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Catalysts
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Enzyme Engineering—the Core of Biocatalysis
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Enzyme Engineering—the Core of Biocatalysis

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1451

Special Issue Editors

Prof. Dr. Xi Chen

E-Mail Website
Guest Editor
Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China
Interests: chemical biology; protein structure; enzyme engineering
Prof. Dr. Francesco Secundo

E-Mail Website
Guest Editor
Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milan, Italy
Interests: biocatalysis; protein conformation; analysis of food samples
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzyme engineering is a pivotal aspect of biocatalysis, focusing on modifying enzymes to enhance their efficiency for industrial, medical, and environmental applications. In organic synthesis, enzymes offer significant advantages over traditional chemical catalysts, such as higher specificity, milder operating conditions, and a reduced environmental footprint. Among the various strategies to optimize enzyme performance for specific industrial uses, enzyme engineering is crucial for developing new enzymes with improved activity, stability under diverse and extreme conditions, and enhanced enantio- and regioselectivity.

Enzyme engineering can be achieved through techniques like directed evolution, rational design, and phylogenetic methods. Directed evolution mimics natural selection by creating enzyme variants through random mutations and selecting those with desirable traits, while rational design involves introducing targeted changes based on detailed knowledge of enzyme structure and function. Phylogenetic methods leverage evolutionary relationships between protein sequences to guide the design process, focusing on conserved regions and predicting beneficial mutations.

Engineered enzymes are instrumental in the development of sustainable technologies, enabling the efficient production of valuable chemicals while minimizing environmental impact. By improving enzyme performance, enzyme engineering plays a critical role in advancing biocatalysis, providing eco-friendly solutions, and driving innovation in green chemistry. It is essential for addressing various industrial challenges while promoting sustainable and environmentally conscious practices.

This special issue aims to collect papers presenting studies where enzymes have been engineered, characterized, and eventually applied for organic synthesis.

Prof. Dr. Xi Chen
Prof. Dr. Francesco Secundo
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 2200 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 engineering
  • biocatalysis
  • directed evolution
  • rational design
  • enzyme modification
  • industrial applications
  • catalytic efficiency
  • sustainable technologies
  • renewable chemicals
  • green chemistry

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Published Papers (2 papers)

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15 pages, 4537 KiB  
Article
Construction of a Cofactor Self-Sufficient Enzyme Cascade System Coupled with Microenvironmental Engineering for Efficient Biosynthesis of Tetrahydrofolate and Its Derivative of L-5-Methyltetrahydrofolate
by Ziting Yan, Lisha Qin, Ruirui Qin, Xin Wang and Kequan Chen
Catalysts 2025, 15(3), 235; https://doi.org/10.3390/catal15030235 - 28 Feb 2025
Viewed by 630
Abstract
Tetrahydrofolate (THF), the biologically active form of folate, serves as a crucial carrier of one-carbon units essential for synthesizing cellular components such as amino acids and purine nucleotides in vivo. It also acts as an important precursor for the production of pharmaceuticals, including [...] Read more.
Tetrahydrofolate (THF), the biologically active form of folate, serves as a crucial carrier of one-carbon units essential for synthesizing cellular components such as amino acids and purine nucleotides in vivo. It also acts as an important precursor for the production of pharmaceuticals, including folinate and L-5-methyltetrahydrofolate (L-5-MTHF). In this study, we developed an efficient enzyme cascade system for the production tetrahydrofolate from folate, incorporating NADPH recycling, and explored its application in the synthesis of L-5-MTHF, a derivative of tetrahydrofolate. To achieve this, we first screened dihydrofolate reductases (DHFRs) from various organisms, identifying SmDHFR from Serratia marcescens as the enzyme with the highest catalytic activity. We then conducted a comparative analysis of formate dehydrogenases (FDHs) from different sources, successfully establishing an NADPH recycling system. To further enhance biocatalytic efficiency, we optimized key reaction parameters, including temperature, pH, enzyme ratio, and substrate concentration. To address the challenge of pH mismatch in dual-enzyme reactions, we employed an enzymatic microenvironment regulation strategy. This involved covalently conjugating SmDHFR with a superfolder green fluorescent protein mutant carrying 30 surface negative charges (−30sfGFP), using the SpyCatcher/SpyTag system. This modification resulted in a 2.16-fold increase in tetrahydrofolate production, achieving a final yield of 4223.4 µM. Finally, we extended the application of this tetrahydrofolate synthesis system to establish an enzyme cascade for L-5-MTHF production with NADH recycling. By incorporating methylenetetrahydrofolate reductase (MTHFR), we successfully produced 389.8 μM of L-5-MTHF from folate and formaldehyde. This work provides a novel and efficient pathway for the biosynthesis of L-5-MTHF and highlights the potential of enzyme cascade systems in the production of tetrahydrofolate-derived compounds. Full article
(This article belongs to the Special Issue Enzyme Engineering—the Core of Biocatalysis)
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16 pages, 1696 KiB  
Review
Recent Advances in the Engineering of Cytochrome P450 Enzymes
by Chang Liu and Xi Chen
Catalysts 2025, 15(4), 374; https://doi.org/10.3390/catal15040374 - 11 Apr 2025
Viewed by 330
Abstract
Cytochrome P450 enzymes (CYPs) are versatile heme-containing monooxygenases involved in the metabolism of endogenous and exogenous compounds, as well as natural product biosynthesis. Their ability to catalyze regio- and stereoselective oxidation reactions makes them valuable in pharmaceuticals, fine chemicals, and biocatalysis. However, wild-type [...] Read more.
Cytochrome P450 enzymes (CYPs) are versatile heme-containing monooxygenases involved in the metabolism of endogenous and exogenous compounds, as well as natural product biosynthesis. Their ability to catalyze regio- and stereoselective oxidation reactions makes them valuable in pharmaceuticals, fine chemicals, and biocatalysis. However, wild-type CYPs suffer from low catalytic efficiency, limited substrate specificity, and instability under industrial conditions. Recent advances in protein engineering—rational design, semi-rational design, and directed evolution—have enhanced their activity, stability, and substrate scope. These strategies have enabled CYPs to be engineered for applications like C–H functionalization, carbene transfer, and complex molecule biosynthesis. Despite progress, challenges remain in optimizing efficiency, expanding substrate ranges, and scaling production for industrial use. Future directions include integrating CYPs with other biocatalysts, improving high-throughput screening, and applying machine learning to enzyme design. This review highlights recent developments and the promising future of engineered CYPs in sustainable chemistry, drug development, and high-value chemical production. Full article
(This article belongs to the Special Issue Enzyme Engineering—the Core of Biocatalysis)
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