many attractive features for the synthetic chemist. In many cases, the high selectivity and ability to tailor specific enzyme features via protein engineering already make it the catalyst of choice. From the perspective of sustainability, several features such as catalysis under mild conditions and use of a renewable and biodegradable catalyst also look attractive. Nevertheless, to be sustainable at a larger scale it will be essential to develop processes operating at far higher concentrations of product, and which make better use of the enzyme via improved stability. In this Concept, it is argued that a particular emphasis on these specific metrics is of particular importance for the future implementation of biocatalysis in industry, at a level that fulfills its true potential.
Collapse
Affiliation(s)
- John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| |
Collapse
|
226
|
Yan X, Zhang J, Tan H, Liu Z, Jiang K, Tian W, Zheng M, Lin Z, Deng Z, Qu X. A Pair of Atypical KAS III Homologues with Initiation and Elongation Functions Program the Polyketide Biosynthesis in Asukamycin. Angew Chem Int Ed Engl 2022; 61:e202200879. [DOI: 10.1002/anie.202200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaoli Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Hongqun Tan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhihao Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Kai Jiang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| |
Collapse
|
227
|
Huang X, Yang Y. The Many Facets of Green Organometallic Chemistry: A Foreword. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
228
|
Xu W, Chen Y, Li D, Wang Z, Xu J, Wu Q. Rational design of fatty acid photodecarboxylase enables the efficient decarboxylation of medium- and short-chain fatty acids for the production of gasoline bio-alkanes. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
229
|
García-Cebollada H, López A, Sancho J. Protposer: the web server that readily proposes protein stabilizing mutations with high PPV. Comput Struct Biotechnol J 2022; 20:2415-2433. [PMID: 35664235 PMCID: PMC9133766 DOI: 10.1016/j.csbj.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mutations. Unfortunately, even the best currently used predictors fail to compute the stability of protein variants with sufficient accuracy and their usefulness as tools to guide the rational stabilisation of proteins is limited. We present here Protposer, a protein stabilising tool based on a different approach. Instead of quantifying changes in stability, Protposer uses structure- and sequence-based screening modules to nominate candidate mutations for subsequent evaluation by a logistic regression model, carefully trained to avoid overfitting. Thus, Protposer analyses PDB files in search for stabilization opportunities and provides a ranked list of promising mutations with their estimated success rates (eSR), their probabilities of being stabilising by at least 0.5 kcal/mol. The agreement between eSRs and actual positive predictive values (PPV) on external datasets of mutations is excellent. When Protposer is used with its Optimal kappa selection threshold, its PPV is above 0.7. Even with less stringent thresholds, Protposer largely outperforms FoldX, Rosetta and PoPMusiC. Indicating the PDB file of the protein suffices to obtain a ranked list of mutations, their eSRs and hints on the likely source of the stabilization expected. Protposer is a distinct, straightforward and highly successful tool to design protein stabilising mutations, and it is freely available for academic use at http://webapps.bifi.es/the-protposer.
Collapse
|
230
|
Wang R, Zhang J, Luo Z, Xie T, Xiao Q, Pei X, Wang A. Controllably crosslinked dual enzymes enabled by genetic-encoded non-standard amino acid for efficiently enantioselective hydrogenation. Int J Biol Macromol 2022; 205:682-691. [PMID: 35247424 DOI: 10.1016/j.ijbiomac.2022.02.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/30/2022] [Accepted: 02/26/2022] [Indexed: 12/17/2022]
Abstract
In traditional method for preparing crosslinked enzymes aggregates using glutaraldehyde, random linkage is inevitable, which often destroys the enzyme active sites and severely decreases the activity. To address this issue, using genetic encode expanding, nonstandard amino acids (NSAAs) were inserted into enzyme proteins at the preselected sites for crosslinking. When aldehyde ketone reductase (AKR), alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) were utilized as model enzymes, their mutants containing p-azido-L-phenylalanine were bio-orthogonally crosslinked with diyne to form crosslinked dual enzymes (CLDEs) acting as a cascade biological oxidation and reduction system. Then, the resultant self-purified CLDEs were characterized using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM), etc. In the asymmetric synthesis of (S)-1-(2,6-dichloro-3-fluorophenyl) ethanol using CLDEs, high product yield (76.08%), ee value (99.99%) and reuse stability were achieved. The yield and ee value were 12.05 times and 1.39 times higher than those using traditional crosslinked enzyme aggregates, respectively. Thus, controllable insertion NSAAs in number and location can engender reasonable linkage and metal-free self-purification for target enzyme proteins. This facile and sustainable method could be further expanded to other dual and multienzyme systems for cascade biocatalysis.
Collapse
Affiliation(s)
- Ru Wang
- College of Medicine, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Jing Zhang
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Tian Xie
- College of Medicine, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China.
| |
Collapse
|
231
|
Wang L, Wei S, Wang X, Lu Y, Zhou X, Wang J. Experimental investigation of optical anisotropy of polymethyl methacrylate aligned by metal–organic framework via in situ polymerization and direct chain‐introduction. J Appl Polym Sci 2022. [DOI: 10.1002/app.52471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Lele Wang
- School of Telecommunication and Information Engineering Nanjing University of Posts and Telecommunications Nanjing China
| | - Shuli Wei
- School of Telecommunication and Information Engineering Nanjing University of Posts and Telecommunications Nanjing China
| | - Xianling Wang
- School of Telecommunication and Information Engineering Nanjing University of Posts and Telecommunications Nanjing China
| | - Yunqing Lu
- School of Telecommunication and Information Engineering Nanjing University of Posts and Telecommunications Nanjing China
| | - Xinhui Zhou
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials Nanjing University of Posts & Telecommunications Nanjing China
| | - Jin Wang
- School of Telecommunication and Information Engineering Nanjing University of Posts and Telecommunications Nanjing China
| |
Collapse
|
232
|
Fessner ND, Badenhorst CPS, Bornscheuer UT. Enzyme Kits to Facilitate the Integration of Biocatalysis into Organic Chemistry – First Aid for Synthetic Chemists. ChemCatChem 2022. [DOI: 10.1002/cctc.202200156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nico D. Fessner
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Christoffel P. S. Badenhorst
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Uwe T. Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| |
Collapse
|
233
|
Hayes RL, Vilseck JZ, Brooks CL. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods. J Chem Theory Comput 2022; 18:2114-2123. [PMID: 35255214 PMCID: PMC9700482 DOI: 10.1021/acs.jctc.1c00948] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alchemical free energy methods are playing a growing role in molecular design, both for computer-aided drug design of small molecules and for computational protein design. Multisite λ dynamics (MSλD) is a uniquely scalable alchemical free energy method that enables more efficient exploration of combinatorial alchemical spaces encountered in molecular design, but simulations have typically been limited to a few hundred ligands or sequences. Here, we focus on coupling between sites to enable scaling to larger alchemical spaces. We first discuss updates to the biasing potentials that facilitate MSλD sampling to include coupling terms and show that this can provide more thorough sampling of alchemical states. We then harness coupling between sites by developing a new free energy estimator based on the Potts models underlying direct coupling analysis, a method for predicting contacts from sequence coevolution, and find it yields more accurate free energies than previous estimators. The sampling requirements of the Potts model estimator scale with the square of the number of sites, a substantial improvement over the exponential scaling of the standard estimator. This opens up exploration of much larger alchemical spaces with MSλD for molecular design.
Collapse
Affiliation(s)
- Ryan L Hayes
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jonah Z Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
234
|
Nanoemulsion-directed growth of MOFs with versatile architectures for the heterogeneous regeneration of coenzymes. Nat Commun 2022; 13:1879. [PMID: 35388007 PMCID: PMC8986779 DOI: 10.1038/s41467-022-29535-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/08/2022] [Indexed: 11/08/2022] Open
Abstract
As one of the most appealing strategies for the synthesis of nanomaterials with various architectures, emulsion-directed methods have been rarely used to control the structure of metal-organic frameworks (MOFs). Herein, we report a versatile salt-assisted nanoemulsion-guided assembly to achieve continuous architecture transition of hierarchical Zr-based MOFs. The morphology of nanoemulsion can be facilely regulated by tuning the feed ratio of a dual-surfactant and the introduced amount of compatible hydrophobic compounds, which directs the assembly of MOFs with various architectures such as bowl-like mesoporous particle, dendritic nanospheres, walnut-shaped particles, crumpled nanosheets and nanodisks. The developed dendritic nanospheres with highly open and large mesochannels is successfully used as matrix for the co-immobilization of coenzymes and corresponding enzymes to realize the in situ heterogeneous regeneration of NAD+. This strategy is expected to pave a way for exploring sophisticated hierarchical MOFs which can be competent for practical applications with bulk molecules involved. Controlling the structure of hierarchical metal-organic frameworks via soft template remains a challenge. Here, the authors report a salt-assisted nanoemulsion-guided strategy to achieve continuous structure transition of hierarchical Zr-based MOFs.
Collapse
|
235
|
Kurtuldu A, Eşgin H, Yetim NK, Semerci F. Immobilization Horseradish Peroxidase onto UiO-66-NH2 for Biodegradation of Organic Dyes. J Inorg Organomet Polym Mater 2022. [DOI: 10.1007/s10904-022-02310-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
236
|
Ju SB, Seo MJ, Yeom SJ. In Vitro One-Pot 3-Hydroxypropanal Production from Cheap C1 and C2 Compounds. Int J Mol Sci 2022; 23:ijms23073990. [PMID: 35409349 PMCID: PMC8999356 DOI: 10.3390/ijms23073990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/02/2022] [Accepted: 04/02/2022] [Indexed: 12/04/2022] Open
Abstract
One- or two-carbon (C1 or C2) compounds have been considered attractive substrates because they are inexpensive and abundant. Methanol and ethanol are representative C1 and C2 compounds, which can be used as bio-renewable platform feedstocks for the biotechnological production of value-added natural chemicals. Methanol-derived formaldehyde and ethanol-derived acetaldehyde can be converted to 3-hydroxypropanal (3-HPA) via aldol condensation. 3-HPA is used in food preservation and as a precursor for 3-hydroxypropionic acid and 1,3-propanediol that are starting materials for manufacturing biocompatible plastic and polytrimethylene terephthalate. In this study, 3-HPA was biosynthesized from formaldehyde and acetaldehyde using deoxyribose-5-phosphate aldolase from Thermotoga maritima (DERATma) and cloned and expressed in Escherichia coli for 3-HPA production. Under optimum conditions, DERATma produced 7 mM 3-HPA from 25 mM substrate (formaldehyde and acetaldehyde) for 60 min with 520 mg/L/h productivity. To demonstrate the one-pot 3-HPA production from methanol and ethanol, we used methanol dehydrogenase from Lysinibacillus xylanilyticus (MDHLx) and DERATma. One-pot 3-HPA production via aldol condensation of formaldehyde and acetaldehyde from methanol and ethanol, respectively, was investigated under optimized reaction conditions. This is the first report on 3-HPA production from inexpensive alcohol substrates (methanol and ethanol) by cascade reaction using DERATma and MDHLx.
Collapse
Affiliation(s)
- Su-Bin Ju
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yong-bong-ro 77, Gwangju 61186, Korea;
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea;
| | - Min-Ju Seo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea;
| | - Soo-Jin Yeom
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yong-bong-ro 77, Gwangju 61186, Korea;
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea;
- Correspondence:
| |
Collapse
|
237
|
Crans DC, Brown M, Roess DA. Vanadium compounds promote biocatalysis in cells through actions on cell membranes. Catal Today 2022. [DOI: 10.1016/j.cattod.2020.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
238
|
Current Trends in Acetins Production: Green versus Non-Green Synthesis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072255. [PMID: 35408654 PMCID: PMC9000466 DOI: 10.3390/molecules27072255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022]
Abstract
To utilize excess glycerol produced from the biodiesel industry, researchers are developing innovative methods of transforming glycerol into value-added chemicals. One strategy adopted is the conversion of glycerol into acetins, which are esters of glycerol that have wide applications in cosmetics, pharmaceuticals, food and fuel additives, and plasticizers and serve as precursors for other chemical compounds. Acetins are synthesized either by traditional chemical methods or by biological processes. Although the chemical methods are efficient, productive, and commercialized, they are "non-green", meaning that they are unsafe for the environment and consumers. On the other hand, the biological process is "green" in the sense that it protects both the environment and consumers. It is, however, less productive and requires further effort to achieve commercialization. Thus, both methodologies have benefits and drawbacks, and this study aims to present and discuss these. In addition, we briefly discuss general strategies for optimizing biological processes that could apply to acetins production on an industrial scale.
Collapse
|
239
|
Zetzsche LE, Chakrabarty S, Narayan ARH. The Transformative Power of Biocatalysis in Convergent Synthesis. J Am Chem Soc 2022; 144:5214-5225. [PMID: 35290055 PMCID: PMC10082969 DOI: 10.1021/jacs.2c00224] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Achieving convergent synthetic strategies has long been a gold standard in constructing complex molecular skeletons, allowing for the rapid generation of complexity in comparatively streamlined synthetic routes. Traditionally, biocatalysis has not played a prominent role in convergent laboratory synthesis, with the application of biocatalysts in convergent strategies primarily limited to the synthesis of chiral fragments. Although the use of enzymes to enable convergent synthetic approaches is relatively new and emerging, combining the efficiency of convergent transformations with the selectivity achievable through biocatalysis creates new opportunities for efficient synthetic strategies. This Perspective provides an overview of recent developments in biocatalytic strategies for convergent transformations and offers insights into the advantages of these methods compared to their small molecule-based counterparts.
Collapse
Affiliation(s)
- Lara E. Zetzsche
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Suman Chakrabarty
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alison R. H. Narayan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| |
Collapse
|
240
|
Taily IM, Saha D, Banerjee P. Direct Synthesis of Paracetamol via Site-Selective Electrochemical Ritter-type C-H Amination of Phenol. Org Lett 2022; 24:2310-2314. [PMID: 35312329 DOI: 10.1021/acs.orglett.2c00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The synthesis of paracetamol still relies on multistep protocols involving the utilization of a stoichiometric amount of oxidizing/reducing or other corrosive agents. Herein we report a regioselective electrochemical Ritter-type reaction at the C(sp2)-H of unprotected phenol toward the environmentally benign and direct synthesis of paracetamol. The reaction proceeds under exogenous oxidant- and catalyst-free conditions. The protocol is scalable, can be deployed to a variety of phenols, and offers a sustainable alternative for the synthesis of paracetamol.
Collapse
Affiliation(s)
- Irshad Maajid Taily
- Department of Chemistry, Indian Institute of Technology Ropar, Lab no. 406, S. S. Bhatnagar Block, Rupnagar, Punjab 140001, India
| | - Debarshi Saha
- Department of Chemistry, Indian Institute of Technology Ropar, Lab no. 406, S. S. Bhatnagar Block, Rupnagar, Punjab 140001, India
| | - Prabal Banerjee
- Department of Chemistry, Indian Institute of Technology Ropar, Lab no. 406, S. S. Bhatnagar Block, Rupnagar, Punjab 140001, India
| |
Collapse
|
241
|
Parvez A, Ravikumar Y, Bisht R, Yun J, Wang Y, Chandrika SP, Zabed HM, Qi X. Functional and Structural Roles of the Dimer Interface in the Activity and Stability of Clostridium butyricum 1,3-Propanediol Oxidoreductase. ACS Synth Biol 2022; 11:1261-1271. [PMID: 35258945 DOI: 10.1021/acssynbio.1c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosynthesis of 1,3-propanediol (1,3-PD) by 1,3-propanediol oxidoreductase (PDOR) is often limited by the stability issues. To address this issue, the goal of the present study was to engineer the Clostridium butyricum PDOR dimeric interface. The interface exists between the chains and plays a role in the synthesis of 1,3-PD, which is hindered by the increased temperature and pH. Herein, we engineered PDOR by HotSpot Wizard 3.0 and molecular dynamics simulations, improving its thermal stability, pH tolerance, and catalytic properties with respect to the wild-type PDOR activity at 37 °C. Compared to the activity of the wild-type PDOR, the N298C mutant showed 0.5-fold greater activity at pH 8.0, while the P299E mutant showed significantly increased activity of over five fold at pH 4.0. Further structural comparisons between the wild-type and P299E mutant revealed that the extraordinary stability of the P299E mutant could be due to the formation of additional hydrogen bonds and salt bridges. The N298C mutant also exhibits thermal stability at a broad range of temperature at pH 8 with respect to wild-type PDOR and other mutants. The molecular dynamics simulations revealed that stability profiles of P299E mutants at pH 4.0 are attributed to identical root mean square deviation values and stable conformations in the motif region present in the dimer interface of the enzyme. These findings suggest that the dimer interface motifs are essential for the compactness and stability of the PDOR enzyme; therefore, engineering the PDOR using a structure-guided approach could aid in improving its activity and stability under various physiological conditions (pH and temperature).
Collapse
Affiliation(s)
- Amreesh Parvez
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Yuvaraj Ravikumar
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Renu Bisht
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi 110021, India
| | - Junhua Yun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Yang Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Sabapathy Poorna Chandrika
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Hossain M. Zabed
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| |
Collapse
|
242
|
Guo J, Gao X, Qian D, Wang H, Jia X, Zhang W, Qin B, You S. Efficient synthesis of an apremilast precursor and chiral β-hydroxy sulfones via ketoreductase-catalyzed asymmetric reduction. Org Biomol Chem 2022; 20:2081-2085. [PMID: 35179164 DOI: 10.1039/d1ob02485j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ketoreductase (KRED)-catalyzed asymmetric reduction of prochiral ketones is an attractive method to synthesize chiral alcohols. Herein, two KREDs LfSDR1-V186A/E141I and CgKR1-F92I with complementary stereopreference were identified towards reduction of apremilast prochiral ketone intermediate 1a. LfSDR1-V186A/E141I exhibited >99% conversion and 99.2% ee yielding an apremilast chiral alcohol intermediate ((R)-2a) at 50 g L-1 substrate loading. Furthermore, we investigated the substrate scope of β-keto sulfones by using LfSDR1-V186A/E141I and CgKR1-F92I to produce both enantiomers of the corresponding β-hydroxy sulfones, with good-to-excellent conversion (up to >99%) and enantioselectivity (up to 99.9% ee) being obtained in most cases. Finally, the gram-scale synthesis of (R)-2a was performed by employing the crude enzyme of LfSDR1-V186A/E141I and BsGDH to afford the desired enantiomer with >99% conversion, 85.9% isolated yield and 99.2% ee. This study presents a biocatalytic strategy to synthesize chiral β-hydroxy sulfones.
Collapse
Affiliation(s)
- Jiyang Guo
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Xiao Gao
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Dong Qian
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Huibin Wang
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Xian Jia
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Wenhe Zhang
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Bin Qin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| | - Song You
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China.
| |
Collapse
|
243
|
Ling FWM, Abdulbari HA, Chin SY. Heterogeneous Microfluidic Reactors: A Review and an Insight of Enzymatic Reactions. CHEMBIOENG REVIEWS 2022. [DOI: 10.1002/cben.202100058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Fiona W. M. Ling
- Universiti Malaysia Pahang Centre for Research in Advanced Fluid & Processes (FLUID CENTRE) Lebuhraya Tun Razak 26300 Gambang, Kuantan Pahang Malaysia
- Universiti Malaysia Pahang Department of Chemical Engineering, College of Engineering Lebuhraya Tun Razak 26300 Gambang, Kuantan Pahang Malaysia
| | - Hayder A. Abdulbari
- Universiti Malaysia Pahang Centre for Research in Advanced Fluid & Processes (FLUID CENTRE) Lebuhraya Tun Razak 26300 Gambang, Kuantan Pahang Malaysia
- Universiti Malaysia Pahang Department of Chemical Engineering, College of Engineering Lebuhraya Tun Razak 26300 Gambang, Kuantan Pahang Malaysia
| | - Sim Yee Chin
- Universiti Malaysia Pahang Department of Chemical Engineering, College of Engineering Lebuhraya Tun Razak 26300 Gambang, Kuantan Pahang Malaysia
| |
Collapse
|
244
|
Efficient Asymmetric Synthesis of (S)-N-Boc-3-Hydroxypiperidine by Coexpressing Ketoreductase and Glucose Dehydrogenase. Catalysts 2022. [DOI: 10.3390/catal12030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
(S)-N-Boc-3-hydroxypiperidine is an important intermediate of the anticancer drug ibrutinib and is mainly synthesized by the asymmetric reduction catalyzed by ketoreductase coupled with glucose dehydrogenase at present. In this study, the coexpression recombinant strains E. coli/pET28-K-rbs-G with single promoter and E. coli/pETDuet-K-G with double promoters were first constructed for the coexpression of ketoreductase and glucose dehydrogenase in the same cell. Then, the catalytic efficiency of E. coli/pET28-K-rbs-G for synthesizing (S)-N-Boc-3-hydroxypiperidine was found to be higher than that of E. coli/pETDuet-K-G due to the more balanced activity ratio and higher catalytic activity. On this basis, the catalytic conditions of E. coli/pET28-K-rbs-G were further optimized, and finally both the conversion of the reaction and the optical purity of the product were higher than 99%. In the end, the cell-free extract was proved to be a better catalyst than the whole cell with the improved catalytic efficiency of different recombinant strains. This study developed a better coexpression strategy for ketoreductase and glucose dehydrogenase by investigating the effect of activity ratios and forms of the biocatalysts on the catalytic efficiency deeply, which provided a research basis for the efficient synthesis of chiral compounds.
Collapse
|
245
|
Meyer J, Meyer L, Kara S. Enzyme immobilization in hydrogels: A perfect liaison for efficient and sustainable biocatalysis. Eng Life Sci 2022; 22:165-177. [PMID: 35382546 PMCID: PMC8961036 DOI: 10.1002/elsc.202100087] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Biocatalysis is an established chemical synthesis technology that has by no means been restricted to research laboratories. The use of enzymes for organic synthesis has evolved greatly from early development to proof-of-concept - from small batch production to industrial scale. Different enzyme immobilization strategies contributed to this success story. Recently, the use of hydrogel materials for the immobilization of enzymes has been attracting great interest. Within this review, we pay special attention to recent developments in this key emerging field of research. Firstly, we will briefly introduce the concepts of both biocatalysis and hydrogel worlds. Then, we list recent interesting publications that link both concepts. Finally, we provide an outlook and comment on future perspectives of further exploration of enzyme immobilization strategies in hydrogels.
Collapse
Affiliation(s)
- Johanna Meyer
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Lars‐Erik Meyer
- Biocatalysis and Bioprocessing GroupDepartment of Biological and Chemical EngineeringAarhus UniversityAarhusDenmark
| | - Selin Kara
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
- Biocatalysis and Bioprocessing GroupDepartment of Biological and Chemical EngineeringAarhus UniversityAarhusDenmark
| |
Collapse
|
246
|
|
247
|
Bering L, Thompson J, Micklefield J. New reaction pathways by integrating chemo- and biocatalysis. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
248
|
|
249
|
Yan X, Zhang J, Tan H, Liu Z, Jiang K, Tian W, Zheng M, Lin Z, Deng Z, Qu X. A Pair of Atypical KAS III Homologues with Initiation and Elongation Functions Program the Polyketide Biosynthesis in Asukamycin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaoli Yan
- Wuhan University School of pharmaceutical Sciences CHINA
| | - Jun Zhang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Hongqun Tan
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhihao Liu
- Wuhan University School of pharmaceutical Sciences CHINA
| | - Kai Jiang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Wenya Tian
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Mengmeng Zheng
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhi Lin
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zixin Deng
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xudong Qu
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology 800 Dongchuan Rd. 200240 Shanghai CHINA
| |
Collapse
|
250
|
Xue Y, Zhang XG, Lu ZP, Xu C, Xu HJ, Hu Y. Enhancing the Catalytic Performance of Candida antarctica Lipase B by Chemical Modification With Alkylated Betaine Ionic Liquids. Front Bioeng Biotechnol 2022; 10:850890. [PMID: 35265607 PMCID: PMC8899502 DOI: 10.3389/fbioe.2022.850890] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
Various betaine ionic liquids composed of different chain lengths and different anions were designed and synthesized to modify Candida antarctica lipase B (CALB). The results showed that the catalytic activity of all modified lipases improved under different temperature and pH conditions, while also exhibiting enhanced thermostability and tolerance to organic solvents. With an increase in ionic liquid chain length, the modification effect was greater. Overall, CALB modified by [BetaineC16][H2PO4] performed best, with the modified CALB enzyme activity increased 3-fold, thermal stability increased 1.5-fold when stored at 70°C for 30 min, with tolerance increased 2.9-fold in 50% DMSO and 2.3-fold in 30% mercaptoethanol. Fluorescence and circular dichroism (CD) spectroscopic analysis showed that the introduction of an ionic liquid caused changes in the microenvironment surrounding some fluorescent groups and the secondary structure of the CALB enzyme protein. In order to establish the enzyme activity and stability change mechanisms of the modified CALB, the structures of CALB modified with [BetaineC4][Cl] and [BetaineC16][Cl] were constructed, while the reaction mechanisms were studied by molecular dynamics simulations. Results showed that the root mean square deviation (RMSD) and total energy of modified CALB were less than those of native CALB, indicating that modified CALB has a more stable structure. Root mean square fluctuation (RMSF) calculations showed that the rigidity of modified CALB was enhanced. Solvent accessibility area (SASA) calculations exhibited that both the hydrophilicity and hydrophobicity of the modified enzyme-proteins were improved. The increase in radial distribution function (RDF) of water molecules confirmed that the number of water molecules around the active sites also increased. Therefore, modified CALB has enhanced structural stability and higher hydrolytic activity.
Collapse
Affiliation(s)
| | | | | | | | | | - Yi Hu
- *Correspondence: Hua-Jin Xu, ; Yi Hu,
| |
Collapse
|