What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization

Efficient and easible biocatalysts: Strategies for enzyme improvement. A review

Owing to the environmental friendliness and vast advantages that enzymes offer in the biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the low catalytic activity, stability, and specific selectivity of the enzyme limit the range of the reaction enzymes involved in. A comprehensive understanding of the protein structure and dynamics in terms of molecular details enables us to tackle these limitations effectively and enhance the catalytic activity by enzyme engineering or modifying the supports and solvents. Along with different strategies including computational, enzyme engineering based on DNA recombination, enzyme immobilization, additives, chemical modification, and physicochemical modification approaches can be promising for the wide spread of industrial enzyme usage. This is attributed to the successful application of biocatalysts in industrial and synthetic processes requires a system that exhibits stability, activity, and reusability in a continuous flow process, thereby reducing the production cost. The main goal of this review is to display relevant approaches for improving enzyme characteristics to overcome their industrial application.

Bioactivity Profiling of Daedaleopsis confragosa (Bolton) J. Schröt. 1888: Implications for Its Possible Application in Enhancing Women's Reproductive Health

This study investigates the bioactivity profile of wood-rotting fungal species Daedaleopsis confragosa (Bolton) J. Schröt. 1888, focusing on its antioxidant, cytotoxic, and genotoxic activities and enzyme modulation properties with respect to its possible application in terms of enhancing women's reproductive health. Two types of extracts, including those based on EtOH extraction (DC) and hydrodistillation (DCHD), were investigated. The results indicate that the radical scavenging capacity against the DPPH radical and reduction potential were stronger in the DC extracts owing to the higher total phenolic content (TPC) and total flavonoid content (TFC) (25.30 ± 1.05 mg GAE/g d.w. and 2.84 ± 0.85 mg QE/g d.w., respectively). The same trend was observed in the protein phosphatase-1 (PP1) activity and in the genotoxic activity against the δ virus since only the DC extract exhibited DNA disintegration regarding a dilution of 1:100. Conversely, the DCHD extract exhibited increased hemolytic and cytotoxic effects (339.39% and IC50 = 27.76 ± 0.89 μg/mL-72 h incubation, respectively), along with greater inhibition of the AChE enzyme (IC50 = 3.11 ± 0.45 mg/mL) and hemolytic activity. These results suggest that terpenoids and steroids may be responsible for the observed activity in DCHD as these compounds could potentially be extracted following the HD procedure. This comprehensive bioactivity profiling offers valuable insights into the potential therapeutic applications of D. confragosa from Serbia and underscores the importance of further investigations for harnessing its pharmacological potential.

Tailoring the interfacial microenvironment of magnetic metal-organic frameworks using amino-acid-based ionic liquids for lipase immobilization

Modifying the carrier interface is a promising method to improve the microenvironment of immobilized enzymes and enhance their activity and stability. In this work, using proline as amino acid, magnetic metal-organic frameworks (MOFs) were modified with an amino-acid-based ionic liquid (AAIL) with two hydroxyl groups followed by adsorption of porcine pancreatic lipase (PPL). The activity recovery of the prepared immobilized lipase (MMOF-AAIL/PPL) was up to 162 % higher than that of MMOF-PPL (70.8 %). The Michaelis constant of MMOF-AAIL/PPL was 0.0742 mM lower than that of MMOF-PPL, but the catalytic efficiency was 0.0223 min-1 which was higher than MMOF-PPL. Furthermore, MMOF-AAIL/PPL maintained 85.6 % residual activity after stored for 40 days and its residual activity was 71.9 % while that for MMOF-PPL was 58.8 % after incubated in 6 M urea for 2 h. Particularly, after ten consecutive cycles, the residual activity of MMOF-AAIL/PPL still reached 84.4 %. In addition, the magnetic properties of the support facilitate the separation process which improves the utilization efficiency of immobilized enzymes.

Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms

The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.

A Review on the Use of Deep Eutectic Solvents in Protection Reactions

Given the recent research on the application of eco-sustainable methods in organic chemistry, we have focused our attention on the derivatization processes for fundamental functional groups in organic chemistry, such as amino, hydroxyl and carbonyl groups. Protection reactions are needed to temporarily block a certain reactive site on a molecule. The use of green solvents in this context has made an excellent contribution to the development of eco-sustainable methods. In recent years, deep eutectic solvents (DESs) have had great success as a new class of green solvents used in various chemical applications, such as extraction or synthetic processes. These solvents are biodegradable and nontoxic. In this framework, a list of relevant works found in the literature is described, considering DESs to be a good alternative to classic toxic solvents in the protection reactions of important functional groups.

Effect of structural stability of lipase in acetonitrile on its catalytic activity in EGCG esterification reaction: FTIR and MD simulation

In this study, (-)-Epigallocatechin-3-O-gallate (EGCG) esterification reaction was catalyzed by Novozym 435, Lipozyme RM, Lipozyme TLIM, and lipase Amano 30SD in acetonitrile. Fourier transform infrared spectroscopy (FTIR) and molecular dynamic (MD) simulations were used to analyze the structural stability of different lipases in acetonitrile and their effect on EGCG esterification reaction. The results showed that conversion rate of EGCG catalyzed by Lipozyme RM was the highest, followed by Lipozyme TLIM. FTIR indicated that the secondary structure of Lipozyme RM was the most stable. MD simulations suggested that whole structural stability of Lipozyme RM in acetonitrile was superior to Novozym 435 and lipase Amano 30SD and similar to Lipozyme TLIM due to their similar conformation, while the active site of Lipozyme RM is more flexible than that of Lipozyme TLIM, which indicated that lipase with stable whole structure and flexible active site may be more conducive to the esterification of EGCG in acetonitrile. This study provided a direction for rapidly screening lipase to synthetize EGCG or other polyphenols esterified derivatives.

Strategies for modulating transglycosylation activity, substrate specificity, and product polymerization degree of engineered transglycosylases

Glycosides are widely used in many fields due to their favorable biological activity. The traditional plant extractions and chemical methods for glycosides production are limited by environmentally unfriendly, laborious protecting group strategies and low yields. Alternatively, enzymatic glycosylation has drawn special attention due to its mild reaction conditions, high catalytic efficiency, and specific stereo-/regioselectivity. Glycosyltransferases (GTs) and retaining glycoside hydrolases (rGHs) are two major enzymes for the formation of glycosidic linkages. Therein GTs generally use nucleotide phosphate activated donors. In contrast, GHs can use broader simple and affordable glycosyl donors, showing great potential in industrial applications. However, most rGHs mainly show hydrolysis activity and only a few rGHs, namely non-Leloir transglycosylases (TGs), innately present strong transglycosylation activities. To address this problem, various strategies have recently been developed to successfully tailor rGHs to alleviate their hydrolysis activity and obtain the engineered TGs. This review summarizes the current modification strategies in TGs engineering, with a special focus on transglycosylation activity enhancement, substrate specificity modulation, and product polymerization degree distribution, which provides a reference for exploiting the transglycosylation potentials of rGHs.

Effects of alcohol concentration and temperature on the dynamics and stability of mutant Staphylococcal lipase

The stability and activity of lipase in organic media are important parameters in determining how quickly biocatalysis proceeds. This study aimed to examine the effects of two commonly used alcohols in industrial applications, methanol (MtOH) and ethanol (EtOH) on the conformational stability and catalytic activity of G210C lipase, a laboratory-evolved mutant of Staphylococcus epidermidis AT2 lipase. Simulation studies were performed using an open-form predicted structure under 30, 40 and 50% of MtOH and EtOH at 25 °C and 45 °C. The overall enzyme structure becomes more flexible with increasing concentration of MtOH and exhibited the highest flexibility in 40% EtOH. In EtOH, the movement of the lid was found to be temperature-dependent with a noticeable shift in the lid position at 45 °C. Lid opening was evidenced at 50% of MtOH and EtOH which was supported by the increase in SASA of hydrophobic residues of the lid and catalytic triad. The active site remained mostly intact. An open-closed lid transition was observed when the structure was re-simulated in water. Experimental evaluation of the lipase stability showed that the half-life reduced when the enzyme was treated with 40% (v/v) and 50% (v/v) of EtOH and MtOH respectively. The finding implies that a high concentration of alcohol and elevated temperature can induce the lid opening of lipase which could be essential for the activation of the enzyme, provided that the catalytic performance in the active site is not compromised.Communicated by Ramaswamy H. Sarma.

Increased Expression Levels of Thermophilic Serine Protease TTHA0724 through Signal Peptide Screening in Bacillus subtilis and Applications of the Enzyme

The thermostable protease TTHA0724 derived from Thermus thermophilus HB8 is an ideal industrial washing enzyme due to its thermophilic characteristics; although it can be expressed in Escherichia coli via pET-22b, high yields are difficult to achieve, leading to frequent autolysis of the host. This paper details the development of a signal peptide library in the expression system of B. subtilis and the optimization of signal peptides for enhanced extracellular expression of TTHA0724. When B. subtilis was used as the host and the optimized signal peptide was used, the expression level of TTHA0724 was 16.7 times higher compared with E. coli. B. subtilis as an expression host does not change the characteristics of TTHA0724. The potential application fields of TTHA0724 are studied. TTHA0724 can be used as a detergent additive at 60 °C, which can sterilize and eliminate mites while thoroughly cleaning protein stains. Soybean meal enzymatic hydrolysis with TTHA0724 at a high temperature produced a higher content of antioxidant peptides. These results indicate that TTHA0724 has great potential for industrial applications.

Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement

With the development of artificial intelligence (AI), tailoring methods for enzyme engineering have been widely expanded. Additional protocols based on optimized network models have been used to predict and optimize lipase production as well as properties, namely, catalytic activity, stability, and substrate specificity. Here, different network models and algorithms for the prediction and reforming of lipase, focusing on its modification methods and cases based on AI, are reviewed in terms of both their advantages and disadvantages. Different neural networks coupled with various algorithms are usually applied to predict the maximum yield of lipase by optimizing the external cultivations for lipase production, while one part is used to predict the molecule variations affecting the properties of lipase. However, few studies have directly utilized AI to engineer lipase by affecting the structure of the enzyme, and a set of research gaps needs to be explored. Additionally, future perspectives of AI application in enzymes, including lipase engineering, are deduced to help the redesign of enzymes and the reform of new functional biocatalysts. This review provides a new horizon for developing effective and innovative AI tools for lipase production and engineering and facilitating lipase applications in the food industry and biomass conversion.

Assessing the compatibility of choline-based deep eutectic solvents for the structural stability and activity of cellulase: Enzyme sustain at high temperature

As a new generation of 'green solvents' deep eutectic solvents (DESs) represents a promising alternative to the conventional solvents. Their environmental-benign nature and designer properties promote their utility in biocatalysis. Enzymes are marginally stable when exposed to physical/chemical disturbances. One such enzyme is cellulase which is a propitious catalyst for the depolymerization of cellulose under mild conditions. Therefore, their stability is a prerequisite condition to match demands of biorefineries. To address this issue of low stability, activity and thermal denaturation of cellulase, there is a need to find a sustainable and suitable co-solvent that is biocompatible with enzymes ultimately to facilitate their application in bio-industries. In this regard, we synthesized three choline-based DESs, choline chloride (ChCl)-glycerol, ChCl-ethylene glycol and ChCl-lactic acid and employed them to analyze their suitability for cellulase. The present study systematically evaluates the influence of the mentioned DESs on stability, activity and thermal stability of cellulase with the help of various spectroscopic techniques. The spectroscopic analysis revealed that the structural stability and activity of the enzyme were improved in presence of ChCl-glycerol and ChCl-ethylene glycol. The thermal stability was also very well maintained in both the DESs. Interestingly, the relative activity of cellulase was >80 % even after incubation at 50 °C after 48 h for both the DESs. This activity preservation behaviour was more pronounced for ChCl-ethylene glycol than ChCl-glycerol. Moreover, temperature variations studies also reveal promising results by maintain conformational intactness. On the other side, ChCl-lactic acid showed a deleterious effect on the enzyme both structurally as well as thermally. The dynamic light scattering (DLS) analysis provides more specific information about the negative influence of ChCl-lactic acid towards cellulase native structure. This DES induces unavoidable alterations in the enzyme structure which leads to the unfolding of enzyme, ultimately, destabilizing it. Overall, our results present a physical insight into how the enzyme stability and activity depend on the nature of DES. Also, the findings will help to facilitate the development and application of DESs as biocatalytic process.

Laccase-catalyzed lignin depolymerization in deep eutectic solvents: challenges and prospects

Lignin has enormous potential as a renewable feedstock for depolymerizing to numerous high-value chemicals. However, lignin depolymerization is challenging owing to its recalcitrant, heterogenous, and limited water-soluble nature. From the standpoint of environmental friendliness and sustainability, enzymatic depolymerization of lignin is of great significance. Notably, laccases play an essential role in the enzymatic depolymerization of lignin and are considered the ultimate green catalysts. Deep eutectic solvent (DES), an efficient media in biocatalysis, are increasingly recognized as the newest and utmost green solvent that highly dissolves lignin. This review centers on a lignin depolymerization strategy by harnessing the good lignin fractionating capability of DES and the high substrate and product selectivity of laccase. Recent progress and insights into the laccase-DES interactions, protein engineering strategies for improving DES compatibility with laccase, and controlling the product selectivity of lignin degradation by laccase or in DES systems are extensively provided. Lastly, the challenges and prospects of the alliance between DES and laccase for lignin depolymerization are discussed. The collaboration of laccase and DES provides a great opportunity to develop an enzymatic route for lignin depolymerization.

Solvent tolerant enzymes in extremophiles: Adaptations and applications

Non-aqueous enzymology has always drawn attention due to the wide range of unique possibilities in biocatalysis. In general, the enzymes do not or insignificantly catalyze substrate in the presence of solvents. This is due to the interfering interactions of the solvents between enzyme and water molecules at the interface. Therefore, information about solvent-stable enzymes is scarce. Yet, solvent-stable enzymes prove quite valuable in the present day biotechnology. The enzymatic hydrolysis of the substrates in solvents synthesizes commercially valuable products, such as peptides, esters, and other transesterification products. Extremophiles, the most valuable yet not extensively explored candidates, can be an excellent source to investigate this avenue. Due to inherent structural attributes, many extremozymes can catalyze and maintain stability in organic solvents. In the present review, we aim to consolidate information about the solvent-stable enzymes from various extremophilic microorganisms. Further, it would be interesting to learn about the mechanism adapted by these microorganisms to sustain solvent stress. Various approaches to protein engineering are used to enhance catalytic flexibility and stability and broaden biocatalysis's prospects under non-aqueous conditions. It also describes strategies to achieve optimal immobilization with minimum inhibition of the catalysis. The proposed review would significantly aid our understanding of non-aqueous enzymology.

Menthol and Fatty Acid-Based Hydrophobic Deep Eutectic Solvents as Media for Enzyme Activation

This research aims to provide insights into the biological efficacy of a newly formed hydrophobic deep eutectic solvent (DES). A DES based on menthol was successfully synthesized with fatty acids. The DESs’ properties as enzyme activators were examined against a neat counterpart. The menthol:decanoic acid (1:1) combination showed improved thermal stability, strong catalytic activity, and reusability for up to four subsequent cycles under ideal conditions (pH 7.0, 40 °C for 2 h). The hydrophobic DES replaced hexane in ester synthesis, where RNL@DES5 showed better fatty acid conversion compared to neat RNL. This study demonstrated promising applications of hydrophobic DESs in non-aqueous organic reactions.

Surface Modification of Magnetic ZIF-90 Nanoparticles Improves the Microenvironment of Immobilized Lipase and Its Application in Esterification

Interactions of enzymes with supports significantly affect the activity and stability of immobilized enzymes. Herein, amino-functionalized ionic liquid (IL)-grafted magnetic zeolitic imidazolate framework-90 (MZIF-90) was prepared and used to immobilize porcine pancreatic lipase (PPL). The nanocomposites were fully characterized; meanwhile, the interactions between ILs and ZIF-90 were calculated based on density functional theory. The prepared biocatalyst (PPL-ILs/MZIF-90) had a lipase loading of 178.3 mg/g and hydrolysis activity up to 287.5 U/g. When the biocatalyst was used to synthesize isoamyl acetate, the reaction media, molar ratio of alcohol/acid, temperature, and reaction time were optimized. Under the optimized reaction conditions (in hexane, alcohol/acid = 3:1, under 45 °C, reacted for 9 h), the ester yield reached 85.5%. The results of the stability test showed that PPL-ILs/MZIF-90 retained 88.7% of the initial activity after storing for 35 days and 92.5% of the initial activity after reusing for seven cycles for synthesizing isoamyl acetate. Moreover, the secondary structure analysis showed that the synthesized supports protected the active conformation of immobilized lipase, which lead to the enhanced catalytic performance. Additionally, the biocatalyst can be easily separated with a magnet, which facilitated the reusability. This study provides insights regarding the application of metal organic framework composites in the field of enzyme catalysis.

Synthesis of Ibuprofen Monoglyceride Using Novozym®435: Biocatalyst Activation and Stabilization in Multiphasic Systems

This work was focused on the enzymatic esterification of glycerol and ibuprofen at high concentrations in two triphasic systems composed of toluene+ibuprofene (apolar) and glycerol or glycerol–water (polar) liquid phases, and a solid phase with the industrial immobilized lipase B from Candida antarctica named Novozym®435 (N435) acting as the biocatalyst. Based on a preliminary study, the concentration of the enzyme was set at 30 g·L−1 and the stirring speed at 720 r.p.m to reduce external mass transfer limitations. To obtain more information on the reaction system, it was conducted at a wide range of temperatures (50 to 80 °C) and initial concentrations of ibuprofen (20–100 g·L−1, that is, 97 to 483 mM). Under these experimental conditions, the external mass transfer, according to the Mears criterion (Me = 1.47–3.33·10−4 << 0.15), was fast, presenting no limitation to the system productivity, regardless of the presence of water and from 50 to 80 °C. Considering that the enzyme is immobilized in a porous ion-exchange resin, limitations due to internal mass transfer can exist, depending on the values of the effectiveness factor (η). It varied from 0.14 to 0.23 at 50 to 80 °C and 0.32–1 mm particle diameter range in the absence of water, and in the same ranges, from 0.40 to 0.66 in the presence of 7.4% w/w water in the glycerol phase. Thus, it is evident that some limitation occurs due to mass transfer inside the pores, while the presence of water in the polar phase increases the productivity 3–4 fold. During the kinetic study, several kinetic models were proposed for both triphasic reacting systems, with and without first-order biocatalyst deactivation, and their fit to all relevant experimental data led to the observation that the best kinetic model was a reversible hyperbolic model with first-order deactivation in the anhydrous reaction system and a similar model, but without deactivation, for the system with added water at zero time. This fact is in sharp contrast to the use of N435 in a water-glycerol monophasic system, where progressive dissolution of ibuprofen in the reacting media, together with a notable enzyme deactivation, is observed.

Heterologous expression and physicochemical characteristics identification of Kunitz protease inhibitor in Brassica napus

A Kunitz protease inhibitor gene (RTI; rti) was cloned from rapeseed and expressed in a Pichia pastoris expression system for the first time. After isolation and purification, the physical and chemical characteristics of the inhibitor were analyzed. The results showed that the induced expression level of the recombinant RTI reached 628 mg/L, and the specific activity of the inhibitor reached 69.6 TIU/mg protein at the shake flask fermentation level; the recombinant RTI retained more than 70% inhibitory activity between 30 and 90 °C and more than 80% inhibitory activity between pH 2.0-11.0. The metal ions Cu²⁺ and CO²⁺ and the organic reagents methanol, ethanol, acetone, and chloroform inhibit its activity. The recombinant RTI interacts with trypsin in a noncompetitive manner and has a strong and specific inhibitory effect on trypsin, a typical Kunitz trypsin inhibitor from plants. Combined with its good physical and chemical properties, recombinant RTI has the potential to be developed into an insect resistance protein.

Efficient Enzymatic Synthesis of Lipophilic Phenolic Glycoside Azelaic Acid Esters and Their Depigmenting Activity

In this paper, an enzymatic route for synthesizing phenolic glycoside azelaic acid esters was successfully set up via lipase-catalyzed esterification and transesterification. Among the lipases tested, Candida antarctica lipase B (Novozyme 435) showed the highest activity in catalyzing esterification and Thermomyces lanuginosus (Lipozyme TLIM) gave the highest substrate conversion in catalyzing transesterification for the synthesis of ester. The addition of 4A molecular sieves into the reaction system is found to be an effective method for in situ absorption of the byproduct water and methanol, with which the substrate conversions of the enzymatic esterification and transesterification were 98.7 and 95.1%, respectively. Also, the main product ratios in transesterification were above 99.0% with lipozyme TLIM as a catalyst because the hydrolysis reaction was hindered. The results of the physical and biological properties indicate that all esters had higher Clog p values than their parent compounds. Also, the esters showed higher intracellular tyrosinase inhibitory and depigmentating activities than phenolic glycosides, azelaic acid (AA), and their physical mixtures due to their higher membrane penetration and tyrosinase inhibitory effects. In particular, piceid 6″-O-azelaic acid ester (PIA) showed the strongest inhibitory effect against melanin production. Its inhibitory rate was 77.4% at a concentration of 0.25 mM, about 4.2 times higher than that of arbutin (18.5%).

Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis

Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.