N-Alkyl-α-amino acids in Nature and their biocatalytic preparation

Opine dehydrogenases, an underexplored enzyme family for the enzymatic synthesis of chiral amines

Opines and opine-type chemicals are valuable natural products with diverse biochemical roles, and potential synthetic building blocks of bioactive compounds. Their synthesis involves reductive amination of ketoacids with amino acids. This transformation has high synthetic potential in producing enantiopure secondary amines. Nature has evolved opine dehydrogenases for this chemistry. To date, only one enzyme has been used as biocatalyst, however, analysis of the available sequence space suggests more enzymes to be exploited in synthetic organic chemistry. This review summarizes the current knowledge of this underexplored enzyme class, highlights key molecular, structural, and catalytic features with the aim to provide a comprehensive general description of opine dehydrogenases, thereby supporting future enzyme discovery and protein engineering studies.

Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications

This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.

Discovery of an Imine Reductase for Reductive Amination of Carbonyl Compounds with Sterically Challenging Amines

The synthesis of structurally diverse amines is of fundamental significance in the pharmaceutical industry due to the ubiquitous presence of amine motifs in biologically active molecules. Biocatalytic reductive amination for amine production has attracted great interest owing to its synthetic advantages. Herein, we report the direct synthesis of a wide range of sterically demanding secondary amines, including several important active pharmaceutical ingredients and pharmaceutical intermediates, via reductive amination of carbonyl substrates and bulky amine nucleophiles employing imine reductases. Key to success for this route is the identification of an imine reductase from Penicillium camemberti with unusual substrate specificity and its further engineering, which empowered the accommodation of a broad range of sterically demanding amine nucleophiles encompassing linear alkyl and (hetero)aromatic (oxy)alkyl substituents and the formation of final amine products with up to >99% conversion. The practical utility of the biocatalytic route has been demonstrated by its application in the preparative synthesis of the anti-hyperparathyroidism drug cinacalcet.

Modular Synthesis of α,α-Diaryl α-Amino Esters via Bi(V)-Mediated Arylation/SN2-Displacement of Kukhtin–Ramirez Intermediates

We report a concise and modular approach to α,α-diaryl α-amino esters from readily available α-keto esters. This mild, one-pot protocol proceeds via ketone umpolung, with in situ formation of a Kukhtin–Ramirez intermediate preceding sequential electrophilic arylation by Bi(V) and S_N2 displacement by an amine. The methodology is compatible with a wide range of anilines and primary amines - including derivatives of drugs and proteinogenic amino acids - Bi(V) arylating agents, and α-keto ester substrates.

Cu(II) Complexes with Proline-Derived Schiff Base Ligand: Chemical Resolution of N,C-Unprotected α-Amino Acids and Their Antibacterial Activity

An operationally simple and convenient resolution method via Cu(II) complexes was reported, efficiently providing valuable enantiopure N,C-unprotected α-amino acids. This protocol features synthetically attractive yields and a stereochemical outcome, using a recyclable Schiff base ligand and inexpensive easily accessible metal copper salts. These novel Cu(II) complexes can be obtained in an enantiopure state by means of column chromatography or recrystallization. Furthermore, all the Cu(II) complexes were evaluated for their antibacterial activities. Among them, complexes (S,2S)-3a, (S,2S)-3g, and (S,2S)-3o showed significant antibacterial activities against Staphylococcus aureus Mu50. Further biological evaluation indicated that they were effective against most of Gram-positive bacteria. It is the first study on the biological activities of transition metal complexes with this type of proline-derived Schiff base ligand.

Highly Sterically Hindered Peptide Bond Formation between α,α-Disubstituted α-Amino Acids and N-Alkyl Cysteines Using α,α-Disubstituted α-Amidonitrile

Peptides and proteins attract enormous attention in many fields of academia and industry. The introduction of unusual amino acids such as α,α-disubstituted α-amino acids or N-alkyl α-amino acids into normal peptide backbones is a well-utilized and useful tool for the modification of properties such as conformation, biological activity, and pharmacological profile. Despite the significant interest in sterically hindered peptides, research on peptides bearing an amide bond between an α,α-disubstituted α-amino acid and an N-alkyl α-amino acid remains underexplored because of the lack of an efficient synthetic approach. Herein, we describe a high-yielding synthetic method to access such extremely sterically hindered peptide bonds between amino acids. The reaction takes place between a peptide with an α,α-disubstituted α-amidonitrile and a second peptide bearing an N-alkyl cysteine, without a coupling reagent.

Efficient cell factories for the production of N-methylated amino acids and for methanol-based amino acid production

The growing world needs commodity amino acids such as L‐glutamate and L‐lysine for use as food and feed, and specialty amino acids for dedicated applications. To meet the supply a paradigm shift regarding their production is required. On the one hand, the use of sustainable and cheap raw materials is necessary to sustain low production cost and decrease detrimental effects of sugar‐based feedstock on soil health and food security caused by competing uses of crops in the feed and food industries. On the other hand, the biotechnological methods to produce functionalized amino acids need to be developed further, and titres enhanced to become competitive with chemical synthesis methods. In the current review, we present successful strain mutagenesis and rational metabolic engineering examples leading to the construction of recombinant bacterial strains for the production of amino acids such as L‐glutamate, L‐lysine, L‐threonine and their derivatives from methanol as sole carbon source. In addition, the fermentative routes for bioproduction of N‐methylated amino acids are highlighted, with focus on three strategies: partial transfer of methylamine catabolism, S‐adenosyl‐L‐methionine dependent alkylation and reductive methylamination of 2‐oxoacids.

Metabolic Engineering for Valorization of Agri- and Aqua-Culture Sidestreams for Production of Nitrogenous Compounds by Corynebacterium glutamicum

Corynebacterium glutamicum is used for the million-ton-scale production of amino acids. Valorization of sidestreams from agri- and aqua-culture has focused on the production of biofuels and carboxylic acids. Nitrogen present in various amounts in sidestreams may be valuable for the production of amines, amino acids and other nitrogenous compounds. Metabolic engineering of C. glutamicum for valorization of agri- and aqua-culture sidestreams addresses to bridge this gap. The product portfolio accessible via C. glutamicum fermentation primarily features amino acids and diamines for large-volume markets in addition to various specialty amines. On the one hand, this review covers metabolic engineering of C. glutamicum to efficiently utilize components of various sidestreams. On the other hand, examples of the design and implementation of synthetic pathways not present in native metabolism to produce sought after nitrogenous compounds will be provided. Perspectives and challenges of this concept will be discussed.

Mild and Expeditious Synthesis of Sulfenyl Enaminones of l-α-Amino Esters and Aryl/Alkyl Amines through NCS-Mediated Sulfenylation

Sulfenylation or selenylation of enaminones of l-α-amino esters requires mild reaction conditions due to the presence of a racemization-prone chiral center and reactive side chains. An N-chlorosuccinimide (NCS)-mediated methodology has been developed for rapid sulfenylation of enaminones of l-α-amino esters and aryl/alkyl amines at room temperature in open air under metal-free conditions. Enaminones of l-α-amino esters bearing aliphatic, aromatic, and heterocyclic side chains react efficiently with diverse aryl/alkyl/heteroaryl thiols (R1SH) in the presence of NCS to afford a library of biologically important sulfenyl enaminones in good-to-excellent yields (71-90%). Under similar reaction conditions, the enaminones also react with benzeneselenol to produce selenyl enaminones in good yield (73-83%). The NCS-mediated pathway generates sulfenyl chloride (R1SCl) as an intermediate which leads to rapid sulfenylation of enaminones through cross-dehydrogenative coupling (CDC) under mild reaction conditions.

Synthetic Enzyme-Catalyzed CO2 Fixation Reactions

In recent years, (de)carboxylases that catalyze reversible (de)carboxylation have been targeted for application as carboxylation catalysts. This has led to the development of proof-of-concept (bio)synthetic CO2 fixation routes for chemical production. However, further progress towards industrial application has been hampered by the thermodynamic constraint that accompanies fixing CO2 to organic molecules. In this Review, biocatalytic carboxylation methods are discussed with emphases on the diverse strategies devised to alleviate the inherent thermodynamic constraints and their application in synthetic CO2 -fixation cascades.

Sustainable Production of N-methylphenylalanine by Reductive Methylamination of Phenylpyruvate Using Engineered Corynebacterium glutamicum

N-alkylated amino acids occur widely in nature and can also be found in bioactive secondary metabolites such as the glycopeptide antibiotic vancomycin and the immunosuppressant cyclosporine A. To meet the demand for N-alkylated amino acids, they are currently produced chemically; however, these approaches often lack enantiopurity, show low product yields and require toxic reagents. Fermentative routes to N-alkylated amino acids like N-methyl-l-alanine or N-methylantranilate, a precursor of acridone alkaloids, have been established using engineered Corynebacterium glutamicum, which has been used for the industrial production of amino acids for decades. Here, we describe metabolic engineering of C. glutamicum for de novo production of N-methylphenylalanine based on reductive methylamination of phenylpyruvate. Pseudomonas putida Δ-1-piperideine-2-carboxylate reductase DpkA containing the amino acid exchanges P262A and M141L showed comparable catalytic efficiencies with phenylpyruvate and pyruvate, whereas the wild-type enzyme preferred the latter substrate over the former. Deletion of the anthranilate synthase genes trpEG and of the genes encoding branched-chain amino acid aminotransferase IlvE and phenylalanine aminotransferase AroT in a strain engineered to overproduce anthranilate abolished biosynthesis of l-tryptophan and l-phenylalanine to accumulate phenylpyruvate. Upon heterologous expression of DpkA^P262A,M141L, N-methylphenylalanine production resulted upon addition of monomethylamine to the medium. In glucose-based minimal medium, an N-methylphenylalanine titer of 0.73 ± 0.05 g L⁻¹, a volumetric productivity of 0.01 g L⁻¹ h⁻¹ and a yield of 0.052 g g⁻¹ glucose were reached. When xylose isomerase gene xylA from Xanthomonas campestris and the endogenous xylulokinase gene xylB were expressed in addition, xylose as sole carbon source supported production of N-methylphenylalanine to a titer of 0.6 ± 0.04 g L⁻¹ with a volumetric productivity of 0.008 g L⁻¹ h⁻¹ and a yield of 0.05 g g⁻¹ xylose. Thus, a fermentative route to sustainable production of N-methylphenylalanine by recombinant C. glutamicum has been established.

Asymmetric Synthesis of N-Substituted α-Amino Esters from α-Ketoesters via Imine Reductase-Catalyzed Reductive Amination

N-Substituted α-amino esters are widely used as chiral intermediates in a range of pharmaceuticals. Here we report the enantioselective biocatalyic synthesis of N-substituted α-amino esters through the direct reductive coupling of α-ketoesters and amines employing sequence diverse metagenomic imine reductases (IREDs). Both enantiomers of N-substituted α-amino esters were obtained with high conversion and excellent enantioselectivity under mild reaction conditions. In addition >20 different preparative scale transformations were performed highlighting the scalability of this system.

Reprogramming natural proteins using unnatural amino acids

Unnatural amino acids have gained significant attention in protein engineering and drug discovery as they allow the evolution of proteins with enhanced stability and activity. The incorporation of unnatural amino acids into proteins offers a rational approach to engineer enzymes for designing efficient biocatalysts that exhibit versatile physicochemical properties and biological functions. This review highlights the biological and synthetic routes of unnatural amino acids to yield a modified protein with altered functionality and their incorporation methods. Unnatural amino acids offer a wide array of applications such as antibody-drug conjugates, probes for change in protein conformation and structure–activity relationships, peptide-based imaging, antimicrobial activities, etc. Besides their emerging applications in fundamental and applied science, systemic research is necessary to explore unnatural amino acids with novel side chains that can address the limitations of natural amino acids.

Incorporation of unnatural amino acids into protein offers wide array of applications in fundamental and applied science.

Structural diversity in the coordination compounds of cobalt, nickel and copper with N-alkylglycinates: crystallographic and ESR study in the solid state

Reactions of N-methylglycine (HMeGly), N-ethylglycine-hydrochloride (H₂EtGlyCl) and N-propylglycine-hydrochloride (H₂PrGlyCl) with cobalt(ii), nickel(ii) and copper(ii) ions in aqueous solutions resulted in ten new coordination compounds [Co(MeGly)₂(H₂O)₂] (1), [{Co(MeGly)₂}₂(μ-OH)₂]·2H₂O (1d), [Cu(MeGly)₂(H₂O)₂] (2α), [Co(EtGly)₂(H₂O)₂] (3), [Ni(EtGly)₂(H₂O)₂] (4), [Cu(μ-EtGly)₂]_n (5p), [Co(PrGly)₂(H₂O)₂] (6), [Ni(PrGly)₂(H₂O)₂] (7), and two polymorphs of [Cu(PrGly)₂(H₂O)₂] (8α and 8β). Compounds were characterized by single-crystal and powder X-ray diffraction, infrared spectroscopy, thermal analysis and X-band electron spin resonance (ESR) spectroscopy. These studies revealed a wide range of structural types including monomeric, dimeric and polymeric architectures, as well as different polymorphs. In all monomeric compounds, except 2α, and in the coordination polymer 5p hydrogen bonds interconnect the molecules into 2D layers with the alkyl chain pointing outward of the layer. In 2α and in the dimeric compound 1d hydrogen bonds link the molecules into 3D structures. 1d with cobalt(iii), and 4 and 7 with nickel(ii) are ESR silent. The ESR spectra of 1, 3 and 6 are characteristic for paramagnetic high-spin cobalt(ii). The ESR spectra of all copper(ii) coordination compounds show that the unpaired copper electron is located in the d_x²−y² orbital, being in agreement with the elongated octahedral geometry.

Interactions in copper, nickel and cobalt complexes with N-methyl-, N-ethyl- and N-propylglycinate: monomers, dimer and polymers.

Fermentative N-Methylanthranilate Production by Engineered Corynebacterium glutamicum

The N-functionalized amino acid N-methylanthranilate is an important precursor for bioactive compounds such as anticancer acridone alkaloids, the antinociceptive alkaloid O-isopropyl N-methylanthranilate, the flavor compound O-methyl-N-methylanthranilate, and as a building block for peptide-based drugs. Current chemical and biocatalytic synthetic routes to N-alkylated amino acids are often unprofitable and restricted to low yields or high costs through cofactor regeneration systems. Amino acid fermentation processes using the Gram-positive bacterium Corynebacterium glutamicum are operated industrially at the million tons per annum scale. Fermentative processes using C. glutamicum for N-alkylated amino acids based on an imine reductase have been developed, while N-alkylation of the aromatic amino acid anthranilate with S-adenosyl methionine as methyl-donor has not been described for this bacterium. After metabolic engineering for enhanced supply of anthranilate by channeling carbon flux into the shikimate pathway, preventing by-product formation and enhancing sugar uptake, heterologous expression of the gene anmt encoding anthranilate N-methyltransferase from Ruta graveolens resulted in production of N-methylanthranilate (NMA), which accumulated in the culture medium. Increased SAM regeneration by coexpression of the homologous adenosylhomocysteinase gene sahH improved N-methylanthranilate production. In a test bioreactor culture, the metabolically engineered C. glutamicum C1* strain produced NMA to a final titer of 0.5 g·L⁻¹ with a volumetric productivity of 0.01 g·L⁻¹·h⁻¹ and a yield of 4.8 mg·g⁻¹ glucose.

Fermentative Production of N-Alkylated Glycine Derivatives by Recombinant Corynebacterium glutamicum Using a Mutant of Imine Reductase DpkA From Pseudomonas putida

Sarcosine, an N-methylated amino acid, shows potential as antipsychotic, and serves as building block for peptide-based drugs, and acts as detergent when acetylated. N-methylated amino acids are mainly produced chemically or by biocatalysis, with either low yields or high costs for co-factor regeneration. Corynebacterium glutamicum, which is used for the industrial production of amino acids for decades, has recently been engineered for production of N-methyl-L-alanine and sarcosine. Heterologous expression of dpkA in a C. glutamicum strain engineered for glyoxylate overproduction enabled fermentative production of sarcosine from sugars and monomethylamine. Here, mutation of an amino acyl residue in the substrate binding site of DpkA (DpkAF117L) led to an increased specific activity for reductive alkylamination of glyoxylate using monomethylamine and monoethylamine as substrates. Introduction of DpkAF117L into the production strain accelerated the production of sarcosine and a volumetric productivity of 0.16 g L-1 h-1 could be attained. Using monoethylamine as substrate, we demonstrated N-ethylglycine production with a volumetric productivity of 0.11 g L-1 h-1, which to the best of our knowledge is the first report of its fermentative production. Subsequently, the feasibility of using rice straw hydrolysate as alternative carbon source was tested and production of N-ethylglycine to a titer of 1.6 g L-1 after 60 h of fed-batch bioreactor cultivation could be attained.