Pentacyclic triterpenes are important representatives of natural products that exhibit a wide variety of biological activities. These activities suggest that these compounds may represent potential medicines for the treatment of cancer and viral, bacterial, or protozoal infections. Naturally occurring triterpenes usually have several drawbacks, such as limited activity and insufficient solubility and bioavailability; therefore, they need to be modified to obtain compounds suitable for drug development. Modifications can be achieved either by methods of standard organic synthesis or with the use of biocatalysts, such as enzymes or enzyme systems within living organisms. In most cases, these modifications result in the preparation of esters, amides, saponins, or sugar conjugates. Notably, while standard organic synthesis has been heavily used and developed, the use of the latter methodology has been rather limited, but it appears that biocatalysis has recently sparked considerably wider interest within the scientific community. Among triterpenes, derivatives of lupane play important roles. This review therefore summarizes the natural occurrence and sources of lupane triterpenoids, their biosynthesis, and semisynthetic methods that may be used for the production of betulinic acid from abundant and inexpensive betulin. Most importantly, this article compares chemical transformations of lupane triterpenoids with analogous reactions performed by biocatalysts and highlights a large space for the future development of biocatalysis in this field. The results of this study may serve as a summary of the current state of research and demonstrate the potential of the method in future applications.

• Klíčová slova
• betulin, betulinic acid, biocatalysis, biotransformation, enzyme, extraction, lupane, lupeol, prodrugs, synthesis,
• MeSH
• biokatalýza * MeSH
• hydrolýza MeSH
• objevování léků MeSH
• oxidace-redukce MeSH
• triterpeny chemická syntéza   chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• lupane MeSH Prohlížeč
• triterpeny MeSH

Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address this issue, the power of machine learning can be harnessed to produce predictive models that enable the in silico study and engineering of improved enzymatic properties. Such machine learning models, however, require the conversion of the complex biological information to a numerical input, also called protein representations. These inputs demand special attention to ensure the training of accurate and precise models, and, in this review, we therefore examine the critical step of encoding protein information to numeric representations for use in machine learning. We selected the most important approaches for encoding the three distinct biological protein representations - primary sequence, 3D structure, and dynamics - to explore their requirements for employment and inductive biases. Combined representations of proteins and substrates are also introduced as emergent tools in biocatalysis. We propose the division of fixed representations, a collection of rule-based encoding strategies, and learned representations extracted from the latent spaces of large neural networks. To select the most suitable protein representation, we propose two main factors to consider. The first one is the model setup, which is influenced by the size of the training dataset and the choice of architecture. The second factor is the model objectives such as consideration about the assayed property, the difference between wild-type models and mutant predictors, and requirements for explainability. This review is aimed at serving as a source of information and guidance for properly representing enzymes in future machine learning models for biocatalysis.

• Klíčová slova
• Biocatalysis, Enzyme engineering, Machine learning, Predictive models, Protein dynamics, Protein representations, Representation learning,
• MeSH
• biokatalýza * MeSH
• enzymy metabolismus   chemie   genetika   MeSH
• neuronové sítě (počítačové) MeSH
• proteiny chemie   metabolismus   MeSH
• strojové učení * MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• enzymy MeSH
• proteiny MeSH

The application of enzymes is a crucial issue for current biotechnological application in pharmaceutical, as well as food and cosmetic industry. Effective platforms for enzyme immobilization are necessary for their industrial use in various biosynthesis procedures. Such platforms must provide high yield of immobilization and retain high activity at various conditions for their large-scale applications. Graphene derivatives such as hydrogenated graphene (graphane) and fluorographene can be applied for enzyme immobilization with close to 100 % yield that can result to activities of the composites significantly exceeding activity of free enzymes. The hydrophobic properties of graphene stoichiometric derivatives allowed for excellent non-covalent bonding of enzymes and their use in various organic solvents. The immobilized enzymes retain their high activities even at elevated temperatures. These findings show excellent application potential of enzyme biocatalysts immobilized on graphene stoichiometric derivatives.

• Klíčová slova
• biocatalysis, enzyme, graphene,
• MeSH
• aktivace enzymů MeSH
• biokatalýza MeSH
• enzymy imobilizované chemie   MeSH
• fluorescenční barviva chemie   MeSH
• grafit chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• koncentrace vodíkových iontů MeSH
• lipasa chemická syntéza   MeSH
• nanostruktury chemie   MeSH
• oxidace-redukce MeSH
• povrchové vlastnosti MeSH
• rozpouštědla chemie   MeSH
• stabilita enzymů MeSH
• vysoká teplota MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• enzymy imobilizované MeSH
• fluorescenční barviva MeSH
• grafit MeSH
• lipasa MeSH
• rozpouštědla MeSH

Quercetin is a flavonoid largely employed as a phytochemical remedy and a food or dietary supplement. We present here a novel biocatalytic methodology for the preparation of quercetin from plant-derived rutin, with both substrate and product being in mostly an undissolved state during biotransformation. This "solid-state" enzymatic conversion uses a crude enzyme preparation of recombinant rutinosidase from Aspergillus niger yielding quercetin, which precipitates from virtually insoluble rutin. The process is easily scalable and exhibits an extremely high space-time yield. The procedure has been shown to be robust and was successfully tested with rutin concentrations of up to 300 g/L (ca 0.5 M) at various scales. Using this procedure, pure quercetin is easily obtained by mere filtration of the reaction mixture, followed by washing and drying of the filter cake. Neither co-solvents nor toxic chemicals are used, thus the process can be considered environmentally friendly and the product of "bio-quality." Moreover, rare disaccharide rutinose is obtained from the filtrate at a preparatory scale as a valuable side product. These results demonstrate for the first time the efficiency of the "Solid-State-Catalysis" concept, which is applicable virtually for any biotransformation involving substrates and products of low water solubility.

• Klíčová slova
• Aspergillus niger, quercetin, rutin, rutinose, rutinosidase, “solid-state biocatalysis”,
• MeSH
• Aspergillus niger enzymologie   genetika   MeSH
• biokatalýza * MeSH
• disacharidy chemie   metabolismus   MeSH
• fungální proteiny genetika   metabolismus   MeSH
• glykosidhydrolasy genetika   metabolismus   MeSH
• Pichia genetika   metabolismus   MeSH
• průmyslová mikrobiologie metody   MeSH
• quercetin chemie   metabolismus   MeSH
• rutin chemie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• beta-rutinosidase MeSH Prohlížeč
• disacharidy MeSH
• fungální proteiny MeSH
• glykosidhydrolasy MeSH
• quercetin MeSH
• rutin MeSH
• rutinose MeSH Prohlížeč

Biotransformation has accompanied mankind since the Neolithic community, when people settled down and began to engage in agriculture [...].

• MeSH
• Bacteria enzymologie   MeSH
• biokatalýza * MeSH
• biosenzitivní techniky MeSH
• biotransformace MeSH
• glykomika MeSH
• houby enzymologie   MeSH
• lidé MeSH
• zemědělství MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• úvodní články MeSH
• úvodníky MeSH

Viable microbial cells are important biocatalysts in the production of fine chemicals and biofuels, in environmental applications and also in emerging applications such as biosensors or medicine. Their increasing significance is driven mainly by the intensive development of high performance recombinant strains supplying multienzyme cascade reaction pathways, and by advances in preservation of the native state and stability of whole-cell biocatalysts throughout their application. In many cases, the stability and performance of whole-cell biocatalysts can be highly improved by controlled immobilization techniques. This review summarizes the current progress in the development of immobilized whole-cell biocatalysts, the immobilization methods as well as in the bioreaction engineering aspects and economical aspects of their biocatalytic applications.

• Klíčová slova
• Biocatalysis, Immobilization methods, Immobilized whole-cell biocatalyst, Multienzyme cascade reactions, Process economics, Reaction engineering,
• MeSH
• bioinženýrství * MeSH
• biokatalýza * MeSH
• bioreaktory * MeSH
• imobilizované buňky * MeSH
• lidé MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Fluorinases, the only enzymes known to catalyze the transfer of fluorine to an organic molecule, are essential catalysts for the biological synthesis of valuable organofluorines. However, the few fluorinases identified so far have low turnover rates that hamper biotechnological applications. Here, we isolated and characterized putative fluorinases retrieved from systematic in silico mining and identified a nonconventional archaeal enzyme from Methanosaeta sp. that mediates the fastest SN2 fluorination rate reported to date. Furthermore, we demonstrate enhanced production of fluoronucleotides in vivo in a bacterial host engineered with this archaeal fluorinase, paving the way toward synthetic metabolism for efficient biohalogenation.

• Publikační typ
• časopisecké články MeSH

• MeSH
• design s pomocí počítače MeSH
• enzymy chemie   genetika   metabolismus   MeSH
• katalýza MeSH
• proteinové inženýrství metody   MeSH
• proteiny chemie   genetika   metabolismus   MeSH
• řízená evoluce molekul * MeSH
• Publikační typ
• kongresy MeSH
• Názvy látek
• enzymy MeSH
• proteiny MeSH

Multienzyme processes represent an important area of biocatalysis. Their efficiency can be enhanced by optimization of the stoichiometry of the biocatalysts. Here we present a workflow for maximizing the efficiency of a three-enzyme system catalyzing a five-step chemical conversion. Kinetic models of pathways with wild-type or engineered enzymes were built, and the enzyme stoichiometry of each pathway was optimized. Mathematical modeling and one-pot multienzyme experiments provided detailed insights into pathway dynamics, enabled the selection of a suitable engineered enzyme, and afforded high efficiency while minimizing biocatalyst loadings. Optimizing the stoichiometry in a pathway with an engineered enzyme reduced the total biocatalyst load by an impressive 56 %. Our new workflow represents a broadly applicable strategy for optimizing multienzyme processes.

• Klíčová slova
• biocatalysis, biotransformations, kinetic modeling, multienzyme reaction, stoichiometry optimization,
• MeSH
• algoritmy MeSH
• biokatalýza * MeSH
• chemické modely MeSH
• enzymy chemie   MeSH
• kinetika MeSH
• proteinové inženýrství MeSH
• průběh práce MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• enzymy MeSH

Design and development of scale-down approaches, such as microbioreactor (μBR) technologies with integrated sensors, are an adequate solution for rapid, high-throughput and cost-effective screening of valuable reactions and/or production strains, with considerably reduced use of reagents and generation of waste. A significant challenge in the successful and widespread application of μBRs in biotechnology remains the lack of appropriate software and automated data interpretation of μBR experiments. Here, it is demonstrated how mathematical models can be usedas helpful tools, not only to exploit the capabilities of microfluidic platforms, but also to reveal the critical experimental conditions when monitoring cascade enzymatic reactions. A simplified mechanistic model was developed to describe the enzymatic reaction of glucose oxidase and glucose in the presence of catalase inside a commercial microfluidic platform with integrated oxygen sensor spots. The proposed model allowed an easy and rapid identification of the reaction mechanism, kinetics and limiting factors. The effect of fluid flow and enzyme adsorption inside the microfluidic chip on the optical sensor response and overall monitoring capabilities of the presented platform was evaluated via computational fluid dynamics (CFD) simulations. Remarkably, the model predictions were independently confirmed for μL- and mL- scale experiments. It is expected that the mechanistic models will significantly contribute to the further promotion of μBRs in biocatalysis research and that the overall study will create a framework for screening and evaluation of critical system parameters, including sensor response, operating conditions, experimental and microbioreactor designs.

• Klíčová slova
• Bioprocess modeling, Computational fluid dynamics, Enzymatic biocatalysis, Mechanistic modeling, Microbioreactor, Oxygen monitoring,
• MeSH
• biokatalýza MeSH
• biologické modely * MeSH
• bioreaktory * MeSH
• glukosaoxidasa metabolismus   MeSH
• katalasa metabolismus   MeSH
• mikrofluidní analytické techniky * MeSH
• optická vlákna * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• glukosaoxidasa MeSH
• katalasa MeSH