Halohydrin Dehalogenase Research Articles

Improving the enantioselectivity of halohydrin dehalogenase for the synthesis of (R)-benzyl glycidyl ether via biocatalytic azidolysis

Halohydrin dehalogenases (HHDHs) are valuable biocatalysts for the synthesis of enantiopure benzyl glycidyl ether (BGE) and its derivatives, which are important synthetic intermediates for anti-cancer and anti-obesity drugs. However, all the reported HHDHs exhibit low enantioselectivity. In this study, we screened site-saturation mutagenesis libraries of AbHHDH at positions R89, A136, V137, P178, N179, F180, I181, Y186 and F187 for mutants with enhanced enantioselectivity toward BGE. The four improved variant R89V, R89Y, R89K and V137I were identified, and the double mutant R89Y/V137I showed 2.9-fold higher enantioselectivity than the wild type. The regions of HHDH containing the identified mutations were analyzed by homology modeling to explain the changes of enantioselectivity. Kinetic resolution of 20 to 100 mM BGE using whole cells of Escherichia coli expressing the mutant R89Y/V137I resulted in (R)-BGE yields of 42 to 32.5%, with ee >99%. This study improves our understanding of the enantioselectivity of HHDHs and contributes improved biocatalysts for the kinetic resolution of BGE.

Conformational Landscapes of Halohydrin Dehalogenases and Their Accessible Active Site Tunnels

Halohydrin dehalogenases (HHDH) are industrially relevant biocatalysts exhibiting a promiscuous epoxide-ring opening reactivity in the presence of small nucleophiles, thus giving access to novel carbon–carbon, carbon–oxygen, carbon–nitrogen, and carbon–sulfur bonds. Recently, the repertoire of HHDH has been expanded, providing access to some novel HHDH subclasses exhibiting a broader epoxide substrate scope. In this work, we develop a computational approach based on the application of linear and non-linear dimensionality reduction techniques to long time-scale Molecular Dynamics (MD) simulations to study the HHDH conformational landscapes. We couple the analysis of the conformational landscapes to CAVER calculations to assess their impact on the active site tunnels and potential ability towards bulky epoxide ring opening reaction. Our study indicates that the analyzed HHDHs subclasses share a common breathing motion of the halide binding pocket, but present large deviations in the loops adjacent to the active site pocket and N-terminal regions. Such conformational differences affect the available tunnels for epoxide binding to the active site. The superior activity of the HHDH G subclass towards bulkier substrates is explained by the additional structural elements delimiting the active site region, its rich conformational heterogeneity, and the substantially wider and frequently observed active site tunnels. This study therefore provides key information for HHDH promiscuity and engineering.

Halohydrin Dehalogenases and Their Potential in Industrial Application – A Viewpoint of Enzyme Reaction Engineering

AbstractAt the moment, there are approx. 100 published papers investigating halohydrin dehalogenases from different aspects; enzymology, molecular biology and reactions they can catalyse. Unquestionably, these enzymes are of great importance and hold an immense potential due to the wide spectrum of different compounds that can be synthesized by their action. These compounds, such as chiral epoxides, β‐substituted alcohols, oxazolidinones etc., significantly enrich the chemist's toolbox and, moreover, open the possibility for the synthesis of even more complex compounds. Still, there are many unknowns, and it is the purpose of this work to demonstrate the possibilities and bottlenecks, in scientific sense, that could further help in broadening the applicative potential of these fascinating enzymes.magnified image

Biphasic Bioelectrocatalytic Synthesis of Chiral β-Hydroxy Nitriles

Two obstacles limit the application of oxidoreductase-based asymmetric synthesis. One is the consumption of high stoichiometric amounts of reduced equivalent. The other is the low solubility of organic substrates, intermediates, and products in the aqueous phase. In order to address the two obstacles of oxidoreductase-based asymmetric synthesis, a biphasic bioelectrocatalytic system was constructed and applied.. In this study, the preparation of chiral β-hydroxy nitriles catalyzed by alcohol dehydrogenase (AdhS) and halohydrin dehalogenase (HHDH) was investigated as a high-value organic product. Diaphorase (DH) was immobilized by cobaltocene-modified poly(allylamine) redox polymer on the electrode surface (DH/Cc-PAA bioelectrode) to realize the effective bioelectrocatalytic NADH regeneration. AdhS is a NAD-dependent dehydrogenase, so the diaphorase modified biocathode was used to regenerate NADH to support the conversion from ethyl 4-chloroacetoacetate (COBE) to ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE) catalyzed by AdhS. The addition of methyl tert-butyl ether (MTBE) as organic phase not only increased the uploading of COBE, but also prevented the spontaneous hydrolysis of COBE and extended the lifetime of DH/Cc-PAA bioelectrode, and finally increased the Faradaic efficiency and the concentration of generated (R)-ethyl-4-cyano-3-hydroxybutyrate ((R)-CHCN). After 10 hours of reaction, the highest concentration of (R)-CHCN in biphasic bioelectrocatalytic system achieve 25.5 mM with 81.2% enantiomeric excess (ee p). The conversion ratio of COBE achieved 85%, which was 8.8 times higher than that of single phase system. Besides COBE, the other two substrates with aromatic ring structures were also used in this biphasic bioelectrocatalytic system to prepare corresponding chiral β-hydroxy nitriles. The results indicate that the biphasic bioelectrocatalytic system has the potential to produce a variety of β-hydroxy nitriles with different structures.

Enzyme immobilization on glass fiber membrane for detection of halogenated compounds

Enzyme immobilization using inorganic membranes has enticed increased attention as they not only improve enzyme stability, but also furnish user-friendly biodevices that can be tailored to different applications. Herein, we explored the suitability of the glass fiber membrane for enzyme immobilization and its application for halocarbon detection. For this, halohydrin dehalogenase (HheC) and bovine serum albumin were crosslinked and immobilized on a glass fiber membrane without membrane functionalization. Immobilized HheC exhibited higher storage stability than its free counterpart over 60 days at 4 °C (67% immobilized vs. 8.1% free) and 30 °C (77% immobilized vs. 57% free). Similarly, the thermal endurance of the immobilized HheC was significantly improved. The practical utility of the membrane-immobilized enzyme was demonstrated by colorimetric detection of 1,3-dichloro-2-propanol (1,3-DCP) and 2,3-dibromo-1-propanol (2,3-DBP) as model analytes. Under optimized conditions, the detection limits of 0.06 mM and 0.09 mM were achieved for 1,3-DCP and 2,3-DBP, respectively. The satisfactory recoveries were observed with spiked river and lake water samples, which demonstrate the application potential of immobilized HheC for screening contaminants in water samples. Our results revealed that the proposed frugal and facile approach could be useful for enzyme stabilization, and mitigation of halocarbon pollution.

Rational design of halohydrin dehalogenase for efficient chiral epichlorohydrin production with high activity and enantioselectivity in aqueous-organic two-phase system

Halohydrin dehalogenases (HHDHs) represent as important biocatalysts for the production of valuable chiral epoxides and β-substituted alcohols. The HHDH from A. radiobacter (HheC) showed great potential for biosynthesis of (S)-epichlorohydrin ((S)-ECH). However, two bottlenecks including self-degradation and enzyme-mediated racemization of product in aqueous solution restricted its wide-spread applications. To solve the problems, the biocatalytic process was performed in aqueous-organic two-phase system and structure-based engineered of HheC was performed. A newly found zigzag tunnel connecting the active site region and outside space, as well as a depressed cave structure in formation of an extra three-pot herringbone channel were demonstrated to play a pivotal role affecting the activity and enantioselectivity of the enzyme. By mutation of the involved amino acid residues, two variants E255 T and E255 G showed significantly improved activity, with specific activity increased from 59.9 U/mg to 101.6 U/mg and 77.5 U/mg, respectively, while one variant Y93 L exhibited high enantioselectivity, with ee value of (S)-ECH maintained at >99 %. In addition, the synergic variant Y93 L/E255 T had both improved catalytic efficiency and enantioselectivity. The results not only facilitate the applicability of HheC for efficient production of (S)-ECH, but also give new insights into the structural-functional relationship of the enzyme.

A paper-based whole-cell screening assay for directed evolution-driven enzyme engineering.

Directed evolution has become an important method to unleash the latent potential of enzymes to make them uniquely suited for human purposes. However, the need for a large reagent volume and sophisticated instrumentation hampers its broad implementation. In an attempt to address this problem, here we report a paper-based high-throughput screening approach that should find broad application in generating desired enzymes. As an example case, the dehalogenation reaction of the halohydrin dehalogenase was adopted for assay development. In addition to visual detection, quantitative measurements were performed by measuring the color intensity of an image that was photographed by a smartphone and processed using ImageJ free software. The proposed method was first validated using a gold standard method and then applied to mutagenesis library screening with reduced consumption of reagents (i.e., ≤ 10μl per assay) and a shorter assay time. We identified two active mutants (P135A and G137A) with improved activities toward four tested substrates. The assay not only consumes less reagents but also eliminates the need for expensive instrumentation. The proposed method demonstrates the potential of paper-based whole-cell screening coupled with digital image colorimetry as a promising approach for the discovery of industrially important enzymes.Key Points• A frugal method was developed for directed enzyme evolution.• Mutagenesis libraries were successfully screened on a paper platform.• Smartphone imaging was efficiently used to measure enzyme activities.

Biphasic Bioelectrocatalytic Synthesis of Chiral β-Hydroxy Nitriles.

Two obstacles limit the application of oxidoreductase-based asymmetric synthesis. One is the consumption of high stoichiometric amounts of reduced cofactor. The other is the low solubility of organic substrates, intermediates, and products in the aqueous phase. In order to address these two obstacles to oxidoreductase-based asymmetric synthesis, a biphasic bioelectrocatalytic system was constructed and applied. In this study, the preparation of chiral β-hydroxy nitriles catalyzed by alcohol dehydrogenase (AdhS) and halohydrin dehalogenase (HHDH) was investigated as a model bioelectrosynthesis, since they are high-value intermediates in statin synthesis. Diaphorase (DH) was immobilized by a cobaltocene-modified poly(allylamine) redox polymer on the electrode surface (DH/Cc-PAA bioelectrode) to achieve effective bioelectrocatalytic NADH regeneration. Since AdhS is a NAD-dependent dehydrogenase, the diaphorase-modified biocathode was used to regenerate NADH to support the conversion from ethyl 4-chloroacetoacetate (COBE) to ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE) catalyzed by AdhS. The addition of methyl tert-butyl ether (MTBE) as an organic phase not only increased the uploading of COBE but also prevented the spontaneous hydrolysis of COBE, extended the lifetime of DH/Cc-PAA bioelectrode, and increased the Faradaic efficiency and the concentration of generated (R)-ethyl-4-cyano-3-hydroxybutyrate ((R)-CHCN). After 10 h of reaction, the highest concentration of (R)-CHCN in the biphasic bioelectrocatalytic system was 25.5 mM with 81.2% enantiomeric excess (eep). The conversion ratio of COBE achieved 85%, which was 8.8 times higher than that achieved with the single-phase system. Besides COBE, two other substrates with aromatic ring structures were also used in this biphasic bioelectrocatalytic system to prepare the corresponding chiral β-hydroxy nitriles. The results indicate that the biphasic bioelectrocatalytic system has the potential to produce a variety of β-hydroxy nitriles with different structures.

Enzyme-based detection of epoxides using colorimetric assay integrated with smartphone imaging.

Epoxides are widely used chemicals, the determination of which is of paramount importance. Herein, we present an enzyme-based approach for noninstrumental detection of epoxides in standard solution and environmental samples. Halohydrin dehalogenase (HheC) as a biological recognition element and epichlorohydrin as a model analyte were evaluated for sensing. The detection is based on the color change of the pH indicator dye bromothymol blue caused by the HheC-catalyzed ring-opening of the epoxide substrate. The color change is then exploited for the determination of epoxide using a smartphone as an image acquisition and data processing device, eliminating the need for computer-based image analysis software. The color parameters were systematically evaluated to determine the optimum quantitative analytical parameter. Under optimal conditions, the proposed enzyme-based detection system showed a linear range of 0.13-2mM with a detection limit of 0.07mM and an assay time of 8Min. In addition, the repeatability expressed as relative standard deviation was found to be below 5% (n=6). Validation with gas chromatographic analyses showed that the proposed enzyme-based epoxide detection could be an alternative way in the quantitative determination of epoxides, and particularly useful in resource-limited settings.

A high-throughput screening assay for the directed evolution-guided discovery of halohydrin dehalogenase mutants for epoxide ring-opening reaction

Halohydrin dehalogenases (HHDHs) are valuable biocatalysts involved in the synthesis of β-substituted alcohols via their nucleophile-mediated ring-opening activity. To use directed evolution to unleash the latent potential of HHDHs for the synthesis of β-substituted alcohols, we report a high-throughput assay for screening HHDHs mutagenesis libraries. The assay is performed in a 96-well microtiter plate format using a cell-free extract or whole-cells in the presence of the desired nucleophile. The developed method relies upon the color change of bromothymol blue, due to the pH change caused by HHDH-catalyzed ring-opening of the epoxide substrate. The assay was validated using gas chromatography and subsequently applied to high-throughput screening of halohydrin dehalogenase HheC mutagenesis library. Active mutants were found for the tested substrates. Due to its simplicity and flexibility towards the use of nucleophiles and epoxides, the method is an attractive alternative to the existing assays for HHDH epoxide ring-opening reaction and could be helpful in the rapid discovery of industrial biocatalysts.

Synthesis of Chiral 5‐Aryl‐2‐oxazolidinones via Halohydrin Dehalogenase‐Catalyzed Enantio‐ and Regioselective Ring‐Opening of Styrene Oxides

AbstractAn efficient biocatalytic approach for enantio‐ and regioselective ring‐opening of styrene oxides with cyanate was developed by using the halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1, generating the corresponding chiral 5‐aryl‐2‐oxazolidinones in up to 47% yield and 90% ee. Additionally, the origin of enantioselectivity and regioselectivity of the HheC‐catalyzed cyanate‐mediated ring‐opening process was uncovered by single enantiomer bioconversions and molecular docking study.magnified image

Significant improvement of the enantioselectivity of a halohydrin dehalogenase for asymmetric epoxide ring opening reactions by protein engineering.

Halohydrin dehalogenases (HHDHs) have attracted much attention due to their ability to synthesize enantiomerically enriched epoxides and β-haloalcohols. However, most of the HHDHs exhibit low enantioselectivity. Here, a HHDH from the alphaproteobacteria isolate 46_93_T64 (AbHHDH), which shows only poor enantioselectivity in the catalytic resolution of rac-PGE (E = 9.9), has been subjected to protein engineering to enhance its enantioselectivity. Eight mutants (R89K, R89Y, V137I, P178A, N179Q, N179L, F187L, F187A) showed better enantioselectivity than the wild type. The best single mutant N179L (E = 93.0) showed a remarkable 9.4-fold increase in the enantioselectivity. Then, the single mutations were combined to produce the double, triple, quadruple, and quintuple mutants. Among the combinational mutants, the best variant (R89Y/N179L) showed an increased E value of up to 48. The E values of the variants N179L and R89Y/N179L for other epoxides 2-7 were 12.2 to > 200, which showed great improvement compared to 1.2 to 10.5 for the wild type. Using the variant N179L, enantiopure (R)-PGE with > 99% ee could be readily prepared, affording a high yield and a high concentration.

Heterologous overexpression of a novel halohydrin dehalogenase from Pseudomonas pohangensis and modification of its enantioselectivity by semi-rational protein engineering

A gene encoding a halohydrin dehalogenase from Pseudomonas pohangensis (PpHHDH) was identified, synthesized and expressed in Escherichia coli. Subsequently, we used protein engineering to enhance the enzyme's enantioselectivity. We created two enantiocomplementary HHDH mutants, N160L and Q159L, which exhibited higher S- and R-selectivity toward PGE, respectively. The exchange of Leu at 159 for Gln led to a 2.3-fold increase in enantioselectivity (E-value of 22.2) compared to the wild-type. In addition, the N160L mutant displayed an inverted enantioselectivity (from ER = 9.8 to ES = 21.6) toward PGE. The wild-type PpHHDH and its variants were purified and characterized. They all displayed maximum activity at pH 7.5. The optimum temperature of mutant Q159L and N160L was increased from 35 °C to 40 °C. The wild-type PpHHDH and N160L mutant had good pH stability at pH 5.0–7.5, and Q159L showed an even wider range of pH tolerance, from pH 4.5 to pH 8.0. The mutants N160L and Q159L showed slightly better thermostability than wild-type PpHHDH. For most tested substrates, the two variants showed higher enantioselectivity. These findings further confirmed the importance of amino acid residues at positions 159 and 160 for the enantioselectivity of PpHHDH.

Regioselective Ring‐Opening of Styrene Oxide Derivatives Using Halohydrin Dehalogenase for Synthesis of 4‐Aryloxazolidinones

AbstractA biocatalytic approach towards a range of 4‐aryloxazolidinones is developed using a halohydrin dehalogenase from Ilumatobacter coccineus (HheG) as biocatalyst. The method is based on the HheG‐catalyzed α‐position regioselective ring‐opening of styrene oxide derivatives with cyanate as a nucleophile, producing the corresponding 4‐aryloxazolidinones in moderate to good yields. Synthesis of enantiopure 4‐aryloxazolidinones is also achievable using chiral epoxide materials.magnified image

Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity

HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles. This enzyme provides access to chiral β-substituted alcohols that serve as building blocks in the pharmaceutical industry. Wild-type HheG suffers from low thermostability, which poses a significant drawback for potential applications. In an attempt to thermostabilize HheG by protein engineering, several single mutants at position 123 were identified which displayed up to 14 °C increased apparent melting temperatures and up to three-fold higher activity. Aromatic amino acids at position 123 resulted even in a slightly higher enantioselectivity. Crystal structures of variants T123W and T123G revealed a flexible loop opposite to amino acid 123. In variant T123G, this loop adopted two different positions resulting in an open or partially closed active site. Classical molecular dynamics simulations confirmed a high mobility of this loop. Moreover, in variant T123G this loop adopted a position much closer to residue 123 resulting in denser packing and increased buried surface area. Our results indicate an important role for position 123 in HheG and give first structural and mechanistic insight into the thermostabilizing effect of mutations T123W and T123G.

Selective Ring‐Opening of Di‐Substituted Epoxides Catalysed by Halohydrin Dehalogenases

AbstractHalohydrin dehalogenases (HHDHs) are valuable biocatalysts for the synthesis of β‐substituted alcohols based on their epoxide ring‐opening activity with a number of small anionic nucleophiles. In an attempt to further broaden the scope of substrates accepted by these enzymes, a panel of 22 HHDHs was investigated in the conversion of aliphatic and aromatic vicinally di‐substituted trans‐epoxides using azide as nucleophile. The majority of these HHDHs was able to convert aliphatic methyl‐substituted epoxide substrates to the corresponding azidoalcohols, in some cases even with absolute regioselectivity. HheG from Ilumatobacter coccineus exhibited also high activity towards sterically more demanding di‐substituted epoxides. This further expands the range of β‐substituted alcohols that are accessible by HHDH catalysis.

Enhancement of the thermostability of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by constructing a combinatorial smart library.

Halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) is a key enzyme in preparing β-substituted alcohols and optically pure epoxides. However, the weak thermostability of HheC greatly limits its industrial application and needs to be improved. In this study, a combinatorial smart library was constructed and screened for enhancing the thermostability of HheC. Mutation sites Lys203 and Lys204 located at the protein surface were selected and simultaneously randomized with charged amino acids (Arg, Asp, Glu, Lys), resulting in a combinatorial smart library. After screening a total of only 48 clones, three positive variants CSL1 (Lys203Arg), CSL2 (Lys204Arg) and CSL3 (Lys203Arg/Lys204Arg) were obtained. Compared to the wild type HheC, variant CSL2 exhibited an increase in thermal stability with a nearly 6.9-fold improvement of half-life (τ1/2, 55°C) at 55 °C without compromising catalytic activity. In addition, the double mutant CSL3 displayed approximately 3.4-fold higher τ1/2, 55°C value and 1.8-fold higher kcat value toward 1,3-dicholoro-2-propanol (1,3-DCP) than that of the wild-type HheC. Homology modeling analysis highlights that the newly gained hydrogen bonds and optimizing charge-charge interactions at the protein surface might contribute to the overall conformational stabilization, leading to improving the thermostability of HheC.

Exploring the Biocatalytic Scope of a Novel Enantioselective Halohydrin Dehalogenase from an Alphaproteobacterium

A gene encoding halohydrin dehalogenase from an alphaproteobacterium (AbHHDH) was identified, cloned and over-expressed in Escherichia coli. AbHHDH was able to catalyze the stereoselective dehalogenation of prochiral and racemic halohydrins. It showed the highest enantioselectivity in the dehalogenation of 20 mM (R,S)-2-bromo-1-phenylethanol, which yielded (S)-2-bromo-1-phenylethanol with 99% ee and 34.5% yield. Moreover, AbHHDH catalyzed the azidolysis of epoxides with low to moderate (S)-enantioselectivity. The highest enantioselectivity (E = 18.6) was observed when (R,S)-benzyl glycidyl ether was used as the substrate. A sequential kinetic resolution catalyzed by HHDH was employed for the synthesis of chiral 1-chloro-3-phenoxy-2-propanol. We prepared enantiopure (S)-isomer with a high enantiopurity of ee > 99% and a yield of 30.7% (E-value: 21.3) by kinetic resolution of 20 mM substrate. The (S)-isomer with 99% ee readily obtained from 40 to 150 mM (R,S)-1-chloro-3-phenoxy-2-propanol. Taken together, the results of this study demonstrate the applicability of this HHDH for the production of optically active compounds.

Highly α-position regioselective ring-opening of epoxides catalyzed by halohydrin dehalogenase from Ilumatobacter coccineus: a biocatalytic approach to 2-azido-2-aryl-1-ols.

Halohydrin dehalogenases are usually recognized as strict β-position regioselective enzymes in the nucleophile-mediated ring-opening of epoxides. Here we found the HheG from Ilumatobacter coccineus exhibited excellent α-position regioselectivity in the azide-mediated ring-opening of styrene oxide derivatives 1a–1k, producing the corresponding 2-azido-2-aryl-1-ols 2a–2k with the yields up to 96%.

Molecular modification of a halohydrin dehalogenase for kinetic regulation to synthesize optically pure (S)-epichlorohydrin

Asymmetric synthesis of chiral epichlorohydrin (ECH) from 1,3-dichloro-2-propanol (1,3-DCP) using halohydrin dehalogenases (HHDHs) is of great value due to the 100% theoretical yield and high enantioselectivity. The vital problem in the asymmetric synthesis is to prepare optically pure ECH. In this study, key amino acid residues located at halide ion channels of HheC (P175S/W249P) (HheCPS) were modified to regulate the kinetic parameters. HheCPS I81W, F86N and V94R were constructed with the corresponding halide ion channels destroyed. The catalytically efficiencies (kcat/Km) of the three mutants exhibited 0.38-, 0.23- and 0.23-fold decrease toward (S)-ECH and the reverse reaction was significantly inhibited. As the results, (S)-ECH was synthesized with >99% enantiomeric excess (e.e.) and 63.42%, 67.08% and 57.01% yields, respectively, under 20 mM 1,3-DCP as substrate. To our knowledge, this is the first investigation of the molecule kinetic modification of HHDHs and also the first report for the biosynthesis of optically pure (S)-ECH from 1,3-DCP using HHDHs.