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Catalysts
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15th Anniversary of Catalysts: The Future of Enzyme Biocatalysis
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15th Anniversary of Catalysts: The Future of Enzyme Biocatalysis

A special issue of Catalysts (ISSN 2073-4344).

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 2921

Special Issue Editors

Prof. Dr. Evangelos Topakas

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Guest Editor
Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytech Str, Zografou Campus, 15780 Athens, Greece
Interests: biocatalysis; industrial biotechnology; lignocellulose degrading enzymes; novel enzymes; structure-function relationship
Special Issues, Collections and Topics in MDPI journals
Dr. Juan M. Bolivar

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Guest Editor
Department of Chemical Engineering, School of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
Interests: heterogeneous biocatalysts; enzyme stabilization; flow microreactor; process intensification
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Chia-Hung Kuo

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Guest Editor
Department of Seafood Science, 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

Special Issue Information

Dear Colleagues,

Celebrating the 15th anniversary of the Catalysts journal, this Special Issue marks the sustained growth and evolving impact of the Biocatalysis section within the journal. As demonstrated in our Biocatalysis section, enzyme or whole-cell biocatalysis has transitioned from a specialized niche into a central technology for sustainable synthesis and analysis, with over 1000 articles and dozens of dedicated Special Issues to date.

In this anniversary edition, we aim to reflect on historical successes while focusing on frontier developments redefining the field today: advances in machine‑learning‑guided enzyme design, photobiocatalysis, enzymatic cascade engineering, enzyme immobilization for continuous flow, and expanding chemoenzymatic approaches in green chemistry. We encourage contributions that challenge traditional paradigms, propose novel strategies for enzyme discovery and stability, and illustrate industrial translation of emerging tools.

Authors are invited to submit both original research and critical reviews exploring grand themes in biocatalysis—particularly those that harness synthetic biology, artificial intelligence, and process intensification. This collection aims to chart the future trajectory of enzyme or whole-cell catalysis for green synthesis, biomanufacturing, and beyond. We look forward to your innovative contributions.

Prof. Dr. Evangelos Topakas
Dr. Juan M. Bolivar
Prof. Dr. Chia-Hung Kuo
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 250 words) can be sent to the Editorial Office for assessment.

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

  • machine‑learning enzyme design
  • photobiocatalysis
  • immobilized enzymes and flow bioprocesses
  • directed evolution and computational enzyme engineering
  • biocatalysis in sustainable chemical production
  • emerging enzyme classes and non‑natural transformations

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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18 pages, 8623 KB  
Article
Computer-Aided Engineering of Trans-Anethole Oxygenase for Enhanced Catalytic Synthesis of Vanillin from Isoeugenol
by Fukang Hou, Dan Wu, Pengcheng Chen and Pu Zheng
Catalysts 2026, 16(5), 374; https://doi.org/10.3390/catal16050374 - 23 Apr 2026
Viewed by 300
Abstract
Trans-anethole oxygenase (TAO) exhibits broad arylpropene substrate specificity but has low activity in converting isoeugenol to high-value vanillin. Herein, we employed computer-aided rational design to engineer TAO from Pseudomonas putida (PpTAO) for enhanced catalytic efficiency toward isoeugenol. Structural modeling and AlphaFold [...] Read more.
Trans-anethole oxygenase (TAO) exhibits broad arylpropene substrate specificity but has low activity in converting isoeugenol to high-value vanillin. Herein, we employed computer-aided rational design to engineer TAO from Pseudomonas putida (PpTAO) for enhanced catalytic efficiency toward isoeugenol. Structural modeling and AlphaFold 3 docking identified two key catalytic residues, Arg86 and His118. Through substrate channel engineering and computation-guided mutagenesis, a series of targeted variants were constructed. Three variants, H93A, Q207R/G249C, and I59T/F62T, showed significant improvements in whole-cell performance, with activity increases of 1.8-, 2.13-, and 4.83-fold over the wild type (WT), respectively. Purified enzyme kinetics corroborated these findings, as reflected in kcat/Km values that reached 1.6, 2.1, and 4.7 times that of the WT. Mechanistic molecular dynamics simulations revealed that H93A enhances activity by widening the access tunnel, whereas Q207R/G249C exerts beneficial distal effects. Notably, the I59T/F62T variant significantly increases substrate affinity by optimizing hydrophobic interactions within the binding pocket. These results validate the efficacy of computational modeling in enzyme redesign and provide a robust biocatalyst for the sustainable biosynthesis of vanillin. Full article
(This article belongs to the Special Issue 15th Anniversary of Catalysts: The Future of Enzyme Biocatalysis)
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18 pages, 1129 KB  
Article
Controlled Sequential Oxygenation of Polyunsaturated Fatty Acids with a Recombinant Unspecific Peroxygenase from Aspergillus niger
by Carlos Renato Carrillo Avilés, Marina Schramm, Sebastian Petzold, Miguel Alcalde, Martin Hofrichter and Katrin Scheibner
Catalysts 2025, 15(12), 1162; https://doi.org/10.3390/catal15121162 - 11 Dec 2025
Viewed by 862
Abstract
The metabolism of polyunsaturated fatty acids (PUFAs) is a broad research field, and the products identified so far offer potential medical and industrial applications. Epoxy fatty acids (EpFAs) act as lipid mediators that modulate renal function, angiogenesis, vascular dilatation and inflammation; moreover, they [...] Read more.
The metabolism of polyunsaturated fatty acids (PUFAs) is a broad research field, and the products identified so far offer potential medical and industrial applications. Epoxy fatty acids (EpFAs) act as lipid mediators that modulate renal function, angiogenesis, vascular dilatation and inflammation; moreover, they regulate monocyte aggregation and are involved in cardiovascular and metabolic diseases. On the other hand, EpFAs are precursors of environmentally friendly products for the plastics industry, in which the grade of epoxidation of the compounds gives the polymeric material different advantageous characteristics. The controlled chemical synthesis of poly epoxidized PUFAs is challenging as the reactions are non-selective. In contrast, the biosynthetic route based on cytochrome P450 monooxygenases and lipoxygenases is highly selective but ineffective due to the instability of the enzymes in cell-free systems. Fungal unspecific peroxygenases (UPOs, EC 1.11.2.1) with P450-like activity offer a suitable alternative for the selective synthesis of EpFAs from PUFAs. Here we demonstrate that a recombinant unspecific peroxygenase from Aspergillus niger (rAniUPO) is able to sequentially epoxidize eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) to 14,15-17,18 diepoxyeicosatrienoic acid (14,15-17,18 diEpETrE) and 16,17-19,20-diepoxydocosatetraenoic acid (16,17-19,20 diEpDTE), respectively, while arachidonic acid is transformed into 13-hydroxy-14,15-epoxyeicosatrienoic acid (14,15-hepoxilin B3). Optimal production for these oxygenated derivatives (up to 15 mg) was achieved using 2 mM hydrogen peroxide as the co-substrate. The obtained molecules were identified using high-resolution mass spectrometry and their structure was verified by NMR. Our results demonstrate the suitability of UPOs for the synthesis of EpFAs that can be used in medical research and industrial applications. Full article
(This article belongs to the Special Issue 15th Anniversary of Catalysts: The Future of Enzyme Biocatalysis)
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Graphical abstract

25 pages, 3623 KB  
Article
Fusarium proliferatum PSA-3 Produces Xylanase-Aggregate to Degrade Complex Arabinoxylan
by Kanlaya Thattha, Lakha Salaipeth, Saengchai Akeprathumchai, Ken-Lin Chang, Takashi Watanabe and Paripok Phitsuwan
Catalysts 2025, 15(10), 988; https://doi.org/10.3390/catal15100988 - 16 Oct 2025
Viewed by 1232
Abstract
Xylanolytic enzymes of the Fusarium species are closely associated with pathogenesis, where they soften plant cell walls to facilitate infection and nutrient uptake. This study investigated the xylanolytic system of Fusarium proliferatum PSA-3, a strain isolated from mango leaves showing dark spot symptoms. [...] Read more.
Xylanolytic enzymes of the Fusarium species are closely associated with pathogenesis, where they soften plant cell walls to facilitate infection and nutrient uptake. This study investigated the xylanolytic system of Fusarium proliferatum PSA-3, a strain isolated from mango leaves showing dark spot symptoms. When cultivated on rice straw under solid-state fermentation, PSA-3 produced high xylanase activity against rye arabinoxylan (50.2 U) and beechwood xylan (56.8 U). Partial purification by ion-exchange and gel-filtration chromatography yielded a large xylanase aggregate (158 kDa), which appeared as a smear at the top of the gel under native conditions. Mild denaturation resolved the aggregate into at least four active proteins of ~25, 35, 48, and 63 kDa, indicating that multiple xylanases assemble into a functional aggregate. The aggregate retained activity across pH 4.0–8.0, with an optimum at pH 5.0 and 50 °C, and was resistant to Ni2+, Fe2+, Co2+, and β-mercaptoethanol, but inhibited by SDS. Hydrolysis of xylo-oligosaccharides (DP 2–6), purified xylans, and plant-derived xylans confirmed predominantly endo-type action with debranching activity toward A2XX and A2,3XX. These findings reveal a natural xylanase aggregate in F. proliferatum, providing a potential mechanism for efficient degradation of arabinoxylan-rich cell walls and offering targets for antifungal strategies and biotechnological applications. Full article
(This article belongs to the Special Issue 15th Anniversary of Catalysts: The Future of Enzyme Biocatalysis)
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