CC bond formation using ThDP-dependent lyases

An enzyme catalyzed umpolung strategy for the green synthesis of Schiff bases and their derivatives

In organic chemistry, the umpolung reaction is an important concept that significantly expands the chemical space and provides unique structures. Although prior research focused on constructing complex molecular frameworks using phase transfer catalysts, the umpolung reaction is well known for its roles in 1,4-conjugate addition and Stetter reactions. Herein, we reported a novel enzymatic approach using immobilized transaminase CV2025 to catalyze the umpolung conjugate addition reaction. This method facilitates the nucleophilic addition of 2-(nitrophenyl)-N-(trifluoromethyl) imine to cyclopentanone, efficiently synthesized a complex imine and its derivatives up to 78% yield. Unlike traditional methods, this enzymatic strategy eliminates the need of a transition metal or chemical (acid, base) catalyst, broadens the substrate scope, and operates under milder conditions. Mechanistic studies, supported by molecular dynamics calculations and alanine scanning mutagenesis, identified key residues influencing regioselectivity. This study presents a sustainable, enzyme-catalyzed method for constructing complex frameworks with broad potential in pharmaceutical synthesis and beyond.

Structural insights into two thiamine diphosphate-dependent enzymes and their synthetic applications in carbon-carbon linkage reactions

The α-hydroxy-β-keto acid synthases are thiamine diphosphate-dependent enzymes catalysing carbon-carbon linkage reactions in the biosynthesis of primary metabolites and various secondary metabolites. However, the substrate selectivity and catalytic stereoselectivity of α-hydroxy-β-keto acid synthases are poorly understood, greatly hindering their synthetic application in generating diverse carbon frameworks. We here report the discovery of two new α-hydroxy-β-keto acid synthases CsmA and BbmA, which show different substrate selectivities in catalysing carbon-carbon coupling reactions between two β-keto acids. Four crystal structures of CsmA or BbmA complexed with thiamine diphosphate and their substrates were determined, clearly revealing their structural bases of substrate selectivity and catalytic stereoselectivity. Substrate scope expansion enables us to generate 120 α-hydroxy-β-keto acids together with 240 NaBH4-reduction products. Furthermore, we applied CsmA and BbmA into enzymatic total synthesis, generating 36 γ-butyrolactone-containing furanolides. These results provide new structural insights into the catalyses of α-hydroxy-β-keto acid synthases and highlight their great potential in carboligation catalysis and synthetic applications.

Diversity of ThDP-Dependent Enzymes Forming Chiral Tertiary Alcohols

Thiamine diphosphate (ThDP)-dependent enzymes are well known biocatalysts for CC bond-forming reactions. While this enzyme class is mainly investigated for the formation of acyloins of secondary alcohols, recent studies have expanded its scope to utilize ketones as electrophiles in asymmetric carboligation reactions for the formation of tertiary alcohols. Chiral tertiary alcohols are ubiquitous motifs in natural products and important building blocks for the synthesis of bioactive compounds. ThDP-dependent enzymes are emerging as one of the most promising classes of biocatalysts for synthesizing a wide range of products due to the variety of possible substrate combinations, accessible starting materials, high enantioselectivity, and advantageous self-regeneration of the catalytic ThDP cofactor. This review provides an overview of the ThDP-dependent enzymes (e.g., decarboxylase, DC; transketolase, TK; α-keto acid dehydrogenase 2, αKADH2) that form tertiary alcohols, focusing on the substrate scope and diversity of physiological functions. The available toolbox and the characterized reactions shall serve as a starting point for future studies. Inspired by nature, an even broader diversity of classes and substrate specificities is expected in this field.

Apparent Reversal of Allosteric Response in Mycobacterium tuberculosis MenD Reveals Links to Half-of-Sites Reactivity

Redox-active molecules play critical roles in various biological functions, including cellular respiration. In bacterial electron transport chains, menaquinones serve as key electron carriers. The first committed enzyme in the menaquinone biosynthesis pathway of Mycobacterium tuberculosis (Mtb), MenD, is allosterically inhibited by 1,4-dihydroxy-2-naphthoic acid (DHNA), the first redox-active metabolite in the pathway. Structural asymmetries in Mtb-MenD suggest that this enzyme operates via a half-of-sites mechanism for catalysis. Here, we investigate the interplay between its catalytic and allosteric mechanisms. Using molecular dynamics (MD) simulations, mutagenesis, kinetic and binding assays, and structural analyses, we identified and characterised mutants of two residues, D141 and D306, involved in stabilising asymmetric conformations associated with allostery. These mutations had complex effects on Mtb-MenD's reaction kinetics, with the D306 mutants showing an apparent reversal of the allosteric response to DHNA. Our findings indicate that asymmetric active site conformations may facilitate optimal binding of cofactors and substrates, while the transition between alternating active site conformations is essential for the catalytic cycle. DHNA binding stabilises asymmetry in the tetramer, likely promoting the binding of cofactors, substrates, or reaction intermediates. However, DHNA interferes with the transition between alternating conformations, ultimately impairing turnover and catalytic cycling in Mtb-MenD.

Taming Highly Enolizable Aldehydes via Enzyme Catalysis for Enantiocomplementary Construction of β-Hydroxyphosphonates

Taming highly enolizable aldehydes for catalytic asymmetric C-C coupling with nucleophiles remains an elusive challenge compared to widely explored simple alkyl or aryl aldehydes. Herein, we use ThDP-dependent enzymes to realize the direct C-C coupling of highly enolizable 2-phosphonate aldehydes with in situ-generated dynamically reversible nucleophiles (acyl anions). Unlike NHC-mediated reactions that yield complex mixtures of multiple adducts, our enzymatic process selectively produces biologically active β-hydroxy phosphonates with high yields (up to 95%) and excellent enantioselectivities (up to 99% ee). The products can be obtained on gram scales and exhibit rich reactivity for downstream transformations to afford diverse molecules. PfBAL (or its mutant A28G) and PaBAL enzymes serve as enantiocomplementary pairs, enabling the synthesis of both product configurations. Mechanistic studies proved that the entrance directions of the active cavities of these two enzyme pairs were distinct, leading to acyl anions formed from these two enzyme pairs attacking 2-phosphonate aldehydes from different orientations.

Installation of an organocatalyst into a protein scaffold creates an artificial Stetterase

Using a protein scaffold covalently functionalised with a thiamine-inspired N-heterocyclic carbene (NHC), we created an artificial Stetterase (ArtiSt) which catalyses a stereoselective, intramolecular Stetter reaction. We demonstrate that ArtiSt functions under ambient conditions with low catalyst loading. Furthermore, activity can be increased >20 fold by altering the protein scaffold.

Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection

Burkholderiales bacteria have emerged as a promising source of structurally diverse natural products that are expected to play important ecological and industrial roles. This order ranks in the top three in terms of predicted natural product diversity from available genomes, warranting further genome sequencing efforts. However, a major hurdle in obtaining the predicted products is that biosynthetic genes are often 'silent' or poorly expressed. Here we report complementary strain isolation, genomics, metabolomics, and synthetic biology approaches to enable natural product discovery. First, we built a collection of 316 rhizosphere-derived Burkholderiales strains over the course of five years. We then selected 115 strains for sequencing using the mass spectrometry pipeline IDBac to avoid strain redundancy. After predicting and comparing the biosynthetic potential of each strain, a biosynthetic gene cluster that was silent in the native Paraburkholderia megapolitana and Paraburkholderia acidicola producers was cloned and activated by heterologous expression in a Burkholderia sp. host, yielding megapolipeptins A and B. Megapolipeptins are unusual polyketide, nonribosomal peptide, and polyunsaturated fatty acid hybrids that show low structural similarity to known natural products, highlighting the advantage of our Burkholderiales genomics-driven and synthetic biology-enabled pipeline to discover novel natural products.

Recent advances in enzymatic carbon-carbon bond formation

Enzymatic carbon-carbon (C-C) bond formation reactions have become an effective and invaluable tool for designing new biological and medicinal molecules, often with asymmetric features. This review provides a systematic overview of key C-C bond formation reactions and enzymes, with the focus of reaction mechanisms and recent advances. These reactions include the aldol reaction, Henry reaction, Knoevenagel condensation, Michael addition, Friedel-Crafts alkylation and acylation, Mannich reaction, Morita-Baylis-Hillman (MBH) reaction, Diels-Alder reaction, acyloin condensations via Thiamine Diphosphate (ThDP)-dependent enzymes, oxidative and reductive C-C bond formation, C-C bond formation through C1 resource utilization, radical enzymes for C-C bond formation, and other C-C bond formation reactions.

Re-investigation of in vitro activity of acetohydroxyacid synthase I holoenzyme from Escherichia coli

Acetohydroxyacid synthase (AHAS) is one of the key enzymes of the biosynthesis of branched-chain amino acids, it is also an effective target for the screening of herbicides and antibiotics. In this study we present a method for preparing Escherichia coli AHAS I holoenzyme (EcAHAS I) with exceptional stability, which provides a solid ground for us to re-investigate the in vitro catalytic properties of the protein. The results show EcAHAS I synthesized in this way exhibits similar function to Bacillus subtilis acetolactate synthase in its catalysis with pyruvate and 2-ketobutyrate (2-KB) as dual-substrate, producing four 2-hydroxy-3-ketoacids including (S)-2-acetolactate, (S)-2-aceto-2-hydroxybutyrate, (S)-2-propionyllactate, and (S)-2-propionyl-2-hydroxybutyrate. Quantification of the reaction indicates that the two substrates almost totally consume, and compound (S)-2-aceto-2- hydroxybutyrate forms in the highest yield among the four major products. Moreover, the protein also condenses two molecules of 2-KB to furnish (S)-2-propionyl-2-hydroxybutyrate. Further exploration manifests that EcAHAS I ligates pyruvate/2-KB and nitrosobenzene to generate two arylhydroxamic acids N-hydroxy-N-phenylacetamide and N-hydroxy-N-phenyl- propionamide. These findings enhance our comprehension of the catalytic characteristics of EcAHAS I. Furthermore, the application of this enzyme as a catalyst in construction of C-N bonds displays promising potential.

Valorization of single-carbon chemicals by using carboligases as key enzymes

Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.

The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase

Benzoic acid decarboxylases offer an elegant alternative to CO2 fixation by reverse reaction-carboxylation, which is named the bio-Kolbe-Schmitt reaction, but they are unfavorable to carboxylation. Enhancing the carboxylation efficiency of reversible benzoic acid decarboxylases is restricted by the unexplained carboxylation mechanisms. The direction of reversible enzyme catalytic reactions depends on whether catalytic residues at the active center of the enzyme are protonated, which is subjected by the pH. Therefore, the forward and reverse reactions could be separated at different pH values. Reversible 2,3-dihydroxybenzoate acid decarboxylase undergoes decarboxylation at pH 5.0 and carboxylation at pH 8.6. However, it is unknown whether the interaction of enzymes with substrates and products in the forward and reverse reactions can be exploited to improve the catalytic activity of reversible enzymes in the unfavorable direction. Here, we identify a V-shaped tunnel of 2,3-dihydroxybenzoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao) through which the substrate travels in the enzyme, and demonstrate that the side chain conformation of a tyrosine residue controls the entry and exit of substrate/product during reversible reactions. Together with the kinetic studies of the mutants, it is clarified that interactions between substrate/product traveling through the enzyme tunnel in 2,3-DHBD_Ao are direction-dependent. These results enrich the understanding of the interactions of substrates/products with macromolecular reversible enzymes in different reaction directions, thereby demonstrating a possible path for engineering decarboxylases with higher carboxylation efficiency. KEY POINTS: • The residue Trp23 of 2,3-DHBD_Ao served as a switch to control the entry and exit of catechol • A V-shaped tunnel of 2,3-DHBD_Ao for decarboxylation and carboxylation reactions was identified • The results provide a promising strategy for engineering decarboxylases with direction-dependent residues inside the substrate/product traveling tunnel of the enzyme.

Binding Interactions and Inhibition Mechanisms of Gold Complexes in Thiamine Diphosphate-Dependent Enzymes

Thiamine diphosphate (ThDP)-dependent enzymes possess the unique ability to generate a carbene within their active site. In this study, we sought to harness this carbene to produce a Au(I) N-heterocyclic complex directly in the active site of ThDP enzymes, thereby establishing a novel platform for artificial metalloenzymes. Because direct metalation of ThDP proved challenging, we synthesized a ThDP mimic that acts as a competitive inhibitor with a high affinity (Ki = 1.5 μM). Upon metalation with Au(I), we observed that the complex became a more potent inhibitor (Ki = 0.7 μM). However, detailed analysis of the inhibition mode, native mass spectrometry, and size exclusion experiments revealed that the complex does not bind specifically to the active site of ThDP enzymes. Instead, it exhibits unspecific binding and exceeds the 1:1 stoichiometry. Similar binding patterns were observed for other Au(I) species. These findings prompt an important question regarding the inherent propensity of ThDP enzymes to bind strongly to Au. If this phenomenon holds true, it could pave the way for the development of Au-based drugs targeting these enzymes.

A Customized Bayesian Algorithm to Optimize Enzyme-Catalyzed Reactions

Design of experiments (DoE) plays an important role in optimizing the catalytic performance of chemical reactions. The most commonly used DoE relies on the response surface methodology (RSM) to model the variable space of experimental conditions with the fewest number of experiments. However, the RSM leads to an exponential increase in the number of required experiments as the number of variables increases. Herein we describe a Bayesian optimization algorithm (BOA) to optimize the continuous parameters (e.g., temperature, reaction time, reactant and enzyme concentrations, etc.) of enzyme-catalyzed reactions with the aim of maximizing performance. Compared to existing Bayesian optimization methods, we propose an improved algorithm that leads to better results under limited resources and time for experiments. To validate the versatility of the BOA, we benchmarked its performance with biocatalytic C-C bond formation and amination for the optimization of the turnover number. Gratifyingly, up to 80% improvement compared to RSM and up to 360% improvement vs previous Bayesian optimization algorithms were obtained. Importantly, this strategy enabled simultaneous optimization of both the enzyme's activity and selectivity for cross-benzoin condensation.

Conversion of Similar Xenochemicals to Dissimilar Products: Exploiting Competing Reactions in Whole-Cell Catalysis

Many enzymes have latent activities that can be used in the conversion of non-natural reactants for novel organic conversions. A classic example is the conversion of benzaldehyde to a phenylacetyl carbinol, a precursor for ephedrine manufacture. It is often tacitly assumed that purified enzymes are more promising catalysts than whole cells, despite the lower cost and easier maintenance of the latter. Competing substrates inside the cell have been known to elicit currently hard-to-predict selectivities that are not easily measured inside the living cell. We employ NMR spectroscopic assays to rationally combine isomers for selective reactions in commercial S. cerevisiae. This approach uses internal competition between alternative pathways of aldehyde clearance in yeast, leading to altered selectivities compared to catalysis with the purified enzyme. In this manner, 4-fluorobenzyl alcohol and 2-fluorophenylacetyl carbinol can be formed with selectivities in the order of 90%. Modification of the cellular redox state can be used to tune product composition further. Hyperpolarized NMR shows that the cellular reaction and pathway usage are affected by the xenochemical. Overall, we find that the rational construction of ternary or more complex substrate mixtures can be used for in-cell NMR spectroscopy to optimize the upgrading of similar xenochemicals to dissimilar products with cheap whole-cell catalysts.

Optimized enantioselective (S)-2-hydroxypropiophenone synthesis by free- and encapsulated-resting cells of Pseudomonas putida

BACKGROUND

Aromatic α-hydroxy ketones, such as S-2-hydroxypropiophenone (2-HPP), are highly valuable chiral building blocks useful for the synthesis of various pharmaceuticals and natural products. In the present study, enantioselective synthesis of 2-HPP was investigated by free and immobilized whole cells of Pseudomonas putida ATCC 12633 starting from readily-available aldehyde substrates. Whole resting cells of P. putida, previously grown in a culture medium containing ammonium mandelate, are a source of native benzoylformate decarboxylase (BFD) activity. BFD produced by induced P. putida resting cells is a highly active biocatalyst without any further treatment in comparison with partially purified enzyme preparations. These cells can convert benzaldehyde and acetaldehyde into the acyloin compound 2-HPP by BFD-catalyzed enantioselective cross-coupling reaction.

RESULTS

The reaction was carried out in the presence of exogenous benzaldehyde (20 mM) and acetaldehyde (600 mM) as substrates in 6 mL of 200 mM phosphate buffer (pH 7) for 3 h. The optimal biomass concentration was assessed to be 0.006 g dry cell weight (DCW) mL^- 1. 2-HPP titer, yield and productivity using the free cells were 1.2 g L^- 1, 0.56 g 2-HPP/g benzaldehyde (0.4 mol 2-HPP/mol benzaldehyde), 0.067 g 2-HPP g^- 1 DCW h^- 1, respectively, under optimized biotransformation conditions (30 °C, 200 rpm). Calcium alginate (CA)-polyvinyl alcohol (PVA)-boric acid (BA)-beads were used for cell entrapment. Encapsulated whole-cells were successfully employed in four consecutive cycles for 2-HPP production under aerobic conditions without any noticeable beads degradation. Moreover, there was no production of benzyl alcohol as an unwanted by-product.

CONCLUSIONS

Bioconversion by whole P. putida resting cells is an efficient strategy for the production of 2-HPP and other α-hydroxyketones.

Synthesis of Novel 1,4-Diketone Derivatives and Their Further Cyclization

One of the important reactions to obtain a new carbon-carbon bond is the Stetter reaction, which is generally via a nucleophilic catalyst like cyanide or thiazolium-NHC catalysts. In particular, 1,4-diketones with very functional properties are obtained by the Stetter reaction with the intermolecular reaction of an aldehyde and an α,β-unsaturated ketone. In this study, we synthesized new derivatives (substituted arenoxy) of 1,4-diketone compounds (2a-2n) with useful features by a new version of the Stetter reaction method. In our work, arenoxy benzaldehyde derivatives with different structures as the Michael donor and methyl vinyl ketone as the Michael acceptor were used for the intermolecular Stetter reaction. The reaction was catalyzed by 3-benzyl-5-(2-hydroxyethyl)-4-methylthiazolium chloride (3b), using triethylamine for the basic medium and dimethyl sulfoxide as the solvent. As a result, some novel arenoxy-substituted 1,4-diketones were gained with good yields at room temperature within 24 h through an intermolecular Stetter reaction. In addition, new furan and pyrrole derivatives were prepared by performing the cyclization reaction with one of the obtained new diketone compounds.

Polyphosphate Kinases Phosphorylate Thiamine Phosphates

Polyphosphate kinases (PPKs) catalyze the reversible transfer of the γ-phosphate moiety of ATP (or of another nucleoside triphosphate) to a growing chain of polyphosphate (polyP). In this study, we describe that PPKs of various sources are additionally able to phosphorylate thiamine diphosphate (ThP2) to produce thiamine triphosphate (ThP3) and even thiamine tetraphosphate in vitro using polyP as phosphate donor. Furthermore, all tested PPK2s, but not PPK1s, were able to phosphorylate thiamine monophosphate (ThP1) to ThP2 and ThP3 although at low efficiency. The predicted masses and identities of the mono- and oligo-phosphorylated thiamine metabolites were identified by high-performance liquid chromatography tandem mass spectrometry. Moreover, the biological activity of ThP2, that was synthesized by phosphorylation of ThP1 with polyP and PPK, as a cofactor of ThP2-dependent enzymes (here transketolase TktA from Escherichia coli) was confirmed in a coupled enzyme assay. Our study shows that PPKs are promiscuous enzymes in vitro that could be involved in the formation of a variety of phosphorylated metabolites in vivo.

Frontiers in the enzymology of thiamin diphosphate-dependent enzymes

Enzymes that use thiamin diphosphate (ThDP), the biologically active derivative of vitamin B1, as a cofactor play important roles in cellular metabolism in all domains of life. The analysis of ThDP enzymes in the past decades have provided a general framework for our understanding of enzyme catalysis of this protein family. In this review, we will discuss recent advances in the field that include the observation of "unusual" reactions and reaction intermediates that highlight the chemical versatility of the thiamin cofactor. Further topics cover the structural basis of cooperativity of ThDP enzymes, novel insights into the mechanism and structure of selected enzymes, and the discovery of "superassemblies" as reported, for example, acetohydroxy acid synthase. Finally, we summarize recent findings in the structural organisation and mode of action of 2-keto acid dehydrogenase multienzyme complexes and discuss future directions of this exciting research field.

Functional Versatility of the Human 2-Oxoadipate Dehydrogenase in the L-Lysine Degradation Pathway toward Its Non-Cognate Substrate 2-Oxopimelic Acid

The human 2-oxoadipate dehydrogenase complex (OADHc) in L-lysine catabolism is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA and NADH (+H⁺). Genetic findings have linked the DHTKD1 encoding 2-oxoadipate dehydrogenase (E1a), the first component of the OADHc, to pathogenesis of AMOXAD, eosinophilic esophagitis (EoE), and several neurodegenerative diseases. A multipronged approach, including circular dichroism spectroscopy, Fourier Transform Mass Spectrometry, and computational approaches, was applied to provide novel insight into the mechanism and functional versatility of the OADHc. The results demonstrate that E1a oxidizes a non-cognate substrate 2-oxopimelate (OP) as well as OA through the decarboxylation step, but the OADHc was 100-times less effective in reactions producing adipoyl-CoA and NADH from the dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3). The results revealed that the E2o is capable of producing succinyl-CoA, glutaryl-CoA, and adipoyl-CoA. The important conclusions are the identification of: (i) the functional promiscuity of E1a and (ii) the ability of the E2o to form acyl-CoA products derived from homologous 2-oxo acids with five, six, and even seven carbon atoms. The findings add to our understanding of both the OADHc function in the L-lysine degradative pathway and of the molecular mechanisms leading to the pathogenesis associated with DHTKD1 variants.

Asymmetric Synthesis of N-Substituted 1,2-Amino Alcohols from Simple Aldehydes and Amines by One-Pot Sequential Enzymatic Hydroxymethylation and Asymmetric Reductive Amination

The chiral N-substituted 1,2-amino alcohol motif is found in many natural and synthetic bioactive compounds. In this study, enzymatic asymmetric reductive amination of α-hydroxymethyl ketones with enantiocomplementary imine reductases (IREDs) enabled the synthesis of chiral N-substituted 1,2-amino alcohols with excellent ee values (91-99 %) in moderate to high yields (41-84 %). Furthermore, a one-pot, two-step enzymatic process involving benzaldehyde lyase-catalyzed hydroxymethylation of aldehydes and subsequent asymmetric reductive amination was developed, offering an environmentally friendly and economical way to produce N-substituted 1,2-amino alcohols from readily available simple aldehydes and amines. This methodology was then applied to rapidly access a key synthetic intermediate of anti-malaria and cytotoxic tetrahydroquinoline alkaloids.

Engineering the 2-Oxoglutarate Dehydrogenase Complex to Understand Catalysis and Alter Substrate Recognition

The E. coli 2-oxoglutarate dehydrogenase complex (OGDHc) is a multienzyme complex in the tricarboxylic acid cycle, consisting of multiple copies of three components, 2-oxoglutarate dehydrogenase (E1o), dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3), which catalyze the formation of succinyl-CoA and NADH (+H+) from 2-oxoglutarate. This review summarizes applications of the site saturation mutagenesis (SSM) to engineer E. coli OGDHc with mechanistic and chemoenzymatic synthetic goals. First, E1o was engineered by creating SSM libraries at positions His260 and His298.Variants were identified that: (a) lead to acceptance of substrate analogues lacking the 5-carboxyl group and (b) performed carboligation reactions producing acetoin-like compounds with good enantioselectivity. Engineering the E2o catalytic (core) domain enabled (a) assignment of roles for pivotal residues involved in catalysis, (b) re-construction of the substrate-binding pocket to accept substrates other than succinyllysyldihydrolipoamide and (c) elucidation of the mechanism of trans-thioesterification to involve stabilization of a tetrahedral oxyanionic intermediate with hydrogen bonds by His375 and Asp374, rather than general acid–base catalysis which has been misunderstood for decades. The E. coli OGDHc is the first example of a 2-oxo acid dehydrogenase complex which was evolved to a 2-oxo aliphatic acid dehydrogenase complex by engineering two consecutive E1o and E2o components.

Shortening Synthetic Routes to Small Molecule Active Pharmaceutical Ingredients Employing Biocatalytic Methods

Biocatalysis, using enzymes for organic synthesis, has emerged as powerful tool for the synthesis of active pharmaceutical ingredients (APIs). The first industrial biocatalytic processes launched in the first half of the last century exploited whole-cell microorganisms where the specific enzyme at work was not known. In the meantime, novel molecular biology methods, such as efficient gene sequencing and synthesis, triggered breakthroughs in directed evolution for the rapid development of process-stable enzymes with broad substrate scope and good selectivities tailored for specific substrates. To date, enzymes are employed to enable shorter, more efficient, and more sustainable alternative routes toward (established) small molecule APIs, and are additionally used to perform standard reactions in API synthesis more efficiently. Herein, large-scale synthetic routes containing biocatalytic key steps toward >130 APIs of approved drugs and drug candidates are compared with the corresponding chemical protocols (if available) regarding the steps, reaction conditions, and scale. The review is structured according to the functional group formed in the reaction.

Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity

Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.

Practical Enzymatic Production of Carbocycles

The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.

Chemoenzymatic Production of Enantiocomplementary 2-Substituted 3-Hydroxycarboxylic Acids from L-α-Amino Acids

A two-enzyme cascade reaction plus in situ oxidative decarboxylation for the transformation of readily available canonical and non-canonical L-α-amino acids into 2-substituted 3-hydroxy-carboxylic acid derivatives is described. The biocatalytic cascade consisted of an oxidative deamination of L-α-amino acids by an L-α-amino acid deaminase from Cosenzaea myxofaciens, rendering 2-oxoacid intermediates, with an ensuing aldol addition reaction to formaldehyde, catalyzed by metal-dependent (R)- or (S)-selective carboligases namely 2-oxo-3-deoxy-l-rhamnonate aldolase (YfaU) and ketopantoate hydroxymethyltransferase (KPHMT), respectively, furnishing 3-substituted 4-hydroxy-2-oxoacids. The overall substrate conversion was optimized by balancing biocatalyst loading and amino acid and formaldehyde concentrations, yielding 36-98% aldol adduct formation and 91- 98% ee for each enantiomer. Subsequent in situ follow-up chemistry via hydrogen peroxide-driven oxidative decarboxylation afforded the corresponding 2-substituted 3-hydroxycarboxylic acid derivatives.

Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations

Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to decipher the details of the reaction mechanisms, including elucidation of the identity of the metal cofactors and the origins of substrate specificity.

Decarboxylases are of growing potential for biocatalytic applications, as they can be used in the synthesis of novel compounds of, e.g., pharmaceutical interest. They can also be employed in the reverse direction, providing a strategy to synthesize value‐added chemicals by CO₂ fixation. A number of non-redox metal-dependent decarboxylases from the amidohydrolase superfamily have been demonstrated to have promiscuous carboxylation activities and have attracted great attention in the recent years. The computational mechanistic studies provide insights that are important for the further modification and utilization of these enzymes in industrial processes. The discussed enzymes are: 5‐carboxyvanillate decarboxylase, γ‐resorcylate decarboxylase, 2,3‐dihydroxybenzoic acid decarboxylase, and iso-orotate decarboxylase.

Intramolecular Stereoselective Stetter Reaction Catalyzed by Benzaldehyde Lyase

The reliable design and prediction of enzyme promiscuity to access transformations not observed in nature remains a long-standing challenge. Herein, we present the first example of an intramolecular stereoselective Stetter reaction catalyzed by benzaldehyde lyase, guided by the rational structure screening of various ThDP-dependent enzymes using molecular dynamics (MD) simulations. After optimization, high productivity (up to 99 %) and stereoselectivity (up to 99:1 e.r.) for this novel enzyme function was achieved.

Quaternary Charge-Transfer Complex Enables Photoenzymatic Intermolecular Hydroalkylation of Olefins

Intermolecular C-C bond-forming reactions are underdeveloped transformations in the field of biocatalysis. Here we report a photoenzymatic intermolecular hydroalkylation of olefins catalyzed by flavin-dependent 'ene'-reductases. Radical initiation occurs via photoexcitation of a rare high-order enzyme-templated charge-transfer complex that forms between an alkene, α-chloroamide, and flavin hydroquinone. This unique mechanism ensures that radical formation only occurs when both substrates are present within the protein active site. This active site can control the radical terminating hydrogen atom transfer, enabling the synthesis of enantioenriched γ-stereogenic amides. This work highlights the potential for photoenzymatic catalysis to enable new biocatalytic transformations via previously unknown electron transfer mechanisms.

Bio-inspired NHC-organocatalyzed Stetter reaction in aqueous conditions

The first bio-inspired N-Heterocyclic Carbene (NHC)-catalyzed Stetter reaction in aqueous medium is reported with benzaldehyde and chalcone as model substrates. A screening of azolium salts as precatalysts revealed the remarkable efficiency of synthetic thiazolium salt 8 (up to 90% conversion in pure water at 75 °C). The reaction was successfully extended to various simple aldehyde substrates. The effect of temperature was also investigated in order to extend the reaction to lower temperature allowing a potential application to sensitive biomolecules. This study highlighted the influence of both solvent and temperature on the 1,4-diketone 3/benzoin 4 ratio. New precatalysts 26 and 27 were designed and synthesized to explore a possible compartmentalization of the reaction in aqueous conditions. Owing to the use of inexpensive metal-free N-Heterocyclic Carbene (NHC) as a bioinspired catalyst, we anticipate that this green strategy in aqueous conditions will be attractive for bioconjugation of many biomolecule-type aldehydes and enone derivatives.

Biocatalysis - Key enabling tools from biocatalytic one-step and multi-step reactions to biocatalytic total synthesis

In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.

Rigorous Model-Based Design and Experimental Verification of Enzyme-Catalyzed Carboligation under Enzyme Inactivation

Enzyme catalyzed reactions are complex reactions due to the interplay of the enzyme, the reactants, and the operating conditions. To handle this complexity systematically and make use of a design space without technical restrictions, we apply the model based approach of elementary process functions (EPF) for selecting the best process design for enzyme catalysis problems. As a representative case study, we consider the carboligation of propanal and benzaldehyde catalyzed by benzaldehyde lyase from Pseudomonas fluorescens (PfBAL) to produce (R)-2-hydroxy-1-phenylbutan-1-one, because of the substrate dependent reaction rates and the challenging substrate dependent PfBAL inactivation. The apparatus independent EPF concept optimizes the material fluxes influencing the enzyme catalyzed reaction for the given process intensification scenarios. The final product concentration is improved by 13% with the optimized feeding rates, and the optimization results are verified experimentally. In general, the rigorous model driven approach could lead to selecting the best existing reactor, designing novel reactors for enzyme catalysis, and combining protein engineering and process systems engineering concepts.

Understanding the molecular properties of the E1 subunit (SucA) of α-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin

Enantioselective ligation of acetaldehydes into (R)-acetoin by SucA from Vibrio vulnificus.

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.

Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites

Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the overall understanding of the kinetics and mechanism of the individual reactions.

In this paper we use density functional theory calculations to systematically study the different cofactor states in terms of energies and geometries. Benzoylformate decarboxylase (BFDC), which is a well characterized chiral catalyst, serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as inhibitor). Overall, the calculations reveal that the relative stabilities of the cofactor states are greatly affected by the presence and identity of the bound ligands. A surprising finding is that benzoylformate binding, while favoring ylide formation, provided even greater stabilization to a catalytically inactive tricyclic state. Conversely, the inhibitor binding greatly destabilized the ylide formation. Together, these observations have significant implications for the reaction kinetics of the ThDP-dependent enzymes, and, potentially, for the use of unnatural substrates in such reactions.