α-Nucleophilic Addition to α,β-Unsaturated Carbonyl Compounds via Photocatalytically Generated α-Carbonyl Carbocations

We report the photocatalytic oxidation of α-carbonyl radicals of amides or esters to the corresponding α-carbonyl carbocations through super photoreductant CBZ6 induced redox-neutral photocatalysis. The α-carbonyl radicals are formed by the β-addition of alkyl radicals generated in situ by the photocatalytic fragmentation of N-hydroxyphthalimide esters to the α,β-unsaturated amides and esters. This method enables the α-nucleophilic addition of hydroxyl or alkoxyl radicals to amides and esters without any prefunctionalization.

C-Alkylated flavonoids from the whole plants of Desmodium caudatum and their anti-TMV activity

BACKGROUND

Natural products are important sources of biopesticides to control plant virus, and flavonoids are identified as promising anti-tobacco mosaic virus (TMV) agents. Since Desmodium caudatum is a rich source of flavonoids, this study focuses on the discovery of the new anti-TMV active flavonoids from D. caudatum and their possible mode of action.

RESULTS

Three new (compounds 1-3) and nine known (compounds 4-12) C-alkylated flavonoids were isolated from D. caudatum. To the best of our knowledge, the framework of 1-3 was reported in natural products for the first time. In addition, 1-3, 5, and 6 showed notable anti-TMV activity with inhibition rates in the range of 35.8-64.3% at a concentration of 50 μg/mL, and these rates are higher than that of positive control (with inhibition rates of 34.6% ± 2.8). In addition, the structure-activity relationship study revealed that the (pyrrol-2-yl)methyl moiety on flavone can significantly increases the activity. This result is helpful to find new anti-TMV inhibitors.

CONCLUSION

C-Alkylated flavonoids showed potent activities against TMV with multiple modes of actions. The increase of defense-related enzyme activities, up-regulate the expression of defense related genes, down-regulate the expression of Hsp70 protein by inhibiting the related Hsp genes that are involved in tobacco resistance to TMV. By the actions mentioned earlier, the infection of TMV was influenced, thereby achieving the effects of control of TMV. The successful isolation of the earlier-mentioned flavonoids provide the new source of biopesticides to TMV proliferation, and also contribute to the utilization of D. caudatum. © 2023 Society of Chemical Industry.

Geobarrettin D, a Rare Herbipoline-Containing 6-Bromoindole Alkaloid from Geodia barretti

Geobarrettin D (1), a new bromoindole alkaloid, was isolated from the marine sponge Geodia barretti collected from Icelandic waters. Its structure was elucidated by 1D, and 2D NMR (including 1H-15N HSQC, 1H-15N HMBC spectra), as well as HRESIMS data. Geobarrettin D (1) is a new 6-bromoindole featuring an unusual purinium herbipoline moiety. Geobarrettin D (1) decreased secretion of the pro-inflammatory cytokine IL-12p40 by human monocyte derived dendritic cells, without affecting secretion of the anti-inflammatory cytokine IL-10. Thus, compound 1 shows anti-inflammatory activity.

Open Nitrogen Site-Induced Kinetic Resolution and Catalysis of a Gold Nanocluster

The emerging metal nanocluster provides a platform for the investigation of structural features, unique properties, and structure-property correlation of nanomaterials at the atomic level. Construction of open sites on the surface of the metal nanocluster is a long-pursued but challenging goal. Herein, we realized the construction of "open organic sites" in a metal nanocluster for the first time. Specifically, we introduce the PNP (2,6-bis(diphenylphosphinomethyl)pyridine) pincer ligand in the synthesis of the gold nanocluster, enabling the construction of a structurally precise Au₈(PNP)₄ nanocluster. The rigidity and the unique bonding mode of PNP lead to open nitrogen sites on the surface of the Au₈(PNP)₄ nanocluster, which have been utilized as multifunctional sites in this work for efficient kinetic resolution and catalysis. The gold pincer nanocluster and the open nitrogen site-induced performance will be enlightening for the construction of multifunctional metal nanoclusters.

Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis

A key step in the biosynthesis of numerous polyketides is the stereospecific formation of a spiroacetal (spiroketal). We report here that spiroacetal formation in the biosynthesis of the macrocyclic polyketides ossamycin and oligomycin involves catalysis by a novel spiroacetal cyclase. OssO from the ossamycin biosynthetic gene cluster (BGC) is homologous to OlmO, the product of an unannotated gene from the oligomycin BGC. The deletion of olmO abolished oligomycin production and led to the isolation of oligomycin-like metabolites lacking the spiroacetal structure. Purified OlmO catalyzed complete conversion of the major metabolite into oligomycin C. Crystal structures of OssO and OlmO reveal an unusual 10-strand β-barrel. Three conserved polar residues are clustered together in the β-barrel cavity, and site-specific mutation of any of these residues either abolished or substantially diminished OlmO activity, supporting a role for general acid/general base catalysis in spiroacetal formation.

AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis

Macrocyclization is an important process that affords morphed scaffold in biosynthesis of bioactive natural products. Nature has adapted diverse biosynthetic strategies to form macrocycles. In this work, we report the identification and characterization of a small enzyme AvmM that can catalyze the construction of a 16-membered macrocyclic ring in the biosynthesis of alchivemycin A (1). We show through in vivo gene deletion, in vitro biochemical assay and isotope labelling experiments that AvmM catalyzes tandem dehydration and Michael-type addition to generate the core scaffold of 1. Mechanistic studies by crystallography, DFT calculations and MD simulations of AvmM reveal that the reactions are achieved with assistance from the special tenuazonic acid like moiety of substrate. Our results thus uncover an uncharacterized macrocyclization strategy in natural product biosynthesis.

Macrocyclization is an important process in bioactive natural product synthesis. Here, the authors report on the study of a macrocyclic ring constructing enzyme in the biosynthesis of alchivemycin A and using gene deletion, biochemical assays and isotope labelling show the enzyme catalyses tandem dehydration and Michael-type addition.

Machine learning and semi-empirical calculations: a synergistic approach to rapid, accurate, and mechanism-based reaction barrier prediction

Modern QM modelling methods, such as DFT, have provided detailed mechanistic insights into countless reactions. However, their computational cost inhibits their ability to rapidly screen large numbers of substrates and catalysts in reaction discovery. For a C-C bond forming nitro-Michael addition, we introduce a synergistic semi-empirical quantum mechanical (SQM) and machine learning (ML) approach that allows the prediction of DFT-quality reaction barriers in minutes, even on a standard laptop using widely available modelling software. Mean absolute errors (MAEs) are obtained that are below the accepted chemical accuracy threshold of 1 kcal mol-1 and substantially better than SQM methods without ML correction (5.71 kcal mol-1). Predictive power is shown to hold when the ML models are applied to an unseen set of compounds from the toxicology literature. Mechanistic insight is also achieved via the generation of full SQM transition state (TS) structures which are found to be very good approximations for the DFT-level geometries, revealing important steric interactions in some TSs. This combination of speed, accuracy, and mechanistic insight is unprecedented; current ML barrier models compromise on at least one of these important criteria.

Polyene Macrolactams from Marine and Terrestrial Sources: Structure, Production Strategies, Biosynthesis and Bioactivities

Over the past few decades (covering 1972 to 2022), astounding progress has been made in the elucidation of structures, bioactivities and biosynthesis of polyene macrolactams (PMLs), but they have only been partially summarized. PMLs possess a wide range of biological activities, particularly distinctive fungal inhibitory abilities, which render them a promising drug candidate. Moreover, the unique biosynthetic pathways including β-amino acid initiation and pericyclic reactions were presented in PMLs, leading to more attention from inside and outside the natural products community. According to current summation, in this review, the chem- and bio-diversity of PMLs from marine and terrestrial sources are considerably rich. A systematic, critical and comprehensive overview is in great need. This review described the PMLs’ general structural features, production strategies, biosynthetic pathways and the mechanisms of bioactivities. The challenges and opportunities for the research of PMLs are also discussed.

Polyketide β-branching: diversity, mechanism and selectivity

Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.

Reactivity prediction in aza-Michael additions without transition state calculations: the Ames test for mutagenicity

Animal testing remains a contentious ethical issue in predictive toxicology. Thus, a fast, versatile, low-cost quantum chemical model is presented for predicting the risk of Ames mutagenicity in a series of 1,4 Michael acceptor type compounds. This framework eliminates the need for transition state calculations, and uses an intermediate structure to probe the reactivity of aza-Michael acceptors. This model can be used in a variety of settings e.g., the design of targeted covalent inhibitors and polyketide biosyntheses.

Total Synthesis of Acaulide and Acaulone A

Acaulide and acaulone A, which contain 14-membered macrodiolides, were isolated from a culture of Acaulium sp. H-JQSF. The antiosteoporosis activity of acaulide is expected to contribute to drug discovery research for an aging society. We herein report the first total synthesis of acaulide, acaulone A, and 10-keto-acaudiol A. Acaulide and acaulone A were synthesized via the late stage Michael addition to the 14-membered macrodiolide, which was inspired by plausible biosynthetic pathways. This approach succeeded in the construction of the acaulide skeleton, which revealed the specific conformation of the 14-membered macrodiolide for late stage functionalization.

Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a β-Amino Acid Starter Unit in Cremimycin Biosynthesis

The flavin adenine dinucleotide-dependent oxidase CmiS2 catalyzes the oxidation of N-carboxymethyl-3-aminononanoic acid to produce a 3-aminononanoic acid starter unit for the biosynthesis of cremimycin, a macrolactam polyketide. Although the sequence of CmiS2 is similar with that of the well-characterized glycine oxidase ThiO, the chemical structure of the substrate of CmiS2 is different from that of ThiO substrate glycine. Here, we present the biochemical and structural characterization of CmiS2. Kinetic analysis revealed that CmiS2 has a strong preference for N-carboxymethyl-3-aminononanoic acid over other substrates such as N-carboxymethyl-3-aminobutanoic acid and glycine, suggesting that CmiS2 recognizes the nonanoic acid moiety of the substrate as well as the glycine moiety. We determined the crystal structure of CmiS2 in complex with a substrate analogue, namely, S-carboxymethyl-3-thiononanoic acid, which enabled the identification of key amino acid residues involved in substrate recognition. We discovered that Asn49, Arg243, and Arg334 interact with the carboxyl group of the nonanoic acid moiety, while Pro46, Leu52, and Ile335 recognize the alkyl chain of the nonanoic acid moiety via hydrophobic interaction. These residues are highly conserved in CmiS2 homologues involved in the biosynthesis of related macrolactam polyketides but are not conserved in glycine oxidases such as ThiO. These results suggest that CmiS2-type enzymes employ a distinct mechanism of substrate recognition for the synthesis of β-amino acids.