Revised Structures for the Kinamycin Antibiotics: 5-Diazobenzo[b]fluorenes Rather Than Benzo[b]carbazole Cyanamides

Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis

Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.

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.

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.

Brønsted/Lewis Acid-Promoted Site-Selective Intramolecular Cycloisomerizations of Aryl-Fused 1,6-Diyn-3-ones for Diversity-Oriented Synthesis of Benzo-Fused Fluorenes and Fluorenones and Naphthyl Ketones

Herein, a facile diversity-oriented approach to access functionalized benzo[a]fluorenes, benzo[b]fluorenones, and naphthyl ketones has been demonstrated via site-selective intramolecular cyclization of aryl-fused 1,6-diyn-3-ones. Synthesis of benzo[a]fluorenes and naphthyl ketones has been achieved selectively using TfOH and AgBF₄, respectively, via in situ-formed acetals. Aryl-fused 1,6-diyn-3-ones undergo triflic acid-mediated intramolecular cyclization, leading to benzo[b]fluorenone derivatives via a radical intermediate as supported by EPR studies. Kinetic studies of these transformations have also been performed by UV-visible spectroscopic analysis to shed light on the reaction profile.

Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis

Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C-C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6-311 + G(d,p)//6-31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10'-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10') of the two reactant molecules maximizes the HOMO-LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2- anion. In particular, the significant π-π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C-C coupling. The distortion/interaction-activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C-C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π-π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.

The Symbiotic Relationship Between Drug Discovery and Organic Chemistry

All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.

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.

Applications of Friedel-Crafts reactions in total synthesis of natural products

Over the years, Friedel-Crafts (FC) reactions have been acknowledged as the most useful and powerful synthetic tools for the construction of a special kind of carbon-carbon bond involving an aromatic moiety. Its stoichiometric and, more recently, its catalytic procedures have extensively been studied. This reaction in recent years has frequently been used as a key step (steps) in the total synthesis of natural products and targeted complex bioactive molecules. In this review, we try to underscore the applications of intermolecular and intramolecular FC reactions in the total syntheses of natural products and complex molecules, exhibiting diverse biological properties.

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.

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.

Diazo Compounds: Versatile Tools for Chemical Biology

Diazo groups have broad and tunable reactivity. That and other attributes endow diazo compounds with the potential to be valuable reagents for chemical biologists. The presence of diazo groups in natural products underscores their metabolic stability and anticipates their utility in a biological context. The chemoselectivity of diazo groups, even in the presence of azido groups, presents many opportunities. Already, diazo compounds have served as chemical probes and elicited novel modifications of proteins and nucleic acids. Here, we review advances that have facilitated the chemical synthesis of diazo compounds, and we highlight applications of diazo compounds in the detection and modification of biomolecules.

Identification of natural inhibitors of Entamoeba histolytica cysteine synthase from microbial secondary metabolites

Amebiasis is a common worldwide diarrheal disease, caused by the protozoan parasite, Entamoeba histolytica. Metronidazole has been a drug of choice against amebiasis for decades despite its known side effects and low efficacy against asymptomatic cyst carriers. E. histolytica is also capable of surviving sub-therapeutic levels of metronidazole in vitro. Novel drugs with different mode of action are therefore urgently needed. The sulfur assimilatory de novo L-cysteine biosynthetic pathway is essential for various cellular activities, including the proliferation and anti-oxidative defense of E. histolytica. Since the pathway, consisting of two reactions catalyzed by serine acetyltransferase (SAT) and cysteine synthase (CS, O-acetylserine sulfhydrylase), does not exist in humans, it is a rational drug target against amebiasis. To discover inhibitors against the CS of E. histolytica (EhCS), the compounds of Kitasato Natural Products Library were screened against two recombinant CS isozymes: EhCS1 and EhCS3. Nine compounds inhibited EhCS1 and EhCS3 with IC50 values of 0.31-490 μM. Of those, seven compounds share a naphthoquinone moiety, indicating the structural importance of the moiety for binding to the active site of EhCS1 and EhCS3. We further screened >9,000 microbial broths for CS inhibition and purified two compounds, xanthofulvin and exophillic acid from fungal broths. Xanthofulvin inhibited EhCS1 and EhCS3. Exophillic acid showed high selectivity against EhCS1, but exhibited no inhibition against EhCS3. In vitro anti-amebic activity of the 11 EhCS inhibitors was also examined. Deacetylkinamycin C and nanaomycin A showed more potent amebicidal activity with IC50 values of 18 and 0.8 μM, respectively, in the cysteine deprived conditions. The differential sensitivity of trophozoites against deacetylkinamycin C in the presence or absence of L-cysteine in the medium and the IC50 values against EhCS suggest the amebicidal effect of deacetylkinamycin C is due to CS inhibition.

Bioactive Phytochemicals: Bioactivity, Sources, Preparations, and/or ModificationsviaSilver Tetrafluoroborate Mediation

This review provides an overview of the biological activities, natural occurrences, and the silver tetrafluoroborate- (AgBF4-) mediated synthesis of proanthocyanidins, glycosides, N-heterocyclic alkaloid analogues (of pyrrole, morphine, quinoline, isoquinoline, and indole), furan analogues, and halocompounds. AgBF4has been reviewed as an effective reaction promoter, used extensively in the synthesis of relevant biologically active compoundsviacarbon-carbon and carbon-heteroatom bonds formation. The literatures from 1979 to April 2014 were reviewed.

Kinamycin biosynthesis employs a conserved pair of oxidases for B-ring contraction

A conserved pair of oxidases is characterized as nature's machinery for benzofluorenone formation.

Prekinamycin and an isosteric-isoelectronic analogue exhibit comparable cytotoxicity towards K562 human leukemia cells

The diazo functionality of the kinamycins may not be an absolute requirement for bioactivity.

Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica

The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.

Synthesis of the N-(tert-butyloxycarbonyl)-O-triisopropylsilyl-D-pyrrolosamine Glycal of Lomaiviticin A & B via Epimerization of L-Threonine

An efficient synthesis of the N-(tert-butyloxycarbonyl)-O-triisopropylsilyl-D-pyrrolosamine glycal of lomaiviticin A (1) and lomaiviticin B (2) is described. The synthesis is highlighted by the epimerization of the L-threonine-derived oxazolidine 10 to oxazolidine 11. This key epimerization reaction, which serves to establish the correct relative configuration of the carbohydrate unit, was made possible only after conformational analysis indicated that substituted oxazolidines may adopt conformations that preclude enolization.

Kinamycin F downregulates cyclin D3 in human leukemia K562 cells

The bacterial metabolite kinamycin F, which contains an unusual and potentially reactive diazo group, is being investigated as an antitumor agent with a potentially novel target. Treatment of K562 cells with kinamycin F induced erythroid differentiation, a rapid apoptotic response, induction of caspase-3/7 activities and a delayed cell cycle progression through the S and G(2)/M phases. Kinamycin F caused a selective reduction of cyclin D3 protein, which appeared to be mediated at the level of transcription, rather than by affecting the stability of either cyclin D3 protein or mRNA. Thus cyclin D3 is a potential target of kinamycin F.

A phosphine-mediated conversion of azides into diazo compounds

N2 the mild: Diazo compounds are extremely versatile intermediates for synthetic organic chemistry, but their synthesis can be challenging in the presence of delicate functional groups. The Staudinger ligation has inspired a mild method for the conversion of a broad range of azides into their diazo compound derivatives through an acyl triazene intermediate.

Recent advances in the chemistry and biology of naturally occurring antibiotics

Ever since the world-shaping discovery of penicillin, nature's molecular diversity has been extensively screened for new medications and lead compounds in drug discovery. The search for agents intended to combat infectious diseases has been of particular interest and has enjoyed a high degree of success. Indeed, the history of antibiotics is marked with impressive discoveries and drug-development stories, the overwhelming majority of which have their origin in natural products. Chemistry, and in particular chemical synthesis, has played a major role in bringing naturally occurring antibiotics and their derivatives to the clinic, and no doubt these disciplines will continue to be key enabling technologies. In this review article, we highlight a number of recent discoveries and advances in the chemistry, biology, and medicine of naturally occurring antibiotics, with particular emphasis on total synthesis, analogue design, and biological evaluation of molecules with novel mechanisms of action.

Diels-Alder reactions using 4,7-dioxygenated indanones as dienophiles for regioselective construction of oxygenated 2,3-dihydrobenz[f]indenone skeleton

Regioselective construction of 4,8,9-trioxygenated 2,3-dihydrobenz[f]indenones, key intermediates for the synthesis of kinamycin antibiotics, was achieved via Diels-Alder reactions (DAR) using 4,7-dioxygenated indanone-type compounds as dienophiles. Reaction of indanetrione with 1-methoxybutadiene gave a 1 : 1 mixture of undesired 4,5,9-trioxygenated 2,3-dihydrobenz[f]indenone and [4.4.3]propellane. The addition of Lewis acid did not affect the product ratio, whereas the use of the 6-bromoindanetrione exclusively afforded the latter propellane. On the other hand, DAR of benzyne derived from bromoindan and furan gave 5,8-epoxy-2,3-dihydrobenz[f]indene, which was subjected to acid-induced ring opening to give 2,3-dihydrobenz[f]indenone with undesired 4,5,9-trioxy functions.