Amine-Mediated Enzymatic Carboxylation of Phenols Using CO2 as Substrate Increases Equilibrium Conversions and Reaction Rates

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Substrate Promiscuity of Thermoplasma acidophilum Malic Enzyme for CO2 Fixation Reaction

CO2 fixation technology has gained attention as a method to effectively utilize the abundant CO2 in the atmosphere by converting it into useful chemicals. However, since CO2 is a highly stable molecule, many of the currently developed methods for chemical CO2 fixation require harsh conditions and reactive reagents. The establishment of efficient and sustainable processes is eagerly awaited. In this study, we investigated a biocatalytic process and achieved a carboxylation reaction under mild conditions (37 °C, 0.1 MPa CO2) using a biocatalyst, Thermoplasma acidophilum NADP+-malic enzyme (TaME), and gaseous CO2 by coupling enzymatic coenzyme regeneration. We also demonstrated for the first time that the carboxylation reaction by ME proceeds not only with pyruvate, a natural substrate, but also with 2-ketoglutarate.

A pushed biosynthesis of 2,6-dihydroxybenzoic acid by the recombinant 2,3-dihydroxybenzoic acid decarboxylase immobilized on novel amino-modified lignin-containing cellulose nanocrystal aerogel

Production of 2,6-dihydroxybenzoic acid (2,6-DHBA) via enzymatic carboxylation of resorcinol by decarboxylases is of great promising but shows depressed equilibrium conversion. In this study, 2,3-dihydroxybenzoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao) pushing the conversion towards carboxylation for efficient 2,6-DHBA biosynthesis was achieved. Meanwhile, a novel amino-modified and lignin-doped cellulose nanocrystal aerogel (A-LCNCA) with high specific surface area and prominent CO2 capture was prepared for 2,3-DHBD_Ao immobilization. 2,3-DHBD_Ao@A-LCNC contributed a further enhanced conversion of carboxylation with the maximal conversion of 76.2 %, which was correlated to both the activity of 2,3-DHBD_Ao and the high CO2 loading capacity of A-LCNCA. Moreover, 2,3-DHBD_Ao@A-LCNC exhibited superior performances in a wider range of temperature and higher concentrations of substrate, with a prolonged storage period longer than 30 days. After seven cycles reuse, 2,3-DHBD_Ao@A-LCNCA could retain 85.3 % of its original activity. These results suggest a considerable potential of 2,3-DHBD_Ao@A-LCNCA in the selective biosynthesis of 2,6-DHBA.

Enzymatic Carboxylation of Resorcinol in Aqueous Triethanolamine at Elevated CO2 Pressure

The fixation of CO2 by enzymatic carboxylation for production of valuable carboxylic acids is one way to recycle carbon. Unfortunately, this type of reaction is limited by an unfavourable thermodynamic equilibrium. An excess of the C1 substrate is required to increase conversions. Solvents with a high CO2 solubility, such as amines, can provide the C1 substrate in excess. Here, we report on the effect of CO2 pressures up to 1100 kPa on the enzymatic carboxylation of resorcinol in aqueous triethanolamine. Equilibrium yields correlate to the bicarbonate concentration. However, inhibition is observed at elevated pressure, severely reducing the enzyme activity. The reaction yields were reduced at higher pressures, whereas at ambient pressure, higher yields were achieved. Overall, CO2 pressures above 100 kPa have been demonstrated to be counterproductive for improving the biotransformation, as productivity decreases rapidly for only a modest improvement in conversion. It is expected that CO2 carbamylation intensifies at elevated CO2 pressures, causing the inhibition of the enzyme. To further increase the reaction yield, the in situ product precipitation is tested by the addition of the quaternary ammonium salt tetrabutylammonium bromide.

Enzymatic Conversion of CO2: From Natural to Artificial Utilization

Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.

Structural Basis of Salicylic Acid Decarboxylase Reveals a Unique Substrate Recognition Mode and Access Channel

Salicylic acid (SA) decarboxylase from Trichosporon moniliiforme (TmSdc), which reversibly catalyses the decarboxylation of SA to yield phenol, is of significant interest because of its potential for the production of benzoic acid derivatives under environmentally friendly reaction conditions. TmSdc showed a preference for C2 hydroxybenzoate derivatives, with k_cat/K_m of SA being 3.2 × 10³ M^-1 s^-1. Here, we presented the first crystal structures of TmSdc, including a complex with SA. The three conserved residues of Glu8, His169, and Asp298 are the catalytic residues within the TIM-barrel domain of TmSdc. Trp239 forms a unique hydrophobic recognition site by interacting with the phenyl ring of SA, while Arg235 is responsible for recognizing the hydroxyl group at the C2 of SA via hydrogen bond interactions. Using a semi-rational combinatorial active-site saturation test, we obtained the TmSdc mutant MT3 (Y64T/P191G/F195V/E302D), which exhibited a 26.4-fold increase in k_cat/K_m with SA, reaching 8.4 × 10⁴ M^-1 s^-1. Steered molecular dynamics simulations suggested that the structural changes in MT3 relieved the steric hindrance within the substrate access channel and enlarged the substrate-binding pocket, leading to the increased activity by improving substrate access. Our data elucidate the unique substrate recognition mode and the substrate entrance tunnel of SA decarboxylase.

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.

Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus oryzae

Broad substrate tolerance and excellent regioselectivity, as well as independence from sensitive cofactors have established benzoic acid decarboxylases from microbial sources as efficient biocatalysts. Robustness under process conditions makes them particularly attractive for preparative-scale applications. The divalent metal-dependent enzymes are capable of catalyzing the reversible non-oxidative (de)carboxylation of a variety of electron-rich (hetero)aromatic substrates analogously to the chemical Kolbe-Schmitt reaction. Elemental mass spectrometry supported by crystal structure elucidation and quantum chemical calculations verified the presence of a catalytically relevant Mg2+ complexed in the active site of 2,3-dihydroxybenoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao). This unique example with respect to the nature of the metal is in contrast to mechanistically related decarboxylases, which generally have Zn2+ or Mn2+ as the catalytically active metal.

Microbubble enhanced mass transfer efficiency of CO2 capture utilizing aqueous triethanolamine for enzymatic resorcinol carboxylation

The present study focuses on the aeration of aqueous triethanolamine acting as reaction medium for biocatalytic carboxylations. For enhancing mass transfer in a bubble column reactor, microbubble aeration is applied and compared to conventional macrobubble aeration. Application of a 0.5 μm porous sparger enables microbubble CO₂ aeration with bubble size distributions below 150 μm in Sauter mean diameter, correlating with the highest measured mass transfer rates. During CO₂ saturation of the aqueous triethanolamine, bubble size distributions changed according to the level of CO₂ saturation. For microbubbles, less foaming was observed compared to macrobubble aeration by a 10 μm porous sparger. This microbubble effect is attributed to their accelerated dissolution assisted by the Laplace pressure lowering the amount of bubbles reaching the surface of the liquid. The experiments reveal that the rate of interfacial area generation, which is calculated based on measured bubble size distributions, influences the biocatalyst activity.

An inline method to investigate microbubble enhanced mass transfer and its effect on a model biocatalyst utilizing CO₂ for carboxylation.

Carboxylation of Hydroxyaromatic Compounds with HCO3− by Enzyme Catalysis: Recent Advances Open the Perspective for Valorization of Lignin-Derived Aromatics

This review focuses on recent advances in the field of enzymatic carboxylation reactions of hydroxyaromatic compounds using HCO3− (as a CO2 source) to produce hydroxybenzoic and other phenolic acids in mild conditions with high selectivity and moderate to excellent yield. Nature offers an extensive portfolio of enzymes catalysing reversible decarboxylation of hydroxyaromatic acids, whose equilibrium can be pushed towards the side of the carboxylated products. Extensive structural and mutagenesis studies have allowed recent advances in the understanding of the reaction mechanism of decarboxylase enzymes, ultimately enabling an improved yield and expansion of the scope of the reaction. The topic is of particular relevance today as the scope of the carboxylation reactions can be extended to include lignin-related compounds in view of developing lignin biorefinery technology.