Some New Developments in Reductive Amtnation with Cofactor Regeneration

Changing the Electron Acceptor Specificity of Rhodobacter capsulatus Formate Dehydrogenase from NAD+ to NADP. Int J Mol Sci 2023;24:16067. [PMID: 38003259 PMCID: PMC10671435 DOI: 10.3390/ijms242216067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Formate dehydrogenases catalyze the reversible oxidation of formate to carbon dioxide. These enzymes play an important role in CO2 reduction and serve as nicotinamide cofactor recycling enzymes. More recently, the CO2-reducing activity of formate dehydrogenases, especially metal-containing formate dehydrogenases, has been further explored for efficient atmospheric CO2 capture. Here, we investigate the nicotinamide binding site of formate dehydrogenase from Rhodobacter capsulatus for its specificity toward NAD+ vs. NADP+ reduction. Starting from the NAD+-specific wild-type RcFDH, key residues were exchanged to enable NADP+ binding on the basis of the NAD+-bound cryo-EM structure (PDB-ID: 6TG9). It has been observed that the lysine at position 157 (Lys157) in the β-subunit of the enzyme is essential for the binding of NAD+. RcFDH variants that had Glu259 exchanged for either a positively charged or uncharged amino acid had additional activity with NADP+. The FdsBL279R and FdsBK276A variants also showed activity with NADP+. Kinetic parameters for all the variants were determined and tested for activity in CO2 reduction. The variants were able to reduce CO2 using NADPH as an electron donor in a coupled assay with phosphite dehydrogenase (PTDH), which regenerates NADPH. This makes the enzyme suitable for applications where it can be coupled with other enzymes that use NADPH.

Crystal Structures and Catalytic Mechanism of l-erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering for Asymmetric Synthesis of β-Amino Acids

Amino acid dehydrogenases (AADHs) have shown considerable potential as biocatalysts in the asymmetric synthesis of chiral amino acids. However, compared to the widely studied α-AADHs, limited knowledge is available about β-AADHs that enable the synthesis of β-amino acids. Herein, we report the crystal structures of a l-erythro-3,5-diaminohexanoate dehydrogenase and its variants, the only known member of β-AADH family. Crystal structure analysis, site-directed mutagenesis studies and quantum chemical calculations revealed the differences in the substrate binding and catalytic mechanism from α-AADHs. A number of rationally engineered variants were then obtained with improved activity (by 110-800 times) toward various aliphatic β-amino acids without an enantioselectivity trade-off. Two β-amino acids were prepared by using the outstanding variants with excellent enantioselectivity (>99 % ee) and high isolated yields (86-87 %). These results provide important insights into the molecular mechanism of 3,5-DAHDH, and establish a solid foundation for further design of β-AADHs for the asymmetric synthesis of β-amino acids.

Enantioselective biocatalytic formal α-amination of hexanoic acid to l-norleucine

A three-step one-pot biocatalytic cascade enabled the enantioselective formal α-amination of hexanoic acid to l-norleucine in >97% ee.

Enzymatic asymmetric synthesis of chiral amino acids

This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.

Establishing a Mathematical Equations and Improving the Production of L-tert-Leucine by Uniform Design and Regression Analysis

L-tert-Leucine (L-Tle) and its derivatives are extensively used as crucial building blocks for chiral auxiliaries, pharmaceutically active ingredients, and ligands. Combining with formate dehydrogenase (FDH) for regenerating the expensive coenzyme NADH, leucine dehydrogenase (LeuDH) is continually used for synthesizing L-Tle from α-keto acid. A multilevel factorial experimental design was executed for research of this system. In this work, an efficient optimization method for improving the productivity of L-Tle was developed. And the mathematical model between different fermentation conditions and L-Tle yield was also determined in the form of the equation by using uniform design and regression analysis. The multivariate regression equation was conveniently implemented in water, with a space time yield of 505.9 g L^-1 day^-1 and an enantiomeric excess value of >99 %. These results demonstrated that this method might become an ideal protocol for industrial production of chiral compounds and unnatural amino acids such as chiral drug intermediates.

Construction of a tunable multi-enzyme-coordinate expression system for biosynthesis of chiral drug intermediates

Systems that can regulate and coordinate the expression of multiple enzymes for metabolic regulation and synthesis of important drug intermediates are poorly explored. In this work, a strategy for constructing a tunable multi-enzyme-coordinate expression system for biosynthesis of chiral drug intermediates was developed and evaluated by connecting protein-protein expressions, regulating the strength of ribosome binding sites (RBS) and detecting the system capacity for producing chiral amino acid. Results demonstrated that the dual-enzyme system had good enantioselectivity, low cost, high stability, high conversion rate and approximately 100% substrate conversion. This study has paved a new way of exploring metabolic mechanism of functional genes and engineering whole cell-catalysts for synthesis of chiral α-hydroxy acids or chiral amino acids.

Engineering of alanine dehydrogenase from Bacillus subtilis for novel cofactor specificity

The l-alanine dehydrogenase of Bacillus subtilis (BasAlaDH), which is strictly dependent on NADH as redox cofactor, efficiently catalyzes the reductive amination of pyruvate to l-alanine using ammonia as amino group donor. To enable application of BasAlaDH as regenerating enzyme in coupled reactions with NADPH-dependent alcohol dehydrogenases, we alterated its cofactor specificity from NADH to NADPH via protein engineering. By introducing two amino acid exchanges, D196A and L197R, high catalytic efficiency for NADPH was achieved, with k_cat /K_M  = 54.1 µM^-1  Min^-1 (K_M  = 32 ± 3 µM; k_cat  = 1,730 ± 39 Min^-1 ), almost the same as the wild-type enzyme for NADH (k_cat /K_M  = 59.9 µM^-1  Min^-1 ; K_M  = 14 ± 2 µM; k_cat  = 838 ± 21 Min^-1 ). Conversely, recognition of NADH was much diminished in the mutated enzyme (k_cat /K_M  = 3 µM^-1  Min^-1 ). BasAlaDH(D196A/L197R) was applied in a coupled oxidation/transamination reaction of the chiral dicyclic dialcohol isosorbide to its diamines, catalyzed by Ralstonia sp. alcohol dehydrogenase and Paracoccus denitrificans ω-aminotransferase, thus allowing recycling of the two cosubstrates NADP⁺ and l-Ala. An excellent cofactor regeneration with recycling factors of 33 for NADP⁺ and 13 for l-Ala was observed with the engineered BasAlaDH in a small-scale biocatalysis experiment. This opens a biocatalytic route to novel building blocks for industrial high-performance polymers.

An exceptionally DMSO-tolerant alcohol dehydrogenase for the stereoselective reduction of ketones

A novel short-chain alcohol dehydrogenase from Paracoccus pantotrophus DSM 11072, which is applicable for hydrogen transfer, has been identified, cloned, and overexpressed in E. coli. The enzyme stereoselectively reduces several ketones in a sustainable substrate-coupled approach using 2-propanol (5% v/v) as hydrogen donor. The enzyme maintained its activity in organic co-solvents in biphasic as well as monophasic systems and was even active in micro-aqueous media (1% v/v aqueous buffer). In general, a higher conversion was observed at higher log P values of the solvent, however, DMSO, which exhibits the lowest log P value of all solvents investigated, was not only tolerated but led to a higher conversion and relative activity (110-210%). For example, the conversion after 24 h in 15% v/v DMSO was double that for the reaction performed in buffer. This tolerance to DMSO may be attributed to the ability of the wild-type strain to adapt and grow in media with high sulfur content.

Biocatalytic reductions: from lab curiosity to "first choice"

Enzyme-catalyzed reductions have been studied for decades and have been introduced in more than 10 industrial processes for production of various chiral alcohols, alpha-hydroxy acids and alpha-amino acids. The earlier hurdle of expensive cofactors was taken by the development of highly efficient cofactor regeneration methods. In addition, the accessible number of suitable dehydrogenases and therefore the versatility of this technology is constantly increasing and currently expanding beyond asymmetric production of alcohols and amino acids. Access to a large set of enzymes for highly selective C=C reductions and reductive amination of ketones for production of chiral secondary amines and the development of improved D-selective amino acid dehydrogenases will fuel the next wave of industrial bioreduction processes.

Mechanism and applications of phosphite dehydrogenase

Phosphite dehydrogenase catalyzes the NAD+-dependent oxidation of hydrogen phosphonate (common name phosphite) to phosphate in what amounts to a formal phosphoryl transfer reaction from hydride to hydroxide. This review places the enzyme in the context of phosphorus redox metabolism in nature and discusses the results of mechanistic investigations into its reaction mechanism. The potential of the enzyme as a NAD(P)H cofactor regeneration system is discussed as well as efforts to engineer the cofactor specificity of the protein.

Recent developments in pyridine nucleotide regeneration

NAD(P)-dependent oxidoreductases are valuable tools for the synthesis of chiral compounds. Due to the high cost of the pyridine cofactors, in situ cofactor regeneration is required for preparative applications. In recent years, existing regeneration methodologies have been improved and new approaches have been devised. These include the use of newly discovered dehydrogenases that are stable in high contents of organic solvent and novel enzymes that can regenerate either the reduced or oxidized forms of the cofactor. The use of electrochemical methods has allowed cofactor regeneration for monooxygenases and natural or engineered whole-cell systems provide alternatives to approaches relying on purified enzymes.

Practical asymmetric enzymatic reduction through discovery of a dehydrogenase-compatible biphasic reaction media

[reaction: see text] An enzyme-compatible biphasic reaction media for the asymmetric biocatalytic reduction of ketones with in situ cofactor regeneration has been developed. In this biphasic reaction media, which is advantageous for reactions at higher substrate concentrations, both enzymes (alcohol dehydrogenase and FDH from Candida boidinii) remain stable. The reductions with poorly water-soluble ketones were carried out at substrate concentrations of 10-200 mM, and the optically active (S)-alcohols were formed with moderate to good conversions and with up to >99% ee.

Preparative resolution of the enantiomers of tert-leucine derivatives by simulated moving bed chromatography

The enantiomers of two different derivatives of tert-leucine were separated by continuous chromatography on chiral stationary phases applying the simulated moving bed technique. About 1 kg of racemic N-carbobenzoxy-tert-leucine was resolved on the cellulose-based phase Chiralcel OD using a mixture of heptane/ethanol and 0.1% of trifluoroacetic acid modifier as the mobile phase, while 520 g of the N-Boc-tert-leucine-benzylester was resolved on the amylose-based phase Chiralpak AD with a mixture of heptane/2-propanol as the mobile phase. In both instances the corresponding enantiomers were obtained in high yield and high optical purity.

New alcohol dehydrogenases for the synthesis of chiral compounds

The enantioselective reduction of carbonyl groups is of interest for the production of various chiral compounds such as hydroxy acids, amino acids, hydroxy esters, or alcohols. Such products have high economic value and are most interesting as additives for food and feed or as building blocks for organic synthesis. Enzymatic reactions or biotransformations with whole cells (growing or resting) for this purpose are described. Although conversions with whole cells are advantageous with respect to saving expensive isolation of the desired enzymes, the products often lack high enantiomeric excess and the process results in low time-space-yield. For the synthesis of chiral alcohols, only lab-scale syntheses with commercially available alcohol dehydrogenases have been described yet. However, most of these enzymes are of limited use for technical applications because they lack substrate specificity, stability (yeast ADH) or enantioselectivity (Thermoanaerobium brockii ADH). Furthermore, all enzymes so far described are forming (S)-alcohols. Quite recently, we found and characterized several new bacterial alcohol dehydrogenases, which are suited for the preparation of chiral alcohols as well as for hydroxy esters in technical scale. Remarkably, of all these novel ADHs the (R)-specific enzymes were found in strains of the genus Lactobacillus. Meanwhile, these new enzymes were characterized extensively. Protein data (amino acid sequence, bound cations) confirm that these catalysts are novel enzymes. (R)-specific as well as (S)-specific ADHs accept a broad variety of ketones and ketoesters as substrates. The applicability of alcohol dehydrogenases for chiral syntheses as an example for the technical use of coenzyme-dependent enzymes is demonstrated and discussed in this contribution. In particular NAD-dependent enzymes coupled with the coenzyme regeneration by formate dehydrogenase proved to be economically feasible for the production of fine chemicals.