Microbial epoxide hydrolases for preparative biotransformations

Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases

Epoxide hydrolases (EHs), which catalyze the transformation of epoxides to diols, are present in many eukaryotic and prokaryotic organisms. They have recently drawn considerable attention from organic chemists owing to their application in the semisynthesis of enantiospecific diol compounds. Here, we report the crystal structures of BoEH from Bosea sp. PAMC 26642 and CaEH from Caballeronia sordidicola PAMC 26510 at 1.95 and 2.43 Å resolution, respectively. Structural analysis showed that the overall structures of BoEH and CaEH commonly possess typical α/β hydrolase fold with the same ring-opening residues (Tyr-Tyr) and conserved catalytic triad residues (Asp-Asp-His). However, the two enzymes were found to have significantly different sequence compositions in the cap domain region, which is involved in the formation of the substrate-binding site in both enzymes. Enzyme activity assay results showed that BoEH had the strongest activity toward the linear aliphatic substrates, whereas CaEH had a higher preference for aromatic- and cycloaliphatic substrates. Computational docking simulations and tunnel identification revealed important residues with different substrate-binding preferences. Collectively, structure comparison studies, together with ligand docking simulation results, suggested that the differences in substrate-binding site residues were highly correlated with substrate specificity.

Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid

Microbial epoxide hydrolases, cis-epoxysuccinate hydrolases (CESHs), have been utilized for commercial production of enantiomerically pure L(+)- and D(-)-tartaric acids for decades. However, the stereo-catalytic mechanism of CESH producing L(+)-tartaric acid (CESH[L]) remains unclear. Herein, the crystal structures of two CESH[L]s in ligand-free, product-complexed, and catalytic intermediate forms were determined. These structures revealed the unique specific binding mode for the mirror-symmetric substrate, an active catalytic triad consisting of Asp-His-Glu, and an arginine providing a proton to the oxirane oxygen to facilitate the epoxide ring-opening reaction, which has been pursued for decades. These results provide the structural basis for the rational engineering of these industrial biocatalysts.

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

Enantioselective Synthesis of Spiro-oxiranes: An Asymmetric Addition/Aldol/Spirocyclization Domino Cascade

Enantioenriched spiro-oxiranes bearing three contiguous stereocenters were synthesized using a rhodium-catalyzed asymmetric addition/aldol/spirocyclization sequence. Starting from a linear substrate, the cascade enabled the formation of a spirocyclic framework in a single step. sp² - and sp-hybridized carbon nucleophiles were found to be competent initiators for this cascade, giving arylated or alkynylated products, respectively. Derivatization studies demonstrated the synthetic versatility of both the epoxide and the alkyne moieties of the products. DFT calculations were used to reconcile spectroscopic discrepancies observed between the solution- and solid-state structures of the products.

Enantiomeric Tartaric Acid Production Using cis-Epoxysuccinate Hydrolase: History and Perspectives

Tartaric acid is an important chiral chemical building block with broad industrial and scientific applications. The enantioselective synthesis of l(+)- and d(−)-tartaric acids has been successfully achieved using bacteria presenting cis-epoxysuccinate hydrolase (CESH) activity, while the catalytic mechanisms of CESHs were not elucidated clearly until very recently. As biocatalysts, CESHs are unique epoxide hydrolases because their substrate is a small, mirror-symmetric, highly hydrophilic molecule, and their products show very high enantiomeric purity with nearly 100% enantiomeric excess. In this paper, we review over forty years of the history, process and mechanism studies of CESHs as well as our perspective on the future research and applications of CESH in enantiomeric tartaric acid production.

Enzymatic synthesis of enantiopure alcohols: current state and perspectives

Enantiomerically pure alcohols, as key intermediates, play an essential role in the pharmaceutical, agrochemical and chemical industries. Among the methods used for their production, biotechnological approaches are generally considered a green and effective alternative due to their mild reaction conditions and remarkable enantioselectivity. An increasing number of enzymatic strategies for the synthesis of these compounds has been developed over the years, among which seven primary methodologies can be distinguished as follows: (1) enantioselective water addition to alkenes, (2) enantioselective aldol addition, (3) enantioselective coupling of ketones with hydrogen cyanide, (4) asymmetric reduction of carbonyl compounds, (5) (dynamic) kinetic resolution of racemates, (6) enantioselective hydrolysis of epoxides, and (7) stereoselective hydroxylation of unactivated C-H bonds. Some recent reviews have examined these approaches separately; however, to date, no review has included all the above mentioned strategies. The aim of this mini-review is to provide an overview of all seven enzymatic strategies and draw conclusions on the effect of each approach.

Structural insight into the catalytic mechanism of a cis-epoxysuccinate hydrolase producing enantiomerically pure d(-)-tartaric acid

Crystal structure determination and mutagenesis analysis of a cis-epoxysuccinate hydrolase which produces enantiomerically pure d(-)-tartaric acids revealed a zinc ion and essential residues in the stereoselective mechanism for the catalytic reaction of the small mirror symmetric substrate.

Biotransformation of polyunsaturated fatty acids to bioactive hepoxilins and trioxilins by microbial enzymes

Hepoxilins (HXs) and trioxilins (TrXs) are involved in physiological processes such as inflammation, insulin secretion and pain perception in human. They are metabolites of polyunsaturated fatty acids (PUFAs), including arachidonic acid, eicosapentaenoic acid and docosahexaenoic acid, formed by 12-lipoxygenase (LOX) and epoxide hydrolase (EH) expressed by mammalian cells. Here, we identify ten types of HXs and TrXs, produced by the prokaryote Myxococcus xanthus, of which six types are new, namely, HXB₅, HXD₃, HXE₃, TrXB₅, TrXD₃ and TrXE₃. We succeed in the biotransformation of PUFAs into eight types of HXs (>35% conversion) and TrXs (>10% conversion) by expressing M. xanthus 12-LOX or 11-LOX with or without EH in Escherichia coli. We determine 11-hydroxy-eicosatetraenoic acid, HXB₃, HXB₄, HXD₃, TrXB₃ and TrXD₃ as potential peroxisome proliferator-activated receptor-γ partial agonists. These findings may facilitate physiological studies and drug development based on lipid mediators.

Hepoxilins (HXs) and trioxilins (TrXs) are lipid metabolites with roles in inflammation and insulin secretion. Here, the authors discover a prokaryotic source of HXs and TrXs, identify the biosynthetic enzymes and heterologously express HXs and TrXs in E. coli.

Production of tartaric acid using immobilized recominant cis-epoxysuccinate hydrolase

OBJECTIVE

To investigate the expression and immobilization of recombinant cis-epoxysuccinate hydrolase (ESH), and its application in the biological production of L-(+)-tartaric acid.

RESULTS

E. coli BL21 (DE3)/pET11a-ESH (His) was engineered to express recombinant ESH. The enzyme had an activity of 262 U mg^-1. The recombinant ESH was immobilized on agarose Ni-IDA matrix with metal ion affinity interaction to improve its thermostability and pH stability. The immobilization efficiency and activity yield were 94 and 95%, respectively. The specific catalytic efficiency of immobilized ESH was 104 mg U^-1 h^-1 during the continuous enzymatic production process.

CONCLUSION

ESH with a histidine tag was immobilized and used for the continuous production of L-(+)-tartaric acid.

Oxetane Substrates of Human Microsomal Epoxide Hydrolase

Oxetanyl building blocks are increasingly used in drug discovery because of the improved drug-like properties they confer on drug candidates, yet little is currently known about their biotransformation. A series of oxetane-containing analogs was studied and we provide the first direct evidence of oxetane hydrolysis by human recombinant microsomal epoxide hydrolase (mEH). Incubations with human liver fractions and hepatocytes were performed with and without inhibitors of cytochrome P450 (P450), mEH and soluble epoxide hydrolase (sEH). Reaction dependence on NADPH was investigated in subcellular fractions. A full kinetic characterization of oxetane hydrolysis is presented, in both human liver microsomes and human recombinant mEH. In human liver fractions and hepatocytes, hydrolysis by mEH was the only oxetane ring-opening metabolic route, with no contribution from sEH or from cytochrome P450-catalyzed oxidation. Minimally altering the structural elements in the immediate vicinity of the oxetane can greatly modulate the efficiency of hydrolytic ring cleavage. In particular, higher pK_a in the vicinity of the oxetane and an increased distance between the oxetane ring and the benzylic nitrogen improve reaction rate, which is further enhanced by the presence of methyl groups near or on the oxetane. This work defines oxetanes as the first nonepoxide class of substrates for human mEH, which was previously known to catalyze the hydrolytic ring opening of electrophilic and potentially toxic epoxide-containing drugs, drug metabolites, and exogenous organochemicals. These findings will be of value for the development of biologically active oxetanes and may be exploited for the biocatalytic generation of enantiomerically pure oxetanes and diols.

Visualizing the Mechanism of Epoxide Hydrolysis by the Bacterial Virulence Enzyme Cif

The CFTR inhibitory factor (Cif) is an epoxide hydrolase (EH) virulence factor secreted by the bacterium Pseudomonas aeruginosa. Sequence alignments reveal a pattern of Cif-like substitutions that proved to be characteristic of a new subfamily of bacterial EHs. At the same time, crystallographic and mutagenetic data suggest that EH activity is required for virulence and that Cif's active site remains generally compatible with a canonical two-step EH mechanism. A hallmark of this mechanism is the formation of a covalent hydroxyalkyl-enzyme intermediate by nucleophilic attack. In several well-studied EHs, this intermediate has been captured at near stoichiometric levels, presumably reflecting rate-limiting hydrolysis. Here we show by mass spectrometry that only minimal levels of the expected intermediate can be trapped with WT Cif. In contrast, substantial amounts of intermediate are recovered from an active-site mutant (Cif-E153Q) that selectively targets the second, hydrolytic release step. Utilizing Cif-E153Q and a previously reported nucleophile mutant (Cif-D129S), we then captured Cif in the substrate-bound, hydroxyalkyl-intermediate, and product-bound states for 1,2-epoxyhexane, yielding the first crystallographic snapshots of an EH at these key stages along the reaction coordinate. Taken together, our data illuminate the proposed two-step hydrolytic mechanism of a new class of bacterial virulence factor. They also suggest that the failure of WT Cif to accumulate a covalent hydroxyalkyl-enzyme intermediate reflects an active-site chemistry in which hydrolysis is no longer the rate-limiting step, a noncanonical kinetic regime that may explain similar observations with a number of other EHs.

Removal of floral microbiota reduces floral terpene emissions

The emission of floral terpenes plays a key role in pollination in many plant species. We hypothesized that the floral phyllospheric microbiota could significantly influence these floral terpene emissions because microorganisms also produce and emit terpenes. We tested this hypothesis by analyzing the effect of removing the microbiota from flowers. We fumigated Sambucus nigra L. plants, including their flowers, with a combination of three broad-spectrum antibiotics and measured the floral emissions and tissular concentrations in both antibiotic-fumigated and non-fumigated plants. Floral terpene emissions decreased by ca. two thirds after fumigation. The concentration of terpenes in floral tissues did not decrease, and floral respiration rates did not change, indicating an absence of damage to the floral tissues. The suppression of the phyllospheric microbial communities also changed the composition and proportion of terpenes in the volatile blend. One week after fumigation, the flowers were not emitting β-ocimene, linalool, epoxylinalool, and linalool oxide. These results show a key role of the floral phyllospheric microbiota in the quantity and quality of floral terpene emissions and therefore a possible key role in pollination.

Purification and characterization of a novel cis-epoxysuccinate hydrolase from Klebsiella sp. that produces L(+)-tartaric acid

A strain of Klebsiella sp. BK-58 that produces cis-epoxysuccinate was screened and identified. This novel enzyme hydrolyzes cis-epoxysuccinate to L(+)-tartaric acid and was purified to homogeneity. Its molecular mass was 30.1 kDa determined by MALDI-TOF-MS analysis. It was stable up to 50 °C and from pH 5 to 11 with optima at 50 °C and pH 8.5. The enzyme was metal-independent and was strongly inhibited by 1 mM Cu(2+) and Ag(+), and 1 % (w/v) SDS. The K m , V max and turnover number (k cat ) values for cis-epoxysuccinate were 19.3, 2.24 mM min(-1) and 220 s(-1), respectively.

A broadly applicable and practical oligomeric (salen) Co catalyst for enantioselective epoxide ring-opening reactions

The (salen) Co catalyst (4a) can be prepared as a mixture of cyclic oligomers in a short, chromatography-free synthesis from inexpensive, commercially available precursors. This catalyst displays remarkable enhancements in reactivity and enantioselectivity relative to monomeric and other multimeric (salen) Co catalysts in a wide variety of enantioselective epoxide ring-opening reactions. The application of catalyst 4a is illustrated in the kinetic resolution of terminal epoxides by nucleophilic ring-opening with water, phenols, and primary alcohols; the desymmetrization of meso epoxides by addition of water and carbamates; and the desymmetrization of oxetanes by intramolecular ring opening with alcohols and phenols. The favorable solubility properties of complex 4a under the catalytic conditions facilitated mechanistic studies, allowing elucidation of the basis for the beneficial effect of oligomerization. Finally, a catalyst selection guide is provided to delineate the specific advantages of oligomeric catalyst 4a relative to (salen) Co monomer 1 for each reaction class.

Protein engineering for development of new hydrolytic biocatalysts

Hydrolytic enzymes play important roles as biocatalysts in chemical synthesis. The chemical versatility and structurally sturdy features of Candida antarctica lipase B has placed this enzyme as a common utensil in the synthetic tool-box. In addition to catalyzing acyl transfer reactions, a number of promiscuous activities have been described recently. Some of these new enzyme activities have been amplified by mutagenesis. Epoxide hydrolases are of interest due to their potential as catalysts in asymmetric synthesis. This current update discusses recent development in the engineering of lipases and epoxide hydrolases aiming to generate new biocatalysts with refined features as compared to the wild-type enzymes. Reported progress in improvements in reaction atom economy from dynamic kinetic resolution or enantioconvergence is also included.

Biocatalytic synthesis of chiral alcohols and amino acids for development of pharmaceuticals

Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become increasingly important in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes derived there from for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities. In this article, biocatalytic processes are described for the synthesis of chiral alcohols and unntural aminoacids for pharmaceuticals.

Farnesides A and B, sesquiterpenoid nucleoside ethers from a marine-derived Streptomyces sp., strain CNT-372 from Fiji

Farnesides A and B (1, 2), linear sesquiterpenoids connected by ether links to a ribose dihydrouracil nucleoside, were isolated from a marine-derived Streptomyces sp., strain CNT-372, grown in saline liquid culture. The structures of the new compounds were assigned by comprehensive spectroscopic analysis primarily involving 1D and 2D NMR analysis and by comparison of spectroscopic data to the recently reported ribose nucleoside JBIR-68 (3). The farnesides are only the second example of this exceedingly rare class of microbial terpenoid nucleoside metabolites. Farneside A (1) was found to have modest antimalarial activity against the parasite Plasmodium falciparum.

Expression and production of recombinant cis-epoxysuccinate hydrolase in Escherichia coli under the control of temperature-dependent promoter

cis-Epoxysuccinate hydrolase (ESH) from Nocardia tartaricans CAS-52 could catalyze the stereospecific hydrolysis of cis-epoxysuccinate to L-(+)-tartrate. The ESH gene of 762 bp was cloned and its open reading frame (ORF) sequence predicted a protein of 253 amino acids. An expression plasmid carrying the ESH gene under the control of the P(L)P(R) promoter was introduced into Escherichia coli, and the ESH gene was successfully expressed in the recombinant strain. The expression conditions and scale-up production were also studied. Fed-batch fermentation of E. coli Trans 1-T1 transformant was carried out in a 2000 L fermentor to product recombinant ESH. The results showed that wet cell concentration reached to 62.45 g L(-1), and the specific activity of ESH was 380.17 U mg(-1), which could meet the requirements of industrial production of L-(+)-tartaric acid.

Enantioselective synthesis of 2,2-disubstituted terminal epoxides via catalytic asymmetric Corey-Chaykovsky epoxidation of ketones

Catalytic asymmetric Corey-Chaykovsky epoxidation of various ketones with dimethyloxosulfonium methylide using a heterobimetallic La-Li₃-BINOL complex (LLB) is described. The reaction proceeded smoothly at room temperature in the presence of achiral phosphine oxide additives, and 2,2-disubstituted terminal epoxides were obtained in high enantioselectivity (97%–91% ee) and yield (>99%–88%) from a broad range of methyl ketones with 1-5 mol% catalyst loading. Enantioselectivity was strongly dependent on the steric hindrance, and other ketones, such as ethyl ketones and propyl ketones resulted in slightly lower enantioselectivity (88%–67% ee).

Bioresolution of benzyl glycidyl ether using whole cells of Bacillus alcalophilus

The incubation of whole Bacillus alcalophilus cells grown on a mineral supplemented medium (MSM) containing 1% (w/v) sucrose as carbon source, 1.2% (w/v) tryptone as nitrogen source at pH 6.5 and temperature 30 °C in 24 h kinetically resolved benzyl glycidyl ether (1 mg/ml) to provide (S)-benzyl glycidyl ether with 30% ee and (R)-3-benzyloxypropane-1,2-diol with 40% ee.

Biocatalytic synthesis of optically active tertiary alcohols

The enzymatic preparation of optically pure tertiary alcohols under sustainable conditions has received much attention. The conventional chemical synthesis of these valuable building blocks is still hampered by the use of harmful reagents such as heavy metal catalysts. Successful examples in biocatalysis used esterases, lipases, epoxide hydrolases, halohydrin dehalogenases, thiamine diphosphate-dependent enzymes, terpene cyclases, -acetylases, and -dehydratases. This mini-review provides an overview on recent developments in the discovery of new enzymes, their functional improvement by protein engineering, the design of chemoenzymatic routes leading to tertiary alcohols, and the discovery of entirely new biotransformations.