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Biocatalysis in Organic Chemistry and Enzyme Engineering
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Biocatalysis in Organic Chemistry and Enzyme Engineering

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (10 February 2023) | Viewed by 15967

Special Issue Editors

Prof. Dr. Pu Zheng

E-Mail Website
Guest Editor
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
Interests: biocatalysis; biorefinery; fermentation
Dr. Pengcheng Chen

E-Mail Website
Guest Editor
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
Interests: enzyme immobilization; biocatalysis; biomaterial

Special Issue Information

Dear Colleagues,

Humans have utilized enzymes for thousands of years in the form of fermentation to produce and preserve foodstuffs such as cheese, beer, vinegar, and wine. Since the latter half of the 20th century, enzymes as catalysts in synthetic organic chemistry have gained more and more importance. Nevertheless, biocatalysis in organic chemistry suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity, and/or insufficient stability under operating conditions. Developments in enzyme engineering such as recombinant DNA technology and directed evolution are helping us to overcome these limitations. This Special Issue, entitled "Biocatalysis in Organic Chemistry and Enzyme Engineering", is aimed at developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Papers concerning the utilization of natural or engineered enzymes, both free and immobilized, in organic reactions for the production of simple compounds such as biofuels and complex natural products are welcomed. Additionally, we aim to present a discussion of cascade reactions using enzyme mixtures both in vitro and in cells as factories.

Prof. Dr. Pu Zheng
Dr. Pengcheng Chen
Guest Editors

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Keywords

  • More efficient catalysts
  • Enzyme immobilization
  • Biocatalysis in organic systems
  • Value-added products from natural or engineered enzymes
  • Enzyme cascade reaction

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Published Papers (7 papers)

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Research

12 pages, 2442 KiB  
Article
Semi-Rational Design of Diaminopimelate Dehydrogenase from Symbiobacterium thermophilum Improved Its Activity toward Hydroxypyruvate for D-serine Synthesis
by Ziyao Wang, Haojie Qu, Wenqi Li, Yan Xu and Yao Nie
Catalysts 2023, 13(3), 576; https://doi.org/10.3390/catal13030576 - 13 Mar 2023
Cited by 2 | Viewed by 2080
Abstract
D-serine plays an essential role in the field of medicine and cosmetics. Diaminopimelate dehydrogenase (DAPDH) is a kind of oxidoreductase that can reduce keto acid into the corresponding D-amino acid. Because of its high stereoselectivity and lack of by-product production, DAPDH has become [...] Read more.
D-serine plays an essential role in the field of medicine and cosmetics. Diaminopimelate dehydrogenase (DAPDH) is a kind of oxidoreductase that can reduce keto acid into the corresponding D-amino acid. Because of its high stereoselectivity and lack of by-product production, DAPDH has become the preferred enzyme for the efficient one-step synthesis of D-amino acids. However, the types of DAPDH with a reductive amination function reported so far are limited. Although the DAPDH from Symbiobacterium thermophilum (StDAPDH) demonstrates reductive amination activity toward a series of macromolecular keto acids, activity toward hydroxypyruvate (HPPA) for D-serine synthesis has not been reported. In this study, we investigated the activity of the available StDAPDH/H227V toward HPPA by measuring the desired product D-serine. After homologous structure modeling and docking analysis concerning the substrate-binding pocket, four residues, D92, D122, M152, and N253, in the active pocket were predicted for catalyzing HPPA. Through single-point saturation mutation and iterative mutation, a mutant D92E/D122W/M152S was obtained with an 8.64-fold increase in enzyme activity, exhibiting a specific activity of 0.19 U/mg and kcat value of 3.96 s−1 toward HPPA. Using molecular dynamics simulation, it was speculated that the increase in enzyme activity might be related to the change in substrate pocket size and the enhancement of the interactions between the substrate and key residues. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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21 pages, 4484 KiB  
Article
Altering the Regioselectivity of T1 Lipase from Geobacillus zalihae toward sn-3 Acylglycerol Using a Rational Design Approach
by Samah Hashim Albayati, Malihe Masomian, Siti Nor Hasmah Ishak, Adam Thean Chor Leow, Mohd Shukuri Mohamad Ali, Fairolniza Mohd Shariff, Noor Dina Muhd Noor and Raja Noor Zaliha Raja Abd Rahman
Catalysts 2023, 13(2), 416; https://doi.org/10.3390/catal13020416 - 15 Feb 2023
Cited by 4 | Viewed by 2108
Abstract
The regioselectivity characteristic of lipases facilitate a wide range of novel molecule unit constructions and fat modifications. Lipases can be categorized as sn-1,3, sn-2, and random regiospecific. Geobacillus zalihae T1 lipase catalyzes the hydrolysis of the sn-1,3 acylglycerol chain. The [...] Read more.
The regioselectivity characteristic of lipases facilitate a wide range of novel molecule unit constructions and fat modifications. Lipases can be categorized as sn-1,3, sn-2, and random regiospecific. Geobacillus zalihae T1 lipase catalyzes the hydrolysis of the sn-1,3 acylglycerol chain. The T1 lipase structural analysis shows that the oxyanion hole F16 and its lid domain undergo structural rearrangement upon activation. Site-directed mutagenesis was performed by substituting the lid domain residues (F180G and F181S) and the oxyanion hole residue (F16W) in order to study their effects on the structural changes and regioselectivity. The novel lipase mutant 3M switches the regioselectivity from sn-1,3 to only sn-3. The mutant 3M shifts the optimum pH to 10, alters selectivity toward p-nitrophenyl ester selectivity to C14-C18, and maintains a similar catalytic efficiency of 518.4 × 10−6 (s−1/mM). The secondary structure of 3M lipase comprises 15.8% and 26.3% of the α-helix and β-sheet, respectively, with a predicted melting temperature (Tm) value of 67.8 °C. The in silico analysis was conducted to reveal the structural changes caused by the F180G/F181S/F16W mutations in blocking the binding of the sn-1 acylglycerol chain and orientating the substrate to bond to the sn-3 acylglycerol, which resulted in switching the T1 lipase regioselectivity. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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17 pages, 21640 KiB  
Article
Stability Enhancement of Aldehyde Dehydrogenase from Anoxybacillus geothermalis Strain D9 Immobilized onto Seplite LX120
by Wahhida Latip, Nur Ezzati Rosli, Mohd Shukuri Mohamad Ali, Nor Hafizah Ahmad Kamarudin and Raja Noor Zaliha Raja Abd Rahman
Catalysts 2023, 13(2), 368; https://doi.org/10.3390/catal13020368 - 7 Feb 2023
Cited by 4 | Viewed by 1831
Abstract
Enzyme stability is regarded as an important criterion for an industrial biocatalyst. Aldehyde dehydrogenase (ALDH) from A. geothermalis strain D9 was previously reported to exhibit good thermostability. However, this enzyme is still not suited to use in harsh environments. In this current work, [...] Read more.
Enzyme stability is regarded as an important criterion for an industrial biocatalyst. Aldehyde dehydrogenase (ALDH) from A. geothermalis strain D9 was previously reported to exhibit good thermostability. However, this enzyme is still not suited to use in harsh environments. In this current work, we aim to see the viability of ALDH in terms of stability when immobilized into Seplite LX120. The purified ALDH was successfully immobilized via physical adsorption at 4 h with 1.25 mg/mL enzyme loading. The immobilized ALDH exhibited improved stability compared to free ALDH as the optimum temperature increased up to 80 °C and was stable with temperatures ranging from 30 to 90 °C. It was also stable in broad pH, ranging from pH 4 to pH 12. Moreover, more than 50% of the immobilized ALDH activity was retained after being stored at 25 °C and 4 °C for 9 and 11 weeks, respectively. The reusability of immobilized ALDH is up to seven cycles. The corroboration of ALDH immobilized on the Seplite LX120 was verified via Fourier-transform infrared spectroscopy, scanning electron microscopy, and a reduction in the surface area. The improved features of immobilized ALDH, especially in enzyme stability, are important for future applications. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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12 pages, 1643 KiB  
Article
Microfluidics Biocatalysis System Applied for the Synthesis of N-Substituted Benzimidazole Derivatives by Aza-Michael Addition
by Rong-Kuan Jiang, Yue Pan, Li-Hua Du, Ling-Yan Zheng, Zhi-Kai Sheng, Shi-Yi Zhang, Hang Lin, Ao-Ying Zhang, Han-Jia Xie, Zhi-Kai Yang and Xi-Ping Luo
Catalysts 2022, 12(12), 1658; https://doi.org/10.3390/catal12121658 - 16 Dec 2022
Cited by 1 | Viewed by 1584
Abstract
Benzimidazole scaffolds became an attractive subject due to their broad spectrum of pharmacological activities. In this work, a methodology was developed for the synthesis of N-substituted benzimidazole derivatives from benzimidazoles and α, β-unsaturated compounds (acrylonitriles, acrylate esters, phenyl vinyl sulfone) catalyzed by lipase [...] Read more.
Benzimidazole scaffolds became an attractive subject due to their broad spectrum of pharmacological activities. In this work, a methodology was developed for the synthesis of N-substituted benzimidazole derivatives from benzimidazoles and α, β-unsaturated compounds (acrylonitriles, acrylate esters, phenyl vinyl sulfone) catalyzed by lipase TL IM from Thermomyces lanuginosus in continuous-flow microreactors. Investigations were conducted on reaction parameters such as solvent, substrate ratio, reaction temperature, reactant donor/acceptor structures, and reaction time. The transformation is promoted by inexpensive and readily available lipase in methanol at 45 °C for 35 min. A wide range of β-amino sulfone, β-amino nitrile, and β-amino carbonyl compounds were efficiently and selectively synthesized in high yields (76–97%). All in all, a microfluidic biocatalysis system was applied to the synthesis of N-substituted benzimidazole derivatives, and could serve as a promising fast synthesis strategy for further research to develop novel and highly potent active drugs. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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15 pages, 3571 KiB  
Article
CYP153A71 from Alcanivorax dieselolei: Oxidation beyond Monoterminal Hydroxylation of n-Alkanes
by Cheri Louise Jacobs, Rodolpho do Aido-Machado, Carmien Tolmie, Martha Sophia Smit and Diederik Johannes Opperman
Catalysts 2022, 12(10), 1213; https://doi.org/10.3390/catal12101213 - 11 Oct 2022
Cited by 2 | Viewed by 2709
Abstract
Selective oxyfunctionalization of non-activated C–H bonds remains a major challenge in synthetic chemistry. The biocatalytic hydroxylation of non-activated C–H bonds by cytochrome P450 monooxygenases (CYPs), however, offers catalysis with high regio- and stereoselectivity using molecular oxygen. CYP153s are a class of CYPs known [...] Read more.
Selective oxyfunctionalization of non-activated C–H bonds remains a major challenge in synthetic chemistry. The biocatalytic hydroxylation of non-activated C–H bonds by cytochrome P450 monooxygenases (CYPs), however, offers catalysis with high regio- and stereoselectivity using molecular oxygen. CYP153s are a class of CYPs known for their selective terminal hydroxylation of n-alkanes and microorganisms, such as the bacterium Alcanivorax dieselolei, have evolved extensive enzymatic pathways for the oxyfunctionalization of various lengths of n-alkanes, including a CYP153 to yield medium-chain 1-alkanols. In this study, we report the characterization of the terminal alkane hydroxylase from A. dieselolei (CYP153A71) for the oxyfunctionalization of medium-chain n-alkanes in comparison to the well-known CYP153A6 and CYP153A13. Although the expected 1-alkanols are produced, CYP153A71 readily converts the 1-alkanols to the corresponding aldehydes, fatty acids, as well as α,ω-diols. CYP153A71 is also shown to readily hydroxylate medium-chain fatty acids. The X-ray crystal structure of CYP153A71 bound to octanoic acid is solved, yielding an insight into not only the regioselectivity, but also the binding orientation of the substrate, which can be used in future studies to evolve CYP153A71 for improved oxidations beyond terminal n-alkane hydroxylation. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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8 pages, 2121 KiB  
Article
Biosynthesis of 4-hydroxybenzylideneacetone by Whole-Cell Escherichia coli
by Xingmiao Zhu, Pengcheng Chen and Pu Zheng
Catalysts 2022, 12(9), 997; https://doi.org/10.3390/catal12090997 - 4 Sep 2022
Viewed by 1769
Abstract
4-Hydroxy benzylideneacetone (4-HBA) is an organic synthesis intermediate and can be used as a precursor for the synthesis of raspberry ketone. Herein, 2-deoxy-D-ribose 5-phosphate aldolase (DERA) was overexpressed in E. coli BL21 (DE3) as an attractive catalyst for enzymatic aldol reactions. The aldol [...] Read more.
4-Hydroxy benzylideneacetone (4-HBA) is an organic synthesis intermediate and can be used as a precursor for the synthesis of raspberry ketone. Herein, 2-deoxy-D-ribose 5-phosphate aldolase (DERA) was overexpressed in E. coli BL21 (DE3) as an attractive catalyst for enzymatic aldol reactions. The aldol reaction between 4-hydroxybenzaldehyde (4-HBD) and acetone to biosynthesize 4-HBA was catalyzed by whole-cell E. coli BL21 (DE3) (pRSF-Deoc). The yield and 4-HBA concentration were 92.8% and 111.35 mM, respectively, when using 120 mM 4-HBD and acetone as substrates. When the concentration of 4-HBD was increased to 480 mM, 376.4 mM 4-HBA was obtained by a fed-batch strategy with a yield of 78.4%, which was about a 28% improvement compared to the one-time addition strategy. E. coli BL21 (DE3) (pRSF-Deoc) cells were further immobilized with K-carrageenan, and the immobilized cells still maintained a residual activity of above 90% after 10 repeated uses. Our study provides a promising method of biosynthesizing 4-HBA. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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12 pages, 2373 KiB  
Article
Efficient Asymmetric Synthesis of (S)-N-Boc-3-hydroxypiperidine by Coexpressing Ketoreductase and Glucose Dehydrogenase
by Xinxing Gao, Qianqian Pei, Nianqing Zhu, Yi Mou, Jilei Liang, Xin Zhang and Shoushuai Feng
Catalysts 2022, 12(3), 304; https://doi.org/10.3390/catal12030304 - 8 Mar 2022
Cited by 3 | Viewed by 2915
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 [...] Read more.
(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. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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