Epoxyquinone Formation Catalyzed by a Two-Component Flavin-Dependent Monooxygenase Involved in Biosynthesis of the Antibiotic Actinorhodin

Characterization of ActVI-ORF3 and ActVI-ORF4 as Lactonizing and Delactonizing Enzymes in Relation to Metabolic Flux in Actinorhodin Biosynthesis

Actinorhodin (ACT) from Streptomyces coelicolor A3(2) is an aromatic polyketide antibiotic with a benzoisochromanequinone (BIQ) skeleton. Although actVI-ORF3 and actVI-ORF4 are not essential for ACT biosynthesis, homologous genes to these are present in the biosynthetic gene clusters of BIQ lactones. In this study, ActVI-ORF3 was identified as a cofactor-independent enzyme with lactonization activity, using ACT as a substrate. ActVI-ORF3 recognized dihydrokalafungin and 8-hydroxykalafafungin, which share the same pyran-ring configuration as ACT, but not nanaomycin A, which has an opposite configuration. In contrast, ActVI-ORF4 functioned as an NAD(P)-dependent oxidoreductase, catalyzing the delactonization of BIQ lactones. Conversion experiments using isotopically labeled compounds revealed that both lactonization and delactonization reactions of these enzymes yielded products in which the carboxyl oxygen at the C1 position was retained. Subsequently, we reexamined the accumulation of ACT-related compounds in the actVI-ORF3 and actVI-ORF-4 disruptants. The results suggested that ACT intermediates are predominantly pooled in the bacteria as (S)-DNPA rather than in lactone-form. The contribution of ActVI-ORF4 to metabolic flux is not significant, and endogenous reductases can convert these intermediates to the dihydro form, which subsequently re-enters the ACT biosynthetic pathway.

Molecular Networking-Guided Discovery of a New Antitumor Pyranonaphthoquinone from Streptomyces tanashiensis DSM 731: Insights from Single-Molecule Stretching Assays

Guided by molecular networking based on single-molecule stretching assay, an unprecedented pyranonaphthoquinone, methyl kalafunginate (1) and five known compounds 2-6 were isolated from Streptomyces tanashiensis DSM 731. Compound 1 was characterized through a combination of spectroscopic techniques, including 1D and 2D NMR analysis, ECD calculation, and X-ray crystallography. Interestingly, we discovered that compound 1 was spontaneously converted from kalafungin (4) in methanol solution. All isolated compounds, except for compound 3, were assessed for their cytotoxic potential against a panel of five human cancer cell lines: A549, HepG2, BxPC-3, SW620, and C4-2B. Compounds 1, 2, 4, and 5 exhibited remarkable cytotoxicity with IC50 values below 2.382 μM, suggesting their potential as promising anticancer agents. These findings highlight the significance of using a combined approach of single-molecule stretching assays and molecular networking for efficiently discovering novel natural products with potential therapeutic applications.

Genome Mining and Heterologous Expression Guided the Discovery of Antimicrobial Naphthocyclinones from Streptomyces eurocidicus CGMCC 4.1086

A type II polyketide synthase biosynthetic gene cluster (nap) was identified in Streptomyces eurocidicus CGMCC 4.1086 via genome mining. The heterologous expression of the cryptic nap gene cluster in Streptomyces albus J1074 generated dimerized aromatic polyketide naphthocyclinones (1-3), whose structures were determined via extensive analysis using nuclear magnetic resonance and high-resolution electrospray ionization mass spectroscopy. The biological pathway of naphthocyclinone synthesis was revealed via in vivo gene deletion, in vitro biochemical reactions, and comparative genomics. Remarkably, 3 played a crucial role in inhibiting Phytophthora capsici and Phytophthora sojae, with EC₅₀ values of 6.1 and 20.2 μg/mL, respectively. Furthermore, 3 exhibited a potent protective effect against P. capsici and P. sojae in greenhouse tests.

Identification of a C-Glycosyltransferase Involved in Medermycin Biosynthesis

C-Glycosylation in the biosynthesis of bioactive natural products is quite unique, which has not been studied well. Medermycin, as an antitumor agent in the family of pyranonaphthoquinone antibiotics, is featured with unique C-glycosylation. Here, a new C-glycosyltransferase (C-GT) Med-8 was identified to be essential for the biosynthesis of medermycin, as the first example of C-GT to recognize a rare deoxyaminosugar (angolosamine). med-8 and six genes (med-14, -15, -16, -17, -18, and -20 located in the medermycin biosynthetic gene cluster) predicted for the biosynthesis of angolosamine were proved to be functional and sufficient for C-glycosylation. A C-glycosylation cassette composed of these seven genes could convert a proposed substrate into a C-glycosylated product. In conclusion, these genes involved in the C-glycosylation of medermycin were functionally identified and biosynthetically engineered, and they provided the possibility of producing new C-glycosylated compounds.

Total synthesis of griseusins and elucidation of the griseusin mechanism of action

An efficient divergent synthesis of griseusins enabled SAR studies, mechanistic elucidation and evaluation in an axolotl tail regeneration model.

A divergent modular strategy for the enantioselective total synthesis of 12 naturally-occurring griseusin type pyranonaphthoquinones and 8 structurally-similar analogues is described. Key synthetic highlights include Cu-catalyzed enantioselective boration–hydroxylation and hydroxyl-directed C–H olefination to afford the central pharmacophore followed by epoxidation–cyclization and maturation via diastereoselective reduction and regioselective acetylation. Structural revision of griseusin D and absolute structural assignment of 2a,8a-epoxy-epi-4′-deacetyl griseusin B are also reported. Subsequent mechanistic studies establish, for the first time, griseusins as potent inhibitors of peroxiredoxin 1 (Prx1) and glutaredoxin 3 (Grx3). Biological evaluation, including comparative cancer cell line cytotoxicity and axolotl embryo tail inhibition studies, highlights the potential of griseusins as potent molecular probes and/or early stage leads in cancer and regenerative biology.

Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow

Mining of microbial genomes has revealed that actinomycetes harbor far more biosynthetic potential for bioactive natural products than anticipated. Activation of (cryptic) biosynthetic gene clusters and identification of the corresponding metabolites has become a focal point for drug discovery. Here, we applied NMR-based metabolomics combined with bioinformatics to identify novel C-glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 and to elucidate the biosynthetic pathway. Following activation of the cryptic qin gene cluster for a type II polyketide synthase (PKS) by constitutive expression of its pathway-specific activator, bioinformatics coupled to NMR profiling facilitated the chromatographic isolation and structural elucidation of qinimycins A-C (1-3). The intriguing structural features of the qinimycins, including 8-C-glycosylation, 5,14-epoxidation, and 13-hydroxylation, distinguished these molecules from the model pyranonaphthoquinones actinorhodin, medermycin, and granaticin. Another novelty lies in the unusual fusion of a deoxyaminosugar to the pyranonaphthoquinone backbone during biosynthesis of the antibiotics BE-54238 A and B (4, 5). Qinimycins showed weak antimicrobial activity against Gram-positive bacteria. Our work shows the utility of combining bioinformatics, targeted activation of cryptic gene clusters, and NMR-based metabolic profiling as an effective pipeline for the discovery of microbial natural products with distinctive skeletons.

Bifunctionality of ActIV as a Cyclase-Thioesterase Revealed by in Vitro Reconstitution of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2)

Type II polyketide synthases iteratively generate a nascent polyketide thioester of the acyl carrier protein (ACP); this is structurally modified to produce an ACP-free intermediate towards the final metabolite. However, the timing of ACP off-loading is not well defined because of the lack of an apparent thioesterase (TE) among relevant biosynthetic enzymes. Here, ActIV, which had been assigned as a second ring cyclase (CYC) in actinorhodin (ACT) biosynthesis, was shown to possess TE activity in vitro with a model substrate, anthraquinone-2-carboxylic acid-N-acetylcysteamine. In order to investigate its function further, the ACT biosynthetic pathway in Streptomyces coelicolor A3(2) was reconstituted in vitro in a stepwise fashion up to (S)-DNPA, and the product of ActIV reaction was characterized as an ACP-free bicyclic intermediate. These findings indicate that ActIV is a bifunctional CYC-TE and provide clear evidence for the release timing of the intermediate from the ACP anchor.

Characterization of the Biosynthetic Gene Cluster for Benzoxazole Antibiotics A33853 Reveals Unusual Assembly Logic

A33853, which shows excellent bioactivity against Leishmania, is a benzoxazole-family compound formed from two moieties of 3-hydroxyanthranilic acid and one 3-hydroxypicolinic acid. In this study, we have identified the gene cluster responsible for the biosynthesis of A33853 in Streptomyces sp. NRRL12068 through genome mining and heterologous expression. Bioinformatics analysis and functional characterization of the orfs contained in the gene cluster revealed that the biosynthesis of A33853 is directed by a group of unusual enzymes. In particular, BomK, annotated as a ketosynthase, was found to catalyze the amide bond formation between 3-hydroxypicolinic and 3-hydroxyanthranilic acid during the assembly of A33853. BomJ, a putative ATP-dependent coenzyme A ligase, and BomN, a putative amidohydrolase, were further proposed to be involved in the benzoxazole formation in A33853 according to gene deletion experiments. Finally, we have successfully utilized mutasynthesis to generate two analogs of A33853, which were reported previously to possess excellent anti-leishmanial activity.

6-Deoxy-13-hydroxy-8,11-dione-dihydrogranaticin B, an intermediate in granaticin biosynthesis, from Streptomyces sp. CPCC 200532

A new granaticin analogue and its hydrolysis product were isolated from Streptomyces sp. CPCC 200532. Their structures were determined to be 6-deoxy-13-hydroxy-8,11-dione-dihydrogranaticins B (1) and A (2), respectively, by detailed analysis of spectroscopic data. Compound 1 was regarded as an intermediate in granaticin biosynthesis, as it was bioconvertable to granaticin B. Compared to granaticin B, 1 showed similar cytotoxicity against cancer cell line HCT116, but decreased cytotoxicity against cancer cell lines A549, HeLa, and HepG2. Compound 2 displayed lower cytotoxicity than 1 against all four cancer cell lines tested.

Insights into the bioactivity of mensacarcin and epoxide formation by MsnO8

Mensacarcin, a potential antitumour drug, is produced by Streptomyces bottropensis. The structure consists of a three-membered ring system with many oxygen atoms. Of vital importance in this context is an epoxy moiety in the side chain of mensacarcin. Our studies with different mensacarcin derivatives have demonstrated that this epoxy group is primarily responsible for the cytotoxic effect of mensacarcin. In order to obtain further information about this epoxy moiety, inactivation experiments in the gene cluster were carried out to identify the epoxy-forming enzyme. Therefore the cosmid cos2, which covers almost the complete type II polyketide synthase (PKS) gene cluster, was heterologously expressed in Streptomyces albus. This led to production of didesmethylmensacarcin, due to the fact that methyltransferase genes are missing in the cosmid. Further gene inactivation experiments on this cosmid showed that MsnO8, a luciferase-like monooxygenase, introduces the epoxy group at the end of the biosynthesis of mensacarcin. In addition, the protein MsnO8 was purified, and its crystal structure was determined to a resolution of 1.80 Å.

Characterization of the two-component monooxygenase system AlnT/AlnH reveals early timing of quinone formation in alnumycin biosynthesis

Alnumycin A is an aromatic polyketide with a strong resemblance to related benzoisochromanequinone (BIQ) antibiotics, such as the model antibiotic actinorhodin. One intriguing difference between these metabolites is that the positions of the benzene and quinone rings are reversed in alnumycin A in comparison to the BIQ polyketides. In this paper we demonstrate that inactivation of either the monooxygenase alnT gene or the flavin reductase alnH gene results in the accumulation of a novel nonquinoid metabolite, thalnumycin A (ThA), in the culture medium. Additionally, two other previously characterized metabolites, K1115 A and 1,6-dihydroxy-8-propylanthraquinone (DHPA), were identified, which had oxidized into quinones putatively nonenzymatically at the incorrect position in the central ring. None of the compounds isolated contained correctly formed pyran rings, which suggests that on the alnumycin pathway quinone biosynthesis occurs prior to third ring cyclization. The regiochemistry of the two-component monooxygenase system AlnT/AlnH was finally confirmed in vitro by using ThA, FMN, and NADH in enzymatic synthesis, where the reaction product, thalnumycin B (ThB), was verified to contain the expected p-hydroquinone structure in the lateral ring.