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

Alleviating Substrate Inhibition of Leucine Dehydrogenase by Enhancing NAD+ Dissociation Efficiency

Leucine dehydrogenase catalyzes the asymmetric reductive amination of ketoacids to produce valuable chiral unnatural amino acids, but its application is often constrained by substrate inhibition. Here we employed a rational engineering strategy to alleviate substrate inhibition by enhancing the dissociation efficiency of NAD+. Notably, the variant H184A exhibited a 1.53-fold increase in enzyme activity and a 58% improvement in the half-maximal inhibitory concentration for 2-oxobutyric acid, alleviating substrate inhibition.

Reductive N-Heterocyclic Carbene Catalysis via Hydride Transfer: Generating Homoenolates from Unsaturated Esters

In N-heterocyclic carbene (NHC) catalysis, the reduction of NHC-bound acyl azolium species is achieved with progress limited to the generation of ketyl radical intermediates. Here, we report a novel NHC-catalyzed reductive mode for acyl azolium intermediates, which accept a hydride to generate the Breslow intermediate. Then, the reaction of the Breslow intermediate with chalcone results in the formation of cyclopentene, demonstrating a classic umpolung transformation. We expect that this catalytic reductive mode will open new avenues for synthetic transformations.

Imine Reductase-Catalyzed Remote Stereocontrol for Enantiodivergent Synthesis of Cyclohexylidene-Based Axially Chiral Amines

Cyclohexylidene-based amines exhibit unique axial chirality arising from the restricted double bond and have shown great potential in medicinal chemistry. However, their asymmetric synthesis remains challenging due to the long distance between the chirally relevant groups. Herein, we report a highly efficient and asymmetric synthesis of cyclohexylidene-based axially chiral amines from 4-substituted cyclohexanones and primary amines catalyzed by imine reductases (IREDs). Enantiodivergent IREDs were identified to provide convenient access to both enantiomers of chiral products with high yields and enantioselectivity (up to 99% yield, 99:1 or 1:99 enantiomeric ratio). A gram-scale synthesis of cyclohexylidene-based amines was also achieved. Moreover, protein X-ray crystallography and molecular modeling studies were conducted to provide structural insight into the remote stereocontrol of IREDs in generating cyclohexylidene-based axial chirality.

Bridging chemistry and biology for light-driven new-to-nature enantioselective photoenzymatic catalysis

Merging enzymes with light-driven photocatalysis has given rise to the burgeoning field of photoenzymatic catalysis. This approach combines the high reactivity from photoexcitation with the exceptional selectivity of biocatalysis, providing exciting opportunities to tackle challenges in enantioselective radical reactions and to access new-to-nature enzyme reactivities. This tutorial review aims to provide a comprehensive introduction to this interdisciplinary topic, catering to the growing interest from communities in asymmetric catalysis, photocatalysis, radical chemistry, enzyme engineering, and synthetic biology. We summarize the fundamental principles of utilizing light to power enzymatic reactions and different strategies exploring enantioselective photoenzymatic systems, including natural cofactor-based photoenzymatic catalysis, photocatalyst/enzyme synergistic catalysis, synthetic cofactor-based artificial photoenzymes, and cofactor-free photoenzymatic catalysis. We also discuss the challenges and prospects of enantioselective photoenzymatic catalysis in advancing sustainable asymmetric synthesis.

Engineering Atomic Sites and Proton Transfer Microenvironments for Bioinspired Photocatalytic Alcohol-Amine Coupling

Achieving a precise understanding and accurate design of heterogeneous catalysts based on bioinspired principles is challenging yet crucial to digging out optimal materials for artificial catalysis. Here, an ADH-mimicking dual-site photocatalyst (YCuCdS) is developed, and demonstrates the powerful effects of atomic site configuration and proton transfer environments on alcohol-amine coupling. Mechanism studies reveal that the alcohol substrate is effectively dehydrogenated at the Y sites, forming the carbonyl intermediates that rapidly experience condensation with the amine. Meanwhile, the released hydrogen species (Hads) migrate from adjacent Cu sites to active S atoms, promoting H2 production and hindering the over-hydrogenation of imine. As a result, a high imine yield of 92% is achieved, along with an H2 production rate of 7400 µmol g-1 h-1. This work showcases an effective strategy for the design of heterogeneous catalysts with bioinspiration.

Building Localized NADP(H) Recycling Circuits to Advance Enzyme Cascadetronics

The catalytic action of enzymes in a cascade trapped within a mesoporous electrode material is simultaneously energized, controlled and observed through the efficient, reversible electrochemical NAD(P)(H) recycling catalyzed by one of the enzymes. In their nanoconfined state, nicotinamide cofactors are tightly channeled current carriers, mediating multi-step reactions in either direction (oxidation or reduction) with a rapid response time. By incorporating a hydrogen-borrowing enzyme pair, the internal action of which opposes the external voltage bias driving oxidation or reduction, a reduction process can be performed under overall oxidizing conditions, and vice versa. The power of the method to control and resolve complex metabolic pathways is demonstrated using a non-linear, three-enzyme cascade extended by incorporating a fourth enzyme, urease. The latter generates in situ ammonia, which is enzymatically consumed in a reductive process, but the immediate current response to each addition of urea is observed, unusually, by applying an oxidizing potential. A practical consequence is that enzyme-catalyzed electrochemical reduction reactions requiring anaerobic conditions (to avoid O2 interference) can readily be studied under ambient aerobic conditions. The results illustrate how a complex enzyme cascade confined within a porous electrode and connected to an electrical power source manifests characteristics associated with electronic circuits.

From discovery to application: Enabling technology-based optimizing carbonyl reductases biocatalysis for active pharmaceutical ingredient synthesis

The catalytic conversion of chiral alcohols and corresponding carbonyl compounds by carbonyl reductases (alcohol dehydrogenases), which are NAD(P) or NAD(P)H-dependent oxidoreductases, has attracted considerable attention. However, existing carbonyl reductases are insufficient to meet the demands of diverse industrial applications; hence, new enzymes with functions that can expand the toolbox of biocatalysts are urgently required. Developing precisely controlled chiral biocatalysts is of great significance for the efficient development of a broad spectrum of active pharmaceutical ingredients via biosynthesis. In this review, we summarized methods for discovering novel natural carbonyl reductases from various perspectives. Furthermore, advances in protein engineering, utilizing known sequence and structural information as well as catalytic dynamics mechanisms to improve potential functions, are also addressed. The exponential growth in data-driven tools over the past decade has made it possible to de novo design carbonyl reductases. Additionally, various applications of these high-performance carbonyl reductases and different strategies for coenzyme regeneration involving photocatalysis during the reaction process were reviewed. These advancements will bring new opportunities and challenges to the fields of green chemistry and biosynthesis in the future.

Structure-guided design of a Zbasic2-mediated dual-enzyme nanoreactor for chiral amine synthesis

The synthesis of chiral amines is of critical importance but still challenging. Here, we present a self-sufficient and reusable dual-enzyme nanoreactor for chiral amine synthesis, featuring Zbasic2-mediated site-specific immobilization of amine dehydrogenase (AmDH) and glucose dehydrogenase (GDH) onto mesoporous silica nanoflowers (MSN). Molecular dynamics simulations revealed that the Zbasic2 tag was bound to MSN via electrostatic interactions, thus maintaining the fusion enzyme's active pocket accessibility and improving its catalytic performance. Using the Zbasic2 tags, AmDH and GDH were purified and immobilized on MSN in a one-pot process, thus creating the dual-enzyme nanoreactor. The dual-enzyme system exhibited remarkable activity and reusability, achieving high yields of 76-99 % (ee > 99 %) for various chiral amines at a substrate concentration of 400 mM and retaining a yield of 65 % after 10 cycles. This Zbasic2-based platform offers a robust and scalable strategy for sustainable chiral amine synthesis.

Biocatalytic Desymmetrization for the Atroposelective Synthesis of Axially Chiral Biaryls Using an Engineered Imine Reductase

The enzymatic atroposelective synthesis of biaryl compounds is relatively rare, despite considerable attention received by biocatalysis in the academic and industrial sectors. Imine reductases (IREDs) are an important class of enzymes that have been applied in the asymmetric synthesis of chiral amine building blocks. In this study, two IREDs (IR140 and IR189) were identified to catalyze the efficient desymmetrization of biaryls utilizing various amine donors. Further protein engineering enabled the identification of variants (IR189 M8-M9 and IR189 M13-M14) that are able to catalyze the formation of both (R) and (S) atropisomers in excellent yields and atroposelectivities (24 examples, up to 99 % ee and yield). The absolute configuration and rotational barriers were confirmed, and the reactions were readily scaled up to allow isolation of the atropisomeric product in 99 % ee and 82 % yield. The optically pure biaryl amines were further derivatized into various synthetically useful atropisomers. To shed light on the molecular recognition mechanisms, molecular dynamics (MD) simulations were performed, offering plausible explanations for the improved atroposelectivity and enzymatic activity. The current strategy expands the scope of the IRED-catalyzed synthesis of axially chiral biaryl amines, contributing significantly to the field of atroposelective biocatalysis.

Metabolic Blockade-Based Genome Mining of Saccharopolyspora erythraea SCSIO 07745: Discovery and Biosynthetic Pathway of Aminoquinolinone Alkaloids Bearing 6/6/5 Tricyclic and 6/6/6/5 Tetracyclic Scaffolds

Metabolic blockade-based genome mining of the marine sediment-derived Saccharopolyspora erythraea SCSIO 07745 led to the discovery of 11 novel aminoquinolinone alkaloids, oxazoquinolinones A-J (1-10), characterized by an oxazolidone[3,2-α]quinoline-5,8-dione scaffold, and oxazoquinolinone K (11), featuring an unprecedented fused 6/6/6/5 tetracyclic core ring system. Additionally, 5 new biosynthetic intermediates or shunt products (12-16) and a known metabolite sannanine (17) were identified. Their structures were elucidated by extensive spectroscopic analyses and a comparison of electronic circular dichroism and single-crystal X-ray diffraction. On the basis of the functional gene analyses and structures of the intermediates or shunt products, plausible biosynthetic pathways for compounds 1-17 were proposed. Additionally, oxazoquinolinone K (11) obviously inhibited cell invasion of human glioma cell line LN229 cells at 10 μM.

Discovery and Synthetic Applications of a NAD(P)H-Dependent Reductive Aminase from Rhodococcus erythropolis

Reductive amination is one of the most synthetically direct routes to access chiral amines. Several Imine Reductases (IREDs) have been discovered to catalyze reductive amination (Reductive Aminases or RedAms), yet they are dependent on the expensive phosphorylated nicotinamide adenine dinucleotide cofactor NADPH and usually more active at basic pH. Here, we describe the discovery and synthetic potential of an IRED from Rhodococcus erythropolis (RytRedAm) that catalyzes reductive amination between a series of medium to large carbonyl and amine compounds with conversions of up to >99% and 99% enantiomeric excess at neutral pH. RytRedAm catalyzes the formation of a substituted γ-lactam and N-methyl-1-phenylethanamine with stereochemistry opposite to that of fungal RedAms, giving the (S)-enantiomer. This enzyme remarkably uses both NADPH and NADH cofactors with K M values of 15 and 247 μM and turnover numbers k cat of 3.6 and 9.0 s-1, respectively, for the reductive amination of hexanal with allylamine. The crystal structure obtained provides insights into the flexibility to also accept NADH, with residues R35 and I69 diverging from that of other IREDs/RedAms in the otherwise conserved Rossmann fold. RytRedAm thus represents a subfamily of enzymes that enable synthetic applications using NADH-dependent reductive amination to access complementary chiral amine products.

Dynamic Asymmetric Diamination of Allylic Alcohols through Borrowing Hydrogen Catalysis: Diastereo-Divergent Synthesis of Tetrahydrobenzodiazepines

We present herein a catalytic enantioconvergent diamination of racemic allylic alcohols with the construction of two C-N bonds and 1,3-nonadjacent stereocenters. This iridium/chiral phosphoric acid cooperative catalytic system operates through an atom-economical borrowing hydrogen amination/aza-Michael cascade, and converts readily available phenylenediamines and racemic allylic alcohols to 1,5-tetrahydrobenzodiazepines in high enantioselectivity. An intriguing solvent-dependent switch of diastereoselectivity was also observed. Mechanistic studies suggested a dynamic kinetic resolution process involving racemization through a reversible Michael addition, making the last step of asymmetric imine reduction the enantiodetermining step of this cascade process.

Atroposelective Synthesis of Axial Biaryls by Dynamic Kinetic Resolution Using Engineered Imine Reductases

Axially chiral biaryl compounds are ubiquitous scaffolds in natural products, bioactive molecules, chiral ligands and catalysts, but biocatalytic methods for their asymmetric synthesis are limited. Herein, we report a highly efficient biocatalytic route for the atroposelective synthesis of biaryls by dynamic kinetic resolution (DKR). This DKR approach features a transient six-membered aza-acetal-bridge-promoted racemization followed by an imine reductase (IRED)-catalyzed stereoselective reduction to construct the axial chirality under ambient conditions. Directed evolution of an IRED from Streptomyces sp. GF3546 provided a variant (S-IRED-Ss-M11) capable of catalyzing the DKR process to access a variety of biaryl aminoalcohols in high yields and excellent enantioselectivities (up to 98 % yield and >99 : 1 enantiomeric ratio). Molecular dynamics simulation studies on the S-IRED-Ss-M11 variant revealed the origin of its improved activity and atroposelectivity. By exploiting the substrate promiscuity of IREDs and the power of directed evolution, our work further extends the biocatalysts' toolbox to construct challenging axially chiral molecules.

Waste Valorization in a Sustainable Bio-Based Economy: The Road to Carbon Neutrality

The development of sustainable chemistry underlying the quest to minimize and/or valorize waste in the carbon-neutral manufacture of chemicals is followed over the last four to five decades. Both chemo- and biocatalysis have played an indispensable role in this odyssey. in particular developments in protein engineering, metagenomics and bioinformatics over the preceding three decades have played a crucial supporting role in facilitating the widespread application of both whole cell and cell-free biocatalysis. The pressing need, driven by climate change mitigation, for a drastic reduction in greenhouse gas (GHG) emissions, has precipitated an energy transition based on decarbonization of energy and defossilization of organic chemicals production. The latter involves waste biomass and/or waste CO2 as the feedstock and green electricity generated using solar, wind, hydroelectric or nuclear energy. The use of waste polysaccharides as feedstocks will underpin a renaissance in carbohydrate chemistry with pentoses and hexoses as base chemicals and bio-based solvents and polymers as environmentally friendly downstream products. The widespread availability of inexpensive electricity and solar energy has led to increasing attention for electro(bio)catalysis and photo(bio)catalysis which in turn is leading to myriad innovations in these fields.

Synthetic Nicotinamide Cofactors as Alternatives to NADPH in Imine Reductase-Catalyzed Reactions

This study demonstrates the effectiveness of synthetic nicotinamide cofactors as cost-effective alternatives to NADPH in imine reductase (IRED) catalysis. The synthetic cofactors maintained catalytic activity and stereoselectivity, achieving high conversion rates. Molecular docking studies revealed key structural interactions influencing performance. Combining a glucose dehydrogenase (GDH) recycling system further enhanced the stability and efficiency. These findings highlight the potential of synthetic cofactors to reduce costs and improve the feasibility of IRED-catalyzed processes for industrial applications.

Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants

This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. Following the establishment of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was introduced. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. During the past decade, this phenomenon was shown to be general. In some studies, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects. We conclude with suggestions for future work, and call for a unified overall picture of non-additivity and epistasis.

A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening

Native amine dehydrogenases offer sustainable access to chiral amines, so the search for scaffolds capable of converting more diverse carbonyl compounds is required to reach the full potential of this alternative to conventional synthetic reductive aminations. Here we report a multidisciplinary strategy combining bioinformatics, chemoinformatics and biocatalysis to extensively screen billions of sequences in silico and to efficiently find native amine dehydrogenases features using computational approaches. In this way, we achieve a comprehensive overview of the initial native amine dehydrogenase family, extending it from 2,011 to 17,959 sequences, and identify native amine dehydrogenases with non-reported substrate spectra, including hindered carbonyls and ethyl ketones, and accepting methylamine and cyclopropylamine as amine donor. We also present preliminary model-based structural information to inform the design of potential (R)-selective amine dehydrogenases, as native amine dehydrogenases are mostly (S)-selective. This integrated strategy paves the way for expanding the resource of other enzyme families and in highlighting enzymes with original features.

Modular Access to Chiral Amines via Imine Reductase-Based Photoenzymatic Catalysis

The development of catalysts serves as the cornerstone of innovation in synthesis, as exemplified by the recent discovery of photoenzymes. However, the repertoire of naturally occurring enzymes repurposed by direct light excitation to catalyze new-to-nature photobiotransformations is currently limited to flavoproteins and keto-reductases. Herein, we shed light on imine reductases (IREDs) that catalyze the remote C(sp3)-C(sp3) bond formation, providing a previously elusive radical hydroalkylation of enamides for accessing chiral amines (45 examples with up to 99% enantiomeric excess). Beyond their natural function in catalyzing two-electron reductive amination reactions, upon direct visible-light excitation or in synergy with a synthetic photoredox catalyst, IREDs are repurposed to tune the non-natural photoinduced single-electron radical processes. By conducting wet mechanistic experiments and computational simulations, we unravel how engineered IREDs direct radical intermediates toward the productive and enantioselective pathway. This work represents a promising paradigm for harnessing nature's catalysts for new-to-nature asymmetric transformations that remain challenging through traditional chemocatalytic methods.

Biocatalysis: landmark discoveries and applications in chemical synthesis

Biocatalysis has become an important tool in chemical synthesis, allowing access to complex molecules with high levels of activity and selectivity and with low environmental impact. Key discoveries in protein engineering, bioinformatics, recombinant technology and DNA sequencing have contributed towards the rapid acceleration of the field. This tutorial review explores enzyme engineering strategies and high-throughput screening approaches that have been applied for the discovery and development of enzymes for synthetic application. Landmark developments in the field are discussed and have been carefully selected to highlight the diverse synthetic applications of enzymes within the pharmaceutical, agricultural, food and chemical industries. The design and development of artificial biocatalytic cascades is also examined. This tutorial review will give readers an insight into the landmark discoveries and milestones that have helped shape and grow this branch of catalysis since the discovery of the first enzyme.