Kinamycin biosytheesis. Synthesis, detection, and incorporation of kinobscurinone, a benzo[b]fluorenone

Cobalt-Catalyzed Divergence in C(sp3)-H Functionalization of 9H-Fluorene: A Streamlined Approach Utilizing Alcohols

Sustainable chemical production demands the creation of innovative catalysts and catalytic technologies. While the development of coherent and robust catalytic systems using earth-abundant transition metals is essential, it remains a significant challenge. Herein, an expedient divergence strategy for tandem dehydrogenative C(sp3)-H alkylation and cyclization reactions of 9H-fluorene using a newly developed N,N-bidentate cobalt catalytic system is developed. This method capitalizes on the use of abundant and readily accessible alcohol. Demonstrating wide-ranging applicability, the catalytic protocol successfully integrated a diverse array of fluorenes and alcohols. This includes benzylic, heteroaromatic, and aliphatic primary and secondary alcohols, amassing a total of 75 distinct examples. When applied to sterically bulky alcohols, the reaction preferentially undergoes alkenylation, yielding a tetrasubstituted olefin as the main product. In the case of diols, the expected outcome is Dual-fluorescence at both terminal positions. This process leads to difluorination, followed by a cyclization step, culminating in the formation of a relatively unprecedented spiro compound. The scalability of this method has been validated through gram-scale synthesis. Control experiments have shed light on the reaction mechanism, indicating that it progresses through an unsaturated intermediate and adheres to the borrowing hydrogen pathway.

Cascade Cyclization of 1,5-Diynols and (RO)2P(O)SH to Construct Benzo[b]fluorenyl S-Alkyl Phosphorothioates under Catalyst-Free Conditions

An efficient and practical cascade cyclization of 1,5-diynols with (RO)2P(O)SH as the acid promoter and nucleophile under mild conditions was developed. A variety of highly substituted benzo[b]fluorenyl-containing S-alkyl phosphorothioates were successfully constructed in moderate to excellent yields. Furthermore, this protocol exhibited good functional group tolerance, a broad substrate scope, and potential practical applications, with water as the only byproduct. The reaction proceeded with allenyl thiophosphate as a key intermediate, followed by a Schmittel-type cyclization process to produce the target product.

P/N-heteroleptic Cu(I)-photosensitizer-catalyzed domino radical relay annulation of 1,6-enynes with aryldiazonium salts

A visible-light driven photocatalytic construction of benzo[b]fluorenones from 1,6-enynes and aryldiazonium salts has been achieved via a P/N-heteroleptic Cu(I)-photosensitizer-catalyzed domino radical relay annulation process. Preliminary mechanistic studies revealed that the aryl radicals in situ generated from aryldiazonium salts with the excited state of the Cu(I)-photosensitizer played a dual role of a radical initiator and a radical terminator in the concise construction of the highly fused benzo[b]fluorenone scaffold.

O-methyltransferase-like enzyme catalyzed diazo installation in polyketide biosynthesis

Diazo compounds are rare natural products possessing various biological activities. Kinamycin and lomaiviticin, two diazo natural products featured by the diazobenzofluorene core, exhibit exceptional potency as chemotherapeutic agents. Despite the extensive studies on their biosynthetic gene clusters and the assembly of their polyketide scaffolds, the formation of the characteristic diazo group remains elusive. L-Glutamylhydrazine was recently shown to be the hydrazine donor in kinamycin biosynthesis, however, the mechanism for the installation of the hydrazine group onto the kinamycin scaffold is still unclear. Here we describe an O-methyltransferase-like protein, AlpH, which is responsible for the hydrazine incorporation in kinamycin biosynthesis. AlpH catalyses a unique SAM-independent coupling of L-glutamylhydrazine and polyketide intermediate via a rare Mannich reaction in polyketide biosynthesis. Our discovery expands the catalytic diversity of O-methyltransferase-like enzymes and lays a strong foundation for the discovery and development of novel diazo natural products through genome mining and synthetic biology.

Direct Synthesis of Benzo[b]fluorenyl Thiophosphates via Tandem Cyclization of Diynols with (RO)2P(O)SH

A general and metal-free protocol for the construction of benzo[b]fluorenyl thiophosphates was developed through the cascade cyclization of easily prepared diynols and (RO)₂P(O)SH, with water as the only byproduct. The novel transformation involved the allenyl thiophosphate as the key intermediate, followed by Schmittel-type cyclization to achieve the desired products. Notably, (RO)₂P(O)SH acted not only as a nucleophile but also as an acid-promoter to initiate the reaction.

Synthetic and biosynthetic routes to nitrogen-nitrogen bonds

The nitrogen-nitrogen bond is a core feature of diverse functional groups like hydrazines, nitrosamines, diazos, and pyrazoles. Such functional groups are found in >300 known natural products. Such N-N bond-containing functional groups are also found in significant percentage of clinical drugs. Therefore, there is wide interest in synthetic and enzymatic methods to form nitrogen-nitrogen bonds. In this review, we summarize synthetic and biosynthetic approaches to diverse nitrogen-nitrogen-bond-containing functional groups, with a focus on biosynthetic pathways and enzymes.

Manganese catalyzed switchable C-alkylation/alkenylation of fluorenes and indene with alcohols

The usage of earth-abundant, nontoxic transition metals in place of rare noble metals is a central goal in catalysis. This would be especially interesting when the reactivity and selectivity patterns can be tuned. Herein, we introduced the first Mn-catalyzed selective C-alkylation and olefination of fluorene, and indene with alcohols. Various substrates including benzylic, heteroaromatic, and aliphatic primary and secondary alcohols are employed as alkylating agents. Mechanistic investigations and a kinetic study underpin the involvement of the olefinated intermediate to furnish the alkylated product.

An N-heterocyclic carbene-catalyzed switchable reaction of 9-(trimethylsilyl)fluorene and aldehydes: chemoselective synthesis of dibenzofulvenes and fluorenyl alcohols

An N-heterocyclic carbene-catalyzed synthesis of dibenzofulvenes and fluorenyl alcohols was developed. In the presence of 10 mol% NHC (1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) and 4 Å molecular sieves, 9-(trimethylsilyl)fluorene undergoes an olefination reaction with aldehydes to produce dibenzofulvenes in 43-99% yields. However, on reducing the NHC loading to 1 mol% and with the addition of water, 9-(trimethylsilyl)fluorene selectively undergoes nucleophilic addition with aldehydes to afford fluorenyl alcohols in 40-95% yields.

Synthesis of fluorenyl alcohols via cooperative palladium/norbornene catalysis

Herein, we report a novel catalytic synthesis of substituted 9H-fluoren-9-ols starting from aryl iodides and secondary ortho-bromobenzyl alcohols in the presence of palladium/norbornene as a catalytic system. The present protocol exhibits high functional group tolerance, mild reaction conditions and moderate to good yields. This transformation is based on two sequential pathways: (i) Pd(ii)-mediated oxidation of the secondary alcohol to the corresponding ketone and (ii) Pd(0)/norbornene-catalyzed reaction of the in situ generated ortho-bromoacetophenone with the aryl iodide.

One-pot synthesis of benzo[b]fluorenones via a cobalt-catalyzed MHP-directed [3+2] annulation/ring-opening/dehydration sequence

A cobalt-catalyzed MHP-directed [3+2] annulation of benzoyl hydrazines with oxabicyclic alkenes followed by a ring-opening/dehydration sequence is developed for the one-pot synthesis of benzo[b]fluorenones.

The functional differentiation of the post-PKS tailoring oxygenases contributed to the chemical diversities of atypical angucyclines

Angucyclines are one of the largest families of aromatic polyketides with various chemical structures and bioactivities. Decades of studies have made it easy for us to depict the picture of their early biosynthetic pathways. Two families of oxygenases, the FAD-dependent oxygenases and the ring opening oxygenases, contribute to the formation of some unique skeletons of atypical angucyclines. The FAD-dependent oxygenases involved in the biosynthetic gene clusters of typical angucyclines catalyze two hydroxylation reactions at C-12 and C-12b of prejadomycin, while their homolog JadH in jadomycin gene cluster catalyze the C-12 hydroxylation and 4a,12b-dehydration reactions of prejadomycin, which leads to the production of dehydrorabelomycin, a common intermediate during the biosynthesis of atypical angucyclines. Ring opening oxygenases of a unique family of oxygenases catalyze the oxidative C—C bond cleavage reaction of dehydrorabelomycin, followed by different rearrangement reactions, resulting in the formation of the various chemical skeletons of atypical angucyclines. These results suggested that the functional differentiation of these oxygenases could apparently enrich the sources of aromatic polyketides with greater structure diversities.

Discovery of a Diazo-Forming Enzyme in Cremeomycin Biosynthesis

The molecular architectures and potent bioactivities of diazo-containing natural products have attracted the interest of synthetic and biological chemists. Despite this attention, the biosynthetic enzymes involved in diazo group construction have not been identified. Here, we show that the ATP-dependent enzyme CreM installs the diazo group in cremeomycin via late-stage N-N bond formation using nitrite. This finding should inspire efforts to use diazo-forming enzymes in biocatalysis and synthetic biology as well as enable genome-based discovery of new diazo-containing metabolites.

Reconstitution of Kinamycin Biosynthesis within the Heterologous Host Streptomyces albus J1074

Diazofluorene compounds such as kinamycin and lomaiviticin feature unique molecular structures and compelling medicinal bioactivities. However, a complete understanding of the biosynthetic details for this family of natural products has yet to be fully elucidated. In addition, a lack of genetically and technically amenable production hosts has limited access to the full medicinal potential of these compounds. Here, we report the capture of the complete kinamycin gene cluster from Streptomyces galtieri Sgt26 by bacterial artificial chromosome cloning, confirmed by successful production of kinamycin in the heterologous host Streptomyces albus J1074. Sequence analysis and a series of gene deletion experiments revealed the boundary of the cluster, which spans 75 kb DNA. To probe the last step in biosynthesis, acetylation of kinamcyin F to kinamycin D, gene knockout, and complementation experiments identified a single gene product involved with final acetylation conversions. This study provides full genetic information for the kinamycin gene cluster from S. galtieri Sgt26 and establishes heterologous biosynthesis as a production platform for continued mechanistic assessment of compound formation and utilization.

Characterization of the flavoenzyme XiaK as an N-hydroxylase and implications in indolosesquiterpene diversification

Flavoenzymes are ubiquitous in biological systems and catalyze a diverse range of chemical transformations.

Flavoenzymes are ubiquitous in biological systems and catalyze a diverse range of chemical transformations. The flavoenzyme XiaK from the biosynthetic pathway of the indolosesquiterpene xiamycin A is demonstrated to mediate the in vivo biotransformation of xiamycin A into multiple products, including a chlorinated adduct as well as dimers characterized by C–N and N–N linkages that are hypothesized to form via radical-based mechanisms. Isolation and characterization of XiaK in vitro shows that it acts as a flavin-dependent N-hydroxylase that catalyzes the hydroxylation of xiamycin A at the carbazole nitrogen to form N-hydroxyxiamycin, a product which was overlooked in earlier in vivo experiments because its chemical and chromatographic properties are similar to those of oxiamycin. N-Hydroxyxiamycin is shown to be unstable under aerobic conditions, and characterization by electron paramagnetic resonance spectroscopy demonstrates formation of an N-hydroxycarbazole radical adduct. This radical species is proposed to serve as a key intermediate leading to the formation of the multiple xiamycin A adducts. This study suggests that non-enzyme catalyzed reactions may play a greater role in the biosynthesis of natural products than has been previously recognized.

Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis

Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.

Production of Stealthin C Involves an S-N-Type Smiles Rearrangement

The kinamycin family of aromatic polyketide natural products contains an atypical angucycline ring system substituted with a diazo group. The enzymatic chemistry involved in constructing both of these structural features has been largely unexplored. Here we report the in vivo and in vitro production of seongomycin, a shunt product from this pathway, and stealthin C, a proposed biosynthetic precursor to the kinamycins. We show that a single enzyme, the flavin-dependent monooxygenase AlpJ, can generate these metabolites from N-acetyl-l-cysteine and l-cysteine, respectively, and that the synthesis of stealthin C likely proceeds via a nonenzymatic S-N-type Smiles rearrangement. This unexpected route to stealthin C reveals a distinct approach to install aromatic amino groups in metabolites and raises questions about the intermediacy of this species in kinamycin production.

Palladium-catalyzed dearomatizative [2 + 2 + 1] carboannulation of 1,7-enynes with aryl diazonium salts and H2O: facile synthesis of spirocyclohexadienone-fused cyclopenta[c]quinolin-4(5H)-ones

The first 1,7-enyne dearomatizative [2 + 2 + 1] carboannulation using aryl diazonium salts as the one-carbon units is described.

New Insights into the Biosynthesis of Fosfazinomycin

The biosynthetic origin of a unique hydrazide moiety in the phosphonate natural product fosfazinomycin is investigated.

The biosynthetic origin of a unique hydrazide moiety in the phosphonate natural product fosfazinomycin is unknown. This study presents the activities of five proteins encoded in its gene cluster. The flavin-dependent oxygenase FzmM catalyses the oxidation of l-Asp to N-hydroxy-Asp. When FzmL is added, fumarate is produced in addition to nitrous acid. The adenylosuccinate lyase homolog FzmR eliminates acetylhydrazine from N-acetyl-hydrazinosuccinate, which in turn is the product of FzmQ-catalysed acetylation of hydrazinosuccinate. Collectively, these findings suggest a path to N-acetylhydrazine from l-Asp. The incorporation of nitrogen from l-Asp into fosfazinomycin was confirmed by isotope labelling studies. Installation of the N-terminal Val of fosfazinomycin is catalysed by FzmI in a Val-tRNA dependent process.

Discovery of the lomaiviticin biosynthetic gene cluster in Salinispora pacifica

The lomaiviticins are a family of cytotoxic marine natural products that have captured the attention of both synthetic and biological chemists due to their intricate molecular scaffolds and potent biological activities. Here we describe the identification of the gene cluster responsible for lomaiviticin biosynthesis in Salinispora pacifica strains DPJ-0016 and DPJ-0019 using a combination of molecular approaches and genome sequencing. The link between the lom gene cluster and lomaiviticin production was confirmed using bacterial genetics, and subsequent analysis and annotation of this cluster revealed the biosynthetic basis for the core polyketide scaffold. Additionally, we have used comparative genomics to identify candidate enzymes for several unusual tailoring events, including diazo formation and oxidative dimerization. These findings will allow further elucidation of the biosynthetic logic of lomaiviticin assembly and provide useful molecular tools for application in biocatalysis and synthetic biology.

Angucyclines: Biosynthesis, mode-of-action, new natural products, and synthesis

Covering: 1997 to 2010. The angucycline group is the largest group of type II PKS-engineered natural products, rich in biological activities and chemical scaffolds. This stimulated synthetic creativity and biosynthetic inquisitiveness. The synthetic studies used five different strategies, involving Diels-Alder reactions, nucleophilic additions, electrophilic additions, transition-metal mediated cross-couplings and intramolecular cyclizations to generate the angucycline frames. Biosynthetic studies were particularly intriguing when unusual framework rearrangements by post-PKS tailoring oxidoreductases occurred, or when unusual glycosylation reactions were involved in decorating the benz[a]anthracene-derived cores. This review follows our previous reviews, which were published in 1992 and 1997, and covers new angucycline group antibiotics published between 1997 and 2010. However, in contrast to the previous reviews, the main focus of this article is on new synthetic approaches and biosynthetic investigations, most of which were published between 1997 and 2010, but go beyond, e.g. for some biosyntheses all the way back to the 1980s, to provide the necessary context of information.

Benzo[b]fluorenes via Indanone Dianion Annulation. A Short Synthesis of Prekinamycin

[structure: see text]. A rapid construction of benzo[b]fluorenones via reaction of 1-indanone dianions with phthalate diesters is described. Its utility is illustrated with a concise synthesis of prekinamycin.

Annulation strategies for benzo[b]fluorene synthesis: efficient routes to the kinafluorenone and WS-5995 antibiotics

Intramolecular palladium-mediated arylation approaches to benzo[b]fluorenes have been investigated. The methodology has been applied in a short synthesis of tri-O-methylkinafluorenone, providing an effective alternative to Friedel-Crafts-based approaches. During the course of this work, an acid-promoted quinolactonization of naphthoquinones was also developed, providing direct access to either ortho or para isomers as desired. Application of this methodology in syntheses of the antibiotics WS-5995A, WS-5995C, and functional analogues was demonstrated, and antitumoral activity of this class was determined.

Cloning and heterologous expression of the entire gene clusters for PD 116740 from Streptomyces strain WP 4669 and tetrangulol and tetrangomycin from Streptomyces rimosus NRRL 3016

The genes for the complete pathways for two polycyclic aromatic polyketides of the angucyclinone class have been cloned and heterologously expressed. Genomic DNAs of Streptomyces rimosus NRRL 3016 and Streptomyces strain WP 4669 were partially digested with MboI, and libraries (ca. 40-kb fragments) in Escherichia coli XL1-Blue MR were prepared with the cosmid vector pOJ446. Hybridization with the actI probe from the actinorhodin polyketide synthase genes identified two clusters of polyketide genes from each organism. After transfer of the four clusters to Streptomyces lividans TK24, expression of one cluster from each organism was established through the identification of pathway-specific products by high-performance liquid chromatography with photodiode array detection. Peaks were identified from the S. rimosus cluster (pksRIM-1) for tetrangulol, tetrangomycin, and fridamycin E. Peaks were identified from the WP 4669 cluster (pksWP-2) for tetrangulol, 19-hydroxytetrangulol, 8-O-methyltetrangulol, 19-hydroxy-8-O-methyltetrangulol, and PD 116740. Structures were confirmed by 1H nuclear magnetic resonance spectroscopy and high-resolution mass spectrometry.