Towards Understanding Directed Evolution: More than Half of All Amino Acid Positions Contribute to Ionic Liquid Resistance of Bacillus subtilis Lipase A

Ionic liquids (ILs) are attractive (co‐)solvents for biocatalysis. However, in high concentration (>10 % IL), enzymes usually show decreased activity. No general principles have been discovered to improve IL resistance of enzymes by protein engineering. We present a systematic study to elucidate general engineering principles by site saturation mutagenesis on the complete gene bsla. Screening in presence of four [BMIM]‐based ILs revealed two unexpected lessons on directed evolution: 1) resistance improvement was obtainable at 50–69 % of all amino acid positions, thus explaining the success of small sized random mutant libraries; 2) 6–13 % of substitutions led to improved resistance. Among these, 66–95 % were substitutions by chemically different amino acids (e.g., aromatic to polar/aliphatic/charged amino acids), thus indicating that mutagenesis methods introducing such changes should, at least for lipases like BSLA, be favored to improve IL resistance.     

Directed Evolution of Enzymes for Industrial Biocatalysis

Enzymes have the potential to catalyse a wide variety of chemical reactions. They are increasingly being sought as environmentally friendly and cost‐effective alternatives to conventional catalysts used in industries ranging from bioremediation to applications in medicine and pharmaceutics. Despite the benefits, they are not without their limitations. Many naturally occurring enzymes are not suitable for use outside of their native cellular environments. However, protein engineering can be used to generate enzymes tailored for specific industrial applications. Directed evolution is particularly useful and can be employed even when lack of structural information impedes the use of rational design. The aim of this review is to provide an overview of current industrial applications of enzyme technology and to show how directed evolution can be used to modify and to enhance enzyme properties. This includes a brief discussion on library generation and a more detailed focus on library screening methods, which are critical to any directed evolution experiment.     

Improving the Stability and Catalyst Lifetime of the Halogenase RebH By Directed Evolution

We previously reported that the halogenase RebH catalyzes selective halogenation of several heterocycles and carbocycles, but product yields were limited by enzyme instability. Here, we use directed evolution to engineer an RebH variant, 3‐LR, with a T_opt over 5 °C higher than that of wild‐type, and 3‐LSR, with a T_m 18 °C higher than that of wild‐type. These enzymes provided significantly improved conversion (up to fourfold) for halogenation of tryptophan and several non‐natural substrates. This initial evolution of RebH not only provides improved enzymes for immediate synthetic applications, but also establishes a robust protocol for further halogenase evolution.     

Effect of 1-Ethyl-3-methylimidazolium Tetrafluoroborate and Acetate Ionic Liquids on Stability and Amyloid Aggregation of Lysozyme

Amyloid fibrils draw attention as potential novel biomaterials due to their high stability, strength, elasticity or resistance against degradation. Therefore, the controlled and fast fibrillization process is of great interest, which raises the demand for effective tools capable of regulating amyloid fibrillization. Ionic liquids (ILs) were identified as effective modulators of amyloid aggregation. The present work is focused on the study of the effect of 1-ethyl-3-methyl imidazolium-based ILs with kosmotropic anion acetate (EMIM-ac) and chaotropic cation tetrafluoroborate (EMIM-BF₄) on the kinetics of lysozyme amyloid aggregation and morphology of formed fibrils using fluorescence and CD spectroscopy, differential scanning calorimetry, AFM with statistical image analysis and docking calculations. We have found that both ILs decrease the thermal stability of lysozyme and significantly accelerate amyloid fibrillization in a dose-dependent manner at concentrations of 0.5%, 1% and 5% (v/v) in conditions and time-frames when no fibrils are formed in ILs-free solvent. The effect of EMIM-BF₄ is more prominent than EMIM-ac due to the different specific interactions of the anionic part with the protein surface. Although both ILs induced formation of amyloid fibrils with typical needle-like morphology, a higher variability of fibril morphology consisting of a different number of intertwining protofilaments was identified for EMIM-BF_4.     

Evolution of Glucose Dehydrogenase for Cofactor Regeneration in Bioredox Processes with Denaturing Agents

Glucose dehydrogenase (GDH) is a general tool for driving nicotinamide (NAD(P)H) regeneration in synthetic biochemistry. An increasing number of synthetic bioreactions are carried out in media containing high amounts of organic cosolvents or hydrophobic substrates/products, which often denature native enzymes, including those for cofactor regeneration. In this work, we attempted to improve the chemical stability of Bacillus megaterium GDH (BmGDH_M0) in the presence of large amounts of 1-phenylethanol by directed evolution. Among the resulting mutants, BmGDH_M6 (Q252L/E170K/S100P/K166R/V72I/K137R) exhibited a 9.2-fold increase in tolerance against 10 % (v/v) 1-phenylethanol. Moreover, BmGDH_M6 was also more stable than BmGDH_M0 when exposed to hydrophobic and enzyme-inactivating compounds such as acetophenone, ethyl 2-oxo-4-phenylbutyrate, and ethyl (R)-2-hydroxy-4-phenylbutyrate. Coupled with a Candida glabrata carbonyl reductase, BmGDH_M6 was successfully used for the asymmetric reduction of deactivating ethyl 2-oxo-4-phenylbutyrate with total turnover number of 1800 for the nicotinamide cofactor, thus making it attractive for commercial application. Overall, the evolution of chemically robust GDH facilitates its wider use as a general tool for NAD(P)H regeneration in biocatalysis.     

The Evolution of an Amine Dehydrogenase Biocatalyst for the Asymmetric Production of Chiral Amines

The reductive amination of ketones to produce chiral amines is an important transformation in the production of pharmaceutical intermediates. Therefore, industrially applicable enzymatic methods that enable the selective synthesis of chiral amines could be very useful. Using a phenylalanine dehydrogenase scaffold devoid of amine dehydrogenase activity, a robust amine dehydrogenase has been evolved with a single two‐site library allowing for the direct production of (R)‐1‐(4‐fluorophenyl)‐propyl‐2‐amine from para‐fluorophenylacetone with a k_cat value of 6.85 s⁻¹ and a K_M value of 7.75 mM for the ketone substrate. This is the first example of a highly active amine dehydrogenase capable of accepting aliphatic and benzylic ketone substrates. The stereoselectivity of the evolved amine dehydrogenase was very high (>99.8% ee) showing that high selectivity of the wild‐type phenylalanine dehydrogenase was conserved in the evolution process. When paired with glucose/glucose dehydrogenase, NADH cofactor can be effficiently regenerated and the reaction driven to over 93% conversion. The broad specificity, high selectivity, and near complete conversion render this amine dehydrogenase an attractive target for further evolution toward pharmaceutical compounds and subsequent application.     

Advances in Membrane-Bound Catechol-O-Methyltransferase Stability Achieved Using a New Ionic Liquid-Based Storage Formulation

Membrane-bound catechol-O-methyltransferase (MBCOMT), present in the brain and involved in the main pathway of the catechol neurotransmitter deactivation, is linked to several types of human dementia, which are relevant pharmacological targets for new potent and nontoxic inhibitors that have been developed, particularly for Parkinson’s disease treatment. However, the inexistence of an MBCOMT 3D-structure presents a blockage in new drugs’ design and clinical studies due to its instability. The enzyme has a clear tendency to lose its biological activity in a short period of time. To avoid the enzyme sequestering into a non-native state during the downstream processing, a multi-component buffer plays a major role, with the addition of additives such as cysteine, glycerol, and trehalose showing promising results towards minimizing hMBCOMT damage and enhancing its stability. In addition, ionic liquids, due to their virtually unlimited choices for cation/anion paring, are potential protein stabilizers for the process and storage buffers. Screening experiments were designed to evaluate the effect of distinct cation/anion ILs interaction in hMBCOMT enzymatic activity. The ionic liquids: choline glutamate [Ch][Glu], choline dihydrogen phosphate ([Ch][DHP]), choline chloride ([Ch]Cl), 1- dodecyl-3-methylimidazolium chloride ([C12mim]Cl), and 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) were supplemented to hMBCOMT lysates in a concentration from 5 to 500 mM. A major potential stabilizing effect was obtained using [Ch][DHP] (10 and 50 mM). From the DoE 146% of hMBCOMT activity recovery was obtained with [Ch][DHP] optimal conditions (7.5 mM) at −80 °C during 32.4 h. These results are of crucial importance for further drug development once the enzyme can be stabilized for longer periods of time.     

Thermal Properties of Macrocyclic Polyethers: Implications for the Design of Crown Ether-Based Ionic Liquids

The most commonly studied classes of ionic liquids (ILs) comprise relatively large and asymmetric heterocyclic cations (e.g., diakylimidazolium or N-alkylpyridinium) in combination with any of a wide variety of inorganic (e.g., BF₄^?, Cl^?) or organic (e.g., bis[(trifluoromethyl- sulfonyl)imide], Tf₂N^?) anions. Recently it has been shown that ILs can also be formed by complexation reactions of metal cations (e.g., Li⁺, as its Tf₂N^? salt) with various neutral ligands (e.g., cyclohexano-15-crown-5 or alkylamines). Because the upper limit of the useful temperature range of any IL is governed by its thermal stability, and because the thermal stability of a neutral ligand (i.e., its propensity to either volatilize or decompose) is of obvious importance in determining that of an IL prepared from it, a systematic examination of the thermal properties of a series of macrocyclic polyethers of potential utility in the synthesis of new ILs has been undertaken. The results show that the temperature corresponding to the onset of mass loss upon heating (i.e., evaporation and/or decomposition) varies with the ring size, substitution, nature of the donor atoms, and stereochemistry of the macrocycle, but is most strongly influenced by the molecular weight and aromatic content of the compound.     

On the Use of Ionic Liquids to Separate Aromatic Hydrocarbons from a Model Soil

The potential of exploiting ionic liquids (ILs) for an ex situ solvent aromatic extraction technique is envisaged in this work, due to the serious proportions reached by this kind of contaminants associated with the industrial progress. 1-butyl-1-methylpyrrolidinium bis (trifluoromethylsulfonyl) imide, tetraalkyl ammonium sulfate, trihexyl (tetradecyl) phosphonium dicyanamide, 1-hexyl-3-methylimidazolium hexafluorophosphate, 1,3-dimethylimidazolium methyl sulfate, and 1-butyl-3-methylimidazolium methyl sulfate are proposed to efficiently extract benzene, toluene, and ethylbenzene at concentrations over the maximum allowable limit. The extraction procedure is completed with a washing and recycling step with the purpose of achieving a more competitive process.     

Exploring the Absorption Mechanisms of Imidazolium-Based Ionic Liquids to Epigallocatechin Gallate

Imidazolium-based ionic liquids are wildly used in natural product adsorption and purification. In this work, one typical polymeric ionic liquid (PIL) was synthesized by using L-proline as the anion, which exhibited excellent adsorption capacity toward tea polyphenol epigallocatechin gallate (EGCG). The adsorption conditions were optimized with the response surface method (RSM). Under the optimum conditions, the adsorption capacity of the PIL for EGCG can reach as high as 552 mg/g. Dynamics and isothermal research shows that the adsorption process of EGCG by the PIL particularly meets the quasi-second-order kinetic equation and monolayer adsorption mechanism. According to thermodynamic parameter analysis, the adsorption process is endothermic and spontaneous. The results of theoretical calculation by molecular docking also demonstrated the interaction mechanisms between EGCG and the ionic liquid. Considering the wide application of imidazolium-based ionic liquids in component adsorption and purification, the present study can not only be extended to other similar experimental mechanism validation, but also be representative for guiding the synthesis of PIL and optimization of adsorption conditions.     

Upgrading the Topical Delivery of Poorly Soluble Drugs Using Ionic Liquids as a Versatile Tool

Numerous studies are continuously being carried out in pursuit of formulations with higher performance. Problems such as poor drug solubility, which hinders drug incorporation into delivery systems and bioavailability, or limitations concerning the stability and performance of the formulations may cause difficulties, since solving all these drawbacks at once is a huge challenge. Ionic liquids (ILs), due to their tunable nature, may hypothetically be synthesized for a particular application. Therefore, predicting the impact of a particular combination of ions within an IL in drug delivery could be a useful strategy. Eight ILs, two choline amino acid ILs, two imidazole halogenated ILs, and four imidazole amino acid ILs, were prepared. Their applicability at non-toxic concentrations, for improving solubility and the incorporation of the poorly soluble, ferulic, caffeic, and p-coumaric acids, as well as rutin, into topical emulsions, was assessed. Next, the impact of the ILs on the performance of the formulations was investigated. Our study showed that choosing the appropriate IL leads to a clear upgrade of a topical emulsion, by optimizing multiple features of its performance, such as improving the delivery of poorly soluble drugs, altering the viscosity, which may lead to better sensorial features, and increasing the stability over time.     

Directed Evolution of an Antitumor Drug (Arginine Deiminase PpADI) for Increased Activity at Physiological pH

Arginine deiminase (ADI; EC 3.5.3.6) has been studied as a potential antitumor drug for the treatment of arginine‐auxotrophic tumors, such as hepatocellular carcinomas (HCCs) and melanomas. Studies with human lymphatic leukemia cell lines confirmed that ADI is an antiangiogenic agent for treating leukemia. The main limitation of ADI from Pseudomonas plecoglossicida (PpADI) lies in its pH‐dependent activity profile, its pH optimum is at 6.5. A pH shift from 6.5 to 7.5 results in an approximately 80 % drop in activity. (The pH of human plasma is 7.35 to 7.45.) In order to shift the PpADI pH optimum, a directed‐evolution protocol based on an adapted citrulline‐screening protocol in microtiter‐plate format was developed and validated. A proof of concept for ADI engineering resulted in a pH optimum of pH 7.0 and increased resistance under physiological and slightly alkaline conditions. At pH 7.4, variant M2 (K5T/D44E/H404R) is four times faster than the wild‐type PpADI and retains ～50 % of its activity relative to its pH optimum, compared to ～10 % in the case of the wild‐type PpADI.     

Mixtures of Ionic Liquids and Water as a Medium for Efficient Enantioselective Hydrogenation and Catalyst Recycling

In a screening of ligands, ionic liquids and reaction conditions in the Rh‐catalyzed hydrogenation of enamides, a novel multi‐phase reaction system consisting of an ionic liquid (IL) and water (wet ILs) was found to give the most promising results. In many cases such IL/water combinations were superior compared to conventional organic solvents and biphasic ILs/organic co‐solvents media with respect to catalytic performance as well as to catalyst separation and recycling. So far, the best results were obtained with Rh‐ferrocenyl‐diphosphine catalysts (>99% ee). Generally, somewhat lower ees were observed at higher pressure. However, this effect was less pronounced with wet ILs than with conventional solvents. It is shown that IL/water combination allow repeated catalyst recycling without significant loss of activity and that industrially relevant turnover numbers of >10,000 can be obtained.     

Molecular dynamics simulation for the binary mixtures of high pressure carbon dioxide and ionic liquids简

Molecular dynamics simulation with an all-atom force field has been carded out on the two binary sys- tems of [bmim][PF6]-CO2 and [bmim][NO3]-CO2 to study the transport properties, volume expansion and micro- structures. It was found that addition of CO2 in the liquid phase can greatly decrease the viscosity of ionic liquids （ILs） and increase their diffusion coefficient obviously. Furthermore, the volume expansion of ionic liquids was found to increase with the increase of the mole fraction of CO2 in the liquid phase but less than 35% for the two simulated systems, which had a significant difference with CO2 expanded organic solvents. The main reason was that there were some void spaces inter and intra the molecules of ionic liquids. Finally, site to site radial distribution functions and corresponding number integrals were investigated and it was found that the change of microstructures of ILs bv addition CO2 had a great influence on the orooerties of ILs.     

Stetter Reaction in Room Temperature Ionic Liquids and Application to the Synthesis of Haloperidol

Imidazolium‐type room temperature ionic liquids (RTILs) have been used for the Stetter reaction, affording the desired 1,4‐dicarbonyl compounds in good yields. Thiazolium salts and Et₃N are efficient catalysts for this reaction performed in ionic liquid. The possibility to recycle and reuse the solvent has been demonstrated, although it was not possible to recycle the thiazolium catalyst. This method was used in the total synthesis of haloperidol.     

Optimized Hemolysin Type 1 Secretion System in Escherichia coli by Directed Evolution of the Hly Enhancer Fragment and Including a Terminator Region

Type 1 secretion systems (T1SS) have a relatively simple architecture compared to other classes of secretion systems and therefore, are attractive to be optimized by protein engineering. Here, we report a KnowVolution campaign for the hemolysin (Hly) enhancer fragment, an untranslated region upstream of the hlyA gene, of the hemolysin T1SS of Escherichia coli to enhance its secretion efficiency. The best performing variant of the Hly enhancer fragment contained five nucleotide mutations at five positions (A30U, A36U, A54G, A81U, and A116U) resulted in a 2-fold increase in the secretion level of a model lipase fused to the secretion carrier HlyA1. Computational analysis suggested that altered affinity to the generated enhancer fragment towards the S1 ribosomal protein contributes to the enhanced secretion levels. Furthermore, we demonstrate that involving a native terminator region along with the generated Hly enhancer fragment increased the secretion levels of the Hly system up to 5-fold.     

Second‐Generation Engineering of a Thermostable Transketolase (TKGst) for Aliphatic Aldehyde Acceptors with Either Improved or Reversed Stereoselectivity

The transketolase from Geobacillus stearothermophilus (TK_Gst) is a thermostable enzyme with notable high activity and stability at elevated temperatures, but it accepts non‐α‐hydroxylated aldehydes only with low efficiency. Here we report a protein engineering study of TK_Gst based on double‐site saturation mutagenesis either at Leu191 or at Phe435 in combination with Asp470; these are the residues responsible for substrate binding in the active site. Screening of the mutagenesis libraries resulted in several positive variants with activity towards propanal up to 7.4 times higher than that of the wild type. Variants F435L/D470E and L191V/D470I exhibited improved (73 % ee, 3S) and inverted (74 % ee, 3R) stereoselectivity, respectively, for propanal. L191V, L382F/E, F435L, and D470/D470I were concluded to be positive mutations at Leu191, Leu382, Phe435, and Asp470 both for activity and for stereoselectivity improvement. These results should benefit further engineering of TK_Gst for various applications in asymmetric carboligation.     

用变阱宽方阱链流体状态方程模拟离子液体相行为

An equation of state (EOS) for square-well chain fluids with variable range (SWCF-VR) developed based on statistical mechanics for chemical association was employed for the calculations of pressure-volume-temperature (pVT) and phase equilibrium of pure ionic liquids (ILs) and their mixtures. The new molecular parameters for 23 ILs were obtained by fitting their experimental density data over a wide temperature and pressure ranges. The molecular parameters of ILs composed of homologous organic cation and an identical anion such as [Cxmim][NTf2] are good linear with respect to their molecular weight, indicating that the molecular pa-rameters of homologous substances, subsequently pVT and vapor-liquid equilibria vapor-liquid equilibria (VLE) can be predicted using the generalized parameter when no experimental data were available. The new set of parameters were satisfactorily used for calculations of the property of solvent and ILs mixture and the solubility of gas in various ILs at low pressure only using one tem-perature-independent binary interaction parameter.     

Halogenase Engineering for the Generation of New Natural Product Analogues

Halogenases catalyze the incorporation of halogen atoms into organic molecules. Given the importance that halogenation has on the biological activity of small molecules, these enzymes have been subjected to intense engineering efforts to make them more suitable for biotechnology applications. The ability to biohalogenate complex molecules provides, in principle, the opportunity for rapid generation of a series of analogues with new or improved properties. Here we discuss the potential and limitations of using halogenases as biocatalysts, including recent advances in engineering halogenases to generate halogenated natural product analogues.