Computational Study of Mechanism and Enantioselectivity of Imine Reductase from Amycolatopsis orientalis

Imine reductases (IREDs) are NADPH-dependent enzymes (NADPH=nicotinamide adenine dinucleotide phosphate) that catalyze the reduction of imines to amines. They exhibit high enantioselectivity for a broad range of substrates, making them of interest for biocatalytic applications. In this work, we have employed density functional theory (DFT) calculations to elucidate the reaction mechanism and the origins of enantioselectivity of IRED from Amycolatopsis orientalis. Two substrates are considered, namely 1-methyl-3,4-dihydroisoquinoline and 2-propyl-piperideine. A model of the active site is built on the basis of the available crystal structure. For both substrates, different binding modes are first evaluated, followed by calculation of the hydride transfer transition states from each complex. We have also investigated the effect of mutations of certain important active site residues (Tyr179Ala and Asn241Ala) on the enantioselectivity. The calculated energies are consistent with the experimental observations and the analysis of transition states geometries provides insights into the origins of enantioselectivity of this enzyme.     

Facile Access to Chiral Alcohols with Pharmaceutical Relevance Using a Ketoreductase Newly Mined from Pichia guilliermondii

Chiral secondary alcohols with additional functional groups are frequently required as important and valuable synthons for pharmaceuticals, agricultural and other fine chemicals. With the advantages of environmentally benign reaction conditions, broad reaction scope, and high stereoselectivity, biocatalytic reduction of prochiral ketones offers significant potential in the synthesis of optically active alcohols. A CmCR homologous carbonyl reductase from Pichia guilliermondii NRRL Y‐324 was successfully overexpressed. Substrate profile characterization revealed its broad substrate specificity, covering aryl ketones, aliphatic ketones and ketoesters. Furthermore, a variety of ketone substrates were asymmetrically reduced by the purified enzyme with an additionally NADPH regeneration system. The reduction system exhibited excellent enantioselectivity (>99% ee) in the reduction of all the aromatic ketones and ketoesters, except for 2‐bromoacetophenone (93.5% ee). Semi‐preparative reduction of six ketones was achieved with high enantioselectivity (>99% ee) and isolation yields (>80%) within 12 h. This study provides a useful guidance for further application of this enzyme in the asymmetric synthesis of chiral alcohol enantiomers.     

Enantioselective transesterification catalysis by nanosized serine protease subtilisin Carlsberg particles in tetrahydrofuran

Enzyme catalysis in organic solvents is a powerful tool for stereo-selective synthesis but the enantioselectivity is still hard to predict. To overcome this obstacle, we employed a nanoparticulate formulation of subtilisin Carlsberg (SC) and designed a series of 14 structurally related racemic alcohols. They were employed in the model transesterification reaction with vinyl butyrate and the enantioselectivities were determined. In general, short alcohol side chains led to low enantioselectivties, while larger and bulky side chains caused better discrimination of the enantiomers by the enzyme. With several bulky substrates high enantioselectivities with E>100 were obtained. Computational modeling highlighted that key to high enantioselectivity is the discrimination of the R and S substrates by the sole hydrophobic binding pocket based on their size and bulkiness. While bulky S enantiomer side chains could be accommodated within the binding pocket, bulky R enantiomer side chains could not. However, when also the S enantiomer side chain becomes too large and does not fit into the binding pocket anymore, enantioselectivity accordingly drops.     

Enzymatic ketone reduction: mapping the substrate profile of a short-chain alcohol dehydrogenase (YMR226c) from Saccharomyces cerevisiae

A short-chain alcohol dehydrogenase (YMR226c) from Saccharomyces cerevisiae was cloned and expressed in Escherichia coli, and the encoded protein was purified. The activity and enantioselectivity of this recombinant enzyme were evaluated with a series of ketones. The alcohol dehydrogenase (YMR226c) was found to effectively catalyze the enantioselective reductions of aryl-substituted acetophenones, α-chloroacetophenones, aliphatic ketones, and α- and β-ketoesters. While the enantioselectivity for the reduction of β-ketoesters was moderate, the acetophenone derivatives, aromatic α-ketoesters, some substituted α-chloroacetophenones, and aliphatic ketones were reduced to the corresponding chiral alcohols with excellent enantioselectivity. The enantiopreference of this enzyme generally followed Prelog’s rule for the simple ketones. The ester functionality played some role in determining the enzyme’s enantiopreference for the reduction of α- and β-ketoesters. The present study serves as a valuable guidance for the future applications of this versatile biocatalyst.     

Towards a novel explanation of Pseudomonas cepacia lipase enantioselectivity via molecular modelling of the enantiomer trajectory into the active site

In the transesterification reaction between (RS)-2-bromophenyl acetic acid ethyl ester and 1-octanol in n-octane, Pseudomonas cepacia lipase enantioselectivity towards the (R)-isomer is 57. Two strategies are described to investigate the structural basis involved in this enzyme enantioselectivity. Molecular modelling of the tetrahedral intermediate mimicking the transition state enables the identification of two potentially productive substrate-binding modes for each enantiomer. However, the conformations obtained with the faster and slower-reacting enantiomers have equivalent potential energies and most of them possess the hydrogen bonds essential for catalysis. On this basis, it is not possible to distinguish the diastereomeric complexes. The second approach is original and consists in a simple but robust protocol of pseudomolecular dynamics simulations under constraints to map the probable trajectory of the enantiomers in the active site. Enzyme/substrate interaction energy is always found to be lower for the faster-reacting enantiomer, which satisfactorily corroborates the experimental results. Energy differences are attributed to specific interactions of these substrates with a network of hydrophobic residues lining the access path. Furthermore, mechanistic details suggest that the pivoting side chains of the hydrophobic residues act in a concerted step–tooth gear motion whose basic role is to select and guide the substrates towards the active site. With this type of lipase, such dynamic features could be the key explanation of this as yet unexplored enantiorecognition. For the slower-reacting enantiomer, it appears that the concerted motion of the side chains is perturbed when the substrate passes through a bottleneck formed by Val266 and Leu17. The enantioselectivity of mutant Val266Leu with a more bulky side chain at this position supports our assumption: by narrowing the bottleneck, the enantioselectivity was considerably enhanced as much as up to 200.     

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate‐dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohols. BsADH prefers smaller substrates, which cause less protein friction along the reaction coordinate and reduced frequencies of dynamic recrossing. This hypothesis allows a prediction of the trend of enzyme isotope effects for a wide variety of substrates.     

Combinatorial Library Based Engineering of Candida antarctica Lipase A for Enantioselective Transacylation of sec‐Alcohols in Organic Solvent

A method for determining lipase enantioselectivity in the transacylation of sec‐alcohols in organic solvent was developed. The method was applied to a model library of Candida antarctica lipase A (CalA) variants for improved enantioselectivity (E values) in the kinetic resolution of 1‐phenylethanol in isooctane. A focused combinatorial gene library simultaneously targeting seven positions in the enzyme active site was designed. Enzyme variants were immobilized on nickel‐coated 96‐well microtiter plates through a histidine tag (His₆‐tag), screened for transacylation of 1‐phenylethanol in isooctane, and analyzed by GC. The highest enantioselectivity was shown by the double mutant Y93L/L367I. This enzyme variant gave an E value of 100 (R), which is a dramatic improvement on the wild‐type CalA (E=3). This variant also showed high to excellent enantioselectivity for other secondary alcohols tested.     

Enantioselective Aminohydroxylation of Styrenyl Olefins Catalyzed by an Engineered Hemoprotein

Chiral 1,2‐amino alcohols are widely represented in biologically active compounds from neurotransmitters to antivirals. While many synthetic methods have been developed for accessing amino alcohols, the direct aminohydroxylation of alkenes to unprotected, enantioenriched amino alcohols remains a challenge. Using directed evolution, we have engineered a hemoprotein biocatalyst based on a thermostable cytochrome c that directly transforms alkenes to amino alcohols with high enantioselectivity (up to 2500 TTN and 90 % ee) under anaerobic conditions with O‐pivaloylhydroxylamine as an aminating reagent. The reaction is proposed to proceed via a reactive iron‐nitrogen species generated in the enzyme active site, enabling tuning of the catalyst's activity and selectivity by protein engineering.     

tert‐Butyldimethylsilyl‐Directed Highly Enantioselective Approach to Axially Chiral α‐Allenols

A highly efficient and enantioselective synthesis of axially chiral α‐allenols was realized in practical yields with 96–99 % ee or de from TBS‐protected propargylic alcohols, aldehydes, and a commercially available, inexpensive, chiral, secondary amine (S)‐α,α‐diphenylprolinol or its enantiomer followed by desilylation. The easily removable TBS group not only acts as a protecting group, but also as a possible sterically directing group for the excellent enantioselectivity and in situ prevention of possible allene racemization.     

How substrate solvation contributes to the enantioselectivity of subtilisin toward secondary alcohols

The current rule to predict the enantiopreference of subtilisin toward secondary alcohols is based on the size of the substituents at the stereocenter and implies that the active site contains two differently sized pockets for these substituents. Several experiments are inconsistent with the current rule. First, the X-ray structures of subtilisin show there is only one pocket (the S1' pocket) approximately the size of a phenyl group to bind secondary alcohols. Second, the rule often predicts the incorrect enantiomer for reactions in water. To resolve these contradictions, we refine the current rule to show that subtilisin binds only one substituent of a secondary alcohol and leaves the other in solvent. To test this refined empirical rule, we show that the enantioselectivity of a series of secondary alcohols in water varied linearly with the difference in hydrophobicity (log P/P0) of the substituents. This hydrophobicity difference accounts for the solvation of one substituent in water.     

Enantioselectivity in Ruthenium-Catalyzed Propargylic Substitution Reactions of Propargylic Alcohols with Acetone: A DFT Study

The enantioselectivity in the propargylic substitution reactions of propargylic alcohols with acetone catalyzed by optically active thiolate-bridged diruthenium complexes was examined via ωB97X-D level DFT calculations. Some structures with intramolecular dispersion interactions between ligands were found for the ruthenium-allenylidene complex, which is the key intermediate in the catalytic reaction, and it was determined that the structure corresponding to the X-ray crystal structure, which had provided the transition state model for the enantioselectivity in previous studies, was not the most stable among the obtained structures. Then, a variety of transition-state structures for the nucleophilic attack of prop-1-ene-2-ol, which is the enol isomer of acetone, on the γ-carbon of the ruthenium-allenylidene complex were explored. Among the transition-state structures with lower energies, the number of structures leading to the major (R) product was found to be larger than that of structures leading to the minor (S) product, providing enantioselectivity in terms of probability distributions. The introduction of a phenyl group in the thiolate ligand was suggested to increase the selectivity. Thus, we propose the novel transition state model for the asymmetric catalytic reaction system.     

Generation of Oxidoreductases with Dual Alcohol Dehydrogenase and Amine Dehydrogenase Activity

The l -lysine-ϵ-dehydrogenase (LysEDH) from Geobacillus stearothermophilus naturally catalyzes the oxidative deamination of the ϵ-amino group of l -lysine. We previously engineered this enzyme to create amine dehydrogenase (AmDH) variants that possess a new hydrophobic cavity in their active site such that aromatic ketones can bind and be converted into α-chiral amines with excellent enantioselectivity. We also recently observed that LysEDH was capable of reducing aromatic aldehydes into primary alcohols. Herein, we harnessed the promiscuous alcohol dehydrogenase (ADH) activity of LysEDH to create new variants that exhibited enhanced catalytic activity for the reduction of substituted benzaldehydes and arylaliphatic aldehydes to primary alcohols. Notably, these novel engineered dehydrogenases also catalyzed the reductive amination of a variety of aldehydes and ketones with excellent enantioselectivity, thus exhibiting a dual AmDH/ADH activity. We envisioned that the catalytic bi-functionality of these enzymes could be applied for the direct conversion of alcohols into amines. As a proof-of-principle, we performed an unprecedented one-pot “hydrogen-borrowing” cascade to convert benzyl alcohol to benzylamine using a single enzyme. Conducting the same biocatalytic cascade in the presence of cofactor recycling enzymes (i.e., NADH-oxidase and formate dehydrogenase) increased the reaction yields. In summary, this work provides the first examples of enzymes showing “alcohol aminase” activity.     

Ruthenium‐Catalyzed Sequential Reactions: Deracemization of Secondary Benzylic Alcohols

The deracemization of secondary benzylic alcohols proceeds successfully by a two‐step process with the appropriate combination of two different ruthenium complexes for catalysis in the first oxidation and second reduction steps. The sequential catalytic system provides a novel approach to obtaining optically active alcohols, including diols, in high yields with excellent enantioselectivity (up to 95 % ee), in contrast to the conventional kinetic resolution of racemic alcohols.     

Chemically modified mutants of subtilisin Bacillus lentus catalyze transesterification reactions better than wild type

A combined site-directed mutagenesis and chemical modification strategy has been used to create superior enzyme catalysts for the resolution of racemic primary and secondary alcohols using a transesterification reaction. The chemically modified mutant, N62C–S–CH₃, of subtilisin Bacillus lentus catalyzes the transesterification of N-acetyl-L-phenylalanine vinyl ester with β-branched primary alcohols faster than wild type. The cysteine mutant, M222C, of subtilisin Bacillus lentus gives higher yields (98% and 92% yields with 1-phenylethanol and 2-octanol, respectively, versus 19% and 10% for wild type) and better enantioselectivity than wild type when secondary alcohols are used.     

YfeX – A New Platform for Carbene Transferase Development with High Intrinsic Reactivity

Carbene transfer biocatalysis has evolved from basic science to an area with vast potential for the development of new industrial processes. In this study, we show that YfeX, naturally a peroxidase, has great potential for the development of new carbene transferases, due to its high intrinsic reactivity, especially for the N−H insertion reaction of aromatic and aliphatic primary and secondary amines. YfeX shows high stability against organic solvents (methanol and DMSO), greatly improving turnover of hydrophobic substrates. Interestingly, in styrene cyclopropanation, WT YfeX naturally shows high enantioselectivity, generating the trans product with 87 % selectivity for the (R,R) enantiomer. WT YfeX also catalyzes the Si−H insertion efficiently. Steric effects in the active site were further explored using the R232A variant. Quantum Mechanics/Molecular Mechanics (QM/MM) calculations reveal details on the mechanism of Si−H insertion. YfeX, and potentially other peroxidases, are exciting new targets for the development of improved carbene transferases.     

Enzyme catalytic promiscuity: asymmetric aldol addition reaction catalyzed by a novel thermophilic esterase in organic solvent

The asymmetric aldol addition of 2-butanone and 4-nitrobenzaldehyde catalyzed by a novel thermophilic esterase (APE1547) from the archaeon Aeropyrum pernix K1 was successfully conducted in organic solvents. APE1547 exhibited a good enzyme activity and enantioselectivity in the reaction. The effects of organic solvent, temperature, water content, and substrate concentration were investigated. The reaction provided optically active secondary alcohol with satisfying enantioselectivity (71.2 %ee) and enzyme activity (38.1 µmol/g/h) under the optimum conditions. A high yield (68.7%) could be obtained when the reaction time was approximately 120 h.     

Kinetics and Protein‐Inhibitor Docking Studies of Enantiomers of exo‐2‐Norbornyl‐N‐n‐butylcarbamates as Pseudomonas Lipase Inhibitors to Probe the Enantioselectivity of the Enzyme

The Pseudomonas species lipase inhibition shows enantioselectivity for R‐enantiomer over S‐enantiomer of exo‐2‐norbornyl‐N‐n‐butylcarbamates. R‐, S‐, and racemic‐exo‐2‐norbornyl‐N‐n‐butylcarbamates are all characterized as pseudo substrate inhibitors of the enzyme. Thus, the mechanism for Pseudomonas species lipase‐catalyzed hydrolysis of the inhibitor is formation of the first enzyme‐inhibitor Michaelis complex via nucleophilic attack of the active site serine to the inhibitor (K_i step) then formation of the butylcarbamyl enzyme intermediate from this complex (k₂ step). Comparison of bimolecular rate constants (k_i = k₂ / K_i) of the inhibitors indicates that R‐enantiomer is 1.8 times more potent than S‐enantiomer. Thus, Pseudomonas species lipase shows enantioselectivity of 1.8 for R‐exo‐2‐norbornyl‐N‐n‐butyl‐carbamate over S‐exo‐2‐norbornyl‐N‐n‐butylcarbamate. Protein‐ligand interaction studies on both enantiomers of exo‐2‐norbornyl‐N‐n‐butylcarbamate as inhibitors of Pseudomonas species lipase using AutoDock suggest that R‐enantiomer binds more tightly into the active site of the enzyme than S‐enantiomer. The norbornyl ring of S‐exo‐2‐norbornyl‐N‐n‐butylcarbamate is repulsive to Ser 82 and His 251 of the catalytic triad as well as to Met 16 of the oxyanion hole. These repulsions may create few unfavorable interactions between S‐exo‐2‐norbornyl‐N‐n‐butylcarbamate and the enzyme and make this inhibitor a less potent one.     

Enzymatic kinetic resolution of ketorolac

Ketorolac 1 was resolved into each enantiomer by interesterification using lipase B from Candida antarctica. The acid reacted with various alcohols and the ester and acid were resolved up to >99% e.e. when reacted with octanol, which was the best result. To increase reactivity and enantioselectivity, the experimental conditions were adjusted by varying temperature, solvent, alcohols and reaction time.     

Catalytic enantioselective addition of diethylzinc to (hetero)aromatic aldehydes

The asymmetric alkylation with diethylzinc of five heterocyclic aldehydes and benzaldehyde (for comparison) has been studied in the presence of two optically active amino alcohols: (S)-2-amino-1-butanol (AB) and (1S,2R)-N,N-dibutylnorephedrine (DBNE). A number of chiral (hetero)aromatic secondary alcohols were synthesized in high yields (95–98%) with enantioselectivity up to 92% enantiomeric excess (ee) in the presence of DBNE catalyst. Optically active thienyl and 4-pyridyl derivatives were prepared for the first time by catalytic asymmetric alkylation. The influence of the amount of DBNE on the enantioselectivity was investigated. In contrast to benzaldehyde, 2-furan- and 2-thiophene-carbaldehydes, in the case of 3- and 4-pyridinecarbaldehydes the ee values depend directly on the catalyst concentration. © 1998 John Wiley & Sons, Ltd.