Biocatalytic Routes to Enantiomerically Enriched Dibenz[c,e]azepines

Bridged Biaryl Atropisomers by Organocatalyzed Kinetic Asymmetric Alcoholysis

We disclose herein an asymmetric synthesis of axially chiral oxazepine-containing bridged biaryls via CPA-catalyzed kinetic asymmetric alcoholysis. Control experiments showed that this CPA-catalyzed alcoholysis was reversible, and lowering the reaction temperature could almost suppress the reversible reaction, thus providing a series of axially chiral oxazepine-containing bridged biaryl compounds in good to excellent enantioselectivities. The gram-scale reactions and facile derivatizations of the enantioenriched products demonstrate the practical utility of this reaction.

Organocatalytic diastereo- and atropo-selective construction of eight-membered bridged (hetero)biaryls via asymmetric intramolecular [3 + 2] cycloaddition

An unprecedented and straightforward route for the asymmetric construction of privileged atroposelective bridged (hetero)biaryl eight-membered scaffolds has been accomplished through chiral phosphoric acid catalyzed asymmetric intramolecular [3 + 2] cycloaddition of innovative (hetero)biaryl aldehydes with 3-aminooxindole hydrochlorides. A class of eight-membered bridged (hetero)biaryl lactones fused to spiro[pyrrolidine-oxindole] derivatives, possessing both chiral C-C/C-N axes and multiple contiguous stereocenters, were obtained in good yields with excellent enantioselectivities and diastereoselectivities in one step through this direct strategy. In addition, the good scalability and derivatization of the title compounds demonstrated their synthetic utility.

An imine reductase that captures reactive intermediates in the biosynthesis of the indolocarbazole reductasporine

Imine reductases (IREDs) and reductive aminases have been used in the synthesis of chiral amine products for drug manufacturing; however, little is known about their biological contexts. Here we employ structural studies and site-directed mutagenesis to interrogate the mechanism of the IRED RedE from the biosynthetic pathway to the indolocarbazole natural product reductasporine. Cocrystal structures with the substrate-mimic arcyriaflavin A reveal an extended active site cleft capable of binding two indolocarbazole molecules. Site-directed mutagenesis of a conserved aspartate in the primary binding site reveals a new role for this residue in anchoring the substrate above the NADPH cofactor. Variants targeting the secondary binding site greatly reduce catalytic efficiency, while accumulating oxidized side-products. As indolocarbazole biosynthetic intermediates are susceptible to spontaneous oxidation, we propose the secondary site acts to protect against autooxidation, and the primary site drives catalysis through precise substrate orientation and desolvation effects. The structure of RedE with its extended active site can be the starting point as a new scaffold for engineering IREDs and reductive aminases to intercept large substrates relevant to industrial applications.

Biocatalytic reductive aminations with NAD(P)H-dependent enzymes: enzyme discovery, engineering and synthetic applications

Chiral amines are pivotal building blocks for the pharmaceutical industry. Asymmetric reductive amination is one of the most efficient and atom economic methodologies for the synthesis of optically active amines. Among the various strategies available, NAD(P)H-dependent amine dehydrogenases (AmDHs) and imine reductases (IREDs) are robust enzymes that are available from various sources and capable of utilizing a broad range of substrates with high activities and stereoselectivities. AmDHs and IREDs operate via similar mechanisms, both involving a carbinolamine intermediate followed by hydride transfer from the co-factor. In addition, both groups catalyze the formation of primary and secondary amines utilizing both organic and inorganic amine donors. In this review, we discuss advances in developing AmDHs and IREDs as biocatalysts and focus on evolutionary history, substrate scope and applications of the enzymes to provide an outlook on emerging industrial biotechnologies of chiral amine production.

Structure-Based Design of Small Imine Reductase Panels for Target Substrates

Biocatalysis is important in the discovery, development, and manufacture of pharmaceuticals. However, the identification of enzymes for target transformations of interest requires major screening efforts. Here, we report a structure-based computational workflow to prioritize protein sequences by a score based on predicted activities on substrates, thereby reducing a resource-intensive laboratory-based biocatalyst screening. We selected imine reductases (IREDs) as a class of biocatalysts to illustrate the application of the computational workflow termed IREDFisher. Validation by using published data showed that IREDFisher can retrieve the best enzymes and increase the hit rate by identifying the top 20 ranked sequences. The power of IREDFisher is confirmed by computationally screening 1400 sequences for chosen reductive amination reactions with different levels of complexity. Highly active IREDs were identified by only testing 20 samples in vitro. Our speed test shows that it only takes 90 min to rank 85 sequences from user input and 30 min for the established IREDFisher database containing 591 IRED sequences. IREDFisher is available as a user-friendly web interface (https://enzymeevolver.com/IREDFisher). IREDFisher enables the rapid discovery of IREDs for applications in synthesis and directed evolution studies, with minimal time and resource expenditure. Future use of the workflow with other enzyme families could be implemented following the modification of the workflow scoring function.

Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms

The NADPH-dependent imine reductase from Ajellomyces dermatitidis (AdRedAm) catalyzes the reductive amination of certain ketones with amine donors supplied in an equimolar ratio. The structure of AdRedAm has been determined in three forms. The first form, which belongs to space group P3121 and was refined to 2.01 Å resolution, features two molecules (one dimer) in the asymmetric unit in complex with the redox-inactive cofactor NADPH4. The second form, which belongs to space group C21 and was refined to 1.73 Å resolution, has nine molecules (four and a half dimers) in the asymmetric unit, each complexed with NADP+. The third form, which belongs to space group P3121 and was refined to 1.52 Å resolution, has one molecule (one half-dimer) in the asymmetric unit. This structure was again complexed with NADP+ and also with the substrate 2,2-difluoroacetophenone. The different data sets permit the analysis of AdRedAm in different conformational states and also reveal the molecular basis of stereoselectivity in the transformation of fluorinated acetophenone substrates by the enzyme.

Asymmetric Synthesis of Fused-Ring Tetrahydroisoquinolines and Tetrahydro-β-carbolines from 2-Arylethylamines via a Chemoenzymatic Approach

While chiral fused-ring tetrahydroisoquinoline (THIQ) and tetrahydro-β-carboline (THβC) scaffolds have attracted considerable interest due to their wide spectrum of biological activities, the synthesis of optically pure chiral fused-ring THIQs and THβCs remains a challenging task. Herein, a group of active imine reductases were identified to convert the imine precursors into the corresponding enantiocomplementary fused-ring THIQs and THβCs with high enantioselectivity and conversion, establishing an efficient and green chemoenzymatic approach to fused-ring alkaloids from 2-arylethylamines.

Reductive aminations by imine reductases: from milligrams to tons

The synthesis of secondary and tertiary amines through the reductive amination of carbonyl compounds is one of the most significant reactions in synthetic chemistry. Asymmetric reductive amination for the formation of chiral amines, which are required for the synthesis of pharmaceuticals and other bioactive molecules, is often achieved through transition metal catalysis, but biocatalytic methods of chiral amine production have also been a focus of interest owing to their selectivity and sustainability. The discovery of asymmetric reductive amination by imine reductase (IRED) and reductive aminase (RedAm) enzymes has served as the starting point for a new industrial approach to the production of chiral amines, leading from laboratory-scale milligram transformations to ton-scale reactions that are now described in the public domain. In this perspective we trace the development of the IRED-catalyzed reductive amination reaction from its discovery to its industrial application on kg to ton scale. In addition to surveying examples of the synthetic chemistry that has been achieved with the enzymes, the contribution of structure and protein engineering to the understanding of IRED-catalyzed reductive amination is described, and the consequent benefits for activity, selectivity and stability in the design of process suitable catalysts.

IRED-catalyzed reductive aminations have progressed from mg to ton scale, through advances in enzyme discovery, protein engineering and process biocatalysis.

Asymmetric synthesis of dibenzo[b,d]azepines by Cu-catalyzed reductive or borylative cyclization

A copper-catalyzed asymmetric intramolecular reductive cyclization for the synthesis of dibenzo[b,d]azepines is described. Use of 2'-vinyl-biaryl-2-imines as substrates and in situ formed [Cu^I/(Ph-BPE)] as the catalyst enables the synthesis of 7-membered bridged biarylamines containing both central and axial stereogenic elements in high yields (up to 98%) and with excellent diastereo- and enantioselectivities (>20 : 1 d.r., up to 99% ee). Moreover, the same catalyst was found to facilitate a related borylative cyclization to afford versatile boronic ester derivatives. Both reactions proceed under mild conditions (rt) and are applicable to a variety of substituted aromatic and heterocyclic derivatives.

Computer-aided engineering of a branching sucrase for the glucodiversification of a tetrasaccharide precursor of S. flexneri antigenic oligosaccharides

Enzyme engineering approaches have allowed to extend the collection of enzymatic tools available for synthetic purposes. However, controlling the regioselectivity of the reaction remains challenging, in particular when dealing with carbohydrates bearing numerous reactive hydroxyl groups as substrates. Here, we used a computer-aided design framework to engineer the active site of a sucrose-active [Formula: see text]-transglucosylase for the 1,2-cis-glucosylation of a lightly protected chemically synthesized tetrasaccharide, a common precursor for the synthesis of serotype-specific S. flexneri O-antigen fragments. By targeting 27 amino acid positions of the acceptor binding subsites of a GH70 branching sucrase, we used a RosettaDesign-based approach to propose 49 mutants containing up to 15 mutations scattered over the active site. Upon experimental evaluation, these mutants were found to produce up to six distinct pentasaccharides, whereas only two were synthesized by the parental enzyme. Interestingly, we showed that by introducing specific mutations in the active site of a same enzyme scaffold, it is possible to control the regiospecificity of the 1,2-cis glucosylation of the tetrasaccharide acceptor and produce a unique diversity of pentasaccharide bricks. This work offers novel opportunities for the development of highly convergent chemo-enzymatic routes toward S. flexneri haptens.

Sequential Addition of Amines to Nitrile and Carbon-Carbon Multiple Bond: A Route to 7-Amino-5H-dibenzo[c,e]azepines

A rare earth metal-catalyzed sequential inter- and intramolecular C-N bond formation of 2-nitrile-2'-alkenyl(alkynyl)biphenyls with amines has been developed, which provides a straightforward and efficient access to a range of new functional dibenzo[c,e]azepines. This represents the first examples of direct construction of seven-membered azaheterocycle from unsaturated nitriles and amines. Such transformations have the advantages of avoiding the use of additives, easily available starting materials, step- and high atom-economy, mild reaction conditions, and high selectivity.

Recent advances in biocatalysis of nitrogen-containing heterocycles

Nitrogen-containing heterocycles (N-heterocycles) are ubiquitous in both organisms and pharmaceutical products. Biocatalysts are providing green approaches for synthesizing various N-heterocycles under mild reaction conditions. This review summarizes the recent advances in the biocatalysis of N-heterocycles through the discovery and engineering of natural N-heterocycle synthetic pathway, and the design of artificial synthetic routes, with an emphasis on biocatalysts applied in retrosynthetic design for preparing complex N-heterocycles. Furthermore, this review discusses the future prospects and challenges of biocatalysts involved in the synthesis of N-heterocycles.

An Enzymatic Platform for the Highly Enantioselective and Stereodivergent Construction of Cyclopropyl-δ-lactones

Abiological enzymes offers new opportunities for sustainable chemistry. Herein, we report the development of biological catalysts derived from sperm whale myoglobin that exploit a carbene transfer mechanism for the asymmetric synthesis of cyclopropane-fused-δ-lactones, which are key structural motifs found in many biologically active natural products. While hemin, wild-type myoglobin, and other hemoproteins are unable to catalyze this reaction, the myoglobin scaffold could be remodeled by protein engineering to permit the intramolecular cyclopropanation of a broad spectrum of homoallylic diazoacetate substrates in high yields and with up to 99 % enantiomeric excess. Via an alternate evolutionary trajectory, a stereodivergent biocatalyst was also obtained for affording mirror-image forms of the desired bicyclic products. In combination with whole-cell transformations, the myoglobin-based biocatalyst was used for the asymmetric construction of a cyclopropyl-δ-lactone scaffold at a gram scale, which could be further elaborated to furnish a variety of enantiopure trisubstituted cyclopropanes.

Asymmetric Reductive Amination/Ring-Closing Cascade: Direct Synthesis of Enantioenriched Biaryl-Bridged NH Lactams

We report here a Ru-catalyzed enantioselective synthesis of biaryl-bridged NH lactams through asymmetric reductive amination and a spontaneous ring-closing cascade from keto esters and NH₄OAc with H₂ as reductant. The reaction features broad substrate generality and high enantioselectivities (up to >99% ee). To showcase the practical utility, a highly enantioselective synthesis of 5-ethylindolobenzazepinone C, a promising antimitotic agent, has been rapidly completed. Furthermore, the amide group in the products enables versatile elaborations through directed C-H functionalization.

Structural Characterization of an S-enantioselective Imine Reductase from Mycobacterium Smegmatis

NADPH-dependent imine reductases (IREDs) are enzymes capable of enantioselectively reducing imines to chiral secondary amines, which represent important building blocks in the chemical and pharmaceutical industry. Since their discovery in 2011, many previously unknown IREDs have been identified, biochemically and structurally characterized and categorized into families. However, the catalytic mechanism and guiding principles for substrate specificity and stereoselectivity remain disputed. Herein, we describe the crystal structure of S-IRED-Ms from Mycobacterium smegmatis together with its cofactor NADPH. S-IRED-Ms belongs to the S-enantioselective superfamily 3 (SFam3) and is the first IRED from SFam3 to be structurally described. The data presented provide further evidence for the overall high degree of structural conservation between different IREDs of various superfamilies. We discuss the role of Asp170 in catalysis and the importance of hydrophobic amino acids in the active site for stereospecificity. Moreover, a separate entrance to the active site, potentially functioning according to a gatekeeping mechanism regulating access and, therefore, substrate specificity is described.

Enantioselective Reductive Coupling of Imines Templated by Chiral Diboron

We herein report a general, practical, and highly efficient method for asymmetric synthesis of a wide range of chiral vicinal diamines via reductive coupling of imines templated by chiral diboron. The protocol features high enantioselectivity and stereospecificity, mild reaction conditions, simple operating procedures, use of readily available starting materials, and a broad substrate scope. The method signifies the generality of diboron-enabled [3,3]-sigmatropic rearrangement.

Characterization of imine reductases in reductive amination for the exploration of structure-activity relationships

Imine reductases (IREDs) have shown great potential as catalysts for the asymmetric synthesis of industrially relevant chiral amines, but a limited understanding of sequence activity relationships makes rational engineering challenging. Here, we describe the characterization of 80 putative and 15 previously described IREDs across 10 different transformations and confirm that reductive amination catalysis is not limited to any particular subgroup or sequence motif. Furthermore, we have identified another dehydrogenase subgroup with chemoselectivity for imine reduction. Enantioselectivities were determined for the reduction of the model substrate 2-phenylpiperideine, and the effect of changing the reaction conditions was also studied for the reductive aminations of 1-indanone, acetophenone, and 4-methoxyphenylacetone. We have performed sequence-structure analysis to help explain clusters in activity across a phylogenetic tree and to inform rational engineering, which, in one case, has conferred a change in chemoselectivity that had not been previously observed.

Stereodivergent, Chemoenzymatic Synthesis of Azaphilone Natural Products

Selective access to a targeted isomer is often critical in the synthesis of biologically active molecules. Whereas small-molecule reagents and catalysts often act with anticipated site- and stereoselectivity, this predictability does not extend to enzymes. Further, the lack of access to catalysts that provide complementary selectivity creates a challenge in the application of biocatalysis in synthesis. Here, we report an approach for accessing biocatalysts with complementary selectivity that is orthogonal to protein engineering. Through the use of a sequence similarity network (SSN), a number of sequences were selected, and the corresponding biocatalysts were evaluated for reactivity and selectivity. With a number of biocatalysts identified that operate with complementary site- and stereoselectivity, these catalysts were employed in the stereodivergent, chemoenzymatic synthesis of azaphilone natural products. Specifically, the first syntheses of trichoflectin, deflectin-1a, and lunatoic acid A were achieved. In addition, chemoenzymatic syntheses of these azaphilones supplied enantioenriched material for reassignment of the absolute configuration of trichoflectin and deflectin-1a based on optical rotation, CD spectra, and X-ray crystallography.

A Continuing Career in Biocatalysis: Frances H. Arnold

On the occasion of Professor Frances H. Arnold's recent acceptance of the 2018 Nobel Prize in Chemistry, we honor her numerous contributions to the fields of directed evolution and biocatalysis. Arnold pioneered the development of directed evolution methods for engineering enzymes as biocatalysts. Her highly interdisciplinary research has provided a ground not only for understanding the mechanisms of enzyme evolution but also for developing commercially viable enzyme biocatalysts and biocatalytic processes. In this Account, we highlight some of her notable contributions in the past three decades in the development of foundational directed evolution methods and their applications in the design and engineering of enzymes with desired functions for biocatalysis. Her work has created a paradigm shift in the broad catalysis field.

Stereodivergent Intramolecular Cyclopropanation Enabled by Engineered Carbene Transferases

We report the development of engineered myoglobin biocatalysts for executing asymmetric intramolecular cyclopropanations resulting in cyclopropane-fused γ-lactones, which are key motifs found in many bioactive molecules. Using this strategy, a broad range of allyl diazoacetate substrates were efficiently cyclized in high yields with up to 99% enantiomeric excess. Upon remodeling of the active site via protein engineering, myoglobin variants with stereodivergent selectivity were also obtained. In combination with whole-cell transformations, these biocatalysts enabled the gram-scale assembly of a key intermediate useful for the synthesis of the insecticide permethrin and other natural products. The enzymatically produced cyclopropyl-γ-lactones can be further elaborated to furnish a variety of enantiopure trisubstituted cyclopropanes. This work introduces a first example of biocatalytic intramolecular cyclopropanation and provides an attractive strategy for the stereodivergent preparation of fused cyclopropyl-γ-lactones of high value for medicinal chemistry and the synthesis of natural products.

Enantioselective Biocatalytic Reduction of 2 H-1,4-Benzoxazines Using Imine Reductases

A biocatalytic reduction of 2 H-1,4-benzoxazines using imine reductases is reported. This process enables a smooth and enantioselective synthesis of the resulting cyclic amines under mild conditions in aqueous media by means of a catalytic amount of the cofactor NADPH as hydride source as well as glucose as the reducing agent used in stoichiometric amounts for in situ cofactor recycling. Several substrates were studied, and the 3,4-dihydro-2 H-1,4-benzoxazines were obtained with up to 99% ee. In addition, the efficiency of this reduction process based on imine reductases as catalysts has been demonstrated for one 2 H-1,4-benzoxazine on an elevated laboratory scale running at a substrate loading of 10 g L^-1 in the presence of a tailor-made whole-cell catalyst.

Synthesis of chiral seven-membered cyclic sulfonamides through palladium-catalyzed arylation of cyclic imines

An enantioselective palladium-catalyzed addition of arylboronic acids to seven-membered cyclic N-sulfonyl aldimines and ketimines has been developed, giving the chiral cyclic sulfonamides with excellent yields and up to 99% ee.

Intramolecular asymmetric reductive amination: synthesis of enantioenriched dibenz[c,e]azepines

An enantioselective synthesis of dibenz[c,e]azepines containing both central and axial chiralities through a one pot N-Boc deprotection/intramolecular asymmetric reductive amination sequence has been achieved with generally excellent enantiocontrol (up to 97% ee).

An Ir-catalyzed intramolecular asymmetric reductive amination (ARA) of bridged biaryl derivatives has been described. Using this unprecedented approach, synthetically useful dibenz[c,e]azepines containing both central and axial chiralities are obtained with excellent enantiocontrol (up to 97% ee). This methodology represents a rare example of enantioselective chemocatalytic synthesis of chiral dibenz[c,e]azepines featuring a broad substrate scope, and their synthetic utilities are exhibited by derivatizing the products into a chiral amino acid derivative and chiral phosphoramidite ligands, which display excellent enantiocontrol in Rh-catalyzed asymmetric hydrogenation of α-dehydroamino acid derivatives. Remarkably, our method is also applicable to enantioselectively synthesize an allocolchicine analogue.

Chemoenzymatic Synthesis of Substituted Azepanes by Sequential Biocatalytic Reduction and Organolithium-Mediated Rearrangement

Enantioenriched 2-aryl azepanes and 2-arylbenzazepines were generated biocatalytically by asymmetric reductive amination using imine reductases or by deracemization using monoamine oxidases. The amines were converted to the corresponding N'-aryl ureas, which rearranged on treatment with base with stereospecific transfer of the aryl substituent to the 2-position of the heterocycle via a configurationally stable benzyllithium intermediate. The products are previously inaccessible enantioenriched 2,2-disubstituted azepanes and benzazepines.

Terminal Alkenes from Acrylic Acid Derivatives via Non-Oxidative Enzymatic Decarboxylation by Ferulic Acid Decarboxylases

Fungal ferulic acid decarboxylases (FDCs) belong to the UbiD-family of enzymes and catalyse the reversible (de)carboxylation of cinnamic acid derivatives through the use of a prenylated flavin cofactor. The latter is synthesised by the flavin prenyltransferase UbiX. Herein, we demonstrate the applicability of FDC/UbiX expressing cells for both isolated enzyme and whole-cell biocatalysis. FDCs exhibit high activity with total turnover numbers (TTN) of up to 55000 and turnover frequency (TOF) of up to 370 min-1. Co-solvent compatibility studies revealed FDC's tolerance to some organic solvents up 20 % v/v. Using the in-vitro (de)carboxylase activity of holo-FDC as well as whole-cell biocatalysts, we performed a substrate profiling study of three FDCs, providing insights into structural determinants of activity. FDCs display broad substrate tolerance towards a wide range of acrylic acid derivatives bearing (hetero)cyclic or olefinic substituents at C3 affording conversions of up to >99 %. The synthetic utility of FDCs was demonstrated by a preparative-scale decarboxylation.

Sequence-Based In-silico Discovery, Characterisation, and Biocatalytic Application of a Set of Imine Reductases

Imine reductases (IREDs) have recently become a primary focus of research in biocatalysis, complementing other classes of amine-forming enzymes such as transaminases and amine dehydrogenases. Following in the footsteps of other research groups, we have established a set of IRED biocatalysts by sequence-based in silico enzyme discovery. In this study, we present basic characterisation data for these novel IREDs and explore their activity and stereoselectivity using a panel of structurally diverse cyclic imines as substrates. Specific activities of >1 U/mg and excellent stereoselectivities (ee>99 %) were observed in many cases, and the enzymes proved surprisingly tolerant towards elevated substrate loadings. Co-expression of the IREDs with an alcohol dehydrogenase for cofactor regeneration led to whole-cell biocatalysts capable of efficiently reducing imines at 100 mM initial concentration with no need for the addition of extracellular nicotinamide cofactor. Preparative biotransformations on gram scale using these 'designer cells' afforded chiral amines in good yield and excellent optical purity.

Hot off the press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as illisimonin A from Illicium simonsii.

Axial stereocontrol in tropos dibenz[c,e]azepines: the individual and cooperative effects of alkyl substituents

6,7-Dihydro-5H-dibenz[c,e]azepines, a class of secondary amine incorporating a centre-axis chirality relay, can be prepared from N-(2-bromobenzyl)-N-(1-arylalkyl)methanesulfonamides via Pd-catalysed intramolecular direct arylation, and methylated at C(7) via the 5,7-trans diastereoselective addition of methylmagnesium bromide to the derived N-benzylazepinium tetraphenylborate. Using these methods, the 4,5-dimethylated and 4,5,7-trimethylated homologues 13 and 14 were obtained and shown by ¹H NMR spectroscopy to be axially biased in opposite senses, as defined by the respective pseudoaxial or pseudoequatorial orientation of the 5-substituent in the preferred conformers, while retaining their tropos nature (the Arrhenius activation energy, E_A, for the conformational exchange process in 14 was estimated to be 57 kJ mol^-1 using 2D-EXSY NMR spectroscopy at 233-248 K). These results serve to illustrate how substituent effects might be exploited in new designs of bridged biaryl ligand in which tropos dynamics operate in combination with a pre-existing axial stereochemical bias.