Biocatalysts from Biosynthetic Pathways: Enabling Stereoselective, Enzymatic Cycloether Formation on a Gram Scale

C-C Bond Cleavage in the Late-Stage Biosynthesis of Huperzine Alkaloids Occurs via Enzymatic Retro-Aza-Prins Reaction

The demand for novel enzyme-catalyzed reactions in chemical synthesis has spurred the development of many new-to-nature reactions. Additionally, detailed analysis of biosynthetic pathways can uncover unprecedented chemical/enzymatic mechanisms. In this study, we revisited the catalytic mechanism of the 2-oxoglutarate-dependent dioxygenase Pt2OGD-1, involved in the biosynthesis of huperzine alkaloids. Our experimental and computational investigations uncovered a previously unknown enzymatic C-C bond cleavage in the piperidine ring of the alkaloid scaffold, resembling an oxidative retro-aza-Prins reaction. Here, this transformation is initiated by hydrogen abstraction, followed by electron transfer at the 4-position of the heterocycle, triggering ring opening and finally resulting in the loss of a carbon atom as formaldehyde. This discovery expands the toolbox of reactions, enhances our understanding of these enzymes, and may facilitate their application in the biotechnological production of pharmaceutically relevant alkaloid scaffolds as well as the development of biocatalysts with similar activities.

The Relationship between Substrate Structure and Selectivity of Ketoreduction in Multimodular Polyketide Synthases: A Comparative Study of A-Type Ketoreductases from Late Modules Using Complex Precursor Analogues

Ketoreductases (KRs) are domains in the reductive loops of type I polyketide synthases (PKSs) and are responsible for the majority of stereocenters in reduced polyketides. Although the highly stereoselective reduction of ACP-bound β-ketothioester intermediates by KRs is crucial for the overall functioning of PKSs, the substrate-dependent stereoselectivity of KRs is a factor that is not yet fully understood, especially for KR domains in late PKS modules that act on biosynthetic precursors with complex polyketidic moieties. We present studies on the three KR domains FosKR7, PlmKR6, and EryKR6 from the biosynthetic pathways of fostriecin, phoslactomycin, and erythromycin by in vitro assays using close surrogates of the octaketidic FosKR7 biosynthetic precursor, complex derivatives and a diketide in the form of their biomimetic N-acetylcysteamine thioesters. Supported by molecular modeling, specific interactions of the studied KR domains with the extended polyketide moieties of their natural precursors were identified and correlated to the differences in stereoselectivity observed in the in vitro assays. These results reinforce the importance of the substrate-dependent stereoselectivity of KR domains in PKSs and suggest more detailed experimental and structural studies with isolated KRs and full PKS modules that could ultimately lead to improved results in PKS engineering.

Recent Advances in the Synthesis of Diarylheptanoids

In the quest for synthesizing biologically important natural products, medicinal chemists embark on an endless journey. This review focuses on the reports published towards the syntheses of diarylheptanoids, classifying them into linear, tetrahydropyran, diarylether, and biphenyl categories. The synthesis methods for each class from 2013 to 2023 are discussed, providing a comprehensive overview of the advancements in the field. Representative natural product examples are highlighted for each category. The review emphasizes the importance of diarylheptanoids in the realms of chemistry and medicine, showcasing their potential as valuable compounds for medicinal and synthetic chemists.

Microbial synthesis of anthocyanins and pyranoanthocyanins: current bottlenecks and potential solutions

Anthocyanins (ACNs) are secondary metabolites found in plants. Due to their impressive biological activities, ACNs have gained significant popularity and extensive application within the food, pharmaceutical, and nutraceutical industries. A derivative of ACNs: pyranoanthocyanins (PACNs) possesses more stable properties and interesting biological activities. However, conventional methods for the production of ACNs, including chemical synthesis and plant extraction, involve organic solvents. Microbial synthesis of ACNs from renewable biomass, such as amino acids or flavonoids, is considered a sustainable and environmentally friendly method for large-scale production of ACNs. Recently, the construction of microbial cell factories (MCFs) for the efficient biosynthesis of ACNs and PACNs has attracted much attention. In this review, we summarize the cases of microbial synthesis of ACNs, and analyze the bottlenecks in reconstructing the metabolic pathways for synthesizing PACNs in microorganisms. Consequently, there is an urgent need to investigate the mechanisms behind the development of MCFs for PACNs synthesis. Such research also holds significant promise for advancing the production of food pigments. Meanwhile, we propose potential solutions to the bottleneck problem based on metabolic engineering and enzyme engineering. Finally, the development prospects of natural food and biotechnology are discussed.

Combining total synthesis and genetic engineering to probe dihydropyran formation in ambruticin biosynthesis

The ambruticins are a family of potent antifungal polyketide derived natural products isolated from the myxobacterium Sorangium cellulosum. Their unusual structures include a trisubstituted cyclopropyl group and two oxygen heterocycles, a tetrahydropyran (THP) and dihydropyran (DHP). Herein we report a flexible modular approach for the total synthesis of ambruticins which is used to prepare ambruticins F and S as well as in the first total synthesis of 20,21-dihydroambruticin F. The flexible strategy unites 3 fragments via Julia-Kocienski olefinations and provides important standards for investigation of dihydropyran formation in ambruticin biosynthesis. Cultures of wild-type S. cellulosum So ce10 produce mainly ambruticin S and the VS series of metabolites. An efficient electroporation method enabled gene knockout experiments which revealed that the ΔambP-S mutant of S. cellulosum accumulated the bisTHP polyketide 20,21-dihydroambruticin F. In contrast, the ΔambN-S mutant gave ambruticin F with the 20,21-alkene as the major metabolite confirming that AmbP and AmbO (a Rieske enzyme and flavin-dependent monooxygenase respectively) are implicated in 20,21-alkene formation. The results of feeding studies to a Sorangium strain containing only ambP and ambO are in accord with formation of the 20,21-alkene occurring prior to generation of the C3 to C7 dihydroxylated tetrahydropyran in ambruticin biosynthesis.

Novel Biocatalysts from Specialized Metabolism

Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.

Rieske Oxygenase-Catalyzed Oxidative Late-Stage Functionalization during Complex Antifungal Polyketide Biosynthesis

Rieske oxygenases (ROs) from natural product biosynthetic pathways are a poorly studied group of enzymes with significant potential as oxidative functionalization biocatalysts. A study on the ROs JerL, JerP, and AmbP from the biosynthetic pathways of jerangolid A and ambruticin VS-3 is described. Their activity was successfully reconstituted using whole-cell bioconversion systems coexpressing the ROs and their respective natural flavin-dependent reductase (FDR) partners. Feeding authentic biosynthetic intermediates and synthetic surrogates to these strains confirmed the involvement of the ROs in hydroxymethylpyrone and dihydropyran formation and revealed crucial information about the RO's substrate specificity. The pronounced dependence of JerL and JerP on the presence of a methylenolether allowed the precise temporal assignment of RO catalysis to the ultimate steps of jerangolid biosynthesis. JerP and AmbP stand out among the biosynthetic ROs studied so far for their ability to catalyze clean tetrahydropyran desaturation without further functionalizing the formed electron-rich double bonds. This work highlights the remarkable ability of ROs to highly selectively oxidize complex molecular scaffolds.

Molecular Insights into Bifunctional Ambruticin DH3 for Substrate Specificity and Catalytic Mechanism

Dehydratase (DH), a domain located at polyketide synthase (PKS) modules, commonly catalyzes the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As a unique bifunctional dehydratase, AmbDH3 (the DH domain of module 3 of the ambruticin PKS) is verified to be responsible for both dehydration and the following pyran-forming cyclization. Besides, in vitro studies showed that its catalytic efficiency varies with different chiral substrates. However, the detailed molecular mechanism of AmbDH3 remains unclear. In this work, the structural rationale for the substrate specificity (2R/2S- and 6R/6S-substrates) in AmbDH3 was elucidated and the complete reaction pathways including dehydration and cyclization were presented. Both MD simulations and binding free energy calculations indicated AmbDH3 had a stronger preference for 2R-substrates (2R6R-2, 2R6S-3) than 2S-substrates (2S6R-1), and residue H51 and G61 around the catalytic pocket were emphasized by forming stable hydrogen bonds with 2R-substrates. In addition, AmbDH3's mild tolerance at C6 was explained by comparison of substrate conformation and hydrogen bond network in 6S- and 6R-substrate systems. The QM/MM results supported a consecutive one-base dehydration and cyclization mechanism for 2R6S-3 substrate with the energy barrier of 25.2 kcal mol^-1 and 24.5 kcal mol^-1 , respectively. Our computational results uncover the substrate recognition and catalytic process of the first bifunctional dehydratase-cyclase AmbDH3, which will shed light on the application of multifunctional DH domains in PKSs for diverse natural product analogs and benefit the chemoenzymatic synthesis of stereoselective pyran-containing products.

Towards understanding oxygen heterocycle-forming biocatalysts: a selectivity study of the pyran synthase PedPS7

Intramolecular oxa-Michael addition-catalysing cyclases are widespread in polyketide biosynthetic pathways. Although they have significant potential in biotechnology and chemoenzymatic synthesis of chiral heterocycles, they have only scarcely been studied. Here, we present detailed investigations on the selectivity profile of the pyran synthase PedPS7 showing that it combines broad substrate tolerance with high selectivity for the formation of up to two new stereocentres and relaxed precursor stereoisomer discrimination. Two of the four possible tetrahydropyran stereoisomers are reliably accessible by this enzyme. The results indicate fundamental differences between the individual subtypes of intramolecular oxa-Michael addition-catalysing cyclases.

Enantioselective Total Synthesis of the Putative Biosynthetic Intermediate Ambruticin J

The family of anti-fungal natural products known as the ambruticins are structurally distinguished by a pair of pyran rings adorning a divinylcyclopropane core. Previous characterization of their biosynthesis, including the expression of a genetically modified producing organism, revealed that the polyketide synthase pathway proceeds via a diol intermediate, known as ambruticin J. Herein, we report the first enantioselective total synthesis of the putative PKS product, ambruticin J, according to a triply convergent synthetic route featuring a Suzuki-Miyaura cross-coupling and a Julia-Kocienski olefination for fragment assembly. This synthesis takes advantage of synthetic methodology previously developed by our laboratory for the stereoselective generation of the trisubstituted cyclopropyl linchpin.

Ambruticins: tetrahydropyran ring formation and total synthesis

The ambruticins are a family of polyketide natural products which exhibit potent antifungal activity. Gene knockout experiments are in accord with the proposal that the tetrahydropyran ring of the ambruticins is formed via the AmbJ catalysed epoxidation of the unsaturated 3,5-dihydroxy acid, ambruticin J, followed by regioselective cyclisation to ambruticin F. Herein, a convergent approach to the total synthesis of ambruticin J is described as well as model studies involving epoxidation and cyclisations of unsaturated hydroxy esters to give tetrahydropyrans and tetrahydrofurans. The total synthesis involves preparation of three key fragments which were united via a Suzuki-Miyaura cross-coupling and Julia-Kocienski olefination to generate the required carbon framework. Global deprotection to a triol and selective oxidation of the primary alcohol gave, after hydrolysis of the lactone, ambruticin J.

Cross-linking of a polyketide synthase domain leads to a recyclable biocatalyst for chiral oxygen heterocycle synthesis

The potential of polyketide synthase (PKS) domains for chemoenzymatic synthesis can often not be tapped due to their low stability and activity in vitro. In this proof-of-principle study, the immobilisation of the heterocycle-forming PKS domain AmbDH3 as a cross-linked enzyme aggregate (CLEA) is described. The AmbDH3-CLEA showed good activity recovery, stability and recyclability. Repetitive reactions on the semi-preparative scale were performed with high conversion and isolated yield. Similar to that observed for the free enzyme, the aggregate retained substrate tolerance and the ability for kinetic resolution. This first example of a successful enzymatic PKS domain immobilisation demonstrates that cross-linking can in principle be applied to this type of enzyme to increase its applicability for chemoenzymatic synthesis.

Cross-linking of the polyketide synthase domain AmbDH3 led to an active aggregate with improved properties for the chemoenzymatic synthesis of chiral oxygen heterocycles, such as recyclability and facile purification.

The ambruticins and jerangolids - chemistry, biology and chemoenzymatic synthesis of potent antifungal drug candidates

Covering: 1977 to 2020The ambruticins and jerangolids are myxobacterial reduced polyketides, which are produced via highly unusual biosynthetic pathways containing a plethora of non-canonical enzymatic transformations. Since the discovery of the first congeners in the late 1970s, they have been in the focus of drug development due to their good antifungal activity and low toxicity in mammals, which result from interaction with an unusual innercellular target in fungi. Despite significant efforts, which have led to the development of various total syntheses, their structural complexity has yet avoided full exploitation of their pharmacological potential. This article summarises biological, total and semisynthetic as well as biosynthetic studies on both compounds. An outlook on the biosynthesis-based approaches to them and their derivatives is presented. Due to the structural and biosynthetic characteristics of the ambruticins and jerangolids, chemoenzymatic processes that make use of their biosynthetic pathway enzymes are particularly promising to gain efficient access to derivative libraries for structure activity relationship studies.