Biosynthesis‐Assisted Structural Elucidation of the Bartolosides,Chlorinated Aromatic Glycolipids from Cyanobacteria

The isolation of the bartolosides, unprecedented cyanobacterial glycolipids featuring aliphatic chains with chlorine substituents and C‐glycosyl moieties, is reported. Their chlorinated dialkylresorcinol (DAR) core presented a major structural‐elucidation challenge. To overcome this, we discovered the bartoloside (brt) biosynthetic gene cluster and linked it to the natural products through in vitro characterization of the DAR‐forming ketosynthase and aromatase. Bioinformatic analysis also revealed a novel potential halogenase. Knowledge of the bartoloside biosynthesis constrained the DAR core structure by defining key pathway intermediates, ultimately allowing us to determine the full structures of the bartolosides. This work illustrates the power of genomics to enable the use of biosynthetic information for structure elucidation.     

A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones

Enzymatic core components from trans‐acyltransferase polyketide synthases (trans‐AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans‐AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N‐acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)‐tethered intermediates, we show that the enzyme inserts oxygen into β‐ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non‐hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.     

Pseudotargeted screening and determination of constituents in Qishen granule based on compound biosynthetic correlation using UHPLC coupled with high‐resolution MS

Detection and determination of many known/unknown compounds in traditional Chinese medicines have always been challenging. To comprehensively identify compounds in Qishen granule, which is a widely prescribed herbal formula for treating chronic heart failure, a pseudotargeted screening method was proposed based on compound biosynthetic correlation using ultra high‐performance liquid chromatography coupled with high‐resolution mass spectrometry. Firstly, all possible compounds of Qishen granule were classified into nine types according to their core skeletons, and potential analogue molecular formulas were predicted according to core compound‐related biosynthetic correlations, such as methylation, hydroxylation, and glucosidation. Secondly, nine pseudocompound databases consisting of core compounds, deduced biosynthetic correlations, and predicted analogue molecular formulas were established. Then, compounds of interest were directly located by pseudotargeted screening of high resolution mass spectrometry data and further verified by target tandem mass spectrometry. As a result, 213 constituents were identified and 21 of them were determined as potential new compounds. This demonstrated that pseudotargeted screening based on compound biosynthetic correlations significantly facilitated the processing of extremely large information data and improved the efficiency of compound identification. This research provided essential data for exploration of effective substances in Qishen granule and enriched the methodology for comprehensive characterization of constituents in complex traditional Chinese medicines.     

Taichunamides: Prenylated Indole Alkaloids from Aspergillus taichungensis (IBT 19404)

Seven new prenylated indole alkaloids, taichunamides A–G, were isolated from the fungus Aspergillus taichungensis (IBT 19404). Taichunamides A and B contained an azetidine and 4‐pyridone units, respectively, and are likely biosynthesized from notoamide S via (+)‐6‐epi‐stephacidin A. Taichunamides C and D contain endoperoxide and methylsulfonyl units, respectively. This fungus produced indole alkaloids containing an anti‐bicyclo[2.2.2]diazaoctane core, whereas A. protuberus and A. amoenus produced congeners with a syn‐bicyclo[2.2.2]diazaoctane core. Plausible biosynthetic pathways to access these cores within the three species likely arise from an intramolecular hetero Diels–Alder reaction.     

Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi

The reisolation and structural revision of brassicicene D is described, and inspired us to reassign the core skeletons of brassicicenes C–H, J and K, ranging from dicyclopenta[a,d]cyclooctane to tricyclo[9.2.1.0^3,7]tetradecane using quantum‐chemical predictions and experimental validation strategies. Three novel, highly modified fusicoccanes, brassicicenes L–N, were also isolated from the fungus Alternaria brassicicola, and their structures were unequivocally established by spectroscopic data, ECD calculations, and crystallography. The reassigned structures represent the first class of bridgehead double‐bond‐containing natural products with a bicyclo[6.2.1]undecane carbon skeleton. Furthermore, their stabilities were first predicted with olefin strain energy calculations. Collectively, these findings extend our view of the application of computational predictions and biosynthetic logic‐based structure elucidation to address problems related to the structure and stability of natural products.     

Biosynthesis of the Central Piperidine Nitrogen Heterocycle in Series a Thiopeptides

Thiopeptides, arising from complex posttranslational modifications of a genetically encoded precursor peptide, are of great interest due to their structural complexity and important biological activities. All of these antibiotics share a macrocyclic peptidyl core that contains a central, six‐membered nitrogen heterocycle and are classified into five series a—e based on the oxidation state of the central nitrogenous ring. Here, we report that the biosynthesis of the central piperidine heterocycle of series a thiopeptides relies on the activity of homologues of an F₄₂₀H₂‐dependent reductase TppX₄ by exploiting and characterizing the piperidine‐containing thiopeptin biosynthetic gene (tpp) cluster in Streptomyces tateyamensis. In vitro reconstruction of TppX₄ activity demonstrated that the piperidine heterocycle of thiopeptins was transformed from a dehydropiperidine heterocycle, and TppX₄ tolerated the changes in the C‐termini and macrocyclic peptidyl core of substrate and also tolerated dehyropiperidine‐containing monocyclic or bicyclic thiopeptides. The identification of TppX₄ and its substrate tolerance enriches the biosynthetic toolbox for development of additional thiopeptide analogs for clinical drug screening.     

Characterization of the Core Oligosaccharide and the O‐Antigen Biological Repeating Unit from Halomonas stevensii Lipopolysaccharide: The First Case of O‐Antigen Linked to the Inner Core

A novel core structure among bacterial lipopolysaccharides (LPS) that belong to the genus Halomonas has been characterized. H. stevensii is a moderately halophilic microorganism, as are the majority of the Halomonadaceae. It brought to light the pathogenic potential of this genus. On account of their role in immune system elicitation, elucidation of LPS structure is the mandatory starting point for a deeper understanding of the interaction mechanisms between host and pathogen. In this paper we report the structure of the complete saccharidic portion of the LPS from H. stevensii. In contrast to the finding that the O‐antigen is usually covalently linked to the outer core oligosaccharide, we could demonstrate that the O‐polysaccharide of H. stevensii is linked to the inner core of an LPS. By means of high‐performance anion‐exchange chromatography with pulsed amperometric detection we were able to isolate the core decasaccharide as well as a tridecasaccharide constituted by the core region plus one O‐repeating unit after alkaline degradation of the LPS. The structure was elucidated by one‐ and two‐dimensional NMR spectroscopy, ESI Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry, and chemical analysis.     

Synthesis of 8‐Desmethoxy Psymberin: A Putative Biosynthetic Intermediate Towards the Marine Polyketide Psymberin

The synthesis of a putative biosynthetic precursor of psymberin including a formal synthesis of the natural product is described. The key step towards the densely functionalized tetrahydropyran core was an enantioselective catalytic Mukaiyama aldol reaction using a titanium(IV)–BINOL catalyst system. syn‐Selective reduction followed by ozonolysis led to a rapid assembly of the tetrahydropyran ring. This flexible approach also allows the synthesis of similar fragments of other complex molecules such as bryostatins and pederins. The syn‐selective coupling between the tetrahydropyran and the aromatic aldehyde was achieved using a boron‐mediated aldol reaction which was followed by further transformations to complete the synthesis of the precursor as well as the formal synthesis of the natural product.     

Biosynthesis of Indole Diterpene Lolitrems: Radical‐Induced Cyclization of an Epoxyalcohol Affording a Characteristic Lolitremane Skeleton

Lolitrems are tremorgenic indole diterpenes that exhibit a unique 5/6 bicyclic system of the indole moiety. Although genetic analysis has indicated that the prenyltransferase LtmE and the cytochrome P450 LtmJ are involved in the construction of this unique structure, the detailed mechanism remains to be elucidated. Herein, we report the reconstitution of the biosynthetic pathway for lolitrems employing a recently established genome‐editing technique for the expression host Aspergillus oryzae. Heterologous expression and bioconversion of the various intermediates revealed that LtmJ catalyzes multistep oxidation to furnish the lolitrem core. We also isolated the key reaction intermediate with an epoxyalcohol moiety. This observation allowed us to establish the mechanism of radical‐induced cyclization, which was firmly supported by density functional theory calculations and a model experiment with a synthetic analogue.     

Aplysiasecosterol A: A 9,11‐Secosteroid with an Unprecedented Tricyclic γ‐Diketone Structure from the Sea Hare Aplysia kurodai

A new 9,11‐secosteroid having an unprecedented tricyclic γ‐diketone structure, aplysiasecosterol A ( 1 ), was isolated from the sea hare Aplysia kurodai. The structure was determined by one‐ and two‐dimensional NMR spectroscopic analysis, molecular modeling studies, a comparison of experimental and calculated ECD spectra, and a modified Mosher′s method. Aplysiasecosterol A ( 1 ) exhibited cytotoxicity against human myelocytic leukemia HL‐60 cells. A biosynthetic pathway for 1 from a known cholesterol was proposed and includes twice α‐ketol rearrangements and an intramolecular acetalization.     

Epigenetic Genome Mining of an Endophytic Fungus Leads to the Pleiotropic Biosynthesis of Natural Products

The small‐molecule biosynthetic potential of most filamentous fungi has remained largely unexplored and represents an attractive source for the discovery of new compounds. Genome sequencing of Calcarisporium arbuscula, a mushroom‐endophytic fungus, revealed 68 core genes that are involved in natural product biosynthesis. This is in sharp contrast to the predominant production of the ATPase inhibitors aurovertin B and D in the wild‐type fungus. Inactivation of a histone H3 deacetylase led to pleiotropic activation and overexpression of more than 75 % of the biosynthetic genes. Sampling of the overproduced compounds led to the isolation of ten compounds of which four contained new structures, including the cyclic peptides arbumycin and arbumelin, the diterpenoid arbuscullic acid A, and the meroterpenoid arbuscullic acid B. Such epigenetic modifications therefore provide a rapid and global approach to mine the chemical diversity of endophytic fungi.     

Iterative Assembly of Two Separate Polyketide Chains by the Same Single‐Module Bacterial Polyketide Synthase in the Biosynthesis of HSAF

Antifungal HSAF (heat‐stable antifungal factor, dihydromaltophilin) is a polycyclic tetramate macrolactam from the biocontrol agent Lysobacter enzymogenes. Its biosynthetic gene cluster contains only a single‐module polyketide synthase–nonribosomal peptide synthetase (PKS‐NRPS), although two separate hexaketide chains are required to assemble the skeleton. To address the unusual biosynthetic mechanism, we expressed the biosynthetic genes in two “clean” strains of Streptomyces and showed the production of HSAF analogues and a polyene tetramate intermediate. We then expressed the PKS module in Escherichia coli and purified the enzyme. Upon incubation of the enzyme with acyl‐coenzyme A and reduced nicotinamide adenine dinucleotide phosphate (NADPH), a polyene was detected in the tryptic acyl carrier protein (ACP). Finally, we incubated the polyene–PKS with the NRPS module in the presence of ornithine and adenosine triphosphate (ATP), and we detected the same polyene tetramate as that in Streptomyces transformed with the PKS‐NRPS alone. Together, our results provide evidence for an unusual iterative biosynthetic mechanism for bacterial polyketide–peptide natural products.     

Synthesis of Novel Core Cross‐Linked Star‐Based Polyrotaxane End‐Capped via “CuAAC” Click Chemistry

The first example of core cross‐linked star (CCS) polyrotaxane was prepared using the poly(ϵ‐caprolactone) (PCL) CCS three‐dimensional (3D) scaffold. The 3D CCS polymer was firstly prepared through the “arm‐first” approach. Then, the “arms” of the resultant PCL CCS polymer were threaded with α‐cyclodextrins (α‐CDs). The threaded α‐CDs were permanently locked by the “click” reaction of terminal alkyne functionalities of the star polymers with the azide‐functionalized end caps to afford the CCS polyrotaxanes. All analytical results confirm the formation of the CCS polyrotaxanes and reveal their characteristics, including fluorescence under UV, a channel‐type crystalline structure, a two‐step thermal decomposition, and a unique core‐shell structure in great contrast to the polymer precursors.     

An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces

Carquinostatin A (CQS), a potent neuroprotective substance, is a unique carbazole alkaloid with both an ortho‐quinone function and an isoprenoid moiety. We identified the entire gene cluster responsible for CQS biosynthesis in Streptomyces exfoliatus through heterologous production of CQS and gene deletion. Biochemical characterization of seven CQS biosynthetic gene products (CqsB1–7) established the total biosynthetic pathway of CQS. Reconstitution of CqsB1 and CqsB2 showed that the synthesis of the carbazole skeleton involves CqsB1‐catalyzed decarboxylative condensation of an α‐hydroxyl‐β‐keto acid intermediate with 3‐hydroxybutyryl‐ACP followed by CqsB2‐catalyzed oxidative cyclization. Based on crystal structures and mutagenesis‐based biochemical assays, a detailed mechanism for the unique deprotonation‐initiated cyclization catalyzed by CqsB2 is proposed. Finally, analysis of the substrate specificity of the biosynthetic enzymes led to the production of novel carbazoles.     

Paranolin: a New Xanthene‐Based Metabolite from Paraphaeosphaeria nolinae

A new xanthene‐based, polycyclic metabolite, paranolin (= (2R,3aS,12aR)‐3,3a‐dihydro‐3a‐hydroxy‐8‐(hydroxymethyl)‐2‐(1‐hydroxy‐1‐methylethyl)‐9‐methoxy‐10‐methylfuro[3,2‐d]xanthen‐6(2H)‐one; 1 ) was isolated from a culture of Paraphaeosphaeria nolinae (IFB‐E011), an endophytic fungus residing in the normal stem of the artemisinin‐producing plant Artemisia annua (Asteraceae). The structure of 1 was elucidated by extensive spectroscopic analyses. Although not substantially active against the human colon (SW1116) and human cervical carcinoma (Hela) cell lines, this metabolite seems to be the first example of a xanthene‐derived secondary metabolite. Its possible biosynthetic origin (Scheme) and its significance as a phyllogenetic marker are discussed in brief.     

Bacterial Alkaloids Prevent Amoebal Predation

Bacterial defense mechanisms have evolved to protect bacteria against predation by nematodes, predatory bacteria, or amoebae. We identified novel bacterial alkaloids (pyreudiones A–D) that protect the producer, Pseudomonas fluorescens HKI0770, against amoebal predation. Isolation, structure elucidation, total synthesis, and a proposed biosynthetic pathway for these structures are presented. The generation of P. fluorescens gene‐deletion mutants unable to produce pyreudiones rendered the bacterium edible to a variety of soil‐dwelling amoebae.     

Mining Symbionts of a Spider‐Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones

A spider‐transmitted fungus (Rhizopus microsporus) that was isolated from necrotic human tissue was found to harbor endofungal bacteria (Burkholderia sp.). Metabolic profiling of the symbionts revealed a complex of cytotoxic agents (necroximes). Their structures were characterized as oxime‐substituted benzolactone enamides with a peptidic side chain. The potently cytotoxic necroximes are also formed in symbiosis with the fungal host and could have contributed to the necrosis. Genome sequencing and computational analyses revealed a novel modular PKS/NRPS assembly line equipped with several non‐canonical domains. Based on gene‐deletion mutants, we propose a biosynthetic model for bacterial benzolactones. We identified specific traits that serve as genetic handles to find related salicylate macrolide pathways (lobatamide, oximidine, apicularen) in various other bacterial genera. Knowledge of the biosynthetic pathway enables biosynthetic engineering and genome‐mining approaches.     

Isolation,evaluation of bioactivity and structure determination of amethinol A,a prototypic amethane diterpene from Isodon amethystoides bearing a six/five/seven‐membered carbon‐ring system

We report the isolation of a novel diterpene, designated as `amethane', from Isodon amethystoides (Lamiaceae). The diterpene [amethinol A; systematic name: (4aR,4bR,7R,10aS)‐4b,7‐dihydroxy‐7‐isopropyl‐1,1‐dimethyl‐9‐oxododecahydrobenzo[a]azulene‐4a(2H)‐carboxylic acid], possesses a unique skeleton containing a six/five/seven‐membered tricyclic system. Intermolecular O—H…O close contacts were found to the carboxyl, carbonyl and hydroxy groups, connecting molecules into a two‐dimensional structure. A possible biosynthetic pathway has been proposed. In addition, the compound was evaluated for its biological activities against different disease targets, and was found to significantly attenuate RORγt‐dependent autoimmune responses.     

Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs

2‐Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo‐oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS‐containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.

     

Homology Modeling and Molecular Docking Studies of (S)‐Scoulerine 9‐O‐Methyltransferase from Coptis chinensis

(S)‐Scoulerine 9‐O‐methyltransferase (SMT), belonging to the S‐adenosyl‐L‐methionine (SAM)‐dependent O‐methyltransferase family, is an essential enzyme in the berberine biosynthetic pathways. In order to study the interactions of SMT with its substrate and further to understand the catalytic mechanism and substrate specificity, a three dimensional model of SMT from Coptis chinensis was constructed by homology modeling using the crystal structure of caffeic acid/5‐hydroxyferulic acid 3/5‐O‐methyltransferase (COMT) as a template. The three dimensional structure of SMT, which was mainly composed of α‐helices and some β‐sheets, was similar to that of COMT. In contrast with COMT, the non‐conserved residues in the substrate binding pocket of SMT might be responsible for their differences in the substrate specificity. Val119 and Asp254 in SMT were the key residues for orienting substrate for methylation as both residues had H‐bonds with (S)‐scoulerine. The methylation of (S)‐scoulerine involved deprotonation of the 9‐hydroxyl group by His253 and Asp254 in SMT followed by a nucleophilic attack on the SAM‐methyl resulting in the product, (S)‐tetrahydrocolumbamine.