Harnessing ortho-Quinone Methides in Natural Product Biosynthesis and Biocatalysis

Acid-Catalyzed Solvent-Switchable Chemoselective N-Alkylation and para C-Alkylation of Unprotected Arylamines Utilizing ortho-Quinone Methides

Nitrogen-containing compounds, such as anilines, represent some of the most prevalent and valuable chemical entities within the field of chemistry. However, their high reactivity, which frequently lacks selectivity, has constrained their application in various chemical transformations, including the alkylation of alcohols. In the present study, we successfully accomplished site-selective para and N-H alkylation of anilines by utilizing ortho-quinone methides under mild conditions. The regioselective para-alkylation was conducted with unprotected anilines in a metal-free environment, while N-H alkylations were effectively performed under similarly mild conditions. DFT calculations were carried out to understand the distinctive chemoselectivity of N-alkylation and C-alkylation of unprotected arylamines with different nonpolar (toluene) and polar protic (HFIP) solvents. Furthermore, the different transition state models identified in our calculations shed light on the intricate interplay between solvent effects and reaction selectivity.

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.

o-Quinone methides in natural product synthesis: an update

In recent years, ortho-quinone methides have emerged as indispensable reactive species for enhancing synthetic efficiency in accessing various bioactive natural products. Importantly, the emulation of nature's patterns and strategies has yielded numerous refined synthetic pathways for the construction of intricate molecules. o-Quinone methides (o-QMs) have demonstrated remarkable versatility in organic synthesis, especially in strategies guided by biomimetic logic. This review aims to delve into bio-inspired strategies employed over the past five years in the total synthesis of natural products involving ortho-quinone methides.

Defining the Synthetic Scope of ortho-Quinone Methides by Quantifying their Electrophilicity

A series of aryl-substituted ortho-quinone methides (oQMs) was synthesised and structurally characterised. Kinetic studies of the nucleophilic additions of carbanions (reference nucleophiles) to oQMs were used to determine second-order rate constants k2 for the carbon-carbon bond forming reactions (20 °C, DMSO) at the oQMs' exocyclic π-bond. Analysing the kinetic data by the linear free energy relationship lg k2=sN(N+E) revealed the Mayr electrophilicities E of the oQMs. The electrophilicities E of oQMs correlate linearly with Hammett substituent constants and experimentally determined reduction potentials Ep red as well as with quantum-chemically calculated methyl anion affinities (MAAs), which provides valuable tools for prediciting the reactivity of further types of oQMs. Embedding the oQMs in Mayr's reactivity scales enables to predict novel nucleophilic reaction partners for oQMs and can productively be used to prepare simple Michael adducts as well as 4+2 or 4+1 cyclisation products as demonstrated in this work by several novel reactions with neutral or negatively charged C-, N-, and S-nucleophiles.

Genome mining of nonenzymatic ortho-quinone methide-based pseudonatural products from ascidian-derived fungus Diaporthe sp.SYSU-MS4722

Ortho-quinone methides (o-QMs), generated by oxidative dehydration of clavatol, are highly reactive intermediates in biosynthesis that give rise to a variety of clavatol-containing pseudonatural products (PNPs) in fungi through intra- and intermolecular nonenzymatic cyclization/addition reaction, and some compounds have significant biological activities. Here we report our genome mining efforts on a cryptic clavatol biosynthetic gene cluster (BGC) from an ascidian-derived fungus Diaporthe sp. SYSU-MS4722. The core genes NR-PKS (DiaG), Esterase (DiaF) derived from the fungus Diaporthe sp. SYSU-MS4722 clavatol BGC and the known α-ketoglutarate-dependent nonheme iron enzymes (ClaD) were heterologously expressed in the Aspergillus oryzae NSAR1 (A. oryzae NSAR1). Thirteen new monomeric, dimeric, and trimeric clavatol-based PNPs (7-19), together with three known compounds (20-22) were isolated from the above transformant. Their structures including absolute configurations were elucidated by spectroscopic analysis (UV, IR, HR-ESI-MS, 1D and 2D NMR data), complemented with the X-ray crystallography, the comparison of the experimental and calculated ECD spectra, and gauge-independent atomic orbital (GIAO) NMR calculations. Based on the structural characteristics, their plausible biosynthetic pathways were proposed. Notably, Compounds 8, 9, 14 and 16 exhibited potent anti-fibrotic activity with EC50 values of 28.9, 10.0, 3.5 and 30.1 μM, respectively.

Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction

Non-heme iron (FeII), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of FeII/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features.

Biosynthesis of Tetramate Derivatives in Penicillium crustosum Reveals the Involvement of ortho-Quinone Methide in Crosstalk of Multiple Pathways

Genome mining and gene deletion experiments in Penicillium crustosum proved the involvement of the PKS-NRPS PemA and the trans-enoyl reductase PemB in the formation of three enantiomeric clavatol-containing tetramate pairs. Overexpression of a transcription factor significantly improved the product yields. Feeding experiments provided evidence for their formation via 1,4-Michael addition of hydroxyclavatol to two tetramates from the Pem pathway. This study provides another example of the involvement of reactive intermediates in multiple biosynthetic pathways.

Fast and Selective Cysteine Conjugation Using para-Quinone Methides

An efficient and selective method for cysteine conjugation utilizing para-quinone methides (p-QMs) was developed. p-QM labeling exhibits high specificity toward the cysteine residue, as evidenced by its reactivity with various amino acid derivatives, peptides, and proteins. Notably, the p-QM-cysteine reactions display robust kinetics with rate constants up to 1.67 × 104 M-1·s-1. Furthermore, p-QM conjugation enables us to attach a fluorescent probe to a HER2 nanobody, resulting in selective labeling of HER2-positive SK-BR-3 cells.

Targeted Discovery of a Natural ortho-Quinone Methide Precursor and Green Generation of Its Oligomers

ortho-Quinone methides (o-QMs) are a class of highly reactive intermediates that serve as important nonisolable building blocks (NBBs) in organic synthesis and small-molecule library construction. Because of their instability and nonisolability, most reported o-QMs are generated through in situ chemical synthesis, and only a few natural o-QMs have been reported due to the lack of directed discovery strategies. Herein, a new natural o-QM precursor (trichophenol A, 2) was identified from the fungal strain of Trichoderma sp. AT0167 through genome mining, which was generated by trilA (nonreducing polyketide synthase) and trilB (2-oxoglutarate dependent dioxygenase). Combinatorial biosynthesis via two other known NRPKS genes with trilA and trilB was performed, leading to the generation of five new trichophenol o-QM oligomers (trichophenols D-H, 5-9). The strategy combining genome mining with combinatorial biosynthesis not only targetedly uncovered a new natural o-QM precursor but also produced various new molecules through oligomerization of the new o-QM and its designated o-QM acceptors without chemical synthesis and isolation of intermediates, which was named NBB genome mining-combinatorial biosynthesis strategy for o-QM molecule library construction. This study provides a new strategy for the targeted discovery of natural o-QMs and small-molecule library construction with natural o-QMs.

Biosynthetic Strategies of Berberine Bridge Enzyme-like Flavoprotein Oxidases toward Structural Diversification in Natural Product Biosynthesis

Berberine bridge enzyme-like oxidases are often involved in natural product biosynthesis and are seen as essential enzymes for the generation of intricate pharmacophores. These oxidases have the ability to transfer a hydride atom to the FAD cofactor, which enables complex substrate modifications and rearrangements including (intramolecular) cyclizations, carbon-carbon bond formations, and nucleophilic additions. Despite the diverse range of activities, the mechanistic details of these reactions often remain incompletely understood. In this Review, we delve into the complexity that BBE-like oxidases from bacteria, fungal, and plant origins exhibit by providing an overview of the shared catalytic features and emphasizing the different reactivities. We propose four generalized modes of action by which BBE-like oxidases enable the synthesis of natural products, ranging from the classic alcohol oxidation reactions to less common amine and amide oxidation reactions. Exploring the mechanisms utilized by nature to produce its vast array of natural products is a subject of considerable interest and can lead to the discovery of unique biochemical activities.

Photocatalytic (3 + 3) Annnulation of Vinyldiazo Compounds and Aminocyclopropanes

A (3 + 3) annulation of aminocyclopropanes and vinyldiazo compounds enabled by organo-photocatalysis is described. The reaction allows the regioselective synthesis of cyclohexenes bearing adjacent amino and carbonyl groups with broad functional group tolerance. In a departure from previous reports, our work demonstrated that a distonic radical cation can be preferentially intercepted by weakly nucleophilic vinyldiazo compounds, followed by an exclusive 6-endo radical cyclization for ring closure. Based on the interaction between adjacent amino and ester groups, the products can be further converted to cyclohexene-fused 1,3-oxazinane and azetidine.

Discovery of Latent Cannabichromene Cyclase Activity in Marine Bacterial Flavoenzymes

Production of phytocannabinoids remains an area of active scientific interest due to the growing use of cannabis by the public and the underexplored therapeutic potential of the over 100 minor cannabinoids. While phytocannabinoids are biosynthesized by Cannabis sativa and other select plants and fungi, structural analogs and stereoisomers can only be accessed synthetically or through heterologous expression. To date, the bioproduction of cannabinoids has required eukaryotic hosts like yeast since key, native oxidative cyclization enzymes do not express well in bacterial hosts. Here, we report that two marine bacterial flavoenzymes, Clz9 and Tcz9, perform oxidative cyclization reactions on phytocannabinoid precursors to efficiently generate cannabichromene scaffolds. Furthermore, Clz9 and Tcz9 express robustly in bacteria and display significant tolerance to organic solvent and high substrate loading, thereby enabling fermentative production of cannabichromenic acid in Escherichia coli and indicating their potential for biocatalyst development.

Total Synthesis of (±)-Rubriflordilactone A

A new and efficient synthesis of rubriflordilactone A has been realized. The key transformations include the following: (1) an intramolecular Prins cyclization to establish the seven-membered ring containing two contiguous stereocenters; (2) a Mukaiyama hydration/oxa-Michael cascade to construct the B-ring; and (3) an unprecedented stereocontrol intermolecular o-QM type [4 + 2]-cycloaddition to rapidly assemble core structure of rubriflordilactone A.

Biomimetic Synthesis of an Antiviral Cinnamoylphloroglucinol Collection from Cleistocalyx operculatus: A Synthetic Strategy Based on Biogenetic Building Blocks

A synthetic strategy based on biogenetic building blocks for the collective and divergent biomimetic synthesis of cleistoperlones A-F, a cinnamoylphloroglucinol collection discovered from Cleistocalyx operculatus, has been developed. These syntheses proceeded successfully in only six to seven steps starting from commercially available 1,3,5-benzenetriol and involving oxidative activation of stable biogenetic building blocks as a crucial step. Key features of the syntheses include a unique Michael addition/ketalization/1,6-addition/enol-keto tautomerism cascade reaction for the construction of the dihydropyrano[3,2-d]xanthene tetracyclic core of cleistoperlones A and B, and a rare inverse-electron-demand hetero-Diels-Alder cycloaddition for the establishment of benzopyran ring in cleistoperlones D-F. Moreover, cleistoperlone A exhibited significant antiviral activity against acyclovir-resistant strains of herpes simplex virus type 1 (HSV-1/Blue and HSV-1/153).

Cascade Annulation Strategy for Expeditious Assembly of Hydroxybenzo[c]chromen-6-ones and Their Photophysical Property Studies

A 1,8-diazabicyclo[5.4.0]undec-7-ene-promoted cascade double-annulation of ortho-alkynyl quinone methide (in situ generated from modular propargylamine) for constructing of 2-aryl-4-hydroxybenzo[c]chromen-6-ones is developed. This synthetic strategy offers remarkable operational simplicity as it allows the use of benchtop-grade solvents without the need for predrying measures and inert atmosphere protection. Additionally, it demonstrates good functional group compatibility. The photophysical properties of these compounds were also examined, revealing bright fluorescence with high quantum yields.

gem-Difluoro-Masked o-Quinone Methides Generated by Photocatalytic Radical (3+3) Annulation and Their (4+1) Cycloaddition with Sulfur Ylides

A visible light-promoted radical (3+3) annulation of vinyldiazo compounds and bromodifluoromethyl alkynyl ketones for the construction of gem-difluoro-masked o-quinone methides (o-QMs) is described. The reactivity of this new type of o-QM precursor is demonstrated by its (4+1) cycloaddition with sulfur ylides, affording monofluorinated aromatic benzofurans by the elimination of HBr without external oxidants.

Asymmetric (4+1) Annulations by Cascade Allylation and Transient σ-Alkyl-Pd(II) Initiated Allylic Csp3 -H Activation

A unique Pd-catalyzed approach for asymmetric (4+1) annulations via cascade allylation and transient σ-alkyl-Pd(II) initiated methylene Csp3 -H activation is reported. The enolate fragment derived from the decarboxylation of vinyl methylene carbonate is crucial to stabilize the key intermediate. These reactions enable the synthesis of various useful dihydrobenzofurans with excellent enantioselectivity, typically >95 : 5 er, and exclusive (Z)-stereoselectivity. Compared with the well-established annulations via Heck-type C-H activations, this protocol showcases a conceptually new way to generate σ-alkyl-Pd(II) species that could initiate challenging asymmetric Csp3 -H activations.

Isolation of new compounds related to xyloketals biosynthesis implies an alternative pathway for furan-fused-chromene formation

In fungi, there is a rare group of natural products harboring the 2,3,3a,9a-tetrahydro-4H-furo[2,3-b]chromene skeleton, represented by xyloketal B, which display a wide range of biological activities and have drawn significant attention. In this work, four new analogues simpliketals A-D (1-4), as well as two other new compounds simplilactones A and B (5 and 6), were isolated from Simplicillium sp. AHK071-01. Their structures were elucidated by extensive NMR spectroscopic methods, ¹³C NMR calculation, single-crystal X-ray diffraction, and ECD calculation. In addition, five known compounds (7-11) including alboatrin (7) were also obtained. Based on the structural similarity of the above compounds, we inferred that compounds 5, 6, and 8-11 might be biosynthetically related with 1-4 and 7, which allowed us to propose an alternative biosynthetic route to generate the furan-fused chromene skeleton of this class of compounds, instead of a previously presumed polyketide-terpenoid hybrid pathway. Finally, cytotoxicity assays showed that 1-4 exhibited weak inhibitory activity on PANC-1 cells and that 2 and 3 possessed moderate activity against SH-SY5Y cells.

Recent Advances in Quinone Methide Chemistry for Protein-Proximity Capturing

Here we summarize the most recent findings in the chemical-, photo-, or enzyme-triggered generation of nitrogen and oxygen anions leading to the formation of quinone methide intermediates (QMIs). This short review is divided into two categories: generation of nitrogen and oxygen anions. Based on quinone methide intermediates (QMIs), proximate capture of a wide range of proteins has been widely determined and studied. Generally, the triggers include, photoirradiation using 365/254 nm UV light, small molecules (ROS/TBAF/s-tetrazine), metal catalysis (iridium catalysis), and enzymes (NQO1/β-galactosidase). New directions including far-red light, heat, force, microwave, and more practical approaches are explored and illustrated.

1 Introduction

2 Generation of the Nitrogen Anion

3 Generation of the Oxygen Anion

4 Conclusion

Reactivity of quinone methides with carbenes generated from α-diazocarbonyl compounds and related compounds

Over the years, quinone methides have broadly been applied in synthesis and biological systems for synthesizing heterocyclic compounds and biologically active molecules. In this feature article, we have discussed the novel and uncovered reactivity of o-quinone methides, p-quinone methides, aza-o-quinone methides, and indolyl-2-methides with carbenes generated from α-diazocarbonyl compounds and related compounds. Two in situ-generated transient intermediates undergo cycloannulation reactions, metathesis-type reactions, 1,6-conjugate addition reactions, cyclopropanation reactions, and many other transformations to access nitrogen- and oxygen-containing heterocyclic compounds and beyond. The reactivity of quinone methides and carbenes is observed in various metal catalysts, Brønsted-acids, Lewis acids, phase transfer catalysts, additives, and visible-light-induced transformations.

Diastereoselective Synthesis of Chromeno[3,2-d]isoxazoles via Brønsted Acid Catalyzed Tandem 1,6-Addition/Double Annulations of o-Hydroxyl Propargylic Alcohols

A Brønsted acid catalyzed tandem process to access densely functionalized chromeno[3,2-d]isoxazoles with good to excellent yields and diastereoselectivities was disclosed. The procedure is proposed to involve a 1,6-conjugate addition/electrophilic addition/double annulations process of alkynyl o-quinone methides (o-AQMs) in situ generated from o-hydroxyl propargylic alcohols with nitrones. Mild conditions, good functional group compatibility, easy scale-up of the reaction, and further product transformation demonstrated its potential application.

Stereochemical and Biosynthetic Rationalisation of the Tropolone Sesquiterpenoids

This review summarises the known structures, biological activities, and biosynthetic pathways of the tropolone sesquiterpenoid family of fungal secondary metabolites. Synthesis of this knowledge allows likely structural and stereochemical misassignments to be revised and shows how the compounds can be divided into three main biosynthetic classes based on the stereochemistry of key biosynthetic steps.