Recent trends in biocatalysis engineering

Recent insight into the advances and prospects of microbial lipases and their potential applications in industry

Enzymes play a crucial role in various industrial sectors. These biocatalysts not only ensure sustainability and safety but also enhance process efficiency through their unique specificity. Lipases possess versatility as biocatalysts and find utilization in diverse bioconversion reactions. Presently, microbial lipases are gaining significant focus owing to the rapid progress in enzyme technology and their widespread implementation in multiple industrial procedures. This updated review presents new knowledge about various origins of microbial lipases, such as fungi, bacteria, and yeast. It highlights both the traditional and modern purification methods, including precipitation and chromatographic separation, the immunopurification technique, the reversed micellar system, the aqueous two-phase system (ATPS), and aqueous two-phase flotation (ATPF), moreover, delves into the diverse applications of microbial lipases across several industries, such as food, vitamin esters, textile, detergent, biodiesel, and bioremediation. Furthermore, the present research unveils the obstacles encountered in employing lipase, the patterns observed in lipase engineering, and the application of CRISPR/Cas genome editing technology for altering the genes responsible for lipase production. Additionally, the immobilization of microorganisms' lipases onto various carriers also contributes to enhancing the effectiveness and efficiencies of lipases in terms of their catalytic activities. This is achieved by boosting their resilience to heat and ionic conditions (such as inorganic solvents, high-level pH, and temperature). The process also facilitates the ease of recycling them and enables a more concentrated deposition of the enzyme onto the supporting material. Consequently, these characteristics have demonstrated their suitability for application as biocatalysts in diverse industries.

Biocatalytic approach for the synthesis of chiral alcohols for the development of pharmaceutical intermediates and other industrial applications: A review

Biocatalysis has emerged as a strong tool for the synthesis of active pharmaceutical ingredients (APIs). In the early twentieth century, whole cell biocatalysis was used to develop the first industrial biocatalytic processes, and the precise work of enzymes was unknown. Biocatalysis has evolved over the years into an essential tool for modern, cost-effective, and sustainable pharmaceutical manufacturing. Meanwhile, advances in directed evolution enable the rapid production of process-stable enzymes with broad substrate scope and high selectivity. Large-scale synthetic pathways incorporating biocatalytic critical steps towards >130 APIs of authorized pharmaceuticals and drug prospects are compared in terms of steps, reaction conditions, and scale with the corresponding chemical procedures. This review is designed on the functional group developed during the reaction forming alcohol functional groups. Some important biocatalyst sources, techniques, and challenges are described. A few APIs and their utilization in pharmaceutical drugs are explained here in this review. Biocatalysis has provided shorter, more efficient, and more sustainable alternative pathways toward existing small molecule APIs. Furthermore, non-pharmaceutical applications of biocatalysts are also mentioned and discussed. Finally, this review includes the future outlook and challenges of biocatalysis. In conclusion, Further research and development of promising enzymes are required before they can be used in industry.

Biocatalyst immobilization on magnetic nano-architectures for potential applications in condensation reactions

In this review article, a perspective on the immobilization of various hydrolytic enzymes onto magnetic nanoparticles for synthetic organic chemistry applications is presented. After a first part giving short overview on nanomagnetism and highlighting advantages and disadvantages of immobilizing enzymes on magnetic nanoparticles (MNPs), the most important hydrolytic enzymes and their applications were summarized. A section reviewing the immobilization techniques with a particular focus on supporting enzymes on MNPs introduces the reader to the final chapter describing synthetic organic chemistry applications of small molecules (flavour esters) and polymers (polyesters and polyamides). Finally, the conclusion and perspective section gives the author's personal view on further research discussing the new idea of a synergistic rational design of the magnetic and biocatalytic component to produce novel magnetic nano-architectures.

Multidomain chimeric enzymes as a promising alternative for biocatalysts improvement: a minireview

Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.

Microbial bioprocess performance in nanoparticle-mediated composting

Microbial composting is one of the most cost-effective techniques for degradation, remediation, nutrition, etc. Currently, there is faster growth and development in nanotechnology in different sectors. This development leads nanoparticles (NPs) to enter into the composts in different ways. First, unintentional entry of NPs into the composts via: waste discharge, buried solid waste, surface runoff, direct disposal into wastes (consumer goods, food, pharmaceuticals, and personal care products). Second, intentional mediation of the NPs in the composting process is a novel approach developed to enhance the degradation rate of wastes and as a nutrient for plants. The presence of NPs in the composts can cause nanotoxicity. Conversely, their presence might also be beneficial, such as soil reclamations, degradation, etc. Alternatively, metal NPs are also helpful for all living organisms, including microorganisms, in various biological processes, such as DNA replication, precursor biosynthesis, respiration, oxidative stress responses, and transcription. NPs show exemplary performance in multiple fields, whereas their role in composting process is worth studying. Consequently, this article aids the understanding of the role of NPs in the composting process and how far their presence can be beneficial. This article reviews the significance of NPs in: the composting process, microbial bioprocess performance during nano composting, basic life cycle assessment (LCA) of NP-mediated composting, and mode of action of the NPs in the soil matrix. This article also sheds insight on the notion of nanozymes and highlights their biocatalytic characterization, which will be helpful in future composting research.

Enzymatic synthesis of new antimicrobial peptides for food purposes

Growing consumer awareness of the potential negative health effects of synthetic antibiotics has prompted the search for more natural preservatives that can improve the safety and quality of food. In this study we report the enzymatic synthesis of N-α-[Carbobenzyloxy]-Ile-Gln (Z-IQ) which is the precursor of Ile-Gln (IQ), a new antibacterial dipeptide, using an aqueous-organic biphasic system formed by 50% (v/v) ethyl acetate in 0.1 M Tris - HCl buffer pH 8. A partially purified proteolytic extract from the fruits of Solanum granuloso leprosum, named granulosain, proved to be a robust biocatalyst for the synthesis of Z-IQ, eliciting 71 ± 0.10% maximal peptide yield in the above described conditions. After cleaving and purifying IQ dipeptide, antimicrobial activity was assayed against Staphylococcus aureus ATCC 25923, Staphylococcus hominis A17771, and Staphylococcus aureus C00195, and MIC values between 118 ± 0.01 μg/mL and 133.7 ± 0.05 μg/mL were obtained. In addition, IQ showed MIC of 82.4 ± 0.01 μg/mL and 85.0 ± 0.00 μg/mL against Escherichia coli ATCC 25922 and Escherichia coli A17683, respectively. IQ did not show inhibitory activity against single-drug resistance (SDR) strains, such as Klebsiella oxytoca A19438 (SDR) and Pseudomonas aeruginosa C00213 (SDR), and against multidrug-resistant Enterococcus faecalis I00125 (MDR). IQ also caused growth inhibition of Helicobacter pylori NCTC 11638 and three wild-type H. pylori strains, which are sensitive to AML, MTZ, LEV and CLA (H. pylori 659), resistant to LEV (H. pylori 661 SDR), and resistant to MTZ (H. pylori 662 SDR). Finally, this study contributes with a new dipeptide (IQ) that can be used as an antimicrobial agent for food preservation or as a safe ingredient of functional foods.

Creatinase: Using Increased Entropy to Improve the Activity and Thermostability

Improving protein thermostability in mutagenesis-based enzyme engineering was often achieved by enhancing interresidue interactions via mutation to increase the enthalpy penalty of unfolding. However, this approach may trade off the functional activity due to the loss of structural flexibility of the biomolecule. Here, by performing X-ray crystallography, enzymatic kinetic experiments, neutron scattering, and thermodynamical measurements, we compared the structures, catalytic behaviors, dynamics, and thermostability between a wild-type creatinase and its four-point mutant. We found that the mutant is an entropy-driven thermostable protein with higher structural flexibility, i.e., higher conformational entropy, in the folded state compared to the wild type. The increased conformational entropy of the mutant in the folded state can reduce the entropy gain during unfolding and thus renders it greater thermostability. Moreover, the increased structural flexibility, particularly around the catalytic site, can broaden the mutant's working temperature range and considerably improve its activity at ambient conditions, which is crucial for its application in diagnosing kidney diseases. Complementary all-atom molecular dynamics simulations indicated that the four mutations replaced several of the strong interresidue interactions (electrostatic interactions and hydrogen bonds) with weak hydrophobic interactions. These substitutions not only release the structural flexibility to promote the thermostability and enzymatic activity of the protein but they also preserve the protein structure from collapsing. Our findings may pave a route for the entropy-driven strategy to design proteins with high thermostability and activity.

The Recent Advances in the Utility of Microbial Lipases: A Review

Lipases are versatile biocatalysts and are used in different bioconversion reactions. Microbial lipases are currently attracting a great amount of attention due to the rapid advancement of enzyme technology and its practical application in a variety of industrial processes. The current review provides updated information on the different sources of microbial lipases, such as fungi, bacteria, and yeast, their classical and modern purification techniques, including precipitation and chromatographic separation, the immunopurification technique, the reversed micellar system, aqueous two-phase system (ATPS), aqueous two-phase flotation (ATPF), and the use of microbial lipases in different industries, e.g., the food, textile, leather, cosmetics, paper, and detergent industries. Furthermore, the article provides a critical analysis of lipase-producing microbes, distinguished from the previously published reviews, and illustrates the use of lipases in biosensors, biodiesel production, and tea processing, and their role in bioremediation and racemization.

Hierarchically Structured CA@ZIF-8 Biohybrids for Carbon Dioxide Mineralization

Carbonic anhydrase (CA) is a powerful biocatalyst for carbon dioxide (CO₂) mineralization, of which immobilization is usually used for maintaining its catalytic activity against harsh external stimuli. However, the incorporated materials for CA immobilization would commonly increase the internal diffusion resistance during the catalytic process, thereby decreasing the catalytic efficiency. In our study, poly-L-glutamic acid (PLGA) as the structure regulator was used to induce the synthesis of CA@zeolitic imidazolate framework-8 (CA@ZIF-8) biohybrids. The introduction of PLGA that could coordinate with Zn²⁺ interfered the crystallization of ZIF-8, thereby changing the morphological structure of CA@ZIF-8 biohybrids. With the increase of PLGA amount from 0 to 60 mg, PLGA(x)-CA@ZIF-8 biohybrids were gradually transformed from a dodecahedron structure to a 3D lamellar nano-flower structure, which caused elevated exposed surface area. Accordingly, the loading ratio was increased from 34.6 to 49.8 mg g_cat^-1, while the catalytic activity was elevated from 20.6 to 23.4%. The CO₂ conversion rate was enhanced by nearly two folds compared to PLGA(0)-CA@ZIF-8 under the optimized condition. The final CaCO₃ yield could reach 5.6 mg mg_cat^-1, whereas the reaction system could remain above 80% of the initial reaction activity after 8 cycles.

Production of a recyclable nanobiocatalyst to synthesize quinazolinone derivatives

Nanobiocatalysts (NBCs) are an emerging innovation that paves the way toward sustainable and eco-friendly endeavors. In the quest for a robust and reusable nanobiocatalyst, herein, we report a nanobiocatalyst, namely CALB@MrGO, developed via immobilizing Candida antarctica lipase B onto the surface of Fe3O4-decorated reduced graphene oxide (MrGO). Next, the enormous potential of the NBC (CALB@MrGO) was checked by employing it to synthesize clinically important quinazolinone derivatives in good to excellent yield (70-95%) using differently substituted aryl aldehydes with 2-aminobenzamide. Further, the synthetic utility and generality of this protocol was proved by setting up a gram-scale reaction, which afforded the product in 87% yield. The green chemistry metrics calculated for the gram-scale reaction those prove the greenness of this protocol.

Neuroprotective metabolites via fungal biotransformation of a novel sapogenin, cyclocephagenol

Cyclocephagenol (1), a novel cycloartane-type sapogenin with tetrahydropyran unit, is only encountered in Astragalus species. This rare sapogenin has never been a topic of biological activity or modification studies. The objectives of this study were; (i) to perform microbial transformation studies on cyclocephagenol (1) using Astragalus endophyte, Alternaria eureka 1E1BL1, followed by isolation and structural characterization of the metabolites; (ii) to investigate neuroprotective activities of the metabolites; (iii) to understand structure-activity relationships towards neuroprotection. The microbial transformation of cyclocephagenol (1) using Alternaria eureka resulted in the production of twenty-one (2-22) previously undescribed metabolites. Oxidation, monooxygenation, dehydration, methyl migration, epoxidation, and ring expansion reactions were observed on the triterpenoid skeleton. Structures of the compounds were established by 1D-, 2D-NMR, and HR-MS analyses. The neuroprotective activities of metabolites and parent compound (1) were evaluated against H2O2-induced cell injury. The structure-activity relationship (SAR) was established, and the results revealed that 1 and several other metabolites had potent neuroprotective activity. Further studies revealed that selected compounds reduced the amount of ROS and preserved the integrity of the mitochondrial membrane. This is the first report of microbial transformation of cyclocephagenol (1).

Unprecedented enhancement and preservation of the peroxidase activity of cytochrome-c packaged with ionic liquid-modified gold nanoparticles by offsetting temperature and time stresses

Inspired by the biocompatibility of ionic liquids and their dexterousness for the preservation of enzyme structure and activity, herein, the interactions of Cyt-c with naked AuNPs and four IL-mediated AuNPs, which were formed by the fabrication of ILs with common cation 1-ethyl-3-methyl-imidazolium (EMIM) and different anions, to obtain AuNP-IL1 [(BF4)^-1 anion], AuNP-IL2 [(CH₃OSO₃)^-1 anion], AuNP-IL3 [(CH₃CH₂OSO₃)^-1 anion], and (AuNP-IL4) [Cl^-1 anion], were studied. Through this work, the peroxidase activity observed in the presence of a lower concentration IL-AuNPs is exceptionally increased (16 fold). IL-AuNPs preferentially counteract the temperature gradient change and long-term solvent preservation effects while persistently maintaining the Cyt-c peroxidase activity without much depreciation. The hydrodynamic diameter (d_H) of the Cyt-c-AuNP system was obtained, which supported the TEM results. Furthermore, to evaluate the effect of Cyt-c interaction with the AuNPs, a Zeta potential analysis was performed. Taken together, the binding of IL-AuNPs with Cyt-c, diameter size analysis, zeta potential, structural integrity evaluation using the DichroWeb software and morphology results suggest the interaction order of the IL-AuNPs to be in a sequence of AuNP-IL2 > AuNP-IL3 > AuNP- IL4 > AuNP-IL1 > Naked AuNPs. Moreover, results indicate that the IL anions play a dominating role in the modulation of interactions between IL-mediated AuNPs and Cyt-c. The study strongly supports the promising character of sulfur-containing IL-mediated AuNPs for Cyt-c immobilization simultaneously opening new avenues for the application of greener and biocompatible nanoparticles with drug delivery and therapeutic applications.

Exploring the Temperature Effect on Enantioselectivity of a Baeyer-Villiger Biooxidation by the 2,5-DKCMO Module: The SLM Approach

Temperature is a crucial parameter for biological and chemical processes. Its effect on enzymatically catalysed reactions has been known for decades, and stereo- and enantiopreference are often temperature-dependent. For the first time, we present the temperature effect on the Baeyer-Villiger oxidation of rac-bicyclo[3.2.0]hept-2-en-6-one by the type II Bayer-Villiger monooxygenase, 2,5-DKCMO. In the absence of a reductase and driven by the hydride-donation of a synthetic nicotinamide analogue, the clear trend for a decreasing enantioselectivity at higher temperatures was observed. "Traditional" approaches such as the determination of the enantiomeric ratio (E) appeared unsuitable due to the complexity of the system. To quantify the trend, we chose to use the 'Shape Language Modelling' (SLM), a tool that allows the reaction to be described at all points in a shape prescriptive manner. Thus, without knowing the equation of the reaction, the substrate ee can be estimated that at any conversion.

Endophytic fungi: a potential source of industrial enzyme producers

Microbial enzymes have gained interest for their widespread use in various industries and medicine due to their stability, ease of production, and optimization. Endophytic fungi in plant tissues produce a wide range of secondary metabolites and enzymes, which exhibit a variety of biological activities. The present review illustrates promising applications of enzymes produced by endophytic fungi and discusses the characteristic features of the enzymes, application of the endophytic fungal enzymes in therapeutics, agriculture, food, and biofuel industries. Endophytic fungi producing ligninolytic enzymes have possible biotechnological applications in lignocellulosic biorefineries. The global market of industrially important enzymes, challenges, and future prospects are illustrated. However, the commercialization of endophytic fungal enzymes for industrial purposes is yet to be explored. The present review suggests that endophytic fungi can produce various enzymes and may become a novel source for upscaling the production of enzymes of industrial use.

Development of a hydrolase mimicking peptide amphiphile and its immobilization on silica surface for stereoselective and enhanced catalysis

Biocatalysis is an important area of modern research and is extensively explored by various industries to attain greener methods in various applications. Supramolecular interactions of short peptides have been under the scanner for developing artificial smart materials inspired from natural systems. Peptide-based artificial enzymes have been proved to show various enzyme-like activities. Therefore, immobilization of catalytic peptides on solid surfaces can be an extremely useful breakthrough for development of cost-effective catalytic formulations. In this work, a series of peptide amphiphiles (PAs) have been systematically analyzed to find the most effective catalyst with esterase like activity. The PA, containing a catalytic triad, 'Asp(Ser)His' in a branched manner, was further immobilized onto silica nanoparticles through covalent bonding method to obtain surface coated catalytic silica nanoparticles. The heterogenous catalytic formulation not only showed enhanced esterase activity than the self-assembled PA in homogenous phase, but also exceeded the activity of natural CV lipase. The catalytic formulation showed high stereoselectivity towards chiral esters. Moreover, the catalyst remained stable at higher temperature, in presence of various denaturant and retained its activity after several catalytic cycles. The ease of separation, robust nature, reusability and high stereoselectivity of the catalyst opens up the possibility of creating new generation heterogeneous catalysts for further industrial applications.

Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems

Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.

Trends in lipase engineering for enhanced biocatalysis

Lipases, also known as triacylglycerol hydrolases (E.C.No. 3.1.1.3), are considered as leading biocatalysts in the lipid modification business. With properties like ease of availability, capability to work in heterogeneous media, stability in organic solvents, property of catalyzing at the lipid-water interface and even in nonaqueous conditions, have made them a versatile choice for applications in the food, flavor, detergent, pharmaceutical, leather, textile, cosmetic, and paper industries [1]. The increasing alertness toward sustainable technologies, lesser waste generation and solvent usage and minimization of energy input has brought light toward the production and usage of recombinant/improved lipases. For example, Novozym 435, a broadly used recombinant lipase isolated from Candida antarctica, dominates the lipase industry and has even created a supplier bias in the market. This shows that there is a desperate need for novel, low-cost lipases with better properties. For this, mining of existing extremophilic genomes seems more rewarding. But considering the diversity of industrial requirements such as types of solvents used or carrier systems employed for enzyme immobilization, tailor-designed enzymes are an unrealized pressing priority. Therefore, protein engineering strategies in collaboration with the discovery of new lipases can serve as a vital tool to obtain tailor-made enzymes with specific characteristics.

Facile mussel-inspired polydopamine-coated 3D-printed bioreactors for continuous flow biocatalysis

Enantiopure alcohol production by a flow system of 3D-printed bioreactor with immobilized Geotrichum candidum acetophenone reductase (GcAPRD).

Chemical Reaction Engineering to Understand Applied Kinetics in Free Enzyme Homogeneous Reactors

Chemical reaction engineering is interested in elucidating the reaction kinetics through the determination of the fundamental influencing variables. The understanding of enzyme kinetics is needed to implement the potential of enzymes to satisfy determined production targets and for the design of the reactor. The quantification of the enzyme kinetics is implemented by the elucidation and building of the kinetic model (it includes one or more kinetic equations). In the context of process development, the kinetic model is not only useful to identify feasibility and for optimizing reaction conditions but also, at an early stage of development it is very useful to anticipate implementation bottlenecks, and so guide reactor setup. In this chapter we describe theoretical and practical considerations to illustrate the methodological framework of kinetic analysis. We take as study cases four archetypal kinetic cases by using as example the hydrolysis of cellobiose catalyzed by a beta-glucosidase. We show the different experimental data that can be obtained by the monitoring of enzymatic reactions in different configuration of free enzyme homogeneous ideal reactors; we show step-by-step the visualization, treatment, and analysis of data to elucidate kinetic models and the procedure for the quantification of kinetic constants. Finally, the performance of different reactors is compared in the interplay with the enzyme kinetics. This book chapter aims at being useful for a broad multidisciplinary audience and different levels of academic development.

Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents

Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.

The Core-Shell Structure, Not Sugar, Drives the Thermal Stabilization of Single-Enzyme Nanoparticles

Trehalose is widely assumed to be the most effective sugar for protein stabilization, but exactly how unique the structure is and the mechanism by which it works are still debated. Herein, we use a polyion complex micelle approach to control the position of trehalose relative to the surface of glucose oxidase within cross-linked and non-cross-linked single-enzyme nanoparticles (SENs). The distribution and density of trehalose molecules in the shell can be tuned by changing the structure of the underlying polymer, poly(N-[3-(dimethylamino)propyl] acrylamide (PDMAPA). SENs in which the trehalose is replaced with sucrose and acrylamide are prepared as well for comparison. Isothermal titration calorimetry, dynamic light scattering, and asymmetric flow field-flow fraction in combination with multiangle light scattering reveal that two to six polymers bind to the enzyme. Binding either trehalose or sucrose close to the enzyme surface has very little effect on the thermal stability of the enzyme. By contrast, encapsulation of the enzyme within a cross-linked polymer shell significantly enhances its thermal stability and increases the unfolding temperature from 70.3 °C to 84.8 °C. Further improvements (up to 92.8 °C) can be seen when trehalose is built into this shell. Our data indicate that the structural confinement of the enzyme is a far more important driver in its thermal stability than the location of any sugar.

Exploring the Diversity and Biotechnological Potential of Cultured and Uncultured Coral-Associated Bacteria

Coral-associated microbes are crucial for the biology of their hosts, contributing to nutrient cycling, adaptation, mitigation of toxic compounds, and biological control of pathogens. Natural products from coral-associated micro-organisms (CAM) may possess unique traits. Despite this, the use of CAM for biotechnological purposes has not yet been adequately explored. Here, we investigated the production of commercially important enzymes by 37 strains of bacteria isolated from the coral species Mussismilia braziliensis, Millepora alcicornis, and Porites astreoides. In-vitro enzymatic assays showed that up to 56% of the isolates produced at least one of the seven enzymes screened (lipase, caseinase, keratinase, cellulase, chitinase, amylase, and gelatinase); one strain, identified as Bacillus amyloliquefaciens produced all these enzymes. Additionally, coral species-specific cultured and uncultured microbial communities were identified. The phylum Firmicutes predominated among the isolates, including the genera Exiguobacterium, Bacillus, and Halomonas, among others. Next-generation sequencing and bacteria culturing produced similar but also complementary data, with certain genera detected only by one or the other method. Our results demonstrate the importance of exploring different coral species as sources of specific micro-organisms of biotechnological and industrial interest, at the same time reinforcing the economic and ecological importance of coral reefs as reservoirs of such diversity.

Nanobiocatalysts: Advancements and applications in enzyme technology

Nanobiocatalysts are one of the most promising biomaterials produced by synergistically integrating advanced biotechnology and nanotechnology. These have a lot of potential to improve enzyme stability, function, efficiencyand engineering performance in bioprocessing. Functional nanostructures have been used to create nanobiocatalystsbecause of their specific physicochemical characteristics and supramolecular nature. This review covers a wide range of nanobiocatalysts including polymeric, metallic, silica and carbon nanocarriers as well as their recent developments in controlling enzyme activity. The enormous potential of nanobiocatalysts in bioprocessing in designing effective laboratory trials forapplications in various fields such as food, pharmaceuticals, biofuel, and bioremediation is also discussed extensively.

Encapsulation of Combi-CLEAs of Glycosidases in Alginate Beads and Polyvinyl Alcohol for Wine Aroma Enhancement

The aromatic expression of wines can be enhanced by the addition of specific glycosidases, although their poor stability remains a limitation. Coimmobilization of glycosidases as cross-linked enzyme aggregates (combi-CLEAs) offers a simple solution yielding highly stable biocatalysts. Nevertheless, the small particle size of combi-CLEAs hinders their recovery, preventing their industrial application. Encapsulation of combi-CLEAs of glycosidases in alginate beads and in polyvinyl alcohol is proposed as a solution. Combi-CLEAS of β-d-glucosidase and α-l-arabinofuranosidase were prepared and encapsulated. The effects of combi-CLEA loading and particle size on the expressed specific activity (IU/gbiocatalyst) of the biocatalysts were evaluated. Best results were obtained with 2.6 mm diameter polyvinyl alcohol particles at a loading of 60 mgcombi-CLEA/gpolyvinyl alcohol, exhibiting activities of 1.9 and 1.0 IU/gbiocatalyst for β-d-glucosidase and α-l-arabinofuranosidase, respectively. Afterwards, the stability of the biocatalysts was tested in white wine. All the encapsulated biocatalysts retained full activity after 140 incubation days, outperforming both free enzymes and nonencapsulated combi-CLEAs. Nevertheless, the alginate-encapsulated biocatalysts showed a brittle consistency, making recovery unfeasible. Conversely, the polyvinyl-encapsulated biocatalyst remained intact throughout the assay. The encapsulation of combi-CLEAs in polyvinyl alcohol proved to be a simple methodology that allows their recovery and reuse to harness their full catalytic potential.

Artificial enzymes bringing together computational design and directed evolution

Enzymes are proteins that catalyse chemical reactions and, as such, have been widely used to facilitate a variety of natural and industrial processes, dating back to ancient times. In fact, the global enzymes market is projected to reach $10.5 billion in 2024. The development of computational and DNA editing tools boosted the creation of artificial enzymes (de novo enzymes) - synthetic or organic molecules created to present abiological catalytic functions. These novel catalysts seek to expand the catalytic power offered by nature through new functions and properties. In this manuscript, we discuss the advantages of combining computational design with directed evolution for the development of artificial enzymes and how this strategy allows to fill in the gaps that these methods present individually by providing key insights about the sequence-function relationship. We also review examples, and respective strategies, where this approach has enabled the creation of artificial enzymes with promising catalytic activity. Such key enabling technologies are opening new windows of opportunity in a variety of industries, including pharmaceutical, chemical, biofuels, and food, contributing towards a more sustainable development.

Challenges and perspectives of the β-galactosidase enzyme

The enzyme β-galactosidase has great potential for application in the food and pharmaceutical industries due to its ability to perform the hydrolysis of lactose, a disaccharide present in milk and in dairy by-products. It can be used in free form, in batch processes, or in immobilized form, which allows continuous operation and provides greater enzymatic stability. The choice of method and support for enzyme immobilization is essential, as the performance of the biocatalyst is strongly influenced by the properties of the material used and by the interaction mechanisms between support and enzyme. Therefore, this review showed the main enzyme immobilization techniques, and the most used supports for the constitution of biocatalysts. Also, materials with the potential for immobilization of β-galactosidases and the importance of their biotechnological application are presented. KEY POINTS: • The main methods of immobilization are physical adsorption, covalent bonding, and crosslinking. • The structural conditions of the supports are determining factors in the performance of the biocatalysts. • Enzymatic hydrolysis plays an important role in the biotechnology industry.

Biosynthesis of a Novel Antibacterial Dipeptide, Using Proteases From South American Native Fruits, Useful as a Food Preservative

Antiacanthain and granulosain are the partially purified proteolytic extracts from the South American native fruits of Bromelia antiacantha (Bertol. ) and Solanum granuloso leprosum, respectively. The aim of this work was to compare the ability of both soluble and immobilized antiacanthain and granulosain f or the synthesis of Z-Tyr-Val-OH, a novel antibacterial dipeptide, in different reaction systems formed by almost anhydrous organic solvents (X_w: 1 × 10⁻⁵) and several percentages of immiscible organic solvents in 100 mM Tris(hydroxymethyl)aminomethane hydrochloride buffer pH 8.0. Soluble antiacanthain in half of the 24 different organic biphasic media showed higher catalytic potential than in 100 mM Tris(hydroxymethyl)aminomethane hydrolchloride buffer pH 8.0. Soluble granulosain showed lower catalytic potential in all liquid-liquid biphasic media than in the same buffer. However, 50% (v/v) ethyl ethanoate in 100 mM Tris(hydroxymethyl)aminomethane hydrolchloride buffer pH 8.0 allowed to express the highest catalytic potential of both soluble enzymes. In 50% v/v ethyl ethanoate, soluble antiacanthain and granulosain catalyzed the synthesis of Z-Tyr-Val-OH with 72 ± 0.15 and 60 ± 0.10% maximal peptide yields, respectively. Multi-point immobilization in glyoxyl-silica did not lead to better peptide yields than soluble enzymes, in that liquid-liquid biphasic medium under the same reaction conditions. Soluble and glyoxyl-silica immobilized antiacanthain in almost anhydrous ethyl ethanoate (X_w: 1 × 10⁻⁵) were able to retain 17.3 and 45% of the initial proteolytic activity of antiacanthain in 100 mM Tris hydrolchloride buffer pH 8.0, respectively, at 40°C under agitation (200 rpm). Soluble and glyoxyl-silica immobilized granulosain were inactivated under the same reaction conditions. Glyoxyl-silica immobilized antiacanthain showed to be a robust biocatalyst in almost anhydrous ethyl ethanoate (X_w: 1 × 10⁻⁵), eliciting the best peptide yield (75 ± 0.13%). The synthesis reaction of Z-Tyr-Val-OH could not proceed when soluble antiacanthain was used under the same conditions. Both peptidases only catalyzed the synthesis reaction under kinetic control, using activated acyl donor substrates. Finally, this work reports a novel broad-spectrum antibacterial peptide that significantly decreased (p ≤ 0.05) the specific growth rates of Gram positive and Gram negative microorganisms at very low concentrations (≥15 and 35 μg/ml, respectively); contributing with a new safe food preservative of applying for different food systems.

Immobilization of Pseudomonas stutzeri lipase through Cross-linking Aggregates (CLEA) for reactions in Deep Eutectic Solvents

The use of deep eutectic solvents (DES) with buffer as cosolvent (up to 10 % v/v) leads to low-viscous media in which lipases can perform synthetic reactions, instead of hydrolysis. This paper explores the immobilization of Pseudomonas stutzeri lipase (TL) in cross-linking aggregates (CLEA) to deliver robust derivatives that are active in media like choline chloride - glycerol DES with buffer as cosolvent. While the free TL enzyme was markedly inactive in these media, TL-CLEA derivatives perform esterifications and can be reused several times. Overall, results are consistent with previous experiments reported for other lipases in these DES-water media and confirm that CLEA immobilization turns out a very useful and straightforward alternative for generating active (bio)catalysts for DES-aqueous media systems. Immobilized systems open the possibility of performing continuous processes in low-viscous DES-buffer media.

Ile258Met mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase significantly enhances catalytic efficiency, cofactor affinity, and thermostability

NAD(H)-dependent 7α-hydroxysteroid dehydrogenase catalyzes the oxidation of chenodeoxycholic acid to 7-oxolithocholic acid. Here, we designed mutations of Ile258 adjacent to the catalytic pocket of Brucella melitensis 7α-hydroxysteroid dehydrogenase. The I258M variant gave a 4.7-fold higher k_cat, but 4.5-fold lower K_M, compared with the wild type, resulting in a 21.8-fold higher k_cat/K_M value for chenodeoxycholic acid oxidation. It presented a 2.0-fold lower K_M value with NAD⁺, suggesting stronger binding to the cofactor. I258M produced 7-oxolithocholic acid in the highest yield of 92.3% in 2 h, whereas the wild-type gave 88.4% in 12 h. The I258M mutation increased the half-life from 20.8 to 31.1 h at 30 °C. Molecular dynamics simulations indicated increased interactions and a modified tunnel improved the catalytic efficiency, and enhanced rigidity at three regions around the ligand-binding pocket increased the enzyme thermostability. This is the first report about significantly improved catalytic efficiency, cofactor affinity, and enzyme thermostability through single site-mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase. KEY POINTS: • Sequence and structure analysis guided the site mutation design. • Thermostability, catalytic efficiency and 7-oxo-LCA production were determined. • MD simulation was performed to indicate the improvement by I258M mutation.

Different strategies for the lipase immobilization on the chitosan based supports and their applications

Immobilized enzymes have received incredible interests in industry, pharmaceuticals, chemistry and biochemistry sectors due to their various advantages such as ease of separation, multiple reusability, non-toxicity, biocompatibility, high activity and resistant to environmental changes. This review in between various immobilized enzymes focuses on lipase as one of the most practical enzyme and chitosan as a preferred biosupport for lipase immobilization and provides a broad range of studies of recent decade. We highlight several aspects of lipase immobilization on the surface of chitosan support containing various types of lipase and immobilization techniques from physical adsorption to covalent bonding and cross-linking with their benefits and drawbacks. The recent advances and future perspectives that can improve the present problems with lipase and chitosan such as high-price of lipase and low mechanical resistance of chitosan are also discussed. According to the literature, optimization of immobilization methods, combination of these methods with other techniques, physical and chemical modifications of chitosan, co-immobilization and protein engineering can be useful as a solution to overcome the mentioned limitations.

Recent advances in artificial enzyme cascades for the production of value-added chemicals

Enzyme cascades are efficient tools to perform multi-step synthesis in one-pot in a green and sustainable manner, enabling non-natural synthesis of valuable chemicals from easily available substrates by artificially combining two or more enzymes. Bioproduction of many high-value chemicals such as chiral and highly functionalised molecules have been achieved by developing new enzyme cascades. This review summarizes recent advances on engineering and application of enzyme cascades to produce high-value chemicals (alcohols, aldehydes, ketones, amines, carboxylic acids, etc) from simple starting materials. While 2-step enzyme cascades are developed for versatile enantioselective synthesis, multi-step enzyme cascades are engineered to functionalise basic chemicals, such as styrenes, cyclic alkanes, and aromatic compounds. New cascade reactions have also been developed for producing valuable chemicals from bio-based substrates, such as ʟ-phenylalanine, and renewable feedstocks such as glucose and glycerol. The challenges in current process and future outlooks in the development of enzyme cascades are also addressed.

Evaluation of biological activities, structural and conformational properties of bovine beta- and alpha-trypsin isoforms in aqueous-organic media

The study of the biological activity of trypsin isoforms in aqueous-organic media is of great interest to various fields of knowledge and biochemistry applications. Thus enzymatic, structural, and energetic properties of bovine β- and α-trypsin isoforms were compared in aqueous-organic media using 30 mg of each isoform. The results showed that the changes induced on the structure and activity of the same trypsin isoform occur at different concentrations. Better results for activity (ionic strength of 0.11 mol·L^-1, at 37 °C and pH 8.0) were found in 0-40% of ethanolic media in which the activity for β-trypsin was about 60% higher than ɑ-trypsin. The ethanolic system does not cause significant changes in the level of secondary structure but the β-trypsin isoform undergoes a major rearrangement. The use of until 60% (v/v) ethanol showed that β-trypsin presents a denaturation process 17% more cooperative. The organic solvent causes redistribution in the supramolecular arrangement of both isoforms: all concentrations used induced the β-trypsin molecules to rearrange into agglomerates. The ɑ-trypsin rearranges into agglomerates up to 60% (v/v) of ethanol and aggregates at 80% (v/v) of ethanol. Both isoforms keep the enzymatic activity up to 60% (v/v) of ethanol.

Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods

Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.

CLytA-DAAO Chimeric Enzyme Bound to Magnetic Nanoparticles. A New Therapeutical Approach for Cancer Patients?

D-amino acid oxidase (DAAO) is an enzyme that catalyzes the oxidation of D-amino acids generating H2O2. The enzymatic chimera formed by DAAO bound to the choline-binding domain of N-acetylmuramoyl-L-alanine amidase (CLytA) induces cytotoxicity in several pancreatic and colorectal carcinoma and glioblastoma cell models. In the current work, we determined whether the effect of CLytA-DAAO immobilized in magnetic nanoparticles, gold nanoparticles, and alginate capsules offered some advantages as compared to the free CLytA-DAAO. Results indicate that the immobilization of CLytA-DAAO in magnetic nanoparticles increases the stability of the enzyme, extending its time of action. Besides, we compared the effect induced by CLytA-DAAO with the direct addition of hydrogen peroxide, demonstrating that the progressive generation of reactive oxygen species by CLytA-DAAO is more effective in inducing cytotoxicity than the direct addition of H2O2. Furthermore, a pilot study has been initiated in biopsies obtained from pancreatic and colorectal carcinoma and glioblastoma patients to evaluate the expression of the main genes involved in resistance to CLytA-DAAO cytotoxicity. Based on our findings, we propose that CLytA-DAAO immobilized in magnetic nanoparticles could be effective in a high percentage of patients and, therefore, be used as an anti-cancer therapy for pancreatic and colorectal carcinoma and glioblastoma.

Enzymes and biopolymers. The opportunity for the smart design of molecular delivery systems

Enzymes exhibit a tremendous potential due to the catalytic activity in response to physiological conditions and specific microenvironments. Exploiting these properties in combination with the versatility of biopolymers, a fascinating field for the rational development of a new class of "smart" delivery systems for therapeutic molecules is proposed. Many strategies have been recently developed to produce matrices with the desirable properties of molecular release, and enzymes could be playing a relevant role in modify the chemical composition of the polymers, the porosity and surface area of the matrices and modulate the kinetic of controlled release. Enzyme based computational systems have appeared as a relevant complementary tool to design novel smart bioactive matrices for programmable drug delivery. The present review is reporting the recent advances and projections of smart biopolymeric matrices activated by enzymes for sustained release of therapeutic molecules, highlighting various applications in the area of advanced drug delivery.

Enhanced enzymatic activity and stability by in situ entrapment of α-Glucosidase within super porous p(HEMA) cryogels during synthesis

Here, poly(2-hydroxyethyl methacrylate) (p(HEMA)) cryogel were prepared in the presence 0.48, 0.96, and 1.92 mL of α-Glucosidase enzyme (0.06 Units/mL) solutions to obtain enzyme entrapped superporous p(HEMA) cryogels, donated as α-Glucosidase@p(HEMA)-1, α-Glucosidase@p(HEMA)-2, and α-Glucosidase@p(HEMA)-3, respectively. The enzyme entrapped p(HEMA) cryogels revealed no interruption for hemolysis and coagulation of blood rendering viable biomedical application in blood contacting applications. The α-Glucosidase@p(HEMA)-1 was found to preserve its' activity% 92.3 ± 1.4 % and higher activity% against free α-Glucosidase enzymes in 15-60℃ temperature, and 4-9 pH range. The Km and Vmax values of α-Glucosidase@p(HEMA)-1 cryogel was calculated as 3.22 mM, and 0.0048 mM/min, respectively versus 1.97 mM, and 0.0032 mM/min, for free enzymes. The α-Glucosidase@p(HEMA)-1 cryogel was found to maintained enzymatic activity more than 50 % after 10 consecutive uses, and also preserved their activity more than 50 % after 10 days of storage at 25 ℃, whereas free α-Glucosidase enzyme maintained only 1.9 ± 0.9 % activity under the same conditions.

Improving laccase thermostability with aqueous natural deep eutectic solvents

The wide-spread use of laccases in industry is often limited due to the enzyme inactivation over time at conditions which exceeds the operating conditions of the enzymes, which are neutral pH and ambient temperatures (30-40 °C). Natural Deep Eutectic Solvents (NADESs) have attracted considerable attention as reaction media in biocatalysis due to their promising compatibility with enzymes and sustainable derivation. In this contribution we demonstrate the possibility of applying aqueous NADESs as incubation media to alter the activity and inhibit thermal inactivation of laccase T. versicolor. For example we show that by incubating 0.25 g L^-1 laccase in an aqueous 25 wt% betaine-xylitol based NADES at 70 °C for 15 min, the measured residual activity of laccase is a near 10 fold greater than the measured residual activity of laccase when incubated without the NADES. Moreover, the comparison of the residual activities of the enzyme in presence betaine, xylitol or NADES is clearly showing the advantage of using a NADES over its individual components. The drastic enhancement of the enzyme thermostability by pre-incubation of laccase in NADES media showcases a facile, cheap and green method of boosting the stability laccase.

Escherichia coli strain engineering for enhanced production of serratiopeptidase for therapeutic applications

Serratiopeptidase is an extracellular zinc-containing metalloprotease that is produced by Serratia marcescens having molecular weight of about 53kD. It has shown therapeutic (anti-inflammatory, anti-fibrinolytic and analgesic) as well as industrial applications (detergents, food processing, leather, paper and brewing etc.). The evolution of Serratia marcescens as an opportunistic pathogen associated with various infections has led researchers to think and develop an alternate strategy for its industrial production. The study presents successful cloning, expression and purification of active serratiopeptidase, using Escherichia coli BL21 [DE3] and pET SUMO vector followed by optimization of synthetic media and culture conditions for enhanced serratiopeptidase production. Initial optimization of physical parameters was done followed by a screening of different carbon and nitrogen sources. The significant media components for serratiopeptidase production as shown by factorial screening experiment were subjected to Response Surface Methodology (RSM) based optimization. The optimized media yielded 86 mg L^-1 of biologically active refolded serratiopeptidase from 20 g L^-1 wet weight of induced pellet as predicted by the equation. The success of the application of a statistical model for designing an optimized media for enhanced serratiopeptidase production also suggests a new insight for the scale-up of serratiopeptidase towards industrial applications.

Design for preparation of more active cross-linked enzyme aggregates of Burkholderia cepacia lipase using palm fiber residue

A new design of cross-linked enzyme aggregates (CLEAs) of Burkholderia cepacia lipase (BCL) based mainly on the use of lignocellulosic residue of palm fiber as an additive was proposed. Different parameters for the preparation of active CLEAs in the hydrolysis of olive oil, such as precipitation agents, crosslinking agent concentration, additives, and coating agents were investigated. The highest activity yield (121.1 ± 0.1%) and volumetric activity (1578.1 ± 2.5 U/mL) were achieved for CLEAs prepared using the combination of a coating step with Triton^® X-100 and polyethyleneimine plus the use of palm fiber as an additive. The variations of the secondary structures of BCL-CLEAs were analyzed by second-derivative infrared spectra, mainly indicating a reduction of the α-helix structure, which was responsible for the lipase activation in the supramolecular structure of the CLEAs. Thus, these results provided evidence of an innovative design of BCL-CLEAs as a sustainable and biocompatible opportunity for biotechnology applications.

Parameterization of Unnatural Amino Acids with Azido and Alkynyl R-Groups for Use in Molecular Simulations

Recent new methods to functionalize proteins at specific amino acid locations use unnatural amino acids that contain azido and alkynyl groups. This capability is unprecedented and enables the creation of site-specific protein devices. Because of the high specificity of these devices, many protein configurations are possible and in silico screens have shown promise in predicting optimal attachment site locations. Therefore, there is significant interest in improving current molecular dynamics (MD) models to include the unique chemistries of these linear moieties. This work uses the force field tool kit to obtain the bonded and nonbonded CHARMM parameters for small molecules that contain azido and alkynyl groups. Next, the reliability of these parameters is tested by running simulated MD analysis to prove that the modeled structures match those found in the literature and quantum theory. Finally, the protein MD simulation compares this parameter set with crystallographic data to give a greater understanding of unnatural amino acid influence on the protein structure.

Improved biosynthesis of 5-hydroxymethyl-2-furancarboxylic acid and furoic acid from biomass-derived furans with high substrate tolerance of recombinant Escherichia coli HMFOMUT whole-cells

The main aim of this work was to firstly develop a selective oxidation approach for biologically converting 5-hydroxymethylfurfural and furfural into the corresponding furan-based carboxylic acids with recombinant Escherichia coli HMFOMUT. Whole-cells of this recombinant strain harbored good biocatalytic activity in a narrow pH range (pH 6.5-7.0), which had high tolerance toward furfural (up to 50 mM) and 5-hydroxymethylfurfural (up to 150 mM), well-known potential inhibitors against microorganisms. 5-Hydroxymethyl-2-furancarboxylic acid and furoic acid could be obtained at 96.9% and 100% yield from 5-hydroxymethylfurfural (150 mM) and furfural (50 mM) at 30 °C and pH 7.0. The improved substrate tolerance of Escherichia coli HMFOMUT is gaining a great interest to synthesize value-added furan-based carboxylic acids, which has potential industrial applications.