Methylamine Dehydrogenase Research Articles

Current Status of Amine Dehydrogenases: From Active Site Architecture to Diverse Applications Across a Broad Substrate Spectrum

AbstractAmine dehydrogenases (AmDHs) are NAD(P)H‐dependent oxidoreductases that catalyze the reductive amination between carbonyl compounds and ammonia as the amine donor yielding valuable amines, typically with excellent enantioselectivity. While nature has provided enzymes with inherent AmDH activities, protein engineering techniques allowed researchers to expand the toolbox of available AmDHs, extend their substrate scope, improve their catalytic activities and stability under synthetically relevant conditions and even enable new reactivity concepts. The biocatalytic synthesis of amines using AmDHs has matured to a point where hundreds of aldehydes or ketones, of varying steric demands and bearing diverse functional groups, can be efficiently transformed. This review offers an overview of the available AmDHs and their substrate spectrum, covering from structural and evolutionary analyses to diverse methods employing these enzymes. Depending on the catalytic activities of other enzymes as reaction partners, AmDHs were applied in kinetic resolution (KR) and deracemization processes, cascade reactions for the amination of alcohols and alkenes or for the synthesis of amines and amino alcohols featuring multiple stereogenic centers. Moreover, the synthetic potential of AmDHs in novel pathways, such as the synthesis of secondary amines or alcohols, presents exciting opportunities for expanding their catalytic repertoire.

Co-immobilization of amine dehydrogenase and glucose dehydrogenase for the biosynthesis of (S)-2-aminobutan-1-ol in continuous flow

Reductive amination by amine dehydrogenases is a green and sustainable process that produces only water as the by-product. In this study, a continuous flow process was designed utilizing a packed bed reactor filled with co-immobilized amine dehydrogenase wh84 and glucose dehydrogenase for the highly efficient biocatalytic synthesis of chiral amino alcohols. The immobilized amine dehydrogenase wh84 exhibited better thermo-, pH and solvent stability with high activity recovery. (S)-2-aminobutan-1-ol was produced in up to 99% conversion and 99% ee in the continuous flow processes, and the space-time yields were up to 124.5 g L-1 d-1. The continuous reactions were also extended to 48 h affording up to 91.8% average conversions. This study showcased the important potential to sustainable production of chiral amino alcohols in continuous flow processes.

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.

Integrating Au Catalysis and Engineered Amine Dehydrogenase for the Chemoenzymatic Synthesis of Chiral Aliphatic Amines

Integrating Au Catalysis and Engineered Amine Dehydrogenase for the Chemoenzymatic Synthesis of Chiral Aliphatic Amines

Biocatalytic Oxidative Amination of para‐Substituted Phenols

AbstractBiocatalytic preparation of chiral amines is a large and burgeoning field in organic chemistry. Many enzymes and routes have been published, including transaminases, imine reductases, reductive aminases, amine dehydrogenases and others. However, all these routes rely on some sacrificial substrate, in the form of either amine donor or cofactor regeneration substrate. Herein, we report the direct oxidative amination of p‐substituted phenols catalyzed by an evolved flavoprotein oxidase, with the consumption of only substrate and O2, and release of H2O2. The substrate scope of the reaction is studied, and is tolerant of a diverse panel including ammonia, primary and secondary amines, and amino acids. The reaction is later employed at preparative scale to generate aminated products in 50–80 % yield. This report establishes flavoprotein oxidase as a new and economical member of the chemist's toolkit for biocatalytic generation of chiral amines, acting as oxidative aminase.

Engineering the substrate acceptance of l-amine dehydrogenase enables the collective biocatalytic synthesis of N-heterocyclic primary amines

Chiral N-heterocyclic primary amines are highly attractive synthons in the pharmaceutical industry. Amine dehydrogenases (AmDHs)-catalyzed direct asymmetric reductive amination of the readily available N-heterocyclic ketones represents a promising approach for synthesizing N-heterocyclic primary amines. However, the limited substrate acceptance of AmDHs restricts their application in biocatalytic synthesis. Here, we engineered the substrate acceptance of L-EsAmDH from Exiguobacterium sibiricum to access a panel of structurally diverse N-heterocyclic ketones. Through reverse substrate design and combining with substrate walking strategy, two active mutants with extended substrate specificity toward N-Boc-4-acetylpiperidine were identified, and two additional rounds of iterative site mutagenesis further increased the activity by 116.3-fold. The optimal mutant M4-2 (L49G/V303A/L307A/T143A) exhibited significantly expanded N-Boc, N-Bn, and N-Cbz-substituted heterocyclic ketones scope, and its practical biocatalytic synthesis performance was verified in the gram-scale synthesis of (R)-4-aminoethyl-1-Boc-piperidine, achieving 95 % conversion, >99 % ee, and an overall isolated yield of 86 % (9.8 g). Our study lays the foundation for the collective biocatalytic synthesis of structurally diverse N-heterocyclic primary amines and gives referable guidance for engineering AmDH family members into versatile biocatalysts.

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.

Efficient synthesis of (R)-4-methoxyamphetamine and its analogues under low ammonium concentration using engineered amine dehydrogenase

Amphetamine and its analogues are widely used in various drugs because of its powerful and diverse effects on the nervous system of the brain, e.g., (R)-4-methoxyamphetamine is the key intermediate in formoterol for the treatment of asthma. Biocatalytic reductive amination of ketone by amine dehydrogenase (AmDH) is a potential method for the synthesis of chiral primary amines, but usually requires a high ammonium concentration to drive the amination reaction. In this study, iterative evolution was performed to generate a LsAmDH mutant W5–5 (T123G/S157T/S275G), which was able to catalyze the reductive amination of 200 mM 4-methoxypropiophenone at 500 mM ammonium concentration to afford (R)-4-methoxyamphetamine with >99% ee and 90% isolated yield. This variant also catalyzed the reductive amination of other phenylacetone analogues with high yields and excellent enantioselectivity at low ammonium concentration. This would greatly reduce the generation of ammonium-containing wastes and make the reaction more economic and greener, laying a foundation for the industrial application of AmDHs.

Methylamine (CH3NH2) dehydrogenase by pristine BN nanotube for H2 storage application: A DFT study

We undertook density functional theory (DFT) computations for inspecting the decomposition and adsorption of methylamine (MLA) onto the surface of a pure boron nitride nano-tube (BNNT). We also obtained the activation energies of viable elementary reactions and the adsorption energies of stable complexes. The most suitable reaction pathway which generated one hydrogen cyanide molecule as well as 4 hydrogen atoms was relatively endothermal. For MLA decomposition, the energy barrier was around 44.6 kcal/mol. Due to the fact that the activation energy for the side reaction which generated NH2 as well as CH3 was somewhat high, reducing the temperature could depress the generation of side products.

Asymmetric Reductive Amination in Organocatalysis and Biocatalysis

AbstractThis review summarizes the recent progress of organocatalytic and biocatalytic asymmetric reductive amination (ARA), a challenging but important topic for drug discovery and the pharmaceutical industry. At present, ARA can be divided into three categories: metal catalysis, organic catalysis, and biocatalysis. In the past decade, transition metal‐catalysed ARA has been well established. Organocatalytic ARA has emerged as a powerful alternative to metal‐catalysed ARA, the hydrogen sources used in organocatalytic ARA are usually Hantzsch esters, benzothiazolines, boranes, and hydrosilanes, which require Lewis base or phosphoric acid catalysts to activate them to give secondary chiral amines. It is worth mentioning that biocatalytic ARA has made remarkable progress in the last decade, amino acid dehydrogenases, amine dehydrogenases, opine dehydrogenases and imine reductases have been successfully used in ARA.

Identification of 7-hydroxyindole as an alternative substrate of MauG by in silico and in vitro analysis

MauG catalyzes the six-electron oxidation of pre-tryptophan tryptophylquinone (preTTQ) cofactor in methylamine dehydrogenase (MADH) to form mature tryptophan tryptophylquinone (TTQ) via long-range electron transfer. To identify alternative substrates for MauG, docking models for 10 tryptophan-like compounds were constructed using Autodock Vina. These demonstrated spontaneous binding to the preTTQ binding site of MauG, with hydroxyindoles most frequently sharing the natural substrate binding site of MauG. To confirm the result of in silico analysis, 7-hydroxyindole was reacted with bis-FeIV of MauG. The spectroscopic change, representing the reactivity of MauG, revealed the highly increased reaction rate (k3) toward 7-hydroxyindole, suggesting that bis-FeIV MauG extracted an electron from the 7-hydroxyindole and then oxidized to di-ferric MauG.

Desymmetric Reductive Amination of 1,3-Cyclopentadiones to Single Stereoisomer of β-Amino Ketones with an All-Carbon Quaternary Stereocenter by Engineered Amine Dehydrogenases

Regio- and stereoselective reductive amination of diketones offers an attractive method to access chiral β-amino ketones with multiple stereocenters which are unique scaffolds and building blocks for bioactive molecules, but it is still a great challenge in organic chemistry. In this study, mutant amine dehydrogenases (LsAmDHs) were created by directed evolution of a l-phenylalanine dehydrogenase from Lysinibacillus sphaericus to catalyze the desymmetric reductive amination of 2,2-disubstituted-1,3-cyclopentadiones. Using these beneficial LsAmDHs, the corresponding (2R, 3R)-β-amino ketones with an all-carbon quaternary stereocenter were prepared with up to 99% de and ee and up to 84% isolated yields. A cyclopenta[b]hydroquinoline derivative was obtained from 2-methyl-2-(2′-bromobenzyl)-1,3-cyclopentadione or 2-methyl-2-(2′-chlorobenzyl)-1,3-cyclopentadione via sequential enzymatic desymmetric reductive amination and an intramolecular Buchwald–Hartwig cross coupling reaction. Molecular docking and dynamics simulations provided some insights into the roles of key mutations on the improved activity and excellent stereoselectivity toward these un-native substrates. This study not only developed biocatalysts to realize the unprecedented desymmetric reductive amination of 2,2-disubstituted-1,3-cyclopentadiones to the single stereoisomer of the corresponding β-amino ketones but also suggested that engineering of amine dehydrogenase provides a useful tool to address the challenges in asymmetric reductive amination of diketones.

Native amine dehydrogenases can catalyze the direct reduction of carbonyl compounds to alcohols in the absence of ammonia

Native amine dehydrogenases (nat-AmDHs) catalyze the (S)-stereoselective reductive amination of various ketones and aldehydes in the presence of high concentrations of ammonia. Based on the structure of CfusAmDH from Cystobacter fuscus complexed with Nicotinamide adenine dinucleotide phosphate (NADP+) and cyclohexylamine, we previously hypothesized a mechanism involving the attack at the electrophilic carbon of the carbonyl by ammonia followed by delivery of the hydride from the reduced nicotinamide cofactor on the re-face of the prochiral ketone. The direct reduction of carbonyl substrates into the corresponding alcohols requires a similar active site architecture and was previously reported as a minor side reaction of some native amine dehydrogenases and variants. Here we describe the ketoreductase (KRED) activity of a set of native amine dehydrogenases and variants, which proved to be significant in the absence of ammonia in the reaction medium but negligible in its presence. Conducting this study on a large set of substrates revealed the heterogeneity of this secondary ketoreductase activity, which was dependent upon the enzyme/substrate pairs considered. In silico docking experiments permitted the identification of some relationships between ketoreductase activity and the structural features of the enzymes. Kinetic studies of MsmeAmDH highlighted the superior performance of this native amine dehydrogenases as a ketoreductase but also its very low activity towards the reverse reaction of alcohol oxidation.

Stereoselective Synthesis of Structurally Diverse (S)‐Lactams via an Engineered Amine Dehydrogenase

AbstractOptically pure lactams have a wide diversity of applications, one of which is serving as important intermediates in the synthesis of agricultural bioactive compounds or pharmaceuticals. Efficient stereoselective synthesis of chiral lactams with low‐cost amine donors under mild conditions is desired for manufacturing of these important chemicals. Herein, a two‐step chemo‐enzymatic strategy has been designed to produce (S)‐lactams by engineering a natural amine dehydrogenase from Thermoanaerobacter thermohydrosulfuricus (TtherAmDH). TtherAmDH was subjected to eight cycles of directed evolution to enhance its reductive amination activity toward keto acid substrates. The variants showed improved specific activity toward 6 tested substrates and gave high stereoselectivities of up to 99% in the asymmetric synthesis of γ‐ and δ‐ lactams. In particular, TtherAmDHV8 showed a 237‐fold higher specific activity toward the model substrate levulinic acid and gave (S)‐5‐methyl‐2‐pyrrolidone in 99% ee with a space‐time yield of 75.3 g L−1 d−1. These results indicate that the engineered amine dehydrogenase TtherAmDH can serve as an efficient biocatalyst for the manufacture of highly valued chiral lactams.magnified image

Cover Feature: Expanding the Substrate Scope of Native Amine Dehydrogenases through In Silico Structural Exploration and Targeted Protein Engineering (ChemCatChem 22/2022)

Cover Feature: Expanding the Substrate Scope of Native Amine Dehydrogenases through <i>In Silico</i> Structural Exploration and Targeted Protein Engineering (ChemCatChem 22/2022)

Continuous Flow Biocatalytic Reductive Amination by Co-Entrapping Dehydrogenases with Agarose Gel in a 3D-Printed Mould Reactor.

Herein, we show how the merge of biocatalysis with flow chemistry aided by 3D-printing technologies can facilitate organic synthesis. This concept was exemplified for the reductive amination of benzaldehyde catalysed by co-immobilised amine dehydrogenase and formate dehydrogenase in a continuous flow micro-reactor. For this purpose, we investigated enzyme co-immobilisation by covalent binding, or ion-affinity binding, or entrapment. Entrapment in an agarose hydrogel turned out to be the most promising solution for this biocatalytic reaction. Therefore, we developed a scalable and customisable approach whereby an agarose hydrogel containing the co-entrapped dehydrogenases was cast in a 3D-printed mould. The reactor was applied to the reductive amination of benzaldehyde in continuous flow over 120 h and afforded 47 % analytical yield and a space-time yield of 7.4 g L day-1 using 0.03 mol% biocatalysts loading. This work also exemplifies how rapid prototyping of enzymatic reactions in flow can be achieved through 3D-printing technology.

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.

Metabolic Engineering for the Comprehensive Utilization of N,N-Dimethylformamide-Containing Wastewater.

N, N-dimethylformamide is frequently present in industrial wastewater and is environmentally detrimental. The current study aims to assess the utilization and biodegradation of N, N-dimethylformamide-containing wastewater to lessen the associated environmental load. Results show that addition of wastewater containing N, N-dimethylformamide to Trichoderma reesei fermentation media enhances cellulase production and facilitates cellulose hydrolysis. However, N, N-dimethylformamide is a cellulase enhancer that is not degraded during cellulase production in T. reesei fermentation and is retained in the N, N-dimethylformamide-enhanced cellulase solution. Indeed, the cellulosic sugar solution generated via lignocellulose hydrolysis with N, N-dimethylformamide-enhanced cellulase retains N, N-dimethylformamide. We further identified three core enzyme modules─N, N-dimethylformamidase, dimethylamine dehydrogenase, and methylamine dehydrogenase enzyme─which were inserted into Escherichia coli to develop metabolically engineered strains. These strains degraded N, N-dimethylformamide and produced succinate using N, N-dimethylformamide-enhanced cellulosic sugar as the substrate. The platform described here can be applied to effectively convert waste into valuable bioproducts.

Expanding the Substrate Scope of Native Amine Dehydrogenases through In Silico Structural Exploration and Targeted Protein Engineering

AbstractNative Amine Dehydrogenases (nat‐AmDHs) are NAD(P)H‐enzymes performing reductive amination, mainly active towards small aliphatic aldehydes and cyclic ketones, due to active site volumes limited by the presence of several bulky amino acids. Herein, inspired by the diversity of residues at these positions among the family, we report the implementation of mutations F140A and W145A in CfusAmDH and their transposition in nine other members. Moderate to high conversions were obtained with substrates not accepted by the native enzymes, notably n‐alkylaldehydes (44.6 %–99.5 % for hexanal to nonanal) and n‐alkylketones (16.0 %–53.7 % for hexan‐2‐one to nonan‐2‐one) with retention of excellent (S)‐enantioselectivity (&gt;99 % ee). Complementary to the reported (R)‐selective AmDHs, the promising mutant CfusAmDH−W145A was further characterized for its synthetic potential. Crystal structure resolution and molecular dynamics gave insights into the cofactor and substrate specificity and the whole structural dynamics, thus providing keys for mutagenesis work on this enzyme family.

Modification of the substrate specificity of leucine dehydrogenase by site-directed mutagenesis based on biocomputing strategies

Synthesis of chiral amines by amine dehydrogenase has the advantages of environmental friendliness, high stereoselectivity, and mild reaction conditions. However, amine dehydrogenase has low catalytic activity, which greatly limits its application in the large-scale synthesis of chiral amines. In this study, a novel amine dehydrogenase was obtained by modifying the substrate specificity of leucine dehydrogenase via computer-aided protein engineering strategy. Furthermore, conservation analysis, homology modeling and molecular docking analysis were carried out via biocomputing strategy to select the mutation sites, and the mutants L52S and T143C were obtained. The enzyme activities of the two mutants to 2-pentanone were 1.55 U/mg and 2.06 U/mg, respectively. The enzyme activity of the latter was 188% and the Tm value was 2.55 °Chigher than those of the original mutant, which laid a foundation for the efficient preparation of chiral amines by using this novel enzyme.