Aromatic Polyketides Research Articles

Aromatic polyketides isolated from the marine-derived fungus Didymella aeria and their neuroprotective activity.

Two novel aromatic polyketides, penicanesins J and K (1, 2), were isolated from the marine-derived fungus Didymella aeria, along with the known compound integrastatin B (3). The structures of the new compounds were determined by NMR spectroscopy and synthetic methods. The isolated compounds were tested for monoamine oxidase (MAO) B inhibition, anti-amyloid beta (Aβ) aggregation, and protective activity against H2O2-induced cell death in human neuroblastoma SH-SY5Y cells. Integrastatin B (3) showed potential activity for inhibition of Aβ aggregation and protection against H2O2-induced cell death.

Multioxidized polyketides from an endophytic Penicillium sp. YUD17006 associated with Gastrodia elata

Three novel, highly oxygenated polyketides, multioketides A−C (1−3), and three previously described multioxidized aromatic polyketides (4−6), were isolated from an endophytic Penicillium sp. YUD17006 associated with Gastrodia elata. Their chemical structures were elucidated using extensive spectroscopic data, electronic circular dichroism calculations, and single X-ray diffraction analysis. All metabolites were characterized by a typical α,β-unsaturated ketone fragment and exhibited a high degree of oxidation. Multioketides A and B were identified as a pair of epimers featuring a rare dihydroisobenzofuranone core. Multioketide C possessed a novel 5/6/6/6 heterotetracyclic chemical architecture with unusual 1,4-dioxin functionalities. Plausible biosynthetic pathways for 1−6 were proposed. Additionally, compound 3 demonstrated weak inhibitory activities against both acetylcholinesterase and protein tyrosine phosphatase 1B.

Hybrid Type I and II Polyketide Synthases Yield Distinct Aromatic Polyketides.

Bacterial aromatic polyketides are compounds with multiple aromatic rings synthesized by bacterial type II polyketide synthases (PKSs), some of which have been developed into clinical drugs. Compounds containing aromatic polyketides synthesized by hybrid type I and type II PKSs are extremely rare. Here, we report the discovery of a gene cluster encoding both modular type I and type II PKSs as well as KAS III through extensive bioinformatics analysis, leading to the characterization of the hybrid polyketide, spirocycline A. The structure of spirocycline A is rare among all aromatic polyketides, featuring a unique starter unit and four spirocycles and forming a dimer. Biosynthetic studies indicate that the starter unit of this molecule is synthesized by type I PKS in collaboration with two trans-acting ketoreductase (KR) and enoylreductase (ER). It is then transferred by KAS III to the type II PKS system, which synthesizes the tricyclic aromatic polyketide backbone. The subsequent formation of the spirocycle and dimerization are carried out by four redox enzymes encoded in the gene cluster. Overall, the discovery of spirocycline A provides a new approach for identifying novel aromatic polyketides and offers potential enzymatic tools for the bioengineering of these hybrid polyketides.

Polyketide Origin of the Indole Ring during the Biosynthesis of Indole Alkaloid Coprisidins.

Coprisidins, a new class of indole alkaloids, feature a 1,4-naphthoquinone moiety attached to C-3 of 2-oxindole. Heterologous expression of a type II polyketide synthase-containing gene cluster resulted in the generation of three coprisidins. Gene disruption and isotope feeding studies suggested that the 2-oxindole moieties of coprisidins originate from a tetracyclic aromatic polyketide through oxidative rearrangements. This represents a novel biosynthetic route for the synthesis of indole rings in nature.

Single-crystal structure, Hirshfeld surface and DFT analyses of chrysomycin A, a marine microbe-derived promising agent for anticancer and antimicrobial therapy

Chrysomycin A (CA) is an important Streptomyces-derived aromatic polyketide with therapeutic potential for treatment of cancer and bacterial infections. In order to prepare highly pure CA for new drug development, a simple and effective strategy to crystallize CA was firstly developed by the liquid phase diffusion method in this work. The single-crystal structure of CA and its Hirshfeld surface property analyses showed that the asymmetric unit of CA crystal consists of one CA molecule and a water in the orthorhombic space group P212121 and it has π-π interactions between benzene rings. CA crystal stacking is consolidated by three intermolecular hydrogen bonds including carbonyl/keto-C-O···H(water), naphthalene-C-O···H(water) and glycoside-O-H···O(water) and van der Waals forces. Furthermore, the HOMO-LUMO energy gap, UV-vis spectral parameters, electrostatic potential, mullliken charge and nonlinear optical properties analyzed in DFT calculations. These results pave a fundamental way for the production of CA using the feasible crystallization approach and the study of molecular mechanisms of action (MoA).

Discovery and Heterologous Expression of Functional 4-O-Dimethylallyl-l-tyrosine Synthases from Lichen-Forming Fungi.

Fungal aromatic prenyltransferases are a family of biosynthetic enzymes that catalyze the prenylation of a range of aromatic substrates during the biosynthesis of bioactive indole alkaloids, diketopiperazines, and meroterpenoids. Their broad substrate scope and soluble nature make these enzymes particularly adept for applications in biocatalysis; for example, the enzymatic derivatization of aromatic drugs improves their bioactivity. Here, we investigated four putative aromatic prenyltransferases from lichen-forming fungi, an underexplored group of organisms that produce more than 1,000 unique metabolites. We successfully expressed two enzymes, annotated as dimethylallyltryptophan synthases, from two lichen species in the heterologous host A. oryzae. Based on their in vivo activity, we hypothesize that these enzymes are in fact 4-O-dimethylallyl-l-tyrosine synthases. Our extensive bioinformatic analysis further confirmed that these and related lichen aromatic prenyltransferases are likely not active on indoles but rather on aromatic polyketides and phenylpropanoids, major metabolites in lichens. Overall, our work provides new insights into fungal aromatic prenyltransferases at the family level and enables future efforts aimed at identifying new candidates for biocatalytic transformations of aromatic compounds.

Total Synthesis of Ganoapplanin Enabled by a Radical Addition/Aldol Reaction Cascade.

The total synthesis of the Ganoderma meroterpenoid ganoapplanin, an inhibitor of T-type voltage-gated calcium channels, is reported. Our synthetic approach is based on the convergent coupling of a readily available aromatic polyketide scaffold with a bicyclic terpenoid fragment. The three contiguous stereocenters of the terpenoid fragment, two of which are quaternary, were constructed by a diastereoselective, titanium-mediated iodolactonization. For the fusion of the two fragments and to simultaneously install the crucial biaryl bond, we devised a highly effective two-component coupling strategy. This event involves an intramolecular 6-exo-trig radical addition of a quinone monoacetal followed by an intermolecular aldol reaction. A strategic late-stage oxidation sequence allowed the selective installation of the remaining oxygen functionalities and the introduction of the characteristic spiro bisacetal structure of ganoapplanin.

Theoretical Studies on the Catalytic Mechanism and Cyclization Pattern of Fungal Polyketide Synthase Product Template Domain

AbstractAromatic polyketides are pharmaceutically significant natural products. Product template (PT) domains from fungal non‐reducing polyketide synthases (NR‐PKSs) control the regioselective aldol cyclization of highly reactive polyketide intermediates, whose instabilities have hindered experimental studies. The molecular basis of PT‐catalyzed cyclization and aromatization remain ambiguous. Herein, we conducted MD simulations and QM/MM calculations to explore the catalytic mechanHism and the cyclization pattern of PksA PT specific for C4−C9. The cyclization mediated by PksA PT is initiated by the C4 deprotonation followed by the aldol condensation in C4−C9 register. PTs which evolve from ancient PKS dehydratases (DHs) perform dehydration reactions to aromatize the cyclized intermediates. In PksA PT, the catalytic His1345 and Asp1543 are responsible for aldol cyclization and aromatization steps, respectively. A keto‐enol tautomerism at C3 assists in the elimination reaction catalyzed by Asp1543 with a water molecule network, different from most DHs of PKSs. The C2−C7 aldol cyclization in PksA PT can occur, but the subsequent dehydration step is kinetically unfeasible and thermodynamically unfavorable, suggesting that the aromatization steps determine the C4−C9 cyclization mode of PksA PT. Overall, these computational investigations provide detailed mechanistic insights into the regiospecific intramolecular cyclization and aromatization controlled by fungal PksA PT.

A new synthetic biology system for investigating the biosynthesis of antibiotics and other secondary metabolites in streptomycetes

We have created a novel synthetic biology expression system allowing easy refactoring of biosynthetic gene clusters (BGCs) as monocistronic transcriptional units. The system is based on a set of plasmids containing a strong kasOp* promoter, RBS and terminators. It allows the cloning of biosynthetic genes into transcriptional units kasOp*-gene(s)-terminator flanked by several rare restriction cloning sites that can be sequentially combined into the artificial BGC in three compatible Streptomyces integration vectors. They allow a simultaneous integration of these BGCs at three different attB sites in the Streptomyces chromosome. The system was validated with biosynthetic genes from two known BGCs for aromatic polyketides landomycin and mithramycin.

The Chemistry of Angucyclines.

Angucyclines and angucyclinones represent a class of natural compounds that belong to the group of aromatic polyketides. They exhibit a wide array of biological properties, such as antimicrobial, antiviral, and cytotoxic. Their considerable therapeutic potential and diverse scaffolds have attracted many synthetic chemists to devise novel strategies to construct their intricate molecular architecture. Over 300 class members have been isolated from natural sources, mainly from bacterial strains of Streptomyces species. This review highlights recent advancements in their synthesis, such as oxidative cyclization, photooxidation, and metal-catalyzed [4+2]-cycloaddition, which has facilitated the efficient and practical total syntheses of various angucycline and angucyclinone natural products.

Isolation and Structure Elucidation of JBIR-157, a Skeletally Novel Aromatic Polyketide Produced by the Heterologous Expression of a Cryptic Gene Cluster.

Heterologous expression of natural compound biosynthetic gene clusters (BGCs) is a robust approach for not only revealing the biosynthetic mechanisms leading to the compounds, but also for discovering new products from uncharacterized BGCs. We established a heterologous expression technique applicable to huge biosynthetic gene clusters for generating large molecular secondary metabolites such as type-I polyketides. As an example, we targeted concanamycin BGC from Streptomyces neyagawaensis IFO13477 (the cluster size of 99 kbp), and obtained a bacterial artificial chromosome (BAC) clone with an insert size of 211 kbp that contains the entire concanamycin BGC. Interestingly, heterologous expression for this BAC clone resulted in two additional aromatic polyketides, ent-gephyromycin, and a new compound designated as JBIR-157, together with the expected concanamycin. Bioinformatic and biochemical analyses revealed that a cryptic biosynthetic gene cluster in this BAC clone was responsible for the production of these type-II polyketide synthases (PKS) compounds. Here, we describe the production, isolation, and structure elucidation of JBIR-157, determined primarily by a series of NMR spectral analyses.

Discovery of a Bacterial Hydrazine Transferase That Constructs the N-Aminolactam Pharmacophore in Albofungin Biosynthesis.

Structural motifs containing nitrogen-nitrogen (N-N) bonds are prevalent in a large number of clinical drugs and bioactive natural products. Hydrazine (N2H4) serves as a widely utilized building block for the preparation of these N-N-containing molecules in organic synthesis. Despite its common use in chemical processes, no enzyme has been identified to catalyze the incorporation of free hydrazine in natural product biosynthesis. Here, we report that a hydrazine transferase catalyzes the condensation of N2H4 and an aromatic polyketide pathway intermediate, leading to the formation of a rare N-aminolactam pharmacophore in the biosynthesis of broad-spectrum antibiotic albofungin. These results expand the current knowledge on the biosynthetic mechanism for natural products with N-N units and should facilitate future development of biocatalysts for the production of N-N-containing chemicals.

Altenuene derivatives produced by an endophyte Alternaria alternata

Two novel aromatic polyketides 1 and 3 and five known compounds, (4S,10S)-talaroflavone (2), altenuene (4), isoaltenuene (5), alternariol (6), and altenusin (7), were isolated from an endophytic strain of Alternaria alternata SI-694. The structures of the new compounds, including their absolute configurations, were elucidated by NMR, IR, UV, and ECD spectroscopies, and the phytotoxicities of the isolated compounds were also evaluated. Altenusin (7) showed moderate cytotoxicity against HL-60 cells, with an IC50 of 6.65 µM, whereas 5, 6, and 7 were phytotoxic against Lactuca sativa, Brassica campestris L., Stellaria aquatica (L.) Scop. and Digitaria ciliaris.

Antibacterial Activity of Defensive Secretions from the Lace Bug Stephanitis svensoni (Drake) (Hemiptera: Tingidae).

Nymphs of Stephanitis svensoni (Drake) (Hemiptera: Tingidae) have numerous glandular setae on their dorsal abdomens. Chemical analysis of the exudates from these setae revealed the presence of 11 compounds, including aliphatic aldehydes, aliphatic ketones, and aromatic polyketides. Among them, 3-oxododecanal, 5-hydroxy-2-heptylchromanone, and 5-hydroxy-2-undecanylchromanone were identified for the first time in the family Tingidae. Previous research has suggested that secretions from nymphs of the genus Stephanitis, belonging to the family Tingidae, function as defensive substances against predators. The exudates of S. svensoni showed antibacterial activity against the Gram-positive bacterium Staphylococcus aureus. Antibacterial tests conducted using preparations of the 10 identified compounds showed antibacterial activity in 3-oxododecanal, 2,6-dihydroxyacetophenone, and 1-(2,6-dihydroxyphenyl)dodecan-1-one. In addition, antibacterial tests against the Gram-negative bacterium Escherichia coli showed activity in 2,6-dihydroxyacetophenone and 1-(2,6-dihydroxyphenyl)dodecan-1-one. Therefore, 2,6-dihydroxyacetophenone and 1-(2,6-dihydroxyphenyl)dodecan-1-one exhibited a wide antibacterial spectrum. Particularly, 1-(2,6-dihydroxyphenyl)dodecan-1-one, which showed antibacterial activity even at low concentrations, holds promise as lead drug compound.

Targeted Discovery of Glycosylated Natural Products by Tailoring Enzyme-Guided Genome Mining and MS-Based Metabolome Analysis.

Glycosides make up a biomedically important class of secondary metabolites. Most naturally occurring glycosides were isolated from plants and bacteria; however, the chemical diversity of glycosylated natural products in fungi remains largely unexplored. Herein, we present a paradigm to specifically discover diverse and bioactive glycosylated natural products from fungi by combining tailoring enzyme-guided genome mining with mass spectrometry (MS)-based metabolome analysis. Through in vivo genes deletion and heterologous expression, the first fungal C-glycosyltransferase AuCGT involved in the biosynthesis of stromemycin was identified from Aspergillus ustus. Subsequent homology-based genome mining for fungal glycosyltransferases by using AuCGT as a probe revealed a variety of biosynthetic gene clusters (BGCs) containing its homologues in diverse fungi, of which the glycoside-producing capability was corroborated by high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. Consequently, 28 fungal aromatic polyketide C/O-glycosides, including 20 new compounds, were efficiently discovered and isolated from the three selected fungi. Moreover, several novel fungal C/O-glycosyltransferases, especially three novel α-pyrone C-glycosyltransferases, were functionally characterized and verified in the biosynthesis of these glycosides. In addition, a proof of principle for combinatorial biosynthesis was applied to design the production of unnatural glycosides in Aspergillus nidulans. Notably, the newly discovered glycosides exhibited significant antiviral, antibacterial, and antidiabetic activities. Our work demonstrates the promise of tailoring enzyme-guided genome-mining approach for the targeted discovery of fungal glycosides and promotes the exploration of a broader chemical space for natural products with a target structural motif in microbial genomes.

Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius

Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or intestinal microbes. Despite the importance of these plant compounds, there is still limited knowledge of how they are metabolized. The Gram-positive aerobic soil bacterium Deinococcus aerius strain TR0125 and other Deinococcus species thrive in a wide range of harsh environments. In this work, we identified a C-glycoside deglycosylation gene cluster in the genome of D. aerius. The cluster includes three genes coding for a GMC-type oxidoreductase (DaCGO1) that oxidizes the glucosyl C3 position in aromatic C-glucosyl compounds, which in turn provides the substrate for the C-glycoside deglycosidase (DaCGD; composed of α+β subunits) that cleaves the glucosyl-aglycone C–C bond. Our results from size-exclusion chromatography, single particle cryo-electron microscopy and X-ray crystallography show that DaCGD is an α2β2 heterotetramer, which represents a novel oligomeric state among bacterial CGDs. Importantly, the high-resolution X-ray structure of DaCGD provides valuable insights into the activation of the catalytic hydroxide ion by Lys261. DaCGO1 is specific for the 6-C-glucosyl flavones isovitexin, isoorientin and the 2-C-glucosyl xanthonoid mangiferin, and the subsequent C–C-bond cleavage by DaCGD generated apigenin, luteolin and norathyriol, respectively. Of the substrates tested, isovitexin was the preferred substrate (DaCGO1, Km 0.047 mM, kcat 51 min−1; DaCGO1/DaCGD, Km 0.083 mM, kcat 0.42 min−1).

Targeted isolation, identification, and antioxidant evaluation of aromatic polyketides from a plant-derived fungus Ophiobolus cirsii LZU-1509

There are >350 species of the Ophiobolus genus, which is not yet very well-known and lacks research reports on secondary metabolites. Three new 3,4-benzofuran polyketides 1–3, a new 3,4-benzofuran polyketide racemate 4, two new pairs of polyketide enantiomers (±)-5 and (±)-7, two new acetophenone derivatives 6 and 8, and three novel 1,4-dioxane aromatic polyketides 9–11, were isolated from a fungus Ophiobolus cirsii LZU-1509 derived from an important medicinal and economic crop Anaphalis lactea. The isolation was guided by LC-MS/MS-based GNPS molecular networking analysis. The planar structures and relative configurations were mainly elucidated by NMR and HR-ESI-MS data. Their absolute configurations were determined by using X-ray diffraction analysis and via comparing computational and experimental ECD, NMR, and specific optical rotation data. 9 possesses an unreported 5/6/6/6/5 five-ring framework with a 1,4-dioxane, and 10 and 11 feature unprecedented 6/6/6/5 and 6/6/5/6 four-ring frames containing a 1,4-dioxane. The biosynthetic pathways of 9–11 were proposed. 1–11 were nontoxic in HT-1080 and HepG2 tumor cells at a concentration of 20 μM, whereas 3 and 5 exerted higher antioxidant properties in the hydrogen peroxide-stimulated model in the neuron-like PC12 cells. They could be potential antioxidant agents for neuroprotection.

An unusual aromatase/cyclase programs the formation of the phenyldimethylanthrone framework in anthrabenzoxocinones and fasamycin

Aromatic polyketides are renowned for their wide-ranging pharmaceutical activities. Their structural diversity is mainly produced via modification of limited types of basic frameworks. In this study, we characterized the biosynthesis of a unique basic aromatic framework, phenyldimethylanthrone (PDA) found in (+)/(-)-anthrabenzoxocinones (ABXs) and fasamycin (FAS). Its biosynthesis employs a methyltransferase (Abx(+)M/Abx(-)M/FasT) and an unusual TcmI-like aromatase/cyclase (ARO/CYC, Abx(+)D/Abx(-)D/FasL) as well as a nonessential helper ARO/CYC (Abx(+)C/Abx(-)C/FasD) to catalyze the aromatization/cyclization of polyketide chain, leading to the formation of all four aromatic rings of the PDA framework, including the C9 to C14 ring and a rare angular benzene ring. Biochemical and structural analysis of Abx(+)D reveals a unique loop region, giving rise to its distinct acyl carrier protein-dependent specificity compared to other conventional TcmI-type ARO/CYCs, all of which impose on free molecules. Mutagenic analysis discloses critical residues of Abx(+)D for its catalytic activity and indicates that the size and shape of its interior pocket determine the orientation of aromatization/cyclization. This study unveils the tetracyclic and non-TcmN type C9 to C14 ARO/CYC, significantly expanding our cognition of ARO/CYCs and the biosynthesis of aromatic polyketide framework.

Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds.

The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.

A Tricyclic Aromatic Polyketide Isolated from the Marine-Derived Fungus Curvularia aeria.

A novel tricyclic polyketide, curvulanone (1), was isolated from the marine-derived fungus Curvularia aeria. The structure of 1 was determined by NMR and single-crystal X-ray crystallography. 1 had a cyclopentabenzopyranone with 3-acetic acid structure that is rarely found in natural compounds. Monoamine oxidase and sirtuin 1 inhibitory test was exhibited and 1 showed their inhibitory activity.