Biotechnological Development of a Practical Synthesis of Ethyl (S)-2-Ethoxy-3-(p-methoxyphenyl)propanoate (EEHP): Over 100-Fold Productivity Increase from Yeast Whole Cells to Recombinant Isolated Enzymes

Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus

Enzyme-catalyzed reaction cascades play an increasingly important role for the sustainable manufacture of diverse chemicals from renewable feedstocks. For instance, dehydratases from the ilvD/EDD superfamily have been embedded into a cascade to convert glucose via pyruvate to isobutanol, a platform chemical for the production of aviation fuels and other valuable materials. These dehydratases depend on the presence of both a Fe-S cluster and a divalent metal ion for their function. However, they also represent the rate-limiting step in the cascade. Here, catalytic parameters and the crystal structure of the dehydratase from Paralcaligenes ureilyticus (PuDHT, both in presence of Mg²⁺ and Mn²⁺ ) were investigated. Rate measurements demonstrate that the presence of stoichiometric concentrations Mn²⁺ promotes higher activity than Mg²⁺ , but at high concentrations the former inhibits the activity of PuDHT. Molecular dynamics simulations identify the position of a second binding site for the divalent metal ion. Only binding of Mn²⁺ (not Mg²⁺ ) to this site affects the ligand environment of the catalytically essential divalent metal binding site, thus providing insight into an inhibitory mechanism of Mn²⁺ at higher concentrations. Furthermore, in silico docking identified residues that play a role in determining substrate binding and selectivity. The combined data inform engineering approaches to design an optimal dehydratase for the cascade.

Alternative design strategies to help build the enzymatic retrosynthesis toolbox

Most of the complex molecules found in nature still cannot be synthesized by current organic chemistry methods. Given the number of enzymes that exist in nature and the incredible potential of directed evolution, the field of synthetic biology contains perhaps all the necessary building blocks to bring about the realization of applied enzymatic retrosynthesis. Current thinking anticipates that enzymatic retrosynthesis will be implemented using conventional cell-based synthetic biology approaches where requisite native, heterologous, designer, and evolved enzymes making up a given multi-enzyme pathway are hosted by chassis organisms to carry out designer synthesis. In this perspective, we suggest that such an effort should not be limited by solely exploiting living cells and enzyme evolution and describe some useful yet less intensive complementary approaches that may prove especially productive in this grand scheme. By decoupling reactions from the environment of a living cell, a significantly larger portion of potential synthetic chemical space becomes available for exploration; most of this area is currently unavailable to cell-based approaches due to toxicity issues. In contrast, in a cell-free reaction a variety of classical enzymatic approaches can be exploited to improve performance and explore and understand a given enzyme's substrate specificity and catalytic profile towards non-natural substrates. We expect these studies will reveal unique enzymatic capabilities that are not accessible in living cells.

Introduction of Chiral Centers to α- and/or β-Positions of Carbonyl Groups by Biocatalytic Asymmetric Reduction of α,β-Unsaturated Carbonyl Compounds

Biocatalytic asymmetric reductions of acyclic and cyclic α,β-unsaturated carbonyl compounds are favorable protocols for introduction of chiral centers to α- and/or β-positions of the carbonyl groups. Representative biocatalytic reductions of electron deficient olefins are compiled from a synthetic point of view according to compound types from the papers in 2012 to early 2022. Applications to syntheses of some enantiomericaly enriched perfumery ingredients are presented to show the feasibility of the biocatalytic reductions.

Chemoenzymatic Synthesis of the Most Pleasant Stereoisomer of Jessemal

We describe the asymmetric synthesis of the most pleasant enantiomer of Jessemal fragrance. The key steps are (i) the one-pot reduction of an α-chloro-tetrasubstituted cyclohexenone to give the chlorohydrin, catalyzed by two stereoselective redox enzymes (an ene-reductase and an alcohol dehydrogenase); (ii) the regioselective epoxide ring-opening with organocuprate or organolithium nucleophiles. Density functional theory calculations together with the Curtin–Hammett principle allowed the rationalization of the regioselectivity.

Two Biotechnological Approaches to the Preparative Synthesis of Natural Dihydrocoumarin

In this work, we describe two different biotechnological processes that provide the natural flavour dihydrocoumarin in preparative scale. Both the presented approaches are based on the enzyme-mediated reduction of natural coumarin. The first one is a whole-cell process exploiting the reductive activity of the yeast Kluyveromyces marxianus, a Generally Recognized As Safe (GRAS) microorganism that possesses high resistance to the substrate toxicity. Differently, the second is based on the reduction of natural coumarin by nicotinamide adenine dinucleotide phosphate (NADPH) and using the Old Yellow Enzyme reductase OYE2 as catalyst. NADPH is used in catalytic amount since the co-factor regeneration is warranted employing an enzymatic system based on glucose oxidation, in turn catalysed by a further enzyme, namely glucose dehydrogenase (GDH). Both processes compare favourably over the previously reported industrial method as they work with higher coumarin concentration (up to 3 g/L for the enzymatic process) yet allowing the complete conversion of the substrate. Furthermore, the two approaches have significant differences. The microbial reduction is experimentally simple but the isolated dihydrocoumarin yield does not exceed 60%. On the contrary, the enzymatic approach requires the use of two specially prepared recombinant enzymes, however, it is more efficient, affording the product in 90% of isolated yield.

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.

Ene-reductase transformation of massoia lactone to δ-decalactone in a continuous-flow reactor

The demand for natural food flavorings increases every year. Biotransformation has become an attractive approach to obtain natural products. In this work, enantiomerically pure (R)-(+)-δ-decalactone was obtained by reduction of the C=C double bond of natural massoia lactone in a continuous-flow reactor. Of 13 different ene-reductases isolated, purified and tested, OYE3 was found to be the most efficient biocatalyst. The selected biocatalyst, either in the form of purified enzyme, cell lysate, whole cells or immobilized cells, was tested in the batch system as well as in the packed-bed flow bioreactor. The biotransformation performed in batch mode, using Ca²⁺-alginate immobilized cells of Escherichia coli BL21(DE3)/pET30a-OYE3, furnished the desired product with complete conversion in 30 min. The process was intensified using a continuous-flow reactor-membrane filtration system (flow 0.1 mL/min, substrate concentration 10 mM, pH 7, 24 °C) with cell lysate as biocatalyst combined with a cofactor regeneration system, which allowed obtaining > 99% bioconversion of massoia lactone.

Oleate Hydratase from Lactobacillus rhamnosus ATCC 53103: A FADH2-Dependent Enzyme with Remarkable Industrial Potential

Recently, we described the preparation of the recombinant oleate hydratase from Lactobacillus rhamnosus ATCC 53103. We observed that the purified C-terminal His-tagged enzyme was completely inactive and the catalytic activity was partially restored only in presence of a large amount of flavin adenine dinucleotide (FAD). In the present work, we assess that this hydratase in the presence of the reduced form of flavin adenine dinucleotide (FADH2) is at least one hundred times as active as in the presence of the same concentration of FAD. By means of two different biochemical processes, we demonstrated unambiguously that oleate hydratase from Lactobacillus rhamnosus ATCC 53103 is a FADH2-dependent enzyme. As a first relevant application of this discovery, we devised a preparative procedure for the stereoselective synthesis of (R)-10-hydroxystearic acid. Accordingly, the hydration of oleic acid (up to 50 g/L) is performed on a multigram scale using the recombinant hydratase and FADH2 generated in situ as cofactor. The produced (R)-10-hydroxystearic acid (ee > 97%) precipitates from the reaction solvent (water/glycerol/ethanol) and is conveniently recovered by simple filtration (>90% yield).

Design and application of a bi-functional redox biocatalyst through covalent co-immobilization of ene-reductase and glucose dehydrogenase

An immobilized bi-functional redox biocatalyst was designed for the asymmetric reduction of alkenes by nicotinamide-dependent ene-reductases. The biocatalyst, which consists of co-immobilized ene-reductase and glucose dehydrogenase, was implemented in biotransformations in the presence of glucose as source of reducing equivalents and catalytic amounts of the cofactor. Enzyme co-immobilization employing glutaraldehyde activated Relizyme HA403/M as support material was performed directly from the crude cell-free extract obtained after protein overexpression in E. coli and cell lysis, avoiding enzyme purification steps. The resulting optimum catalyst showed excellent level of activity and stereoselectivity in asymmetric reduction reactions using either OYE3 from Saccharomyces cerevisiae or NCR from Zymomonas mobilis in the presence of organic cosolvents in up to 20 vol%. The bi-functional redox biocatalyst, which demonstrated remarkable reusability over several cycles, was applied in preparative-scale synthesis at 50 mM substrate concentration and provided access to three industrially relevant chiral compounds in high enantiopurity (ee up to 97 %) and in up to 42 % isolated yield. The present method highlights the potential of (co-)immobilization of ene-reductases, notorious for their poor scalability, and complements the few existing methods available for increasing productivity in asymmetric bioreduction reactions.

Isobutanol production freed from biological limits using synthetic biochemistry

Cost competitive conversion of biomass-derived sugars into biofuel will require high yields, high volumetric productivities and high titers. Suitable production parameters are hard to achieve in cell-based systems because of the need to maintain life processes. As a result, next-generation biofuel production in engineered microbes has yet to match the stringent cost targets set by petroleum fuels. Removing the constraints imposed by having to maintain cell viability might facilitate improved production metrics. Here, we report a cell-free system in a bioreactor with continuous product removal that produces isobutanol from glucose at a maximum productivity of 4 g L⁻¹ h⁻¹, a titer of 275 g L⁻¹ and 95% yield over the course of nearly 5 days. These production metrics exceed even the highly developed ethanol fermentation process. Our results suggest that moving beyond cells has the potential to expand what is possible for bio-based chemical production.

A cell free or synthetic biochemistry approach offers a way to circumvent the many constraints of living cells. Here, the authors demonstrate, via enzyme and process enhancements, the production of isobutanol with the metrics exceeding highly developed ethanol fermentation.

Old yellow enzymes: structures and structure-guided engineering for stereocomplementary bioreduction

Since the first discovery of old yellow enzyme 1 (OYE1) from Saccharomyces pastorianus in 1932, biocatalytic asymmetric reduction of activated alkenes by OYEs has become a valuable reaction in organic synthesis. To access stereocomplementary C=C-bond bioreduction, the mining of novel OYEs and especially the protein engineering of existing OYEs have been performed, which successfully achieved the stereocomplementary reduction in several cases and further raise the potential of applications. In this review, we analyzed the structures, active sites, and substrate recognition of OYEs, which are the bases for their substrate specificity and stereospecificity. Sequence similarity network of OYEs superfamily was also constructed to investigate the scope of characterized OYEs. The structure-guided engineering to switch the stereoselectivity of OYEs and thus access stereocomplementary bioreduction over the last decade (2009-2020) was then reviewed and discussed, which might give new insights into the mining and engineering of related biocatalysts. KEY POINTS: • The sequence similarity network of OYEs superfamily was constructed and annotated. • The structures and active sites of OYEs from different classes were compared. • "Left/right" binding mode was used to explain the stereopreferences of OYEs. • Structure-guided engineering of OYEs to switch their stereoselectivity was reviewed.

The Evolution of Cell Free Biomanufacturing

Cell-free systems are a widely used research tool in systems and synthetic biology and a promising platform for manufacturing of proteins and chemicals. In the past, cell-free biology was primarily used to better understand fundamental biochemical processes. Notably, E. coli cell-free extracts were used in the 1960s to decipher the sequencing of the genetic code. Since then, the transcription and translation capabilities of cell-free systems have been repeatedly optimized to improve energy efficiency and product yield. Today, cell-free systems, in combination with the rise of synthetic biology, have taken on a new role as a promising technology for just-in-time manufacturing of therapeutically important biologics and high-value small molecules. They have also been implemented at an industrial scale for the production of antibodies and cytokines. In this review, we discuss the evolution of cell-free technologies, in particular advancements in extract preparation, cell-free protein synthesis, and cell-free metabolic engineering applications. We then conclude with a discussion of the mathematical modeling of cell-free systems. Mathematical modeling of cell-free processes could be critical to addressing performance bottlenecks and estimating the costs of cell-free manufactured products.

Stereoselectivity Switch in the Reduction of α-Alkyl-β-Arylenones by Structure-Guided Designed Variants of the Ene Reductase OYE1

Ene reductases from the Old Yellow Enzyme (OYE) family are industrially interesting enzymes for the biocatalytic asymmetric reduction of alkenes. To access both enantiomers of the target reduced products, stereocomplementary pairs of OYE enzymes are necessary, but their natural occurrence is quite limited. A library of wild type ene reductases from different sources was screened in the stereoselective reduction of a set of representative α-alkyl-β-arylenones to investigate the naturally available biodiversity. As far as the bioreduction of the ethyl ketone derivatives concerns, the results confirmed the distinctiveness of the OYE3 enzyme in affording the reduced product in the (S) configuration, while all the other tested ene reductases from the Old Yellow Enzymes family showed the same stereoselectivity toward the formation of corresponding (R) enantiomer. A possible determinant role of the "hot spot" residue in position 296 for the stereoselectivity control of these reactions was confirmed by the replacement of Phe296 of OYE1 with Ser as found in OYE3. Further investigations showed that the same stereoselectivity switch in OYE1 could be achieved also by the replacement of Trp116 with Ala and Val, these experimental results being rationalized by structural and docking studies. Moreover, an additive effect on the stereoselectivity of OYE1 was observed when coupling the selected mutations in position 296 and 116, thus providing two extremely enantioselective variants of OYE1 (W116A-F296S, W116V-F296S) showing the opposite stereoselectivity of the wild type enzyme. Lastly, the effects of the mutations on the bioreduction of carvone enantiomers were investigated as well.

Expanding biological applications using cell-free metabolic engineering: An overview

Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.

One-Pot Multi-Enzymatic Synthesis of the Four Stereoisomers of 4-Methylheptan-3-ol

The use of pheromones in the integrated pest management of insects is currently considered a sustainable and environmentally benign alternative to hazardous insecticides. 4-Methylheptan-3-ol is an interesting example of an insect pheromone, because its stereoisomers are active towards different species. All four possible stereoisomers of this compound were prepared from 4-methylhept-4-en-3-one by a one-pot procedure in which the two stereogenic centres were created during two sequential reductions catalysed by an ene-reductase (ER) and an alcohol dehydrogenase (ADH), respectively.

Exploitation of a Multienzymatic Stereoselective Cascade Process in the Synthesis of 2-Methyl-3-Substituted Tetrahydrofuran Precursors

Enantiopure 2-methyl-3-substituted tetrahydrofurans are key precursors of several biologically active products (drugs, flavors, and agrochemicals). Thus, a stereocontrolled and efficient methodology for the obtainment of these synthons is highly desirable. We exploited a two-step multienzymatic stereoselective cascade reduction of α-bromo-α,β-unsaturated ketones to give the corresponding bromohydrins in good yields, with high ee and de values. The cascade process is catalyzed by an ene-reductase and an alcohol dehydrogenase. Further manipulations of these bromohydrins, by two diastereodivergent routes, allowed the preparation of the tetrahydrofuran synthons. One route is based on a lipase catalyzed cleavage of the protecting group. The second route is characterized by a camphor sulfonic acid mediated isomerization of a β-hydroxyepoxide to give the tetrahydrofuran-2-ol. Finally, the synthesis of the most odorous and pleasant stereoisomer of the roasted meat aroma, i.e., (2S,3R)-2-methyl-3-thioacetate tetrahydrofuran, is reported as well.

Stereoselective synthesis of hernandulcin, peroxylippidulcine A, lippidulcines A, B and C and taste evaluation

The first stereoselective synthesis of lippidulcines A, B and C has been accomplished starting from (+)-hernandulcin, which has been prepared on a multigram scale. The previously assigned absolute configurations have been confirmed. The key steps of this synthesis are based on a modified version of the Kornblum–DeLaMare rearrangement, and on a highly regioselective and stereoselective ketone reduction with the MeCBS reagent. The taste evaluations indicate that none of these sesquiterpenes are sweet, instead the lippidulcine A is a cooling agent with a mint after taste.

Stereoselective reduction of aromatic ketones by a new ketoreductase from Pichia glucozyma

A new NADPH-dependent benzil reductase (KRED1-Pglu) was identified from the genome of the non-conventional yeast Pichia glucozyma CBS 5766 and overexpressed in E. coli. The new protein was characterised and reaction parameters were optimised for the enantioselective reduction of benzil to (S)-benzoin. A thorough study of the substrate range of KRED1-Pglu was conducted; in contrast to most other known ketoreductases, KRED1-Pglu prefers space-demanding substrates, which are often converted with high stereoselectivity. A molecular modelling study was carried out for understanding the structural determinants involved in the stereorecognition experimentally observed and unpredictable on the basis of steric properties of the substrates. As a result, a new useful catalyst was identified, enabling the enantioselective preparation of different aromatic alcohols and hydroxyketones.

A Rapid and High-Throughput Assay for the Estimation of Conversions of Ene-Reductase-Catalysed Reactions

A fast and sensitive colorimetric assay (FRED, fast and reliable ene-reductases detection) that allows the estimation of levels of conversion of ene-reductase (ER)-catalysed reactions has been developed. The activated olefin is reduced by ER at the expense of NAD(P)H cofactor, whose regeneration is carried out in situ by the glucose/glucose dehydrogenase system. Subsequently, the consumption of the co-substrate glucose is determined colorimetrically by a multienzymatic system. The FRED assay offers a wide range of possible applications, from enzyme fingerprinting and kinetic analysis, to primary screening of enzyme libraries and optimisation of ERs' performances under different reaction conditions.

Non-hazardous Baeyer-Villiger oxidation of levulinic acid derivatives: alternative renewable access to 3-hydroxypropionates

Baeyer-Villiger monooxygenases catalyze the energetically challenging oxidation of levulinates (4-oxopentanoates) to 3-hydroxypropionic acid (3-HPA) derivates under ambient conditions, replacing propellant-grade H2O2 with aerial oxygen as the oxidant. This reaction enables a new pathway to a platform for chemical 3-HPA, an important intermediate in the non-petrol based production of a variety of bulk chemicals (acrylates, malonates, 1,3-propanediol).

Cell-free metabolic engineering: biomanufacturing beyond the cell

Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.

New developments in 'ene'-reductase catalysed biological hydrogenations

Asymmetric biocatalytic hydrogenations are important reactions performed primarily by members of the Old Yellow Enzyme family. These reactions have great potential in the chemosynthesis of a variety of industrially useful synthons due to the generation of up to two stereogenic centres. In this review, additional enzyme classes capable of asymmetric hydrogenations will be discussed, as will examples of multienzyme cascading reactions. New and improved technology that enhances the commercial viability of biotransformations are included, such as the nicotinamide coenzyme-independent reactions. This review will focus on progress in this field within the last two years, with emphasis on industrial applications of this technology.

Synthesis of robalzotan, ebalzotan, and rotigotine precursors via the stereoselective multienzymatic cascade reduction of α,β-unsaturated aldehydes

A stereoselective synthesis of bicyclic primary or secondary amines, based on tetralin or chroman structural moieties, is reported. These amines are precursors of important active pharmaceutical ingredients such as rotigotine (Neupro), robalzotan, and ebalzotan. The key step is based on a multienzymatic reduction of an α,β-unsaturated aldehyde or ketone to give the saturated primary or secondary alcohol, in a high yield and with a high ee. The catalytic system consists of the combination of an ene-reductase (ER; i.e., OYE2 or OYE3 belonging to the Old Yellow Enzyme family) with an alcohol dehydrogenase (ADH), applying the in situ substrate feeding product removal technology. By this system the formation of the allylic alcohol side product and the racemization of the chirally unstable α-substituted aldehyde intermediate are minimized. The primary alcohols were elaborated via a Curtius rearrangement. The combination of OYE2 with a Prelog or an anti-Prelog ADH allowed the preparation of the secondary alcohols with ee > 99% and de > 87%. The absolute configuration of the primary amines was unambiguously assigned by comparison with authentic samples. The stereochemistry of secondary alcohols was assigned by X-ray crystal structure and NMR analysis of Mosher esters.

A substrate-driven approach to determine reactivities of α,β-unsaturated carboxylic esters towards asymmetric bioreduction

The degree of C=C bond activation in the asymmetric bioreduction of α,β-unsaturated carboxylic esters by ene-reductases was studied, and general recommendations to render these "borderline-substrates" more reactive towards enzymatic reduction are proposed. The concept of "supported substrate activation" was developed. In general, an additional α-halogenated substituent proved to be beneficial for enzymatic activity, whereas β-alkyl or β-aryl substituents were detrimental for the reactivity of nonhalogenated substrates, and α-cyano groups showed little effect. The alcohol moiety of the ester functionality was found to have a strong influence on the reaction rate. Overall, activities were determined by both steric and electronic effects.