Asymmetric synthesis of both antipodes of beta-hydroxy nitriles and beta-hydroxy carboxylic acids via enzymatic reduction or sequential reduction/hydrolysis

Engineering a carbonyl reductase for the scalable preparation of (S)-3-Cyclopentyl-3-hydroxypropanenitrile, the key building block of ruxolitinib

( S )- 3-Cyclopentyl-3-hydroxypropanenitrile is the key precursor for the synthesis of ruxolitinib. The bioreduction of 3-cyclopentyl-3-ketopropanenitrile ( 1a ) offers an attractive method to access this important compound. A carbonyl reductase (PhADH) from Paraburkholderia hospita catalyzed the reduction of 1a giving the ( S )-alcohol ( 1b ) with 85% ee. Rational engineering of PhADH resulted in a double mutant H93C/A139L, which enhanced the enantioselectivity from 85% to >98%, as well as a 6.3-fold improvement in the specific activity. The bioreduction of 1a was performed at 200 g/L (1.5 M) substrate concentration, leading to isolation of ( S )- 1b in 91% yield. Similarly, using this mutant enzyme 3-cyclohexyl-3-ketopropanenitrile ( 2a) and 3-phenyl-3-ketopropanenitrile ( 3a ) were reduced at high concentration affording the corresponding alcohols in >99% ee, and 90% and 92% yield, respectively. The results showed that the variant H93C/A139L was a powerful biocatalyst for reduction of β-substituted-β-ketonitriles.

Predicting enzymatic reactions with a molecular transformer

The use of enzymes for organic synthesis allows for simplified, more economical and selective synthetic routes not accessible to conventional reagents. However, predicting whether a particular molecule might undergo a specific enzyme transformation is very difficult. Here we used multi-task transfer learning to train the molecular transformer, a sequence-to-sequence machine learning model, with one million reactions from the US Patent Office (USPTO) database combined with 32 181 enzymatic transformations annotated with a text description of the enzyme. The resulting enzymatic transformer model predicts the structure and stereochemistry of enzyme-catalyzed reaction products with remarkable accuracy. One of the key novelties is that we combined the reaction SMILES language of only 405 atomic tokens with thousands of human language tokens describing the enzymes, such that our enzymatic transformer not only learned to interpret SMILES, but also the natural language as used by human experts to describe enzymes and their mutations.

Cascaded Biocatalysis and Bioelectrocatalysis: Overview and Recent Advances

Enzyme cascades are plentiful in nature, but they also have potential in artificial applications due to the possibility of using the target substrate in biofuel cells, electrosynthesis, and biosensors. Cascade reactions from enzymes or hybrid bioorganic catalyst systems exhibit extended substrate range, reaction depth, and increased overall performance. This review addresses the strategies of cascade biocatalysis and bioelectrocatalysis for ( a) CO2 fixation, ( b) high value-added product formation, ( c) sustainable energy sources via deep oxidation, and ( d) cascaded electrochemical enzymatic biosensors. These recent updates in the field provide fundamental concepts, designs of artificial electrocatalytic oxidation-reduction pathways (using a flexible setup involving organic catalysts and engineered enzymes), and advances in hybrid cascaded sensors for sensitive analyte detection.

Asymmetric Transfer Hydrogenation of α-Substituted-β-Keto Carbonitriles via Dynamic Kinetic Resolution

A catalytic protocol for the enantio- and diastereoselective reduction of α-substituted-β-keto carbonitriles is described. The reaction involves a DKR-ATH process with the simultaneous construction of β-hydroxy carbonitrile scaffolds with two contiguous stereogenic centers. A wide range of α-substituted-β-keto carbonitriles were obtained in high yields (94%-98%) and excellent enantio- and diastereoselectivities (up to >99% ee, up to >99:1 dr). The origin of the diastereoselectivity was also rationalized by DFT calculations. Furthermore, this methodology offers rapid access to the pharmaceutical intermediates of Ipenoxazone and Tapentadol.

Stereoselective Total Synthesis of (-)-(2S,4R)-3'-Methoxyl Citreochlorol: Preparation and Use of New Proline-Based Auxiliary for Asymmetric Acetate Aldol Reaction

The first stereoselective total synthesis of (-)-(2S,4R)-3'-methoxy citreochlorol and (-)-(2S,4S)-3'-methoxy citreochlorol is demonstrated. A proline-based imidazolidinone was synthesized and used as chiral auxiliary for asymmetric acetate aldol reaction to generate initial chirality in the targeted molecule. Geminal dichloromethane functionality was introduced by the addition of in situ generated dichloromethyllithium to Weinreb's amide functional group.

One-step photostructuring of multiple hydrogel arrays for compartmentalized enzyme reactions in microfluidic devices

A moulding technique is presented for the simultaneous photostructuring on the μm scale of hydrogels with nanomaterials on one substrate, usable for the fabrication of microfluidic double-chamber reactors.

Characterization of a new nitrilase from Hoeflea phototrophica DFL-43 for a two-step one-pot synthesis of (S)-β-amino acids

A nitrilase from Hoeflea phototrophica DFL-43 (HpN) demonstrating excellent catalytic activity towards benzoylacetonitrile was identified from a nitrilase tool-box, which was developed previously in our laboratory for (R)-o-chloromandelic acid synthesis from o-chloromandelonitrile. The HpN was overexpressed in Escherichia coli BL21 (DE3), purified to homogeneity by nickel column affinity chromatography, and its biochemical properties were studied. The HpN was very stable at 30-40 °C, and highly active over a wide range of pH values (pH 6.0-10.0). In addition, the HpN could tolerate against several hydrophilic organic solvents. Steady-state kinetics indicated that HpN was highly active towards benzoylacetonitrile, giving a K_M of 4.2 mM and a k_cat of 170 s^-1, the latter of which is ca. fivefold higher than the highest record reported so far. A cascade reaction for the synthesis of optically pure (S)-β-phenylalanine from benzoylacetonitrile was developed by coupling HpN with an ω-transaminase from Polaromonas sp. JS666 in toluene-water biphasic reaction system using β-alanine as an amino donor. Various (S)-β-amino acids could be produced from benzoylacetonitrile derivatives with moderate to high conversions (73-99%) and excellent enantioselectivity (> 99% ee). These results are significantly advantageous over previous studies, indicating a great potential of this cascade reaction for the practical synthesis of (S)-β-phenylalanine in the future.

DBU-Mediated Diastereoselective Aldol-Type Cyanomethylation of Isatins

An efficient, metal-free approach to 3-substituted 3-hydroxyoxindole by DBU-mediated highly diastereoselective addition of aryl acetonitrile to N-protected isatin under mild conditions has been developed. The reaction proceeds smoothly to produce respective cyanomethylated adducts in good yield and excellent diastereoselectivity. Further transformation of the cyanide group allowed the synthesis of an advance intermediate of corresponding (±) CPC analogue. The mechanistic insight toward the aldol-type cyanomethylation of N-tritylisatin with benzyl cyanide was obtained by DFT calculations.

Formation of a Cationic Vinylimido Group upon C-H Activation of Nitriles by Trialkylamines in the Presence of TaCl5

We report a new CH3CN activation mode where an imido group is directly formed by deprotonation of the nitrile coordinated to the highly Lewis acidic Ta(V) center. The unexpected deprotonation of TaCl5(CH3CN) by NEt3 resulted in isolation of the triethylammonium vinylimido complex [HNEt3][Ta(NC(CH2)NEt3)Cl5]. The reaction is proposed to proceed through rearrangement of the initial nucleophilic carbanion to the electrophilic azaallene/carbocation intermediate. The use of more sterically hindered (i-Pr)CN and weakly nucleophilic N(i-Pr)2Et resulted in the isolation of a vinylimido group formed upon dimerization of deprotonated nitriles, suggesting deprotonation as the first step of the transformation.

An efficient aldol-type direct reaction of isatins with TMSCH2CN

Cesium fluoride catalyzed direct cyanomethylation of various isatins by using trimethylsilyl acetonitrile (TMSAN) as a nucleophile has been developed. The reaction has been explored for a number of isatins, with various substitutions on its aromatic ring. Further, the versatility of the reaction is demonstrated by converting the direct aldol adducts to various corresponding intermediates.

Chemoselective efficient synthesis of functionalized β-oxonitriles through cyanomethylation of Weinreb amides

Homologation of Weinreb amides with cyanomethyllithium: a new route to β-oxonitriles.

Characterization of a putative stereoselective oxidoreductase from Gluconobacter oxydans and its application in producing ethyl (R)-4-chloro-3-hydroxybutanoate ester

A gene encoding an NADH-dependent short-chain dehydrogenase/reductase (gox2036) from Gluconobacter oxydans 621H was cloned and heterogeneously expressed in Escherichia coli. The protein (Gox2036) was purified to homogeneity and biochemically characterized. Gox2036 was a homotetramer with a subunit size of approximately 28 kDa. Gox2036 had a strict requirement for NAD⁺/NADH as the cofactor. Gox2036 displayed preference for oxidation of secondary alcohols and 2,3-diols as well as for reduction of α-diketones, hydroxy ketones, α-ketoesters, and β-ketoesters. However, Gox2036 was poorly active on 1,2-diols and acetoin and showed no activity on primary alcohols, polyols, and aldehydes. The optimum pH values for the oxidation and reduction reactions were 9 and 6, respectively. Gox2036 was highly selective in the reduction of various β-ketones and β-ketoesters. Among the substrates tested, ethyl 4-chloro acetoacetate was reduced to ethyl (R)-4-chloro-3-hydroxybutanoate ester with an excellent conversion yield of 96.9 % and optical purity of >99 % e.e. using an efficient in situ NADH-recycling system involving glucose and a glucose dehydrogenase from Bacillus subtilis (BsGDH).

Biologically active dichapetalins from Dichapetalum gelonioides

A phytochemical investigation of the toxic tropical plant Dichapetalum gelonioides led to the isolation and identification of 14 new dichapetalins (1-14) and the known dichapetalins A (15) and K (16). The structures of the new compounds were determined by analyses of their NMR, MS, electronic circular dichroism, and X-ray diffraction data. The esterification at C-25 by 4-hydroxyphenylpropanoic acid and the hydroxylation at C-2' are unique in this unusual class of natural products. In addition to the known cytotoxicity, an array of biological activities, including antifeedant, nematicidal, antifungal, and NO and AChE inhibitory activities, were observed for this class of compounds. These findings suggested that dichapetalin hybrid triterpenoids as a class have broad biologically active cellular functions including defense against insect herbivores and pathogens.

Enzyme catalysed tandem reactions

To transfer to the laboratory, the excellent efficiency shown by enzymes in Nature, biocatalysis, had to mimic several synthetic strategies used by the living organisms. Biosynthetic pathways are examples of tandem catalysis and may be assimilated in the biocatalysis field for the use of isolated multi-enzyme systems in the homogeneous phase. The concurrent action of several enzymes that work sequentially presents extraordinary advantages from the synthetic point of view, since it permits a reversible process to become irreversible, to shift the equilibrium reaction in such a way that enantiopure compounds can be obtained from prochiral or racemic substrates, reduce or eliminate problems due to product inhibition or prevent the shortage of substrates by dilution or degradation in the bulk media, etc. In this review we want to illustrate the developments of recent studies involving in vitro multi-enzyme reactions for the synthesis of different classes of organic compounds.

Novel anti-Prelog stereospecific carbonyl reductases from Candida parapsilosis for asymmetric reduction of prochiral ketones

The application of biocatalysis to the synthesis of chiral molecules is one of the greenest technologies for the replacement of chemical routes due to its environmentally benign reaction conditions and unparalleled chemo-, regio- and stereoselectivities. We have been interested in searching for carbonyl reductase enzymes and assessing their substrate specificity and stereoselectivity. We now report a gene cluster identified in Candida parapsilosis that consists of four open reading frames including three putative stereospecific carbonyl reductases (scr1, scr2, and scr3) and an alcohol dehydrogenase (cpadh). These newly identified three stereospecific carbonyl reductases (SCRs) showed high catalytic activities for producing (S)-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone with NADPH as the coenzyme. Together with CPADH, all four enzymes from this cluster are carbonyl reductases with novel anti-Prelog stereoselectivity. SCR1 and SCR3 exhibited distinct specificities to acetophenone derivatives and chloro-substituted 2-hydroxyacetophenones, and especially very high activities towards ethyl 4-chloro-3-oxobutyrate, a β-ketoester with important pharmaceutical potential. Our study also showed that genomic mining is a powerful tool for the discovery of new enzymes.