An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity

A Bimolecular Diels-Alder Reaction Mediated by Inclusion in a Polar Bis-calix[4]pyrrole Octa-Imine Cage

We describe using a dynamically self-assembled octa-imine cage as a molecular flask to accelerate a bimolecular Diels-Alder reaction. We investigate the cage's binding properties using 1H NMR spectroscopic titrations, ITC experiments, and X-ray crystallography. We detect and characterize the formation of the ternary complex (Michaelis) in solution. A detailed kinetic analysis of the reaction data supports that the cage's acceleration is provided by including the two reactants, resulting in an effective molarity (EM) of ∼40 M. Exo-selectivity and shift of the reaction's chemical equilibrium are also encountered in the cage's confined space. Our results mimic enzymes' ability to bind two substrates in a polar cavity, using directional interactions, and accelerate their stereoselective reaction, with the potential for cavity engineering to enable other reactions.

An enzymatic dual-oxa Diels-Alder reaction constructs the oxygen-bridged tricyclic acetal unit of (-)-anthrabenzoxocinone

The hetero-Diels-Alder (HDA) reaction is a key method for synthesizing six-membered heterocyclic rings in natural products and bioactive compounds. Despite its importance in synthetic chemistry, naturally occurring enzymatic HDA reactions are rare and limited to a single heteroatom. Here we report Abx(-)F, a bifunctional vicinal oxygen chelate (VOC)-like protein that catalyses dehydration and dual-oxa Diels-Alder reactions to stereoselectively form the oxygen-bridged tricyclic acetal of (-)-anthrabenzoxocinone ((-)-ABX). Isotope assays and density functional theory calculations reveal a dehydration-coordinated, concerted HDA mechanism. The crystal structure of Abx(-)F and NMR complex structures of Abx(-)F with its substrate analogue and (-)-ABX define the reaction's structural basis. Mutational analysis identifies Asp17 as a general base that mediates dehydration, forming an o-quinone methide intermediate for stereoselective dual-oxa HDA. This work establishes the molecular and structural basis of a polyheteroatomic Diels-Alderase, paving the way for designing polyheteroatomic DA enzymatic tools.

Reshaping Interface Interactions of P. litoralis Acyltransferase for Efficient Chemoenzymatic Epoxidation in Aqueous Phase

Epoxides, a class of ethers with a three-membered ring structure, are widely used in the textile, pharmaceutical, and packaging industries. Chemoenzymatic epoxidation presents a promising method for synthesizing epoxides. However, its epoxidation efficiency is hindered by low chemoselective perhydrolysis, which is caused by the hydrolysis side reaction in the aqueous phase. In this study, a chemoenzymatic epoxidation process in the aqueous phase was developed by utilizing an acyltransferase from P. litoralis (PlAcT) for its chemoselective perhydrolysis. Crystal structure analysis, molecular dynamics simulations, and quantum mechanics calculations, along with site-specific mutagenesis, revealed that the selectivity of perhydrolysis is due to a lower energy barrier in the acyl transfer step compared to that in hydrolysis. Furthermore, the mutant PlAcTM3-2 exhibited a 7.6-fold improvement in solvent stability and a 1.3-fold increase in perhydrolysis activity compared to the wild type, achieved by reshaping interface interactions. As a result, the engineered strain Y07, harboring PlAcTM3-2, successfully synthesized compounds 3a-3n with conversions ranging from 11-99%, and the titers of compounds α-pinene oxide(3i), β-pinene oxide(3j), 3-carene oxide(3k), and limonene dioxide(3l-3) reached 55.8, 16.7, 75.2, and 21.4 g/L, respectively. These results demonstrate a sustainable method for chemoenzymatic epoxidation in the aqueous phase.

The Mutually Inspiring Biological and Chemical Synthesis of Fungal Bicyclo[2.2.2]diazaoctane Indole Alkaloids

Fungal indole alkaloids bearing a bicyclo[2.2.2]diazaoctane (BCDO) core structure are a fascinating family of natural products that exhibit a wide spectrum of biological activities. These compounds also display remarkable structural diversity, with many different diastereomers and enantiomers produced by specific fungal strains. The biogenesis of the unique BCDO moiety has long been proposed to involve an intramolecular [4+2] hetero-Diels-Alder (IMDA) reaction, but the exact mechanisms for this hypothetical transformation have remained elusive until recently. This review aims to summarize the whole history of synthetic and biosynthetic studies of fungal BCDO indole alkaloids, by covering the discovery, biomimetic syntheses, total syntheses, biosynthetic pathway elucidation, and biological activities of representative compounds. We highlight the mutual inspiration and corroboration between biological and synthetic chemists in exploring the intriguing biosynthetic mysteries of this family of natural products. We also provide perspectives and clues for the remaining biosynthetic problems.

Enzymatic Ring Contraction for the Biosynthesis of Sulfur-Containing Cyclopentachromone

Cyclopentachromone, distinguished by its 6/6/5 heterotricyclic ring structure, is a key building block in many bioactive natural products, yet its enzymatic origin remains unclear. We identified a new class of cyclopentachromone-containing compounds, termed isochromosulfines, characterized by unique C-S bonds. A distinct FAD-dependent monooxygenase, IscL, was identified to catalyze the formation of the 6/6/5 cyclopentadiene intermediate, 2S-remisporine A, from a 6/6/6 xanthone precursor via benzene ring contraction. The high reactivity of 2S-remisporine A further promotes a spontaneous thiol-Michael addition reaction with thiol-containing compounds, forming the C-S bond in isochromosulfines. Additionally, we demonstrate that IscL homologues mediate a bifurcated pathway of benzene ring modification in the xanthone intermediate, leading to either ring contraction or cleavage, which is determined by a critical residue at position 230 to be phenylalanine or tyrosine. Our findings highlight the pivotal role of IscL in forming the 6/6/5 cyclopentachromone scaffold and offer deep insights into its catalytic mechanism. Our work lays the foundation for genome mining of cyclopentachromone-containing compounds and shows the potential application of IscL in biocatalysis.

Structural diversity, biological activities and biosynthetic pathways of [2 + 2] and [4 + 2] amide alkaloid dimers from Piperaceae: An updated review

The Piperaceae family is distributed widely in tropical and subtropical areas. It encompasses around 5 genera and over 3000 species. They are distinguished by the substantial chemical diversity and potential medicinal applications. Amide alkaloids, as the main secondary metabolites in the Piperaceae family, exhibit various biological activities, and the discovery of [2 + 2] and [4 + 2] amide alkaloid dimers has led to a surge in phytochemical research on Piperaceae plants. Although the identification of these dimers has been gradually increasing in recent years, there remains a lack of comprehensive and systematic evaluations of these compounds. This review aims to summarize the latest advancements in the research on natural amide alkaloid dimers, focusing on their structural diversity, biological activities and biosynthetic pathways, and the enzymatic advances of [2 + 2] and [4 + 2] cyclase enzymes. Until October 2024, research has documented 99 amide alkaloid dimers, including 37 dimers possessing [2 + 2] cyclobutanes skeletons and 62 [4 + 2] cyclohexene skeletons derived from the Piperaceae family. These compounds demonstrate a range of in vitro biological activities including anti-inflammatory, anticancer, acetylcholinesterase inhibitory, anti-platelet aggregation, hepatoprotective, antimalarial, antitubercular, anti-diabetic and notable interactions with CYP3A4 and CYP2D6 enzymes. A systematic review of these [2 + 2] and [4 + 2] amide alkaloid dimers in Piperaceae family can provide a critical scientific foundation and theoretical support for the discovery and development of novel pharmaceutical agents.

Modifications of Prenyl Side Chains in Natural Product Biosynthesis

In recent years, there has been a growing interest in understanding the enzymatic machinery responsible for the modifications of prenyl side chains and elucidating their roles in natural product biosynthesis. This interest stems from the pivotal role such modifications play in shaping the structural and functional diversity of natural products, as well as from their potential applications to synthetic biology and drug discovery. In addition to contributing to the diversity and complexity of natural products, unique modifications of prenyl side chains are represented by several novel biosynthetic mechanisms. Representative unique examples of epoxidation, dehydrogenation, oxidation of methyl groups to carboxyl groups, unusual C-C bond cleavage and oxidative cyclization are summarized and discussed. By revealing the intriguing chemistry and enzymology behind these transformations, this comprehensive and comparative review will guide future efforts in the discovery, characterization and application of modifications of prenyl side chains in natural product biosynthesis.

Engineering a Biosynthetic Pathway for the Production of (+)-Brevianamides A and B in Escherichia coli

The privileged fused-ring system comprising the bicyclo[2.2.2]diazaoctane (BDO) core is prevalent in diketopiperazine (DKP) natural products with potent and diverse biological activities, with some being explored as drug candidates. Typically, only low yields of these compounds can be extracted from native fungal producing strains and the available synthetic routes remain challenging due to their structural complexity. BDO-containing DKPs including (+)-brevianamides A and B are assembled via multi-component biosynthetic pathways incorporating non-ribosomal peptide synthetases, prenyltransferases, flavin monooxygenases, cytochrome P450s and semi-pinacolases. To simplify access to this class of alkaloids, we designed an engineered biosynthetic pathway in Escherichia coli , composed of six enzymes sourced from different kingdoms of life. The pathway includes a cyclodipeptide synthase (NascA), a cyclodipeptide oxidase (DmtD2/DmtE2), a prenyltransferase (NotF), a flavin-dependent monooxygenase (BvnB), and kinases (PhoN and IPK). Cultivated in glycerol supplemented with prenol, the engineered E. coli strain produces 5.3 mg/L of (-)-dehydrobrevianamide E ( 4 ), which undergoes a terminal, ex vivo lithium hydroxide catalyzed rearrangement reaction to yield (+)-brevianamides A and B with a 46% yield and a 92:8 diastereomeric ratio. Additionally, titers of 4 were increased eight-fold by enhancing NADPH pools in the engineered E. coli strain. Our study combines synthetic biology, biocatalysis and synthetic chemistry approaches to provide a five-step engineered biosynthetic pathway for producing complex indole alkaloids in E. coli .

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Hunting for the Intermolecular Diels-Alderase

The Diels-Alder reaction is well known as a concerted [4 + 2] cycloaddition governed by the Woodward-Hoffmann rules. Since Prof. Otto Diels and his student Kurt Alder initially reported the intermolecular [4 + 2] cycloaddition between cyclopentadiene and quinone in 1928, it has been recognized as one of the most powerful chemical transformations to build C-C bonds and construct cyclic structures. This named reaction has been widely used in synthesizing natural products and drug molecules. Driven by the synthetic importance of the Diels-Alder reaction, identifying the enzyme that stereoselectively catalyzes the Diels-Alder reaction has become an intriguing research area in natural product biosynthesis and biocatalysis. With significant progress in sequencing and bioinformatics, dozens of Diels-Alderases have been characterized in microbial natural product biosynthesis. However, few are evolutionally dedicated to catalyzing an intermolecular Diels-Alder reaction with a concerted mechanism. This Account summarizes our endeavors to hunt for the naturally occurring intermolecular Diels-Alderase from plants. Our research journey started from the biomimetic syntheses of D-A-type terpenoids and flavonoids, showing that plants use both nonenzymatic and enzymatic intermolecular [4 + 2] cycloadditions to create complex molecules. Inspired by the biomimetic syntheses, we identify an intermolecular Diels-Alderase hidden in the biosynthetic pathway of mulberry Diels-Alder-type cycloadducts using a biosynthetic intermediate probe-based target identification strategy. This enzyme, MaDA, is an endo-selective Diels-Alderase and is then functionally characterized as a standalone intermolecular Diels-Alderase with a concerted but asynchronous mechanism. We also discover the exo-selective intermolecular Diels-Alderases in Morus plants. Both the endo- and exo-selective Diels-Alderases feature a broad substrate scope, but their mechanisms for controlling the endo/exo pathway are different. These unique intermolecular Diels-Alderases phylogenetically form a subgroup of FAD-dependent enzymes that can be found only in moraceous plants, explaining why this type of [4 + 2] cycloadduct is unique to moraceous plants. Further studies of the evolutionary mechanism reveal that an FAD-dependent oxidocyclase could acquire the Diels-Alderase activity via four critical amino acid mutations and then gradually lose its original oxidative activity to become a standalone Diels-Alderase during the natural evolution. Based on these insights, we designed new Diels-Alderases and achieved the diversity-oriented chemoenzymatic synthesis of D-A products using either naturally occurring or engineered Diels-Alderases. Overall, this Account describes our decade-long efforts to discover the intermolecular Diels-Alderases in Morus plants, particularly highlighting the importance of biomimetic synthesis and chemical proteomics in discovering new intermolecular Diels-Alderases from plants. Meanwhile, this Account also covers the evolutionary and catalytic mechanism study of intermolecular Diels-Alderases that may provide new insights into how to discover and design new Diels-Alderases as powerful biocatalysts for organic synthesis.

Discovery and evolution of [4 + 2] cyclases

[4 + 2] Cyclases are potent biocatalysts that have been bestowed upon microorganisms and plants by nature, equipping them with the powerful tools to utilize and implement the [4 + 2] cycloaddition reaction for constructing the cyclohexene core in synthesizing valuable molecules. Over the past two years, eleven new enzymes have joined this pericyclase club and undergone extensive investigation. In this review, we present a comprehensive overview of recent advancements in characterizing [4 + 2] cyclases with regard to their catalytic mechanism and stereoselectivity. We particularly focus on insights gained from enzyme co-crystal structures, cofactors, as well as the effects of glycosylation. Advancements in understanding the mechanisms of natural [4 + 2] cyclases offer the potential to mimic evolutionary processes and engineer artificial enzymes for the development of valuable and practical biocatalysts.

Expanding chemistry through in vitro and in vivo biocatalysis

Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.

Discovery of a Potent Antiosteoporotic Drug Molecular Scaffold Derived from Angelica sinensis and Its Bioinspired Total Synthesis

Angelica sinensis, commonly known as Dong Quai in Europe and America and as Dang-gui in China, is a medicinal plant widely utilized for the prevention and treatment of osteoporosis. In this study, we report the discovery of a new category of phthalide from Angelica sinensis, namely falcarinphthalides A and B (1 and 2), which contains two fragments, (3R,8S)-falcarindiol (3) and (Z)-ligustilide (4). Falcarinphthalides A and B (1 and 2) represent two unprecedented carbon skeletons of phthalide in natural products, and their antiosteoporotic activities were evaluated. The structures of 1 and 2, including their absolute configurations, were established using extensive analysis of NMR spectra, chemical derivatization, and ECD/VCD calculations. Based on LC-HR-ESI-MS analysis and DFT calculations, a production mechanism for 1 and 2 involving enzyme-catalyzed Diels-Alder/retro-Diels-Alder reactions was proposed. Falcarinphthalide A (1), the most promising lead compound, exhibits potent in vitro antiosteoporotic activity by inhibiting NF-κB and c-Fos signaling-mediated osteoclastogenesis. Moreover, the bioinspired gram-scale total synthesis of 1, guided by intensive DFT study, has paved the way for further biological investigation. The discovery and gram-scale total synthesis of falcarinphthalide A (1) provide a compelling lead compound and a novel molecular scaffold for treating osteoporosis and other metabolic bone diseases.

Reprogramming the Transition States to Enhance C-N Cleavage Efficiency of Rhodococcus opacusl-Amino Acid Oxidase

l-Amino acid oxidase (LAAO) is an important biocatalyst used for synthesizing α-keto acids. LAAO from Rhodococcus opacus (RoLAAO) has a broad substrate spectrum; however, its low total turnover number limits its industrial use. To overcome this, we aimed to employ crystal structure-guided density functional theory calculations and molecular dynamic simulations to investigate the catalytic mechanism. Two key steps were identified: S → [TS1] in step 1 and Int1 → [TS2] in step 2. We reprogrammed the transition states [TS1] and [TS2] to reduce the identified energy barrier and obtain a RoLAAO variant capable of catalyzing 19 kinds of l-amino acids to the corresponding high-value α-keto acids with a high total turnover number, yield (≥95.1 g/L), conversion rate (≥95%), and space-time yields ≥142.7 g/L/d in 12-24 h, in a 5 L reactor. Our results indicated the promising potential of the developed RoLAAO variant for use in the industrial production of α-keto acids while providing a potential catalytic-mechanism-guided protein design strategy to achieve the desired physical and catalytic properties of enzymes.

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.

Fungal P450 Deconstructs the 2,5-Diazabicyclo[2.2.2]octane Ring En Route to the Complete Biosynthesis of 21R-Citrinadin A

Prenylated indole alkaloids (PIAs) possess great structural diversity and show biological activities. Despite significant efforts in investigating the biosynthetic mechanism, the key step in the transformation of 2,5-diazabicyclo[2.2.2]octane-containing PIAs into a distinct class of pentacyclic compounds remains unknown. Here, using a combination of gene deletion, heterologous expression, and biochemical characterization, we show that a unique fungal P450 enzyme CtdY catalyzes the cleavage of the amide bond in the 2,5-diazabicyclo[2.2.2]octane system, followed by a decarboxylation step to form the 6/5/5/6/6 pentacyclic ring in 21R-citrinadin A. We also demonstrate the function of a subsequent cascade of stereospecific oxygenases to further modify the 6/5/5/6/6 pentacyclic intermediate en route to the complete 21R-citrinadin A biosynthesis. Our findings reveal a key enzyme CtdY for the pathway divergence in the biosynthesis of PIAs and uncover the complex late-stage post-translational modifications in 21R-citrinadin A biosynthesis.

Peroxidase-induced C-N bond formation via nitroso ene and Diels-Alder reactions

The formation of new carbon-nitrogen bonds is indisputably one of the most important tasks in synthetic organic chemistry. Here, nitroso compounds offer a highly interesting reactivity that complements traditional amination strategies, allowing for the introduction of nitrogen functionalities via ene-type reactions or Diels-Alder cycloadditions. In this study, we highlight the potential of horseradish peroxidase as biological mediator for the generation of reactive nitroso species under environmentally benign conditions. Exploiting a non-natural peroxidase reactivity, in combination with glucose oxidase as oxygen-activating biocatalyst, aerobic activation of a broad range of N-hydroxycarbamates and hydroxamic acids is achieved. Thus both intra- and intermolecular nitroso-ene as well as nitroso-Diels-Alder reactions are performed with high efficiency. Relying on a commercial and robust enzyme system, the aqueous catalyst solution can be recycled over numerous reaction cycles without significant loss of activity. Overall, this green and scalable C-N bond-forming strategy enables the production of allylic amides and various N-heterocyclic building blocks utilizing only air and glucose as sacrificial reagents.