Enhanced catalytic efficiency and enantioselectivity of epoxide hydrolase from Agrobacterium radiobacter AD1 by iterative saturation mutagenesis for (R)-epichlorohydrin synthesis

Enantioconvergent hydrolysis of racemic 1,2-epoxypentane and 1,2-epoxyhexane by an engineered Escherichia coli strain overexpressing a novel Streptomyces fradiae epoxide hydrolase

In order to excavate microbial epoxide hydrolases (EHs) with desired catalytic properties, a novel EH, SfEH1, was identified based on the genome annotation of Streptomyces fradiae and sequence alignment analysis with local protein library. The SfEH1-encoding gene, sfeh1, was then cloned and over-expressed in soluble form in Escherichia coli/BL21(DE3). The optimal temperature and pH of recombinant SfEH1 (reSfEH1) and reSfEH1-expressing E. coli (E. coli/sfeh1) were both determined as 30 ℃ and 7.0, also indicating that the influences of temperature and pH on reSfEH1's activities were more obvious than those of E. coli/sfeh1 whole cells. Subsequently, using E. coli/sfeh1 as catalyst, its catalytic properties towards thirteen common mono-substituted epoxides were tested, in which E. coli/sfeh1 had the highest activity of 28.5 U/g dry cells for rac-1,2-epoxyoctane (rac-6a), and (R)-1,2-pentanediol ((R)-3b) (or (R)-1,2-hexanediol ((R)-4b)) with up to 92.5% (or 94.1%) ee_p was obtained at almost 100% conversion ratio. Regioselectivity coefficients (α_S and β_R) displayed in the enantioconvergent hydrolysis of rac-3a (or rac-4a) were calculated to be 98.7% and 93.8% (or 95.2% and 98.9%). Finally, the reason of the high and complementary regioselectivity was confirmed by both kinetic parameter analysis and molecular docking simulations.

Gram-Scale Synthesis of (R)-P-Chlorophenyl-1,2-Ethanediol at High Concentration by a Pair of Epoxide Hydrolases

(R)-p-chlorophenyl-1,2-ethanediol (pCPED) is an important intermediate for the synthesis of (R)-eliprodil that is widely applied in the treatment of ischemic stroke. To prepare (R)-pCPED with high enantiomeric excess (eep) and yield via the enantioconvergent hydrolysis of racemic styrene oxide (rac-pCSO) at high concentration, the bi-enzymatic catalysis was designed and investigated by a pair of epoxide hydrolases, a mutant (PvEH1Z4X4-59) of Phaseolus vulgaris EH1 and a mutant (RpEHF361V) of Rhodotorula paludigena RpEH. Firstly, the maximum allowable concentration of rac-pCSO was confirmed. Subsequently, the addition mode and the weight ratio of two Escherichia coli cells were optimized. Finally, under the optimized reaction conditions—the cell weight ratio 20:1 of E. coli/pveh1z4x4-59 to E. coli/rpehF361V, a simultaneous addition mode, and reaction temperature at 25°C—300 mM rac-pCSO in the 100 ml 4% (v/v) Tween-20/phosphate buffer system (100 mM, pH 7.0) was completely hydrolyzed within 5 h, affording (R)-pCPED with 87.8% eep, 93.4% yield, and 8.63 g/L/h space–time yield (STY). This work would be an efficient technical strategy for the preparation of chiral vicinal diols at industrial scale.

Structure-guided improvement in the enantioselectivity of an Aspergillus usamii epoxide hydrolase for the gram-scale kinetic resolution of ortho-trifluoromethyl styrene oxide

Microtuning the substrate-binding pocket (SBP) of EHs has emerged as an effective approach to manipulate their enantio- or regio-selectivities and activities towards target substrates. Here, the enantioselectivity (enantiomeric ratio, E) of AuEH2 towards a racemic (rac-) ortho-trifluoromethyl styrene oxide (o-TFMSO) was improved via microtuning its SBP. Based on the analysis on the crystal structure of AuEH2, its specific residues I192, Y216, R322 and L344 lining the SBP in close to the catalytic triad were identified for site-saturation mutagenesis. After screening, five single-site mutants were selected with E values elevated from 8 to 12-25 towards rac-o-TFMSO. To further improve E, four double-site mutants were constructed by combinatorial mutagenesis of AuEH2^R322V separately with AuEH2^I192V, AuEH2^Y216F, AuEH2^L344A and AuEH2^L344C. Among all the mutants, AuEH2^R322V/L344C possessed the largest E of 83 with activity of 67 U/g wet cell. The kinetic resolution of 200 mM rac-o-TFMSO was conducted at 0 °C for 5.5 h using 80 mg/mL wet cells of E. coli/Aueh2^R322V/L344C, a transformant expressing AuEH2^R322V/L344C, retaining (S)-o-TFMSO with 98.4 % ee_s and 49.3 % yield_s. Furthermore, the molecular docking simulation analysis indicated that AuEH2^R322V/L344C more enantiopreferentially attacks the terminal carbon (C_β) in the oxirane ring of (R)-o-TFMSO than AuEH2.

Improvement in the catalytic performance of a phenylpyruvate reductase from Lactobacillus plantarum by site-directed and saturation mutagenesis based on the computer-aided design

To enhance the specific activity and catalytic efficiency (k _cat/K _m) of an NADH-dependent LpPPR, its directed modification was performed based on the computer-aided design using molecular docking simulation and multiple sequence alignment. Firstly, five single-site variants of an LpPPR-encoding gene (lpppr) were amplified and expressed in E. coli BL21 (DE3). The asymmetric reduction of 20 mM phenylpyruvic acid (PPA) was carried out using 50 mg/mL E. coli/lpppr ^R53Q or /lpppr ^A79V whole wet cells at 37 °C for 20 min, giving d-phenyllactic acid (PLA) with 41.1 or 44.3% yield, being 1.17- or 1.26-fold that by E. coli/lpppr. Secondly, double-site variants were obtained by saturation mutagenesis of Ala79 in LpPPR^R53Q. Among all tested E. coli transformants, E. coli/lpppr ^R53Q/A79V exhibited the highest d-PLA yield of 85.3%. The specific activity and k _cat/K _m of the purified LpPPR^R53Q/A79V increased to 67.5 U/mg and 169.8 mM^-1 s^-1, which were 3.0- and 13.2-fold those of LpPPR, respectively. Finally, the catalytic mechanism analysis of LpPPR^R53Q/A79V by molecular docking simulation indicated that the replacement of Arg53 in LpPPR with Gln expanded its substrate-binding pocket, while that Ala79 with Val formed an additional π-sigma interaction with phenyl group of PPA.

SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s13205-020-02633-3) contains supplementary material, which is available to authorized users.

Greatly enhancing the enantioselectivity of PvEH2, a Phaseolus vulgaris epoxide hydrolase, towards racemic 1,2-epoxyhexane via replacing its partial cap-loop

To achieve the kinetic resolution and enantioconvergent hydrolysis of rac-1,2-epoxyhexane, the E value of PvEH2 was enhanced by substituting its partial cap-loop. Based on the experimental results reported previously and computer-aided analysis, the flexible and variable cap-loop, especially its middle segment, was speculated to be related to the catalytic properties of PvEH2. In view of this, four PvEH2's hybrids, Pv2St, Pv2Pv1, Pv2Vr1 and Pv2Vr2, were designed by substituting the middle segment (¹⁹⁰EGMGSNLNTSMP²⁰¹) of a cap-loop in PvEH2 with the corresponding ones in StEH, PvEH1, VrEH1 and VrEH2, respectively. Then, the hybrid-encoding genes, pv2st, pv2pv1, pv2vr1 and pv2vr2, were constructed by fusion PCR, and expressed in E. coli Rosetta(DE3). The expressed hybrid, Pv2St, displayed the highest specific activity of 35.3 U/mg protein towards rac-1,2-epoxyhexane. The corresponding transformant, E. coli/pv2st, exhibited the largest E value of 24.2, which was 11.5-fold that of E. coli/pveh2 expressing PvEH2. The scale-up kinetic resolution of 280 mM rac-1,2-epoxyhexane was carried out using 40 mg dry cells/mL of E. coli/pv2st at 25 °C for 4.5 h, retaining (S)-1,2-epoxyhexane with >99.5% ee_s and 36.9% yield. Additionally, the chemo-enzymatic enantioconvergent hydrolysis of rac-1,2-epoxyhexane using E. coli/pv2st followed by sulfuric acid produced (R)-hexane-1,2-diol with 73.0% ee_p and 86.5% yield.

Near-perfect kinetic resolution of o-methylphenyl glycidyl ether by RpEH, a novel epoxide hydrolase from Rhodotorula paludigena JNU001 with high stereoselectivity

In order to provide more alternative epoxide hydrolases for industrial production, a novel cDNA gene Rpeh-encoding epoxide hydrolase (RpEH) of Rhodotorula paludigena JNU001 identified by 26S rDNA sequence analysis was amplified by RT-PCR. The open-reading frame (ORF) of Rpeh was 1236 bp encoding RpEH of 411 amino acids and was heterologously expressed in Escherichia coli BL21(DE3). The substrate spectrum of expressed RpEH showed that the transformant E. coli/Rpeh had excellent enantioselectivity to 2a, 3a, and 5a-10a, among which E. coli/Rpeh had the highest activity (2473 U/g wet cells) and wonderful enantioselectivity (E = 101) for 8a, and its regioselectivity coefficients, α_R and β_S, toward (R)- and (S)-8a were 99.7 and 83.2%, respectively. Using only 10 mg wet cells/mL of E. coli/Rpeh, the near-perfect kinetic resolution of rac-8a at a high concentration (1000 mM) was achieved within 2.5 h, giving (R)-8a with more than 99% enantiomeric excess (ee_s) and 46.7% yield and producing (S)-8b with 93.2% ee_p and 51.4% yield with high space-time yield (STY) for (R)-8a and (S)-8b were 30.6 and 37.3 g/L/h.

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.

Manipulating the regioselectivity of a Solanum lycopersicum epoxide hydrolase for the enantioconvergent synthesis of enantiopure alkane- and alkene-1,2-diols

This work engineered a superior double-site mutant SlEH1^W106T/F189L used for the enantioconvergent biosynthesis of (R)-1b–6b with high ee_p values.

Enantioconvergent hydrolysis of m-nitrostyrene oxide at an elevated concentration by Phaseolus vulgaris epoxide hydrolase in the organic/aqueous two-phase system

(R)-m-Nitrophenyl-1,2-ethanediol (m-NPED) is a versatile and highly value-added chiral building block for the synthesis of some bioactive compounds, such as (R)-Nifenalol. To efficiently produce (R)-m-NPED through the enantioconvergent hydrolysis of racemic (rac-) m-nitrostyrene oxide (m-NSO) using the whole resting cells of Escherichia coli/pCold-pveh2 intracellularly expressing PvEH2, an epoxide hydrolase from Phaseolus vulgaris, two reaction systems were investigated. In the Na₂ HPO₄ -NaH₂ PO₄ buffer (50 mmol l^-1 , pH 7·0) system, merely 15 mmol l^-1 rac-m-NSO was successfully subjected to enantioconvergent hydrolysis, producing (R)-m-NPED with 86·0% enantiomeric excess (ee_p ) and 177·6 mg l^-1  h^-1 space-time yield (STY). The experimental result indicated that there is inhibitory effect of rac-m-NSO at high concentration on PvEH2. To efficiently increase the concentration of rac-m-NSO and the STY of (R)-m-NPED, petroleum ether was first selected to construct an organic/aqueous two-phase system. Then, both the volume ratio (v_o /v_b ) of petroleum ether to phosphate buffer and the weight ratio (w_c /w_s ) of E. coli/pCold-pveh2 dry cells to rac-m-NSO were optimized as 2 : 8 and 5 : 1, respectively. In the optimized petroleum ether/phosphate buffer two-phase system, the enantioconvergent hydrolysis of rac-m-NSO at 40 mmol l^-1 (6·6 mg ml^-1 ) was carried out at 25°C for 12 h using 33·0 mg ml^-1 vacuum freeze-dried cells of E. coli/pCold-pveh2, producing (R)-m-NPED with 87·4% ee_p , 82·3% yield and 502·4 mg l^-1  h^-1 STY. SIGNIFICANCE AND IMPACT OF THE STUDY: Epoxide hydrolases play a crucial role in producing enantiopure epoxides and/or vicinal diols. However, numerous biocatalytic reactions of organic compounds, such as epoxides, in aqueous phase suffered various restrictions. Herein, the enantioconvergent hydrolysis of rac-m-NSO in two reaction systems was investigated using the whole cells of Escherichia coli/pCold-pveh2. As a result, the concentration of rac-m-NSO and the space-time yield of (R)-m-NPED in organic/aqueous two-phase system were significantly increased, when compared with those in aqueous phase. To our knowledge, this is the first report about the production of (R)-m-NPED from rac-m-NSO at an elevated concentration by PvEH2 in the two-phase system.

Substantially improving the enantioconvergence of PvEH1, a Phaseolus vulgaris epoxide hydrolase, towards m-chlorostyrene oxide by laboratory evolution

Background

Epoxide hydrolase can regioselectively catalyze the oxirane ring-opening hydrolysis of rac-epoxides producing the corresponding chiral diols. In our laboratory, a gene named pveh1 encoding an EH from Phaseolus vulgaris was cloned. Although the directed modification of PvEH1 was carried out, the mutant PvEH1^Y3 showed a limited degree of enantioconvergence towards racemic (rac-) m-chlorostyrene oxide (mCSO).

Results

PvEH1 and PvEH1^Y3 were combinatively subjected to laboratory evolution to further enhance the enantioconvergence of PvEH1^Y3 towards rac-mCSO. Firstly, the substrate-binding pocket of PvEH1 was identified using a CAVER 3.0 software, and divided into three zones. After all residues in zones 1 and 3 were subjected to leucine scanning, two E. coli transformants, E. coli/pveh1^Y149L and /pveh1^P184L, were selected, by which rac-mCSO was transformed into (R)-m-chlorophenyl-1,2-ethanediol (mCPED) having 55.1% and 27.2% ee_p. Secondly, two saturation mutagenesis libraries, E. coli/pveh1^Y149X and /pveh1^P184X (X: any one of 20 residues) were created at sites Y149 and P184 of PvEH1. Among all transformants, both E. coli/pveh1^Y149L (65.8% α_S and 55.1% ee_p) and /pveh1^P184W (66.6% α_S and 59.8% ee_p) possessed the highest enantioconvergences. Finally, the combinatorial mutagenesis was conducted by replacements of both Y149L and P184W in PvEH1^Y3, constructing E. coli/pveh1^Y3Z2, whose α_S reached 97.5%, higher than that (75.3%) of E. coli/pveh1^Y3. In addition, the enantioconvergent hydrolysis of 20 mM rac-mCSO was performed by E. coli/pveh1^Y3Z2, giving (R)-mCPED with 95.2% ee_p and 97.2% yield.

Conclusions

In summary, the enantioconvergence of PvEH1^Y3Z2 was successfully improved by laboratory evolution, which was based on the study of substrate-binding pocket by leucine scanning. Our present work introduced an effective strategy for the directed modification of enantioconvergence of PvEH1.

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.

Identifying and engineering a critical amino acid residue to enhance the catalytic efficiency of Pseudomonas sp. methyl parathion hydrolase

Methyl parathion hydrolase (MPH) that hydrolyzes a wide range of organophosphorus pesticides can be used to remediate land polluted by the pesticides. Here, the catalytic efficiency of methyl parathion hydrolase from Pseudomonas sp. (WBC-3) was enhanced by searching and engineering a critical site far away from the binding pocket. In the first round, a four-site mutant with a modest increased catalytic efficiency (3.2-fold k_cat/K_m value of the wild type) was obtained with random mutagenesis. By splitting and re-combining the four substitutions in the mutant, the critical site S277, was identified to show the most significant effects of improving binding affinity and catalytic efficiency. With further site-saturation mutagenesis focused on the residue S277, another two substitutions were discovered to have even more significant decrease in K_m (40.2 and 47.6 μM) and increased in k_cat/K_m values (9.5- and 10.3-fold of the wild type) compared to the original four-site mutant (3.0- and 3.2-fold). In the three-dimensional structure, residue S277 is located at a hinge region of a loop, which could act as a "lid" at the substrate entering to the binding pocket. This suggests that substitutions of residue S277 could affect substrate binding via conformational change in substrate entrance region. This work provides a valuable protocol combining random mutagenesis, site-saturation mutagenesis, structural and bioinformatics analyses to obtain mutants with high catalytic efficiency from a screening library of a modest size (3200 strains).