A novel enantioselective epoxide hydrolase from Agromyces mediolanus ZJB120203: Cloning, characterization and application

EnzyKR: a chirality-aware deep learning model for predicting the outcomes of the hydrolase-catalyzed kinetic resolution

Hydrolase-catalyzed kinetic resolution is a well-established biocatalytic process. However, the computational tools that predict favorable enzyme scaffolds for separating a racemic substrate mixture are underdeveloped. To address this challenge, we trained a deep learning framework, EnzyKR, to automate the selection of hydrolases for stereoselective biocatalysis. EnzyKR adopts a classifier-regressor architecture that first identifies the reactive binding conformer of a substrate-hydrolase complex, and then predicts its activation free energy. A structure-based encoding strategy was used to depict the chiral interactions between hydrolases and enantiomers. Different from existing models trained on protein sequences and substrate SMILES strings, EnzyKR was trained using 204 substrate-hydrolase complexes, which were constructed by docking. EnzyKR was tested using a held-out dataset of 20 complexes on the task of predicting activation free energy. EnzyKR achieved a Pearson correlation coefficient (R) of 0.72, a Spearman rank correlation coefficient (Spearman R) of 0.72, and a mean absolute error (MAE) of 1.54 kcal mol-1 in this task. Furthermore, EnzyKR was tested on the task of predicting enantiomeric excess ratios for 28 hydrolytic kinetic resolution reactions catalyzed by fluoroacetate dehalogenase RPA1163, halohydrin HheC, A. mediolanus epoxide hydrolase, and P. fluorescens esterase. The performance of EnzyKR was compared against that of a recently developed kinetic predictor, DLKcat. EnzyKR correctly predicts the favored enantiomer and outperforms DLKcat in 18 out of 28 reactions, occupying 64% of the test cases. These results demonstrate EnzyKR to be a new approach for prediction of enantiomeric outcomes in hydrolase-catalyzed kinetic resolution reactions.

Potential of Y. lipolytica epoxide hydrolase for efficient production of enantiopure (R)-1,2-octanediol

The recombinant Yleh from a tropical marine yeast Yarrowia lipolytica NCIM 3589 exhibited a high epoxide hydrolase activity of 9.34 ± 1.80 µmol min^-1 mg^-1 protein towards 1,2-epoxyoctane (EO), at pH 8.0 and 30 °C. The reaction product was identified as 1,2-Octanediol (OD) by GC-MS using EO and H₂O¹⁸ as substrate, affirming the functionality of Yleh as an epoxide hydrolase. For EO, the K_m, V_max, and k_cat/K_m values were 0.43 ± 0.017 mM, 0.042 ± 0.003 mM min^-1, and 467.17 ± 39.43 mM^-1 min^-1, respectively. To optimize the reaction conditions for conversion of racemic EO by Yleh catalyst to enantiopure (R)-1,2-octanediol, initially, Response Surface Methodology was employed. Under optimized reaction conditions of 15 mM EO, 150 µg purified Yleh at 30 °C a maximal diol production of 7.11 mM was attained in a short span of 65 min with a yield of 47.4%. Green technology using deep eutectic solvents for the hydrophobic substrate (EO) were tested as co-solvents in Yleh catalyzed EO hydrolysis. Choline chloride-Glycerol, produced 9.08 mM OD with an increased OD yield of 60.5%. Thus, results showed that deep eutectic solvents could be a promising solvent for Yleh-catalyzed reactions making Yleh a potential biocatalyst for the biosynthesis of enantiopure synthons.

Significant improvement in catalytic activity and enantioselectivity of a Phaseolus vulgaris epoxide hydrolase, PvEH3, towards ortho-cresyl glycidyl ether based on the semi-rational design

The investigation of substrate spectrum towards five racemic (rac-) aryl glycidyl ethers (1a-5a) indicated that E. coli/pveh3, an E. coli BL21(DE3) transformant harboring a PvEH3-encoding gene pveh3, showed the highest EH activity and enantiomeric ratio (E) towards rac-3a. For efficiently catalyzing the kinetic resolution of rac-3a, the activity and E value of PvEH3 were further improved by site-directed mutagenesis of selected residues. Based on the semi-rational design of an NC-loop in PvEH3, four single-site variants of pveh3 were amplified by PCR, and intracellularly expressed in E. coli BL21(DE3), respectively. E. coli/pveh3^E134K and /pveh3^T137P had the enhanced EH activities of 15.3 ± 0.4 and 16.1 ± 0.5 U/g wet cell as well as E values of 21.7 ± 1.0 and 21.2 ± 1.1 towards rac-3a. Subsequently, E. coli/pveh3^E134K/T137P harboring a double-site variant gene was also constructed, having the highest EH activity of 22.4 ± 0.6 U/g wet cell and E value of 24.1 ± 1.2. The specific activity of the purified PvEH3^E134K/T137P (14.5 ± 0.5 U/mg protein) towards rac-3a and its catalytic efficiency (k_cat/K_m of 5.67 mM^-1 s^-1) for (S)-3a were 1.7- and 3.54-fold those (8.4 ± 0.3 U/mg and 1.60 mM^-1 s^-1) of PvEH3. The gram-scale kinetic resolution of rac-3a using whole wet cells of E. coli/pveh3^E134K/T137P was performed at 20 °C for 7.0 h, producing (R)-3a with 99.4% ee_s and 38.5 ± 1.2% yield. Additionally, the mechanism of PvEH3^E134K/T137P with remarkably improved E value was analyzed by molecular docking simulation.

Investigation of Desulfurization Activity, Reusability, and Viability of Magnetite Coated Bacterial Cells

Background

Magnetic separation using magnetic nanoparticles can be used as a simple method to isolate desulfurizing bacteria from a biphasic oil/water system.

Objectives

Magnetite nanoparticles were applied to coat the surface of Rhodococcus erythropolis IGTS8 and Rhodococcus erythropolis FMF desulfurizing bacterial cells, and the viability and reusability of magnetite-coated bacteria evaluated by using various methods.

Material and Methods

Magnetite nanoparticles were synthesized through a reverse co-precipitation method. Glycine was added during and after the synthesis of magnetite nanoparticles to modify their surface and to stabilize the dispersion of the nanoparticles. The glycine-modified magnetite nanoparticles were immobilized on the surface of both oil-desulfurizing bacterial strains. Reusability of magnetite-coated bacterial cells was evaluated via assessing the desulfurization activity of bacteria via spectrophotometry using Gibb’s assay, after the separation of bacterial cells from 96h-cultures with the application of external magnetic field. In addition, CFU and fluorescence imaging were used to investigate the viability of magnetite-coated and free bacterial cells.

Results

TEM micrographs showed that magnetite nanoparticles have the size approximately 5.35±1.13 nm. Reusability results showed that both magnetite-coated bacterial strains maintain their activity even after 5 × 96h-cycles. The viability results revealed glycine-modified magnetite nanoparticles did not negatively affect the viability of two bacterial strains R. erythropolis IGTS8 and R. erythropolis FMF.

Conclusions

In conclusion, the glycine-modified magnetite nanoparticles have great capacity for immobilization and separation of desulfurizing bacteria from suspension.

Enantioselective Hydrolysis of Styrene Oxide and Benzyl Glycidyl Ether by a Variant of Epoxide Hydrolase from Agromyces mediolanus

Enantiopure epoxides are versatile synthetic intermediates for producing optically active pharmaceuticals. In an effort to provide more options for the preparation of enantiopure epoxides, a variant of the epoxide hydrolase (vEH-Am) gene from a marine microorganism Agromyces mediolanus was synthesized and expressed in Escherichia coli. Recombiant vEH-Am displayed a molecular weight of 43 kDa and showed high stability with a half-life of 51.1 h at 30 °C. The purified vEH-Am exhibited high enantioselectivity towards styrene oxide (SO) and benzyl glycidyl ether (BGE). The vEH-Am preferentially converted (S)-SO, leaving (R)-SO with the enantiomeric excess (ee) >99%. However, (R)-BGE was preferentially hydrolyzed by vEH-Am, resulting in (S)-BGE with >99% ee. To investigate the origin of regioselectivity, the interactions between vEH-Am and enantiomers of SO and BGE were analyzed by molecular docking simulation. In addition, it was observed that the yields of (R)-SO and (S)-BGE decreased with the increase of substrate concentrations. The yield of (R)-SO was significantly increased by adding 2% (v/v) Tween-20 or intermittent supplementation of the substrate. To our knowledge, vEH-Am displayed the highest enantioselectivity for the kinetic resolution of racemic BGE among the known EHs, suggesting promising applications of vEH-Am in the preparation of optically active BGE.

Enhancement of Soluble Expression and Biochemical Characterization of Two Epoxide Hydrolases from Bacillus

Background

Enantiopure epoxides are important intermediates in the synthesis of high-value chiral chemicals. Epoxide hydrolases have been exploited in biocatalysis for kinetic resolution of racemic epoxides to produce enantiopure epoxides and vicinal diols. It is necessary to obtain sufficient stable epoxide hydrolases with high enantioselectivity to meet the requirements of industry.

Objectives

Enhancement of soluble expression and biochemical characterization of epoxide hydrolases from Bacillus pumilus and B. subtilis.

Material and Methods

Homologous genes encoding epoxide hydrolases from B. pumilus and B. subtilis were cloned and expressed in Escherichia coli. The recombinant epoxide hydrolases were characterized biochemically.

Results

Low temperature induction of expression and a C-terminal-fused His-tag enhanced soluble expression of the epoxide hydrolases from the two Bacillus species in E. coli. These epoxide hydrolases could hydrolyze various epoxide substrates, with stereoselectivity toward some epoxides such as styrene oxide and glycidyl tosylate.

Conclusions

The position of the His-tag and the induction temperature were found to play a vital role in soluble expression of these two epoxide hydrolases in E. coli. In view of their catalytic properties, the epoxide hydrolases from Bacillus have potential for application in kinetic resolution of some epoxides to prepare enantiopure epoxides and vicinal diols.

Identification and characterization of a highly S-enantioselective halohydrin dehalogenase from Tsukamurella sp. 1534 for kinetic resolution of halohydrins

Halohydrin dehalogenases are remarkable enzymes which possess promiscuous catalytic activity and serve as potential biocatalysts for the synthesis of chiral halohydrins, epoxides and β-substituted alcohols. The enzyme HheC exhibits a highly R enantioselectivity in the processes of dehalogenation of vicinal halohydrins and ring-opening of epoxides, which attracts more attentions in organic synthesis. Recently dozens of novel potential halohydrin dehalogenases have been identified by gene mining, however, most of the characterized enzymes showed low stereoselectivity. In this study, a novel halohydrin dehalogenase of HheA10 from Tsukamurella sp. 1534 has been heterologously expressed, purified and characterized. Substrate spectrum and kinetic resolution studies indicated the HheA10 was a highly S enantioselective enzyme toward several halohydrins, which produced the corresponding epoxides with the ee (enantiomeric excess) and E values up to >99% and >200 respectively. Our results revealed the HheA10 was a promising biocatalyst for the synthesis of enantiopure aromatic halohydrins and epoxides via enzymatic kinetic resolution of racemic halohydrins. What's more important, the HheA10 as the first individual halohydrin dehalogenase with the highly S enantioselectivity provides a complementary enantioselectivity to the HheC.

Production of (R)-styrene oxide by recombinant whole-cell biocatalyst in aqueous and biphasic system

The enantioselective resolution of racemic styrene oxide (rac-SO) to (R)-SO by whole cells of a recombinant Escherichia coli expressing epoxide hydrolase (EH) activity in aqueous and biphasic system were studied. Some parameters that may alter this bio-resolution, such as the concentration of recombinant cell, substrate and product were evaluated. The effect of the addition of different additives on the course of rac-SO biotransformation was also investigated. The results showed that the yield and the enantiomeric excess (ee) of (R)-SO were dependent on these variables. When the kinetic resolution was conducted with 350 mM of rac-SO, enantiopure (R)-SO with high (≥99%) ee was obtained with a yield of 38.2% yield at 12.2 h in the presence of 10% (v/v) Tween 80. An isooctane/aqueous system was developed to overcome the adverse factors in the aqueous phase, resulting in an improvement of yield from 38.2% to 42.9%. The results will provide a useful guidance for further application of this enzyme in the biocatalytic production of chiral synthons.

Evaluating Ylehd, a recombinant epoxide hydrolase from Yarrowia lipolytica as a potential biocatalyst for the resolution of benzyl glycidyl ether

Glycidyl ethers and their vicinal diols are important building blocks in the organic synthesis of anti-cancer and anti-obesity drugs. Ylehd, an epoxide hydrolase from tropical marine yeast Yarrowia lipolytica, was explored for its enantioselective properties by kinetic, thermodynamic and in silico studies. Kinetic resolution of racemic phenyl glycidyl ether (PGE) yielded (S)-epoxide while for benzyl glycidyl ether (BGE) (R)-epoxide was obtained, with vicinal diols of the opposite configuration. Amongst the enantiomers of PGE and BGE, the (S)-selective conversion of benzyl glycidyl ether to its corresponding diol, (S)-3-benzyloxy-1,2-propanediol while retaining (R)-BGE was most favourable with 95% ee in 20 min. Enantioselective conversion of specific enantiomer of BGE to its corresponding diols was attributed to the favourable kinetic and thermodynamic parameters as well as to the number and proximity of water molecules near the base H325 in the active site pocket. The easily available and highly active Ylehd could be a potential biocatalyst for large scale preparation of pharmaceutically relevant chiral (R)-benzyl glycidyl ether and (S)-3-benzyloxy-1,2-propanediol.

Ylehd, an enantioselective epoxide hydrolase with potential application in resolution of racemic benzyl glycidyl ether.

An Overview on the Enhancement of Enantioselectivity and Stability of Microbial Epoxide Hydrolases

Epoxide hydrolases (EHs; 3.3.2.x) catalyze the enantioselective ring opening of racemic epoxides to the corresponding enantiopure vicinal diols and remaining equivalent unreacted epoxides. These epoxides and diols are used for the synthesis of chiral drug intermediates. With an upsurge in the methods for identification of novel microbial EHs, a lot of EHs have been discovered and utilized for kinetic resolution of racemic epoxides. However, there is still a constraint on the account of limited EHs being successfully applied on the preparative scale for industrial biotransformations. This limitation has to be overcome before application of identified functional EHs on large scale. Many strategies such as optimizing reaction media, immobilizing EHs and laboratory-scale directed evolution of EHs have been adopted for enhancing the industrial potential of EHs. In this review, these approaches have been highlighted which can serve as a pathway for the enrichment of already identified EHs for their application on an industrial scale in future studies.

Enzymatic approaches to the preparation of chiral epichlorohydrin

Enantiomerically pure epichlorohydrin is a key chiral synthon in the preparation of 4-chloro-3-hydroxybutyrate, pheromones,l-carnitine, and β-adrenergic blockers.

Engineering the epoxide hydrolase from Agromyces mediolanus for enhanced enantioselectivity and activity in the kinetic resolution of racemic epichlorohydrin

The biocatalytic production of enantiopure epichlorohydrin (ECH) has been steadily attracting more attention.

Trigger factor assisted folding of the recombinant epoxide hydrolases identified from C. pelagibacter and S. nassauensis

Epoxide hydrolases (EHs), are enantioselective enzymes as they catalyze the kinetic resolution of racemic epoxides into the corresponding enantiopure vicinal diols, which are useful precursors in the synthesis of chiral pharmaceutical compounds. Here, we have identified and cloned two putative epoxide hydrolase genes (cpeh and sneh) from marine bacteria, Candidatus pelagibacter ubique and terrestrial bacteria, Stackebrandtia nassauensis, respectively and overexpressed them in pET28a vector in Escherichia coli BL21(DE3). The CPEH protein (42kDa) was found to be overexpressed as inactive inclusion bodies while SNEH protein (40kDa) was found to form soluble aggregates. In this study, the recombinant CPEH was successfully transformed from insoluble aggregates to the soluble and functionally active form, using pCold TF vector, though with low EH activity. To prevent the soluble aggregate formation of SNEH, it was co-expressed with GroEL/ES chaperone and was also fused with trigger factor (TF) chaperone at its N-terminus. The TF chaperone-assisted correct folding of SNEH led to a purified active EH with a specific activity of 3.85μmol/min/mg. The pure enzyme was further used to biocatalyze the hydrolysis of 10mM benzyl glycidyl ether (BGE) and α-methyl styrene oxide (MSO) with an enantiomeric excess of the product (eep) of 86% and 73% in 30 and 15min, respectively. In conclusion, this is the first report about the heterologous expression of epoxide hydrolases using TF as a molecular chaperone in pCold TF expression vector, resulting in remarkable increase in the solubility and activity of the otherwise improperly folded recombinant epoxide hydrolases.

Purification, gene cloning, and characterization of a novel halohydrin dehalogenase from Agromyces mediolanus ZJB120203

A novel halohydrin dehalogenase (HHDH), catalyzing the transformation of 1,3-dichloro-2-propanol (1,3-DCP) to epichlorohydrin (ECH), was purified from Agromyces mediolanus ZJB120203. The molecular mass of the enzyme was estimated to be 28 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A 735-bp nucleotide fragment was obtained based on the N-terminal and internal amino acid sequences of the purified HHDH. The gene codes a protein sequence with 244 amino acid residues, and the protein sequence shows high similarity to Hhe AAD2 (HHDH from Arthrobacter sp. AD2), defined as Hhe AAm, which is the seventh reported HHDH. Expression of Hhe AAm was carried out in Escherichia coli and purification was performed by nickel-affinity chromatography. The recombinant HheAAm possessed an optimal pH of 8.5 and an optimal temperature of 50 °C and manifested a K m of 4.58 mM and a V max of 3.84 μmol/min(/)mg. The activity of Hhe AAm was not significantly affected by metal ions such as Zn(2+), Ca(2+), Cu(2+), and EDTA, but was strongly inhibited by Hg(2+) and Ag(+). In particular, the Hhe AAm exhibits an enantioselectivity for the conversion of prochiral 1,3-DCP to (S)-ECH. The applications of the Hhe AAm as a catalyst for asymmetric synthesis are promising.