Modification of Substrate Specificity Resulting in an Epoxide Hydrolase with Shifted Enantiopreference for (2,3‐Epoxypropyl)benzene

Random mutagenesis targeted at hotspots of noncatalytic active‐site residues of potato epoxide hydrolase StEH1 combined with an enzyme‐activity screen allowed the isolation of enzyme variants displaying altered enantiopreference in the catalyzed hydrolysis of (2,3‐epoxypropyl)benzene. The wild‐type enzyme favored the S enantiomer with a ratio of 2.5:1, whereas the variant displaying the most radical functional changes showed a 15:1 preference for the R enantiomer. This mutant had accumulated four substitutions distributed over two out of four mutated hotspots: W106L, L109Y, V141K, and I151V. The underlying causes of the enantioselectivity were a decreased catalytic efficiency in the catalyzed hydrolysis of the S enantiomer combined with retained activity with the R enantiomer. The results demonstrate the feasibility of molding the stereoselectivity of this biocatalytically relevant enzyme.     

Characterization of a Cyanobacterial Haloperoxidase and Evaluation of its Biocatalytic Halogenation Potential

Vanadium‐dependent haloperoxidases (VHPOs) are a class of halogenating enzymes found in fungi, lichen, algae, and bacteria. We report the cloning, purification, and characterization of a functional VHPO from the cyanobacterium Acaryochloris marina (AmVHPO), including its structure determination by X‐ray crystallography. Compared to other VHPOs, the AmVHPO features a unique set of disulfide bonds that stabilize the dodecameric assembly of the protein. Easy access by high‐yield recombinant expression, as well as resistance towards organic solvents and temperature, together with a distinct halogenation reactivity, make this enzyme a promising starting point for the development of biocatalytic transformations.     

Biocatalytic Reversal of Advanced Glycation End Product Modification

Advanced glycation end products (AGEs) are a heterogeneous group of molecules that emerge from the condensation of sugars and proteins through the Maillard reaction. Despite a significant number of studies showing strong associations between AGEs and the pathologies of aging-related illnesses, it has been a challenge to establish AGEs as causal agents primarily due to the lack of tools in reversing AGE modifications at the molecular level. Herein, we show that MnmC, an enzyme involved in a bacterial tRNA-modification pathway, is capable of reversing the AGEs carboxyethyl-lysine (CEL) and carboxymethyl-lysine (CML) back to their native lysine structure. Combining structural homology analysis, site-directed mutagenesis, and protein domain dissection studies, we generated a variant of MnmC with improved catalytic properties against CEL in its free amino acid form. We show that this enzyme variant is also active on a CEL-modified peptidomimetic and an AGE-containing peptide that has been established as an authentic ligand of the receptor for AGEs (RAGE). Our data demonstrate that MnmC variants are promising lead catalysts toward the development of AGE-reversal tools and a better understanding of AGE biology.     

Enzymatic Transformations 62. Preparative Scale Synthesis of Enantiopure Glycidyl Acetals using an Aspergillus niger Epoxide Hydrolase‐Catalysed Kinetic Resolution

The hydrolytic kinetic resolution of five glycidaldehyde acetal derivatives was examined using the recombinant Aspergillus niger epoxide hydrolase as biocatalyst. This could successfully be performed, at room temperature, using solely demineralised water as solvent and following a two‐phase methodology allowing us to operate at a global substrate concentration as high as 200 g/L in the reactor. The observed E values were shown to be modest to excellent, depending on the structure of the acetal moiety, indicating that it is possible to achieve this resolution very efficiently just by choosing the right substituents. Both the unreacted (R)‐epoxide and the formed (S)‐diol could thus be obtained in good to excellent ee (ee>99 % for the epoxide). For the best substrates, the reaction could be performed within a few hours by using a biocatalyst over substrate molecular ratio of about 9 to 10×10⁻⁴ mol %. The turnover frequency (TOF) as well as the total turnover number (TON) of the enzyme proved to be excellent as compared to chemical catalysts – reaching respectively values in the order of 6×10² mol sub/mol enz/min and 6×10⁴ mol sub/mol enz. The space‐time yield of the best (two‐phase) reactor could thus reach a value as high as 56 g/L/hour. As a demonstration experiment, a 50‐g scale resolution of glycidaldehyde 2,2‐dimethyltrimethylene acetal was performed.     

Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus jostii RHA1: A Versatile Oxidative Biocatalyst

Eugenol oxidase (EUGO) from Rhodococcus jostii RHA1 had previously been shown to convert only a limited set of phenolic compounds. In this study, we have explored the biocatalytic potential of this flavoprotein oxidase, resulting in a broadened substrate scope and a deeper insight into its structural properties. In addition to the oxidation of vanillyl alcohol and the hydroxylation of eugenol, EUGO can efficiently catalyze the dehydrogenation of various phenolic ketones and the selective oxidation of a racemic secondary alcohol—4‐(1‐hydroxyethyl)‐2‐methoxyphenol. EUGO was also found to perform the kinetic resolution of a racemic secondary alcohol. Crystal structures of the enzyme in complexes with isoeugenol, coniferyl alcohol, vanillin, and benzoate have been determined. The catalytic center is a remarkable solvent‐inaccessible cavity on the si side of the flavin cofactor. Structural comparison with vanillyl alcohol oxidase from Penicillium simplicissimum highlights a few localized changes that correlate with the selectivity of EUGO for phenolic substrates bearing relatively small p‐substituents while tolerating o‐methoxy substituents.     

Increased Enantioselectivity by Engineering Bottleneck Mutants in an Esterase from Pseudomonas fluorescens

Four hydrophobic and bulky amino acid residues (F126, F144, F159, and I225) were identified to form a bottleneck guarding the entrance to the active site of an esterase from Pseudomonas fluorescens (PFE I). Hence, a range of nonpolar amino acids were introduced into PFE I to broaden the substrate range and to increase enantioselectivity while preserving the hydrophobicity of the tunnel. First, single variants were created and then the most enantioselective ones were combined to find cooperative effects. This resulted in several mutants, which showed substantially enhanced enantioselectivity; for instance, in the kinetic resolution of 1‐phenyl‐1‐propyl acetate, with which the wild type only showed E=1.2, two mutants gave E>46. For 1‐phenyl‐1‐ethyl acetate enantioselectivity increased from ～50 to >100 for all mutants studied. Furthermore, higher conversions could be found at shorter reaction times; this indicates that the mutations not only enhanced selectivity, but that also the entrance into the active site was indeed facilitated by these mutations. The experimental results could be explained by computer modeling.     

An Esterase with Superior Activity and Enantioselectivity towards 1,2‐O‐Isopropylideneglycerol Esters Obtained by Protein Design

The Escherichia coli esterase YbfF displays high activity towards 1,2‐O‐isopropylideneglycerol (IPG) butyrate and IPG caprylate, and prefers the R‐enantiomer of these substrates, producing the S‐enantiomer of the IPG product in excess. To improve the potential of the enzyme for the kinetic resolution of racemic esters of IPG, an enhancement of the activity and enantioselectivity would be highly desirable. Molecular docking of the R‐enantiomer of both IPG esters into the active site of YbfF allowed the identification of proximal YbfF active site residues. Four residues (25, 124, 185 and 235) were selected as targets for mutagenesis, in order to enhance YbfF activity and enantioselectivity towards IPG esters. Random mutagenesis at positions 25, 124, 185 and 235 yielded several best YbfF variants with enhanced activity and enantioselectivity towards IPG esters. The best YbfF mutant, W235I, exhibited a 2‐fold higher enantioselectivity than wild‐type YbfF, with an E=38 for IPG butyrate and an E=77 for IPG caprylate. Molecular docking experiments further support the enhanced enantioselectivity shown experimentally and the structural effects of this amino acid substitution on the active site of YbfF are provided. The engineered W235I mutant is an attractive catalyst for practical applications in the kinetic resolution of IPG esters.     

Simple Biocatalytic Access to Enantiopure (S)‐1‐Heteroarylethanols Employing a Microbial Hydrogen Transfer Reaction

Lyophilised cells of various Rhodococcus spp. were employed in an efficient hydrogen transfer‐like process for the asymmetric bioreduction of heteroaryl methyl ketones using 2‐propanol as hydrogen donor. Besides the genus Rhodococcus, only Mycoplana rubra R14 showed a comparable stability towards elevated concentrations of the co‐substrate 2‐propanol. Among the organisms tested, Rhodococcus ruber DSM 44541 and DSM 43338 showed best activity and selectivity. With these strains, the reaction proceeded with high stereoselectivity (ee>99%) and predictable stereochemical outcome regardless of the nature of the heteroaromatic ring system. The reaction could be performed at the exceptional substrate concentration of up to 0.4 mol L⁻¹ in an environmentally friendly aqueous‐organic solvent mixture at room temperature and is easy to handle, thus providing a very practical tool to access enantiopure 1‐heteroarylethanols.     

Combined enzyme and substrate design: grafting of a cooperative two-histidine catalytic motif into a protein targeted at the scissile bond in a designed ester substrate

A histidine-based, two-residue reactive site for the catalysis of hydrolysis of designed sulfonamide-containing para-nitrophenyl esters has been engineered into a scaffold protein. A matching substrate was designed to exploit the natural active site of human carbonic anhydrase II (HCAII) for well-defined binding. In this we took advantage of the high affinity between the active site zinc atom and sulfonamides. The ester substrate was designed to position the scissile bond in close proximity to the His64 residue in the scaffold protein. Three potential sites for grafting the catalytic His-His pair were identified, and the corresponding N62H/H64, F131H/V135H and L198H/P202H mutants were constructed. The most efficient variant, F131H/V135H, has a maximum k(cat)/K(M) value of approximately 14 000 M(-1) s(-1), with a k(cat) value that is increased by a factor of 3 relative to that of the wild-type HCAII, and by a factor of over 13 relative to the H64A mutant. The results show that an esterase can be designed in a stepwise way by a combination of substrate design and grafting of a designed catalytic motif into a well-defined substrate binding site.     

Enhanced fructose oxidase activity in a galactose oxidase variant

Galactose oxidase (GO; EC 1.1.3.9) catalyses the oxidation of a wide range of primary alcohols including mono-, oligo- and polysaccharides. High-resolution structures have been determined for GO, but no structural information is available for the enzyme with bound substrate or inhibitor. Previously, computer-aided docking experiments have been used to develop a plausible model for interactions between GO and the D-galactose substrate. Residues implicated in such interactions include Arg330, Gln406, Phe464, Phe194 and Trp290. In the present study we describe an improved expression system for recombinant GO in the methylotrophic yeast Pichia pastoris. We use this system to express variant proteins mutated at Arg330 and Phe464 to explore the substrate binding model. We also demonstrate that the Arg330 variants display greater fructose oxidase activity than does wild-type GO.     

An Unusual (R)‐Selective Epoxide Hydrolase with High Activity for Facile Preparation of Enantiopure Glycidyl Ethers

A novel epoxide hydrolase (BMEH) with unusual (R)‐enantioselectivity and very high activity was cloned from Bacillus megaterium ECU1001. Highest enantioselectivities (E>200) were achieved in the bioresolution of ortho‐substituted phenyl glycidyl ethers and para‐nitrostyrene oxide. Worthy of note is that the substrate structure remarkably affected the enantioselectivities of the enzyme, as a reversed (S)‐enantiopreference was unexpectedly observed for the ortho‐nitrophenyl glycidyl ether. As a proof‐of‐concept, five enantiopure epoxides (>99% ee) were obtained in high yields, and a gram‐scale preparation of (S)‐ortho‐methylphenyl glycidyl ether was then successfully performed within a few hours, indicating that BMEH is an attractive biocatalyst for the efficient preparation of optically active epoxides.     

Dynamic Kinetic Resolution of Primary Alcohols with an Unfunctionalized Stereogenic Center in the β‐Position

Primary alcohols with an unfunctionalized stereogenic center in the β‐position undergo an enzyme‐ and metal‐catalyzed dynamic kinetic resolution (DKR). The in situ racemization of the primary alcohol, required for the DKR, takes place via: (i) ruthenium‐catalyzed dehydrogenation of the alcohol, (ii) enolization of the aldehyde formed, and (iii) ruthenium‐catalyzed readdition of hydrogen to the aldehyde. The present method widens the scope of metal‐ and enzyme‐catalyzed DKR, which has so far been limited to α‐chiral alcohol and amine derivatives.     

Biocatalytic and Structural Properties of a Highly Engineered Halohydrin Dehalogenase

Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild‐type enzyme in the cyanolysis of ethyl (S)‐3,4‐epoxybutyrate, a conversion yielding ethyl (R)‐4‐cyano‐3‐hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild‐type enzyme, both for dehalogenation and for cyanolysis reactions. The 37‐fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild‐type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)‐3,4‐epoxybutyrate or with ethyl (R)‐4‐cyano‐3‐hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild‐type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.     

Vanadium‐Catalyzed Enantioselective Sulfoxidation and Concomitant,Highly Efficient Kinetic Resolution Provide High Enantioselectivity and Acceptable Yields of Sulfoxides

Simple, inexpensive, preformed vanadium‐Schiff base complexes were facilely prepared and used in enantioselective sulfoxidation. Both the amount of aqueous H₂O₂ and reaction time greatly influenced the ee values and yields of chiral sulfoxides. High enantioselectivities (up to 99% ee) and reasonable yields (>40%) for various chiral sulfoxides were achieved by combining enantioselective sulfoxidation and appropriate concomitant kinetic resolution.     

Epoxide Hydrolase‐Catalysed Kinetic Resolution of a Spiroepoxide,a Key Building Block of Various 11‐Heterosteroids

Two microbial epoxide hydrolases – i.e., Aspergillus niger (AnEH) and Rhodococcus erythropolis (the so‐called “Limonene EH”: LEH) were used to achieve, for the first time, the biocatalysed hydrolytic kinetic resolution (BHKR) of spiroepoxide rac‐ 1 . This compound is a strategic key building block allowing the synthesis of 11‐heterosteroids. Interestingly enough, the two enzymes exhibited opposite and therefore complementary enantioselectivity allowing us to isolate the residual (R,R)‐ 1 (from AnEH) and the residual (S,S)‐ 1 (from LEH) in nearly enantiopure forms (>98 %). Their absolute configurations were determined by X‐ray crystallography. An opposite regioselectivity of the oxirane ring opening for both enantiomers of substrate 1 , determined using H₂¹⁸O labelling and chiral GC‐MS analysis, was also observed, corresponding to an attack at the less substituted carbon atom using AnEH, and at the most substituted carbon atom using LEH. A chemical process‐improving methodology was also developed. This allowed us to obtain both enantiomers of the substrate in high enantiomeric purity (99 %) and optimised quantity. In the case of the AnEH, the use of a biphasic (water/isooctane) reaction medium allowed us to increase the global substrate concentration up to 200 g/ L. The preparation of both enantiomers of 1 clearly paves the way to the preparative scale synthesis and biochemical evaluation of the corresponding 11‐heterosteroid enantiomers.     

Directed evolution of an esterase from Pseudomonas fluorescens yields a mutant with excellent enantioselectivity and activity for the kinetic resolution of a chiral building block

A triple mutant of an esterase from Pseudomonas fluorescens (PFE) that was created by directed evolution exhibited high enantioselectivity (E=89) in a kinetic resolution and yielded the building block (S)-but-3-yn-2-ol. Surprisingly, a mutation close to the active site caused the formation of inclusion bodies, but remote mutations were found to be responsible for the high selectivity. Back mutations gave a variant (double mutant PFE Ile76Val/Val175Ala) that showed excellent selectivity (E=96) and activity (20 min for 50% conversion, which corresponds to 1.25 U per mg of protein).     

Understanding the Plasticity of the α/β Hydrolase Fold: Lid Swapping on the Candida antarctica Lipase B Results in Chimeras with Interesting Biocatalytic Properties

The best of both worlds . Long molecular dynamics (MD) simulations of Candida antarctica lipase B (CALB) confirmed the function of helix α5 as a lid structure. Replacement of the helix with corresponding lid regions from CALB homologues from Neurospora crassa and Gibberella zeae resulted in new CALB chimeras with novel biocatalytic properties. The figure shows a snapshot from the MD simulation.