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Feature Review Papers in Biocatalysis and Enzyme Engineering
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Feature Review Papers in Biocatalysis and Enzyme Engineering

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 6577

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
Prof. Dr. Jose M. Guisan

E-Mail Website
Guest Editor
Department of Biocatalysis, Institute of Catalysis, Spanish Research Council, ICP-CSIC, Campus UAM, 28049 Madrid, Spain
Interests: enzyme engineering: purification, immobilization, stabilization, reactivation; hyperactivation; main enzymes: lipases, penicillin G acylase, endoxylanases, beta-xylosidases, etc.; enzyme processes: fine chemistry, food chemistry, analytical chemistry, green energy; enzyme reactors: stirred tanks, packed beds, etc.
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the ever-evolving landscape of Biocatalysis and Enzyme Engineering, the journal Catalyst’s section of Biocatalysis presents the Special Issue titled “Feature Review Papers in Biocatalysis and Enzyme Engineering”. Spanning from the intricate mechanisms of enzymatic activity to the cutting-edge engineering of biocatalysts for transformative applications, our contributors are expected to offer insights that are both profound and practical. Through this Special Issue, we aim to cover a spectrum of topics, including but not limited to enzyme discovery and engineering, enzyme reaction engineering, and the application of enzymes in industrial processes.

In specific, Review Articles are invited to explore a diverse array of topics, which may include the discovery of novel enzymes, the intricate interplay between enzyme structure and function, the development and analysis of robust and sensitive high-throughput enzyme assays, and scalable biocatalytic synthesis processes for innovative manufacturing. A strong emphasis is placed on the computational design of enzymes through protein engineering, a frontier that holds immense promise for the rational design and optimization of biocatalysts. Your contributions will help in charting the course for future research, driving innovation, and fostering breakthroughs in the field of Biocatalysis and Enzyme Engineering.

The aims and scope of this Special Issue are, however, not limited to the above areas of interest, and potential authors are welcome to submit contributions on other Biocatalysis topics as well. It is a great honour and pleasure to invite you to contribute a Review Article for peer-review and possible publication in this Special Issue.

Prof. Dr. Evangelos Topakas
Prof. Dr. Jose M. Guisan
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 biocatalysis
  • protein engineering
  • computational design
  • high-throughput assays
  • enzyme discovery
  • industrial biocatalysis

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

Published Papers (5 papers)

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Review

22 pages, 8217 KiB  
Review
Cellulosome Systems in the Digestive Tract: Underexplored Enzymatic Machine for Lignocellulose Bioconversion
by Jiajing Qi, Mengke Zhang, Chao Chen, Yingang Feng and Jinsong Xuan
Catalysts 2025, 15(4), 387; https://doi.org/10.3390/catal15040387 - 16 Apr 2025
Viewed by 273
Abstract
Cellulosomes are sophisticated multi-enzyme complexes synthesized and secreted by anaerobic microorganisms, characterized by intricate structural components and highly organized modular assembly mechanisms. These complexes play a pivotal role in the efficient degradation of lignocellulosic biomass, significantly enhancing its bioconversion efficiency, and are thus [...] Read more.
Cellulosomes are sophisticated multi-enzyme complexes synthesized and secreted by anaerobic microorganisms, characterized by intricate structural components and highly organized modular assembly mechanisms. These complexes play a pivotal role in the efficient degradation of lignocellulosic biomass, significantly enhancing its bioconversion efficiency, and are thus regarded as invaluable enzymatic molecular machines. Cellulosomes are not only prevalent in anaerobic bacteria from soil and compost environments but are also integral to the digestive systems of herbivorous animals, primates and termites. The cellulosomes produced by digestive tract microbiota exhibit unique properties, providing novel enzymes and protein modules that are instrumental in biomass conversion and synthetic biology, thereby showcasing substantial application potential. Despite their promise, the isolation and cultivation of digestive tract microorganisms that produce cellulosomes present significant challenges. Additionally, the lack of comprehensive genetic and biochemical studies has impeded a thorough understanding of these cellulosomes, leaving them largely underexplored. This paper provides a comprehensive overview of the digestive tract cellulosome system, with a particular focus on the structural and functional attributes of cellulosomes in various animal digestive tracts. It also discusses the application prospects of digestive tract cellulosomes, highlighting their potential as a treasure in diverse fields. Full article
(This article belongs to the Special Issue Feature Review Papers in Biocatalysis and Enzyme Engineering)
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Graphical abstract

36 pages, 6968 KiB  
Review
Protein Engineering for Industrial Biocatalysis: Principles, Approaches, and Lessons from Engineered PETases
by Konstantinos Grigorakis, Christina Ferousi and Evangelos Topakas
Catalysts 2025, 15(2), 147; https://doi.org/10.3390/catal15020147 - 4 Feb 2025
Viewed by 2160
Abstract
Protein engineering has emerged as a transformative field in industrial biotechnology, enabling the optimization of enzymes to meet stringent industrial demands for stability, specificity, and efficiency. This review explores the principles and methodologies of protein engineering, emphasizing rational design, directed evolution, semi-rational approaches, [...] Read more.
Protein engineering has emerged as a transformative field in industrial biotechnology, enabling the optimization of enzymes to meet stringent industrial demands for stability, specificity, and efficiency. This review explores the principles and methodologies of protein engineering, emphasizing rational design, directed evolution, semi-rational approaches, and the recent integration of machine learning. These strategies have significantly enhanced enzyme performance, even rendering engineered PETase industrially relevant. Insights from engineered PETases underscore the potential of protein engineering to tackle environmental challenges, such as advancing sustainable plastic recycling, paving the way for innovative solutions in industrial biocatalysis. Future directions point to interdisciplinary collaborations and the integration of emerging machine learning technologies to revolutionize enzyme design. Full article
(This article belongs to the Special Issue Feature Review Papers in Biocatalysis and Enzyme Engineering)
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Graphical abstract

20 pages, 1692 KiB  
Review
The Organic-Functionalized Silica Nanoparticles as Lipase Carriers for Biocatalytic Application: Future Perspective in Biodegradation
by Jelena Milovanović, Katarina Banjanac, Jasmina Nikolić, Jasmina Nikodinović-Runić and Nevena Ž. Prlainović
Catalysts 2025, 15(1), 54; https://doi.org/10.3390/catal15010054 - 9 Jan 2025
Cited by 1 | Viewed by 1021
Abstract
Over the past three decades, organic reactions catalyzed by lipase have been extensively studied. To overcome the drawbacks of free enzymes and develop new and sustainable biocatalysts, various insoluble forms of lipases were examined. Especially interesting are lipases immobilized on silica nanoparticles (SiNPs) [...] Read more.
Over the past three decades, organic reactions catalyzed by lipase have been extensively studied. To overcome the drawbacks of free enzymes and develop new and sustainable biocatalysts, various insoluble forms of lipases were examined. Especially interesting are lipases immobilized on silica nanoparticles (SiNPs) due to their promising unique and advantageous physicochemical properties. Therefore, the present paper presents an overview of different organic functionalization methods of SiNP surfaces to create a more favorable microenvironment for lipase molecules. Given the high commercial value of lipases in biotechnological applications, the second part of this paper highlights the key industrial sectors utilizing these nanobiocatalysts. This review discusses the key industrial applications of silica-based lipase nanobiocatalysts, including biodiesel production, flavor ester synthesis, and pharmaceutical applications such as racemization. Special attention is given to emerging technologies, particularly the use of immobilized lipases in polymer biodegradation and polymerization reactions. These advances have paved the way for innovative solutions, such as self-degrading bioplastics, which hold significant promise for sustainable materials and environmental protection. This comprehensive overview underscores the transformative potential of lipase–SiNP nanobiocatalysts in both industrial and environmental contexts. Full article
(This article belongs to the Special Issue Feature Review Papers in Biocatalysis and Enzyme Engineering)
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27 pages, 1100 KiB  
Review
Use of Nicotinamide Mononucleotide as Non-Natural Cofactor
by Tahseena Naaz and Beom Soo Kim
Catalysts 2025, 15(1), 37; https://doi.org/10.3390/catal15010037 - 3 Jan 2025
Viewed by 1678
Abstract
Nicotinamide mononucleotide (NMN) has emerged as a promising non-natural cofactor with significant potential to transform biocatalysis, synthetic biology, and therapeutic applications. By modulating NAD⁺ metabolism, NMN offers unique advantages in enzymatic reactions, metabolic engineering, and regenerative medicine. This review provides a comprehensive analysis [...] Read more.
Nicotinamide mononucleotide (NMN) has emerged as a promising non-natural cofactor with significant potential to transform biocatalysis, synthetic biology, and therapeutic applications. By modulating NAD⁺ metabolism, NMN offers unique advantages in enzymatic reactions, metabolic engineering, and regenerative medicine. This review provides a comprehensive analysis of NMN’s biochemical properties, mechanisms of action, and diverse applications. Emphasis is placed on its role in addressing challenges in multi-enzyme cascades, biofuel production, and the synthesis of high-value chemicals. The paper also highlights critical research gaps, including the need for scalable NMN synthesis methods, improved integration into enzymatic systems, and comprehensive toxicity studies for therapeutic use. Emerging technologies such as AI-driven enzyme design and CRISPR-based genome engineering are discussed as transformative tools for optimizing NMN-dependent pathways. Furthermore, the synergistic potential of NMN with synthetic biology innovations, such as cell-free systems and dynamic regulatory networks, is explored, paving the way for precise and modular biotechnological solutions. Looking forward, NMN’s versatility as a cofactor positions it as a pivotal tool in advancing sustainable bioprocessing and precision medicine. Addressing current limitations through interdisciplinary approaches will enable NMN to redefine the boundaries of metabolic engineering and therapeutic innovation. This review serves as a roadmap for leveraging NMN’s potential across diverse scientific and industrial domains. Full article
(This article belongs to the Special Issue Feature Review Papers in Biocatalysis and Enzyme Engineering)
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35 pages, 4527 KiB  
Review
Biocatalysis with Unconventional Yeasts
by Cecilia Andreu and Marcel·lí del Olmo
Catalysts 2024, 14(11), 767; https://doi.org/10.3390/catal14110767 - 30 Oct 2024
Cited by 1 | Viewed by 1274
Abstract
Biocatalysis is a green and sustainable technology based on the use of natural substances to catalyze chemical reactions. Humans have been unconsciously using biocatalysis for thousands of years to produce food and alcoholic beverages, but it is only since the 19th century that [...] Read more.
Biocatalysis is a green and sustainable technology based on the use of natural substances to catalyze chemical reactions. Humans have been unconsciously using biocatalysis for thousands of years to produce food and alcoholic beverages, but it is only since the 19th century that we have begun to understand its fundamentals and its enormous potential. In fact, advances in our knowledge of enzymes and metabolic pathways and, in recent decades, the introduction of tools such as bioinformatics, DNA sequencing and protein engineering have made biocatalysis a key strategy in fine chemistry and for the production of active pharmaceutical ingredients. In addition, the discovery of new microorganisms adapted to adverse conditions has also been crucial in advancing this avenue. The present review focuses on the use of unconventional yeasts and their enzymes in the most interesting reactions where biocatalysis is applied. It highlights the advantages of using these microorganisms in industrial chemical processes due to their particular phenotypes, such as their ability to withstand high temperatures and pressures, as well as acidic or alkaline environments, high substrate loads, presence of organic solvents, etc. All this results in a wider range of possible substrates and higher efficiency. Examples of the most important reactions in which their use has been described are included, considering both catalysis by wild-type whole cells or their isolated enzymes and their genetically modified variants. All this information will help to understand the current relevance of unconventional yeasts and their enzymes in biocatalysis. Full article
(This article belongs to the Special Issue Feature Review Papers in Biocatalysis and Enzyme Engineering)
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