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Catalysts
Special Issues
State-of-the-Art Enzyme Engineering and Biocatalysis in China
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State-of-the-Art Enzyme Engineering and Biocatalysis in China

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 5718

Special Issue Editors

Dr. Jing Zhao

E-Mail Website
Guest Editor
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, #368 Youyi Road, Wuhan 430062, China
Interests: enzyme engineering; biocatalysis; computational biology; multienzyme cascade reaction
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiandong Zhang

E-Mail Website
Guest Editor
Department of Biological and Pharmaceutical Engineering, College of Biomedical Engineering, Taiyuan University of Technology, No.79 West Yingze Street, Taiyuan 030024, China
Interests: biocatalysis; enzyme discovery; enzyme engineering; cascade biocatalysis

Special Issue Information

Dear Colleagues,

Enzyme engineering and biocatalysis have emerged as powerful tools in various fields of science and industry. These disciplines involve the modification and utilization of enzymes to perform specific reactions, leading to improved catalytic properties and expanded applicability. In recent years, there has been growing interest in enzyme engineering and biocatalysis in China, driven by the need for sustainable and efficient processes in areas such as pharmaceuticals, biofuels, food production, and environmental remediation. The advancements in this field have not only provided novel solutions to complex challenges but also paved the way for the development of greener and more sustainable technologies.

This Special Issue aims to showcase the latest research and advancements in this rapidly evolving field. This collection of articles and reviews brings together contributions from leading scientists and researchers in China, highlighting the diverse applications of enzyme engineering and biocatalysis. The topics covered in this Special Issue include but are not limited to:

(a) The rational design and directed evolution of enzymes for improved catalytic properties.

(b) Biocatalytic transformations for the synthesis of pharmaceuticals, fine chemicals, and bioactive compounds.

(c) Understanding the enzyme structure–activity relationship and catalytic mechanisms.

(d) Immobilization and bioprocess engineering strategies for enhanced reactor performance and recycling of enzymes.

(e) Multi-enzyme cascade reactions or enzymatic–chemical cascade reactions.

(f) Enzyme design or engineering using artificial intelligence techniques.

This Special Issue provides a comprehensive overview of the current research trends and breakthroughs in enzyme engineering and biocatalysis in China, offering valuable insights and perspectives for researchers, scientists, and industrial practitioners in this field.

Dr. Jing Zhao
Prof. Dr. Jiandong Zhang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Catalysts is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • enzyme
  • biocatalysis
  • enzyme discovery
  • enzyme engineering
  • directed evolution
  • rational design
  • enzyme mechanism
  • machine learning
  • multi-enzymatic synthesis/cell-free biosynthesis
  • chemo-enzymatic synthesis

Published Papers (5 papers)

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Research

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12 pages, 3029 KiB  
Article
Studies on Insertion/Deletion Residues for Functional Analysis and Improved Amination Activity in Meso-DAPDH from Corynebacterium glutamicum
by Yaning Zhang, Jiaying Hao, Yongjun Cao, Wenjun Zhao, Hankun Liu, Xiuzhen Gao and Qinyuan Ma
Catalysts 2024, 14(4), 220; https://doi.org/10.3390/catal14040220 - 22 Mar 2024
Viewed by 800
Abstract
Meso-diaminopimelate dehydrogenase (meso-DAPDH) from Corynebacterium glutamicum ATCC13032 (CgDAPDH) is a type I meso-DAPDH that shows obvious preference toward meso-diaminopimelate (meso-DAP) and exhibits almost no amination activity toward 2-keto acids. There are seven distinct conserved insertions and [...] Read more.
Meso-diaminopimelate dehydrogenase (meso-DAPDH) from Corynebacterium glutamicum ATCC13032 (CgDAPDH) is a type I meso-DAPDH that shows obvious preference toward meso-diaminopimelate (meso-DAP) and exhibits almost no amination activity toward 2-keto acids. There are seven distinct conserved insertions and deletions (indels) between type I and type II meso-DAPDH. The current functional analysis of indels is not comprehensive in meso-DAPDH. Continuing from our previous work on these indels, we first examined the functions of the other indels shown as insertion residues in type I CgDAPDH. Alanine mutations in M216, T240, K289, and Q290 lost at least 40% of their activity, highlighting the importance of these four sites in CgDAPDH. Molecular dynamic analysis indicated that the four non-active sites altered the dynamic network of interactions within the protein. Subsequently, these four sites together with the previously identified indel-related residues R180, L176, and H193 were targeted by site-saturation mutagenesis to improve the amination ability of CgDAPDH toward pyruvic acid. The most significant improvement was observed with the mutant CgL176R, which showed a six-fold increase toward pyruvic acid in kcat/Km compared to wild-type CgDAPDH. Overall, our study provides new hotspots and ideas for the subsequent protein engineering of CgDAPDH, which may also be applied to other meso-DAPDHs. Full article
(This article belongs to the Special Issue State-of-the-Art Enzyme Engineering and Biocatalysis in China)
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17 pages, 4497 KiB  
Article
Rational Engineering of Mesorhizobium Imine Reductase for Improved Synthesis of N-Benzyl Cyclo-tertiary Amines
by Zi-Han Zhang, An-Qi Wang, Bao-Di Ma and Yi Xu
Catalysts 2024, 14(1), 23; https://doi.org/10.3390/catal14010023 - 27 Dec 2023
Viewed by 1055
Abstract
The effective synthesis of N-benzyl cyclo-tertiary amines using imine reductase, key components in natural products and pharmaceutical synthesis, is a green approach. Traditional methods faced challenges with enzyme activity and selectivity. This study focused on enhancing Mesorhizobium imine reductase (MesIRED) [...] Read more.
The effective synthesis of N-benzyl cyclo-tertiary amines using imine reductase, key components in natural products and pharmaceutical synthesis, is a green approach. Traditional methods faced challenges with enzyme activity and selectivity. This study focused on enhancing Mesorhizobium imine reductase (MesIRED) for better N-benzyl cyclo-tertiary amine production. Through alanine scanning and consensus mutation, 12 single-site MesIRED mutants were identified from 23 candidates, showing improved conversion of N-benzylpyrrolidine and N-benzylpiperidine. Notably, mutants from I177, V212, I213, and A241 significantly boosted conversions. The best-performing mutant for N-benzylpyrrolidine, MesIREDV212A/I213V (M1), increased conversion from 23.7% to 74.3%. For N-benzylpiperidine, MesIREDV212A/I177A/A241I (M2) enhanced conversion from 22.8% to 66.8%. Tunnel analysis revealed M1 and M2 have more efficient tunnels for larger product movement compared to wild-type MesIRED. Using recombinant E. coli coexpressing MesIRED and glucose dehydrogenase (GDH), high conversions were achieved: 75.1% for N-benzylpyrrolidine (M1) and 88.8% for N-benzylpiperidine (M2). A preparative experiment resulted in 86.2% conversion and 60.2% yield for N-benzylpiperidine. This research offers an efficient method for engineering IRED, significantly improving conversion and selectivity for N-benzyl cyclo-tertiary amines, aiding drug synthesis and providing insights into rational design of other enzymes. Full article
(This article belongs to the Special Issue State-of-the-Art Enzyme Engineering and Biocatalysis in China)
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12 pages, 2444 KiB  
Article
Efficient Synthesis of Pyrrole Disulfides Catalyzed by Lipase in Ethanol
by Feiyang Wen, Yuelin Xu, Fengxi Li, Jinglin Ma, Zhi Wang, Hong Zhang and Lei Wang
Catalysts 2023, 13(12), 1493; https://doi.org/10.3390/catal13121493 - 06 Dec 2023
Viewed by 1025
Abstract
Disulfides, as fundamental scaffolds, are widely present in peptides, natural products, and pharmaceutical molecules. However, traditional synthesis of disulfides often involves the utilization of toxic reagents or environmentally unfriendly reaction conditions. In this work, a green and efficient method was developed for synthesizing [...] Read more.
Disulfides, as fundamental scaffolds, are widely present in peptides, natural products, and pharmaceutical molecules. However, traditional synthesis of disulfides often involves the utilization of toxic reagents or environmentally unfriendly reaction conditions. In this work, a green and efficient method was developed for synthesizing pyrrole disulfides using β-ketothioamides and ethyl cyanoacetate as substrates, with lipase serving as a catalyst. Under the optimal conditions (β-Ketothioamides (1 mmol), ethyl cyanoacetate (1 mmol), PPL (200 U), and EtOH (5 mL)), lipase leads to the formation of pyrrole disulfides in yields of up to 88% at 40 °C. The related mechanism is also speculated in this paper. This approach not only presents a new application of lipase in enzyme catalytic promiscuity, but also offers a significant advancement in the synthetic pathway for pyrrole disulfides and aligns with the current mainstream research direction of green chemistry, contributing to the further development of environmentally friendly biocatalytic processes. Full article
(This article belongs to the Special Issue State-of-the-Art Enzyme Engineering and Biocatalysis in China)
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14 pages, 2177 KiB  
Article
Generating Novel and Soluble Class II Fructose-1,6-Bisphosphate Aldolase with ProteinGAN
by Fangfang Tang, Mengyuan Ren, Xiaofan Li, Zhanglin Lin and Xiaofeng Yang
Catalysts 2023, 13(12), 1457; https://doi.org/10.3390/catal13121457 - 22 Nov 2023
Viewed by 927
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) is an important enzyme involved in central carbon metabolism (CCM) with promising industrial applications. Artificial intelligence models like generative adversarial networks (GANs) can design novel sequences that differ from natural ones. To expand the sequence space of FBA, we applied [...] Read more.
Fructose-1,6-bisphosphate aldolase (FBA) is an important enzyme involved in central carbon metabolism (CCM) with promising industrial applications. Artificial intelligence models like generative adversarial networks (GANs) can design novel sequences that differ from natural ones. To expand the sequence space of FBA, we applied the generative adversarial network (ProteinGAN) model for the de novo design of FBA in this study. First, we corroborated the viability of the ProteinGAN model through replicating the generation of functional MDH variants. The model was then applied to the design of class II FBA. Computational analysis showed that the model successfully captured features of natural class II FBA sequences while expanding sequence diversity. Experimental results validated soluble expression and activity for the generated FBAs. Among the 20 generated FBA sequences (identity ranging from 85% to 99% with the closest natural FBA sequences), 4 were successfully expressed as soluble proteins in E. coli, and 2 of these 4 were functional. We further proposed a filter based on sequence identity to the endogenous FBA of E. coli and reselected 10 sequences (sequence identity ranging from 85% to 95%). Among them, six were successfully expressed as soluble proteins, and five of these six were functional—a significant improvement compared to the previous results. Furthermore, one generated FBA exhibited activity that was 1.69fold the control FBA. This study demonstrates that enzyme design with GANs can generate functional protein variants with enhanced performance and unique sequences. Full article
(This article belongs to the Special Issue State-of-the-Art Enzyme Engineering and Biocatalysis in China)
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Review

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19 pages, 3204 KiB  
Review
Recent Applications of Flavin-Dependent Monooxygenases in Biosynthesis, Pharmaceutical Development, and Environmental Science
by Yuze Guan and Xi Chen
Catalysts 2023, 13(12), 1495; https://doi.org/10.3390/catal13121495 - 06 Dec 2023
Cited by 1 | Viewed by 1274
Abstract
Flavin-dependent monooxygenases (FMOs) have raised substantial interest as catalysts in monooxygenation reactions, impacting diverse fields such as drug metabolism, environmental studies, and natural product synthesis. Their application in biocatalysis boasts several advantages over conventional chemical catalysis, such as heightened selectivity, safety, sustainability, and [...] Read more.
Flavin-dependent monooxygenases (FMOs) have raised substantial interest as catalysts in monooxygenation reactions, impacting diverse fields such as drug metabolism, environmental studies, and natural product synthesis. Their application in biocatalysis boasts several advantages over conventional chemical catalysis, such as heightened selectivity, safety, sustainability, and eco-friendliness. In the realm of biomedicine, FMOs are pivotal in antibiotic research, significantly influencing the behavior of natural products, antimicrobial agents, and the pathways critical to drug synthesis They are also underscored as potential pharmaceutical targets, pivotal in opposing disease progression and viable for therapeutic intervention. Additionally, FMOs play a substantial role in environmental science, especially in pesticide processing and in preserving plant vitality. Their involvement in the biosynthesis of compounds like polyethers, tropolones, and ω-hydroxy fatty acids, with remarkable regio- and stereoselectivity, renders them indispensable in drug discovery and development. As our comprehension of FMOs’ catalytic mechanisms and structures advances, through the use of cutting-edge biotechnologies like computational design and directed evolution, FMOs are poised to occupy an increasingly significant role in both scientific exploration and industrial applications. Full article
(This article belongs to the Special Issue State-of-the-Art Enzyme Engineering and Biocatalysis in China)
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