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Catalysts
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Enzyme and Biocatalysis Application
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Enzyme and Biocatalysis Application

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

Deadline for manuscript submissions: 15 July 2025 | Viewed by 8437

Special Issue Editors

Prof. Dr. Chia-Hung Kuo

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Guest Editor
Department of Seafood Sci-ence, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
Interests: food analysis; food processing; cellulase; lipase esterification and trans esterification; amylase; enzymatic kinetics; ultrasound-assisted enzymatic reaction; enzyme extraction; biotransformation; saccharification; response surface methodology; artificial neural network; wine fermentation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Chwen-Jen Shieh

E-Mail Website
Guest Editor
Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
Interests: biodiesel; lipid biocatalysis; enzyme technology; bioprocess optimization; supercritical fluid technology; Chinese herb medicine biotechnology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yung-Chuan Liu

E-Mail Website
Guest Editor
Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
Interests: fermentation technology; protein engineering; immunoassay; membrane technology; molecular engineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes, with their remarkable specificity, catalyze key reactions essential for various processes that are widely used for pharmaceuticals, biochemical synthesis, agriculture science, food science and environmental remediation. The Special Issue on Enzyme and Biocatalysis Application aims to showcase the latest advancements, methodologies, and applications of enzyme and biocatalysis. It welcomes contributions that explore various aspects of enzyme application, as well as innovative biocatalytic processes in the fields of pharmaceuticals, biochemical synthesis, biotechnology, food science, and environmental remediation. This includes enzyme production, biocatalytic process development, enzymatic synthesis, biotransformation, enzyme engineering and enzyme immobilization. In this Special Issue, we welcome original research articles and reviews focused on all aspects of enzymes applications, such as biocatalysis, process optimization, ultrasonic process, fine chemical production, enzymatic-assisted extraction, enzyme production, biocatalytic processes, environmental protection, bio-reactors, food processes, biomass utilization, bioresource application, bio-transformations, enzymology, biological activity, enzymatic synthesis of value-added chemicals, nanotechnology; environment and biodiversity; and bioremediation and so on. Overall, it aims to highlight the significance of enzymes and biocatalysis in addressing global challenges and advancing sustainable solutions.

Prof. Dr. Chia-Hung Kuo
Prof. Dr. Chwen-Jen Shieh
Prof. Dr. Yung-Chuan Liu
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 production
  • enzyme purification
  • biocatalysis
  • optimization
  • lipase
  • cellulase
  • protease
  • amylase
  • biofuels
  • enzymatic-catalyzed synthesis
  • enzyme immobilization
  • biomass utilization
  • environmental protection
  • glucosidase
  • biotransformation
  • enzymatic kinetics
  • ultrasound-assisted enzymatic reaction
  • bio-reactor
  • enzymatic-assisted extraction
  • experimental design
  • response surface methodology (RSM)

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Published Papers (7 papers)

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Research

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12 pages, 1865 KiB  
Article
Efficient Synthesis of Tetrasubstituted Furans via Lipase-Catalyzed One-Pot Sequential Multicomponent Reaction
by Yongqi Zeng, Yong Tang, Minglu Xu, Dantong Wang, Zhi Wang, Yin Gao and Lei Wang
Catalysts 2025, 15(5), 482; https://doi.org/10.3390/catal15050482 - 15 May 2025
Viewed by 279
Abstract
Tetrasubstituted furans and their derivatives represent a versatile class of important heterocyclic frameworks widely distributed in natural products. These scaffolds also demonstrate significant potential in pharmaceutical chemistry, materials science, and organic synthesis methodologies. In this study, we successfully established a synergistic catalytic system [...] Read more.
Tetrasubstituted furans and their derivatives represent a versatile class of important heterocyclic frameworks widely distributed in natural products. These scaffolds also demonstrate significant potential in pharmaceutical chemistry, materials science, and organic synthesis methodologies. In this study, we successfully established a synergistic catalytic system utilizing benzoylacetonitriles, aldehydes, and benzoyl chlorides as substrates, facilitated by tributylphosphine and immobilized lipase (Novozym 435), to achieve efficient synthesis of cyano-containing tetrasubstituted furans. Under optimized conditions, we obtained a series of target products exhibiting exceptional substrate tolerance with good to excellent isolated yields ranging from 80% to 94%. Additionally, we proposed a reasonable reaction mechanism and verified it through controlled experiments. This methodology not only expands the synthetic utility of lipase in non-natural transformations but also establishes a paradigm of green chemistry for the construction of tetrasubstituted furans. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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17 pages, 28408 KiB  
Article
Immobilization of Enzymes on Electrodes and Electrode Design in Biofuel Cells
by Chang Yen Chen, Adama A. Bojang, Damayanti Damayanti and Ho Shing Wu
Catalysts 2025, 15(3), 253; https://doi.org/10.3390/catal15030253 - 6 Mar 2025
Viewed by 892
Abstract
In an enzyme-based fuel cell system, glucose oxidase and laccase were immobilized on carbon paper as the anode and cathode electrodes. A conductive polymer (polypyrrole) was added to improve conductivity. The mediator and enzymes were mixed in a phosphate-buffer solution for entrapment. A [...] Read more.
In an enzyme-based fuel cell system, glucose oxidase and laccase were immobilized on carbon paper as the anode and cathode electrodes. A conductive polymer (polypyrrole) was added to improve conductivity. The mediator and enzymes were mixed in a phosphate-buffer solution for entrapment. A Nafion 212 membrane separated the two half-cells. Power density measurements were taken at a glucose concentration of 10 mM across different operating voltages. Potassium hexacyanoferrate III was used as a redox mediator in the anode and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) in the cathode to boost power output. The biofuel cells, constructed from acrylic (40 × 50 × 50 mm) with a working volume of 20 × 30 × 40 mm, were assembled using a rubber gasket to secure the Nafion membrane. The use of micropore tape covering the electrodes extended the system’s operational lifespan. Without the micropore tape, the maximum power density was 57.6 μW/cm2 at 0.24 V. With the micropore tape, the cell achieved a maximum power density of 324.9 μW/cm2 at 0.57 V, sustaining performance for 20 days. Thus, micropore tape effectively enhances enzyme retention and biofuel cell performance. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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16 pages, 4142 KiB  
Article
Preparation of Novel ACE Inhibitory Peptides from Skimmed Goat Milk Hydrolyzed by Multi-Enzymes: Process Optimization, Purification, and Identification
by Wenjing Hu, Guowei Shu, Huan Lei, Guanli Du, Zhengxin Liu and Li Chen
Catalysts 2025, 15(2), 140; https://doi.org/10.3390/catal15020140 - 3 Feb 2025
Viewed by 900
Abstract
This study optimizes the process conditions for preparing angiotensin-converting enzyme (ACE) inhibitory peptides from skimmed goat milk (SGM) hydrolyzed by multi-enzymes using response surface methodology. When the enzymatic hydrolysis time was 90 min, the optimal hydrolysis conditions were a pH of 8.49, enzyme-to-substrate [...] Read more.
This study optimizes the process conditions for preparing angiotensin-converting enzyme (ACE) inhibitory peptides from skimmed goat milk (SGM) hydrolyzed by multi-enzymes using response surface methodology. When the enzymatic hydrolysis time was 90 min, the optimal hydrolysis conditions were a pH of 8.49, enzyme-to-substrate ratio (E/S ratio) of 8.04%, and temperature of 61.54 °C. The hydrolysis degree and ACE inhibitory activity were 65.39% ± 0.01% and 84.65% ± 0.03%, respectively. After purification by ultrafiltration, macroporous resin, and gel filtration, the ACE inhibitory activity of F2-2 in the two components of F2 was higher, with the ACE inhibitory rate of 93.97% ± 0.15% and IC50 of 0.121 ± 0.004 mg/mL. The content of hydrophobic amino acids, fatty amino acids, and aromatic amino acids in component F2-2 accounts for 73.17%, 33.86%, and 33.72%, respectively. Eleven peptides were isolated and identified from the F2-2 components of the enzymatic hydrolysate of SGM, including two peptides without an established database. The peptides mainly came from β casein, αS1 casein, and αS2 casein. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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18 pages, 2624 KiB  
Article
GPpred: A Novel Sequence-Based Tool for Predicting Glutamic Proteases Using Optimized Hybrid Encodings
by Ahmad Firoz, Adeel Malik, Nitin Mahajan, Hani Mohammed Ali, Majid Rasool Kamli and Chang-Bae Kim
Catalysts 2024, 14(12), 894; https://doi.org/10.3390/catal14120894 - 5 Dec 2024
Viewed by 1130
Abstract
Glutamic proteases (GPs) represent one of the seven peptidase families described in the MEROPS database of peptidases (also known as proteases, proteinases, and proteolytic enzymes). Currently, the GP family is divided into six sub-families (G1–G6) distributed across three clans (GA, GB, and GC). [...] Read more.
Glutamic proteases (GPs) represent one of the seven peptidase families described in the MEROPS database of peptidases (also known as proteases, proteinases, and proteolytic enzymes). Currently, the GP family is divided into six sub-families (G1–G6) distributed across three clans (GA, GB, and GC). A glutamic acid and another variable amino acid are the catalytic residues in this family. Members of the GP family are involved in a wide variety of biological functions. For example, they act as bacterial and plant pathogens, and are involved in cancer and celiac disease. These enzymes are considered potential drug targets given their crucial roles in numerous biological processes. Characterizing GPs provides insights into their structure–function relationships, enabling the design of specific inhibitors or modulators. Such advancements directly contribute to drug discovery by identifying novel therapeutic targets and guiding the development of potent and selective drugs for various diseases, including cancers and autoimmune disorders. To address the challenges associated with labor-intensive experimental methods, we developed GPpred, an innovative support vector machine (SVM)-based predictor to identify GPs from their primary sequences. The workflow involves systematically extracting six distinct feature sets from primary sequences, and optimization using a recursive feature elimination (RFE) algorithm to identify the most informative hybrid encodings. These optimized encodings were then used to evaluate multiple machine learning classifiers, including K-Nearest Neighbors (KNNs), Random Forest (RF), Naïve Bayes (NB), and SVM. Among these, the SVM demonstrated a consistent performance, with an accuracy of 97% during the cross-validation and independent validation. Computational methods like GPpred accelerate this process by analyzing large datasets, predicting potential enzyme targets, and prioritizing candidates for experimental validation, thereby significantly reducing time and costs. GPpred will be a valuable tool for discovering GPs from large datasets, and facilitating drug discovery efforts by narrowing down viable therapeutic candidates. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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16 pages, 4541 KiB  
Article
Identification of Five Robust Novel Ene-Reductases from Thermophilic Fungi
by Pedro H. Damada and Marco W. Fraaije
Catalysts 2024, 14(11), 764; https://doi.org/10.3390/catal14110764 - 29 Oct 2024
Cited by 1 | Viewed by 1132
Abstract
Ene-reductases (ERs) are enzymes known for catalyzing the asymmetric hydrogenation of activated alkenes. Among these, old yellow enzyme (OYE) ERs have been the most extensively studied for biocatalytic applications due to their dependence on NADH or NADPH as electron donors. These flavin-containing enzymes [...] Read more.
Ene-reductases (ERs) are enzymes known for catalyzing the asymmetric hydrogenation of activated alkenes. Among these, old yellow enzyme (OYE) ERs have been the most extensively studied for biocatalytic applications due to their dependence on NADH or NADPH as electron donors. These flavin-containing enzymes are highly enantio- and stereoselective, making them attractive biocatalysts for industrial use. To discover novel thermostable OYE-type ERs, we explored genomes of thermophilic fungi. Five genes encoding ERs were selected and expressed in Escherichia coli, namely AtOYE (from Aspergillus thermomutatus), CtOYE (from Chaetomium thermophilum), LtOYE (from Lachancea thermotolerans), OpOYE (from Ogatae polymorpha), and TtOYE (from Thermothielavioides terrestris). Each enzyme was purified as a soluble FMN-containing protein, allowing detailed characterization. All ERs exhibited a preference for NADPH, with AtOYE showing the broadest substrate range. Moreover, all the enzymes showed activity toward maleimide and p-benzoquinone, with TtOYE presenting the highest catalytic efficiency. The optimal pH for enzyme activity was between 6 and 7 and the enzymes displayed notable solvent tolerance and thermostability, with CtOYE and OpOYE showing the highest stability (Tm > 60 °C). Additionally, all enzymes converted R-carvone into (R,R)-dihydrocarvone. In summary, this study contributes to expanding the toolbox of robust ERs. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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12 pages, 1191 KiB  
Article
Enzymatic Production of Chitooligosaccharide Using a GH Family 46 Chitosanase from Paenibacillus elgii and Its Antioxidant Activity
by Chien Thang Doan, Thi Ngoc Tran, Anh Dzung Nguyen and San-Lang Wang
Catalysts 2024, 14(11), 761; https://doi.org/10.3390/catal14110761 - 29 Oct 2024
Viewed by 1119
Abstract
Chitooligosaccharide (COS), a natural antioxidant, is a hydrolysis product of chitosan created using enzymatic or chemical methods. COS has received considerable attention recently, making its efficient bioproduction of great value. This study investigated the optimal conditions for the enzymatic method using a GH [...] Read more.
Chitooligosaccharide (COS), a natural antioxidant, is a hydrolysis product of chitosan created using enzymatic or chemical methods. COS has received considerable attention recently, making its efficient bioproduction of great value. This study investigated the optimal conditions for the enzymatic method using a GH family 46 chitosanase from Paenibacillus elgii TKU051 to prepare COS based on the response surface methodology (RSM). The results showed optimal values for chitosan hydrolysis, such as a pH of 5.5, an incubation temperature of 58.3 °C, an [E]/[S] ratio of 118.494 (U/g), and an incubation time of 6.821 h. Under the optimal conditions, the highest reducing sugar level (per substrate, w/w) of the chitosan hydrolysis process that could be reached was 690.587 mg/g. The composition of the obtained COS was analyzed using the thin-layer chromatography (TLC) method, yielding (GlcN)2 and (GlcN)3 as the products. The ascorbic acid equivalent antioxidant capacity (AEAC) of the obtained COS was found to be 1246 mg/100 g (via a DPPH (2,2-diphenyl-1-picrylhydrazyl) radical-scavenging assay) and 3673 mg/100 g (via an ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) radical-scavenging assay). This green and efficient bioproduction method may possess excellent potential for application in bioactive COS preparation. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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Review

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34 pages, 2388 KiB  
Review
Biocatalysis for Lignin Conversion and Valorization: Driving Sustainability in the Circular Economy
by Parushi Nargotra, Vishal Sharma, Hui-Min David Wang, Chwen-Jen Shieh, Yung-Chuan Liu and Chia-Hung Kuo
Catalysts 2025, 15(1), 91; https://doi.org/10.3390/catal15010091 - 20 Jan 2025
Cited by 3 | Viewed by 2168
Abstract
In recent years, lignin derived from lignocellulosic biomass has emerged as a critical component in modern biorefinery systems. The production yield and reactivity of lignin are critical factors for advancing the research and development of lignin-derived biochemicals. The recovery of high-purity lignin, along [...] Read more.
In recent years, lignin derived from lignocellulosic biomass has emerged as a critical component in modern biorefinery systems. The production yield and reactivity of lignin are critical factors for advancing the research and development of lignin-derived biochemicals. The recovery of high-purity lignin, along with carbohydrates, is accomplished through the application of various advanced pretreatment techniques. However, biological pretreatment using lignin-degrading enzymes to facilitate lignin depolymerization is an environmentally benign method for the sustainable production of valuable products that occurs under mild conditions with high substrate specificity. The current review presents the role of biocatalysis in lignin valorization, focusing on lignin-degrading enzymes that facilitate different bond cleavage in the lignocellulosic biomass. The review also highlights the recent advancements in enzyme engineering that have enabled the enhancement of enzyme stability and catalytic efficiency for improving lignin valorization processes. Furthermore, the integration of omics technologies that provide valuable insights into the microbial and enzymatic pathways involved in lignin degradation is presented. The challenges and future prospects in this emerging field of study for a biorefinery concept are also outlined for improving lignin depolymerization efficiency. Full article
(This article belongs to the Special Issue Enzyme and Biocatalysis Application)
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