Rational Biocatalyst Design for a Cyanide-Free Synthesis of Long-Chain Fatty Nitriles from Their Aldoximes

Recently, the capability of the aldoxime dehydratase from Bacillus sp. (OxdB) for the transformation of fatty aldoximes into fatty nitriles with impressive substrate loadings is reported. However, the substrate scope of this biocatalyst turned out to be limited in terms of the chain length with decanal oxime being the substrate with the longest well tolerated n-alkyl chain. Besides the increased bulkiness of the long-chain aldoximes, their strongly decreased water solubility represents a further hurdle for an efficient biotransformation. Addressing this challenge of an expanded substrate spectrum comprising long-chain fatty aldoximes, this work investigates the substrate solubility and enzyme kinetics in combination with molecular modeling in order to find an enzyme mutant being suitable for C12- to C16-aldoximes. Both, fatty aldoxime solubility in water and the active site of the wild-type enzyme OxdB are identified as critical issues for an efficient biotransformation of these substrates. The activity issue is addressed by a rational design of a mutant using a homology modeling as well as a molecular modeling software suitable for enzymes. With the resulting double mutant OxdB-F289A/L293A, this report can achieve successful biotransformations with the C12- to C16-aldoximes at substrate concentrations of 250 × 10⁻³ to 1000 × 10⁻³ m . For example, an excellent conversion of >99% is obtained with tetradecanal oxime. Practical applications: Fatty nitriles with a prolonged chain length of C12 or more are of high interest in industry due to their use for the production of fatty amines on large technical scale. As an alternative route, fatty nitriles can be generated from their aldoximes by means of an aldoxime dehydratase (Oxd) as biocatalyst. The conversion of long-chain fatty aldoximes, however, remained a challenge up to now. This work describes the optimization of the aldoxime dehydratase OxdB from Bacillus sp. for the dehydration of nonsoluble bulky fatty aldoximes. The created variant can convert long chain fatty aldoximes toward the corresponding nitrile as demonstrated for C12- to C16-nitriles. In addition, high conversion (of up to >99%) is achieved when operating at high substrate concentrations of up to 1000 × 10⁻³ m , thus making this approach interesting for industrial applications.     

Kemp Elimination Catalyzed by Naturally Occurring Aldoxime Dehydratases

Recently, the Kemp elimination reaction has been extensively studied in computational enzyme design of new catalysts, as no natural enzyme has evolved to catalyze this reaction. In contrast to in silico enzyme design, we were interested in searching for Kemp eliminase activity in natural enzymes with catalytic promiscuity. Based on similarities of substrate structures and reaction mechanisms, we assumed that the active sites of naturally abundant aldoxime dehydratases have the potential to catalyze the non‐natural Kemp elimination reaction. We found several aldoxime dehydratases that are efficient catalysts of this reaction. Although a few natural enzymes have been identified with promiscuous Kemp eliminase activity, to the best of our knowledge, this is a rare example of Kemp elimination catalyzed by naturally occurring enzymes with high catalytic efficiency.     

The synthesis of oxime reagents from natural and semi‐synthetic phenolic lipid and alkanoic acid resources for the solvent recovery of copper(II)

In a study of the relationship between structure and efficiency towards recovery of copper(II) by chelation/solvent extraction, a series of homologous aldoximes has been synthesised from natural phenolic lipidic, and fatty lipidic renewable sources, for comparison with commercial reagents prepared from petrochemical sources. From cardanol, in technical cashew nut‐shell liquid, isoanacardic aldoxime, [2‐hydroxy‐4‐pentadec(en)yl]aldoxime, and from the natural phenolic lipid, anacardic acid, the isomer, 2‐hydoxy‐6‐pentadec(en)ylaldoxime, have been synthesised. A C₁₁ analogue of anacardic aldoxime from Anacardium giganteum has been prepared. The isomeric n‐octyl aldoximes have been synthesised, the o‐ and p‐isomers from the readily available fatty acid n‐octanoic acid and the m‐isomer from cardanol. Related m‐aldoximes have been prepared from the ketonic intermediates methyl isoamyl and methyl amyl ketones. The solvent extraction properties for copper(II) of the synthesised aldoximes have been compared with those of a current commercial reagent, 2‐hydroxy‐5‐t‐nonylbenzaldoxime (Acorga 5100, Cytec), and two former extractants, 2‐hydroxy‐5‐t‐nonylacetophenone ketoxime (SME 529, Shell) and 2‐hydroxy‐5‐t‐nonylbenzophenone ketoxime (LIX 65N, Henkel). All the aldoximes possessed useful properties in extraction efficiency, notably the isoanacardic and the C₈ aldoximes with the C₈o‐isomer, 2‐hydroxy‐3‐n‐octylbenzaldoxime, exhibited optimal extraction, stripping and phase separation characteristics. Copyright © 2005 Society of Chemical Industry     

Chemoenzymatic synthesis of chiral carboxylic acids via nitriles

BACKGROUND: Enantiomerically pure 1,4‐benzodioxane‐2‐carboxylic acid derivatives are useful building blocks for the synthesis of pharmaceuticals and biologically active compounds whose interaction with their biological target (enzyme, receptor) depends very much on the absolute configuration of the chiral carbon at the 2‐position. The aim of the present work is to investigate the route to racemic nitriles and the subsequent selective enzymatic hydrolysis by nitrilase to optically active 1,4‐benzodioxane‐2‐carboxylic acid and 6‐formyl‐1,4‐benzodioxane‐2‐carboxylic acid. RESULTS: A range of microbial nitrilases from Rhodococcus, Alcaligenes and Pseudomonas strains have been prepared and screened for the desired biotransformations using a chiral high performance liquid chromatography (HPLC) analytical method. The nitrilase from Alcaligenes faecalis ATCC 8750 showed the highest and the nitrilase from Rhodococcus rhodochrous NCIMB 11216 the lowest activity towards 2‐cyano‐6‐formyl‐1,4‐benzodioxane. Lyophilised cells of Rhodococcus R 312 gave the (R)‐1,4‐benzodioxane‐2‐carboxylic acid with high enantioselectivity after 25% conversion. Excellent enantioselectivities for the hydrolysis of both 2‐cyano‐1,4‐benzodioxane as well as 2‐cyano‐6‐formyl‐1,4‐benzodioxane have been achieved and the absolute configuration of 1,4‐benzodioxane‐2‐carboxylic acid was determined to be R by comparison with the specific rotation of commercially available (R)‐1,4‐benzodioxane‐2‐carboxylic acid. CONCLUSIONS: This new nitrilase‐catalysed kinetic resolution of 2‐cyano‐ and 2‐cyano‐6‐formyl‐1,4‐benzodioxane opens a mild route to optically active 1,4‐benzodioxane‐2‐carboxylic acids. As the formyl functional group would be damaged in chemical nitrile hydrolysis, nitrilase‐catalysed hydrolysis solves this synthetic bottleneck and advances nitrilase biocatalytic tools for the preparation of more complex 1,4‐benzodioxane‐2‐carboxylic acids. Copyright © 2007 Society of Chemical Industry     

An Efficient and Improved Method for the Preparation of Nitriles from Primary Amides and Aldoximes†

The pivaloyl chloride‐pyridine system has been utilized as a novel and efficient reagent for the preparation of nitriles from primary amides and aldoximes. The reaction proceeds smoothly under mild reaction conditions and the products are obtained in excellent yields. This method is applicable to a wide range of substrates including aromatic, heterocyclic and aliphatic species. The dehydration takes place at room temperature in the case of primary amides and dichloromethane at reflux temperature is required for rapid conversion in the case of aldoximes.     

A Remarkable Titanium‐Catalyzed Asymmetric Strecker Reaction using Hydrogen Cyanide at Room Temperature

Close to perfect enantioselectivity (up to 98% ee) is obtained for the formation of amino nitriles using hydrogen cyanide (HCN) as the cyanide source at room temperature for the first time. In an operationally simple process, the catalyst generated from a partially hydrolyzed titanium alkoxide (PHTA) and (S)‐N‐salicyl‐β‐amino alcohol ligand, catalyzes the cyanation of imines in a short reaction time.     

Copper‐Dipyridylphosphine‐Polymethylhydrosiloxane: A Practical and Effective System for the Asymmetric Catalytic Hydrosilylation of Ketones

In the presence of the inexpensive and non‐toxic stoichiometric reductant polymethylhydrosiloxane (PMHS), the chiral copper(II)‐dipyridylphosphine catalyst displayed high efficiency in the stereoselective hydrosilylation of a wide scope of aryl alkyl and heteroaromatic ketones under an air atmosphere and mild conditions in good to excellent ees (up to 97%). With certain amounts of sodium tert‐butoxide and tert‐butyl alcohol as additives, the reaction on a 21‐g substrate scale can be conveniently completed within a few hours even at a substrate‐to‐ligand (S/L) ratio of 50,000.     

Isolation and characterization of a nitrile hydratase from a Rhodococcus sp.

A new nitrile hydratase producing strain of Rhodococcus has been found. A method for purification of the nitrile hydratase and a characterization of the enzyme is described. The hydratase is a 52-kdal protein consisting of two subunits of molecular weights, 26 and 23 kdal, respectively. The hydratase exhibits a broad substrate specificity. Aliphatic saturated or unsaturated nitriles, as well as aromatic nitriles, are substrates for the enzyme. Inhibition of the enzyme activity by amides and carboxylic acids was observed. The optimum pH of the hydratase is 7.5. The enzyme is rather unstable, even at room temperature. The enzyme may be applied for the production of acrylamide. For this application of the enzyme, the optimal temperature is about 4°C, where the enzyme exhibits a satisfactory activity and stability.     

Enantioselective Reaction of Imines and Benzyl Nitriles Using Palladium Pincer Complexes with C2‐Symmetric Chiral Bis(imidazoline)s

Enantioselective reactions of a wide variety of benzyl nitriles with N‐tosylimines catalyzed by novel chiral 1,3‐bis(imidazolin‐2‐yl)benzene‐palladium(II) [Phebim‐Pd(II)] complexes have afforded the respective products in high yield with good enantioselectivity. A reaction mechanism is proposed based on X‐ray crystal structures of palladium complexes.     

Hydrolytic Kinetic Resolution of Epoxides Catalyzed by Chromium(III)‐endo,endo‐2,5‐diaminonorbornane‐salen [Cr(III)‐DIANANE‐salen] Complexes. Improved Activity,Low Catalyst Loading

The hydrolytic kinetic resolution (HKR) of terminal epoxides, using chiral chromium(III )‐salen catalysts based on DIANANE (endo,endo‐2,5‐diaminonorbornane), was studied. A broad substrate scope was found for the chromium(III )‐DIANANE catalysts, and very low loadings (down to 0.05 mol %) were needed to achieve high enantiomeric purities of both the remaining epoxides and the product diols (up to >99 % ee). Besides monosubstituted epoxides, 2‐methyl‐2‐n‐pentyloxirane, which is an example for 2,2‐disubstituted epoxides, could be ring‐opened in an asymmetric fashion with water in the presence of an electronically tuned chromium(III )‐DIANANE complex.     

Towards practical Baeyer-Villiger-monooxygenases: design of cyclohexanone monooxygenase mutants with enhanced oxidative stability

Baeyer–Villiger monooxygenases (BVMOs) catalyze the conversion of ketones and cyclic ketones into esters and lactones, respectively. Cyclohexanone monooxygenase (CHMO) from Acinetobacter sp. NCIMB 9871 is known to show an impressive substrate scope as well as exquisite chemo‐, regio‐, and enantioselectivity in many cases. Large‐scale synthetic applications of CHMO are hampered, however, by the instability of the enzyme. Oxidation of cysteine and methionine residues contributes to this instability. Designed mutations of all the methionine and cysteine residues in the CHMO wild type (WT) showed that the amino acids labile towards oxidation are mostly either surface‐exposed or located within the active site, whereas the two methionine residues identified for thermostabilization are buried within the folded protein. Combinatorial mutations gave rise to two stabilized mutants with either oxidative or thermal stability, without compromising the activity or stereoselectivity of the enzyme. The most oxidatively stabilized mutant retained nearly 40 % of its activity after incubation with H₂O₂ (0.2 M ), whereas the wild‐type enzyme's activity was completely abolished at concentrations as low as 5 mM H₂O₂. We propose that oxidation‐stable mutants might well be a “prerequisite” for thermostabilization, because laboratory‐evolved thermostability in CHMO might be masked by a high degree of oxidation instability.     

Kinetic Resolution of α‐Bromoamides: Experimental and Theoretical Investigation of Highly Enantioselective Reactions Catalyzed by Haloalkane Dehalogenases

Haloalkane dehalogenases from five sources were heterologously expressed in Escherichia coli, isolated, and tested for their ability to achieve kinetic resolution of racemic α‐bromoamides, which are important intermediates used in the preparation of bioactive compounds. To explore the substrate scope, fourteen α‐bromoamides, with different Cα‐ and N‐substituents, were synthesized. Catalytic activity towards eight substrates was found, and for five of these compounds the conversion proceeded with a high enantioselectivity (E value >200). In all cases, the (R)‐α‐bromoamide is the preferred substrate. Conversions on a preparative scale with a catalytic amount of enzyme (enzyme:substrate ratio less 1:50 w/w) were all completed within 17–46 h and optically pure α‐bromoamides and α‐hydroxyamides were isolated with good yields (31–50%). Substrate docking followed by molecular dynamics simulations indicated that the high enantioselectivity results from differences in the percentage of the time in which the substrate enantiomers are bound favourably for catalysis. For the preferred (R)‐substrates, the angle between the attacking aspartate oxygen atom of the enzyme, the attacked carbon atom of the substrate, and the displaced halogen atom, is more often in the optimal range (>157°) for reactivity. This can explain the observed enantioselectivity of LinB dehalogenase in a kinetic resolution experiment.     

Enantioselective Carbonyl‐Ene Reactions of Arylglyoxals with a Chiral Palladium(II)‐BINAP Catalyst

The palladium(II)‐BINAP‐catalyzed enantioselective carbonyl‐ene reactions between ten arylglyoxals and five alkenes were systematically investigated and demonstrated good to excellent enantioselectivities with high ee values of up to 93.8 %. The results showed that both arylglyoxals and alkenes exert evident effects on the enantioselectivity. Particularly, the ortho‐methyl substituents of the substrates could increase the enantioselectivity. The achieved excellent enantioselectivities may be due to the corresponding substrate matches well fitting the chiral space created by the chiral palladium(II)‐BINAP catalyst. The ortho‐methyl substituents may improve the fitting of the substrate match to the chiral space created by the chiral catalyst, hence the enantioselectivity is improved. When using dienes (1,4‐diisopropenylbenzene and 1,3‐diisopropenylbenzene) as substrates in this reaction, only one of the two carbon‐carbon double bonds participated into the reaction affording tetrafunctional organic compounds with moderate enantioselectivities of up to 83.8 % ee. The chiral Lewis acid palladium(II) catalyst incorporating (R)‐BINAP, which is a conformationally restricted chiral ligand, is very stable in ionic liquids and could be recycled 21 times with retention of the high enantioselectivity.     

Multi‐Enzymatic Biosynthesis of Chiral β‐Hydroxy Nitriles through Co‐Expression of Oxidoreductase and Halohydrin Dehalogenase

To establish a system for the efficient one bacterial multi‐enzymatic biosynthesis of both (R)‐ and (S)‐β‐hydroxy nitriles, we co‐expressed alcohol dehydrogenases with opposite stereoselectivities, cofactor regeneration enzymes, and a halohydrin dehalogenase in Escherichia coli. By researching cofactor recycling and various co‐expression strategies and by selecting and engineering the halohydrin dehalogenase, we engineered two E. coli strains, which were subsequently used in a cascade of reactions to produce chiral β‐hydroxy nitriles with high enantiomeric excess directly from prochiral α‐halo ketones. Three valuable pharmaceutical intermediates were prepared by means of this catalytic system, and substrate conversion reached about >99%. More importantly, the system is of low cost because there is no need for expensive cofactors or for expression and purification of the component enzymes.

     

Structure-Guided Modulation of the Catalytic Properties of [2Fe−2S]-Dependent Dehydratases

The FeS cluster-dependent dihydroxyacid dehydratases (DHADs) and sugar acid-specific dehydratases (DHTs) from the ilvD/EDD superfamily are key enzymes in the bioproduction of a wide variety of chemicals. We analyzed [2Fe−2S]-dependent dehydratases in silico and in vitro, deduced functionally relevant sequence, structure, and activity relationships within the ilvD/EDD superfamily, and we propose a new classification based on their evolutionary relationships and substrate profiles. In silico simulations and analyses identified several key positions for specificity, which were experimentally investigated with site-directed and saturation mutagenesis. We thus increased the promiscuity of DHAD from Fontimonas thermophila (FtDHAD), showing >10-fold improved activity toward D-gluconate, and shifted the substrate preference of DHT from Paralcaligenes ureilyticus (PuDHT) toward shorter sugar acids (recording a six-fold improved activity toward the non-natural substrate D-glycerate). The successful elucidation of the role of important active site residues of the ilvD/EDD superfamily will further guide developments of this important biocatalyst for industrial applications.     

Active Site Mapping of Human Cathepsin F with Dipeptide Nitrile Inhibitors

Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class II. Cathepsin S is the major processing enzyme of the invariant chain, but cathepsin F acts in macrophages as its functional synergist which is as potent as cathepsin S in invariant chain cleavage. Dedicated low‐molecular‐weight inhibitors for cathepsin F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent–reversible inhibitors, was performed to draw structure–activity relationships for the non‐primed binding region of human cathepsin F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins F, B, L, K and S. Compounds 10 (N‐(4‐phenylbenzoyl)‐leucylglycine nitrile) and 12 (N‐(4‐phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin F, with K_i values <10 nM . With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure–activity relationships for this series of cathepsin F inhibitors.     

Solvent‐Free Non‐Covalent Organocatalysis: Enantioselective Addition of Nitroalkanes to Alkylideneindolenines as a Flexible Gateway to Optically Active Tryptamine Derivatives

A catalytic asymmetric addition of nitroalkanes to alkylideneindolenines, generated in situ from arylsulfonylindoles, is presented. Despite the weakness of the non‐covalent H‐bond interactions between catalyst and substrates, the performance of the bifunctional organocatalyst used was found to be essentially unaffected by the polarity of the reaction medium. Nitroalkanes, mostly used in nearly stoichiometric amounts, could thus function both as solvents and reagents, resulting in a truly solvent‐free reaction. The broad substrate scope shown by the present transformation allowed the preparation of some optically active tryptamine precursors that are not accessible through the previous catalytic asymmetric methods.     

Identification of Suitable Ligands for a Transition Metal‐Catalyzed Reaction: Screening of a Modular Ligand Library in the Enantioselective Hydroboration of Styrene

Based on a general modular synthetic scheme, a variety of chiral bidentate P/P‐, P/S‐, P/N‐, and P/Se‐ligands is accessible in an efficient divergent manner starting from phenol or naphthol derived backbone systems. A library of 20 selected ligands was tested in the Rh‐catalyzed asymmetric hydroboration of styrene to give 1‐phenylethanol in up to 91% ee after oxidative work‐up. It was demonstrated that small variations of the ligand structures lead to pronounced, unpredictable differences in the performance of the in situ generated rhodium complexes. The modular approach should be applicable for the identification and optimization of suitable ligands for other transition metal‐catalyzed transformations with comparably low effort.     

Dehydration of aldoximes on rare earth exchanged (La<Superscript>3+</Superscript>, Ce<Superscript>3+</Superscript>, RE<Superscript>3+</Superscript>, Sm<Superscript>3+</Superscript>) Na–Y zeolites: A facile route for the synthesis of nitriles

Rare earth exchanged Na–Y zeolites, H-mordenite, K-10 montmorillonite clay and amorphous silica-alumina were effectively employed for the continuous synthesis of nitriles. Dehydration of benzaldoxime and 4-methoxybenzaldoxime were carried out on these catalysts at 473 K. Benzonitrile (dehydration product) was obtained in near quantitative yield with benzaldoxime whereas; 4-methoxybenzaldoxime produces both Beckmann rearrangement (4-methoxyphenylformamide) as well as dehydration products (4-methoxy benzonitrile) in quantitative yields. The production of benzonitrile was near quantitative under heterogeneous reaction conditions. The optimal protocol allows nitriles to be synthesized in good yields through the dehydration of aldoximes. Time on stream (TOS) studies show decline in the activity of the catalysts due to neutralization of acid sites by the basic reactant and product molecules and water formed during the dehydration of aldoximes.