Structural and Mutagenesis Studies of the Thiamine-Dependent, Ketone-Accepting YerE from Pseudomonas protegens

Carboligation towards production of hydroxypentanones

2-Hydroxy-3-pentanone and 3-hydroxy-2-pentanone are flavor molecules present in various foods, such as cheese, wine, durian, and honey, where they impart buttery, hay-like, and caramel-sweet aromas. However, their utilization as flavoring agents is constrained by a lack of developed synthesis methods. In this study, we present their synthesis from simple starting compounds available in natural quality, catalyzed by previously characterized ThDP-dependent carboligases. Additionally, we demonstrate that newly discovered homologues of pyruvate dehydrogenase from E. coli (EcPDH E1), namely LaPDH from Leclercia adecarboxylata, CnPDH from Cupriavidus necator, and TcPDH from Tanacetum cinerariifolium, exhibit promising potential for α-hydroxy pentanone synthesis in form of whole-cell biocatalysts. Enzyme stability at varying pH levels, kinetic parameters, and reaction intensification were investigated. CnPDH, for example, exhibits superior stability across different pH levels compared to EcPDH E1. Both α-hydroxy pentanones can be produced with CnPDH in satisfactory yields (74% and 59%, respectively).

Identification and Characterization of Thiamine Diphosphate-Dependent Lyases with an Unusual CDG Motif

The thiamine diphosphate (ThDP)-binding motif, characterized by the canonical GDG(X)24-27N sequence, is highly conserved among ThDP-dependent enzymes. We investigated a ThDP-dependent lyase (JanthE from Janthinobacterium sp. HH01) with an unusual cysteine (C458) replacing the first glycine of this motif. JanthE exhibits a high substrate promiscuity and accepts long aliphatic α-keto acids as donors. Sterically hindered aromatic aldehydes or non-activated ketones are acceptor substrates, giving access to a variety of secondary and tertiary alcohols as carboligation products. The crystal structure solved at a resolution of 1.9 Å reveals that C458 is not primarily involved in cofactor binding as previously thought for the canonical glycine. Instead, it coordinates methionine 406, thus ensuring the integrity of the active site and the enzyme activity. In addition, we have determined the long-sought genuine tetrahedral intermediates formed with pyruvate and 2-oxobutyrate in the pre-decarboxylation states and deciphered the atomic details for their stabilization in the active site. Collectively, we unravel an unexpected role for the first residue of the ThDP-binding motif and unlock a family of lyases that can perform valuable carboligation reactions.

Unifying Scheme for the Biosynthesis of Acyl-Branched Sugars: Extended Substrate Scope of Thiamine-Dependent Enzymes

Thiamine diphosphate (ThDP) dependent enzymes are useful catalysts for asymmetric C−C bond formation through benzoin‐type condensation reactions that result in α‐hydroxy ketones. A wide range of aldehydes and ketones can be used as acceptor substrates; however, the donor substrate range is mostly limited to achiral α‐keto acids and simple aldehydes. By using a unifying retro‐biosynthetic approach towards acyl‐branched sugars, we identified a subclass of (myco)bacterial ThDP‐dependent enzymes with a greatly extended donor substrate range, namely functionalized chiral α‐keto acids with a chain length from C₄ to C₈. Highly enantioenriched acyloin products were obtained in good to high yields and several reactions were performed on a preparative scale. The newly introduced functionalized α‐keto acids, accessible by known aldolase‐catalyzed transformations, substantially broaden the donor substrate range of ThDP‐dependent enzymes, thus enabling a more general use of these already valuable catalysts.

Recent Developments in the Synthesis of β-Diketones

Apart from being one of the most important intermediates in chemical synthesis, broadly used in the formation of C-C bonds among other processes, the β-dicarbonyl structure is present in a huge number of biologically and pharmaceutically active compounds. In fact, mainly derived from the well-known antioxidant capability associated with the corresponding enol tautomer, β-diketones are valuable compounds in the treatment of many pathological disorders, such as cardiovascular and liver diseases, hypertension, obesity, diabetes, neurological disorders, inflammation, skin diseases, fibrosis, or arthritis; therefore, the synthesis of these structures is an area of overwhelming interest for organic chemists. This paper is devoted to the advances achieved in the last ten years for the preparation of 1,3-diketones, using different chemical (Claisen, hydration of alkynones, decarboxylative coupling) or catalytic (biocatalysis, organocatalytic, metal-based catalysis) methodologies: Additionally, the preparation of branched β-dicarbonyl compounds by means of α-functionalization of non-substituted 1,3-diketones are also discussed.

Robust Model Selection: Flatness-Based Optimal Experimental Design for a Biocatalytic Reaction

Considering the competitive and strongly regulated pharmaceutical industry, mathematical modeling and process systems engineering might be useful tools for implementing quality by design (QbD) and quality by control (QbC) strategies for low-cost but high-quality drugs. However, a crucial task in modeling (bio)pharmaceutical manufacturing processes is the reliable identification of model candidates from a set of various model hypotheses. To identify the best experimental design suitable for a reliable model selection and system identification is challenging for nonlinear (bio)pharmaceutical process models in general. This paper is the first to exploit differential flatness for model selection problems under uncertainty, and thus translates the model selection problem to advanced concepts of systems theory and controllability aspects, respectively. Here, the optimal controls for improved model selection trajectories are expressed analytically with low computational costs. We further demonstrate the impact of parameter uncertainties on the differential flatness-based method and provide an effective robustification strategy with the point estimate method for uncertainty quantification. In a simulation study, we consider a biocatalytic reaction step simulating the carboligation of aldehydes, where we successfully derive optimal controls for improved model selection trajectories under uncertainty.

Biosynthesis of Diverse Antimicrobial and Antiproliferative Acyloins in Anaerobic Bacteria

Metabolic profiling and genome mining revealed that anaerobic bacteria have the potential to produce acyloin natural products. In addition to sattazolin A and B, three new sattazolin congeners and a novel acyloin named clostrocyloin were isolated from three strains of Clostridium beijerinckii, a bacterium used for industrial solvent production. Bioactivity profiling showed that the sattazolin derivatives possess antimicrobial activities against mycobacteria and pseudomonads with only low cytotoxicity. Clostrocyloin was found to be mainly active against fungi. The thiamine diphosphate (ThDP)-dependent sattazolin-producing synthase was identified in silico and characterized both in vivo and in in vitro enzyme assays. A related acyloin synthase from the clostrocyloin producer was shown to be responsible for the production of the acyloin core of clostrocyloin. The biotransformation experiments provided first insights into the substrate scope of the clostrocyloin synthase and revealed biosynthetic intermediates.