The biosynthetic gene cluster for the antitumor rebeccamycin: characterization and generation of indolocarbazole derivatives

Rebeccamycin, a halogenated natural product of the indolocarbazole family, is produced by Saccharothrix aerocolonigenes ATCC39243. Several rebeccamycin analogues, which target DNA topoisomerase I or II, have already entered clinical trials as anticancer drugs. Using as a probe an internal fragment of ngt, a Saccharothrix aerocolonigenes gene encoding an indolocarbazole N-glycosyltransferase, we isolated a DNA region that directed the biosynthesis of rebeccamycin when introduced into Streptomyces albus. Sequence analysis of 25.6 kb revealed genes for indolocarbazole core formation, halogenation, glycosylation, and sugar methylation, as well as a regulatory gene and two resistance/secretion genes. Heterologous expression of subsets of these genes resulted in production of deschloro-rebeccamycin, 4'-demethyldeschloro-rebeccamycin, and deschloro-rebeccamycin aglycone. The cloned genes should help to elucidate the molecular basis for indolocarbazole biosynthesis and set the stage for the generation of novel indolocarbazole analogues by genetic engineering.     

Deciphering indolocarbazole and enediyne aminodideoxypentose biosynthesis through comparative genomics: insights from the AT2433 biosynthetic locus

AT2433, an indolocarbazole antitumor antibiotic, is structurally distinguished by its aminodideoxypentose-containing disaccharide and asymmetrically halogenated N-methylated aglycon. Cloning and sequence analysis of AT2433 gene cluster and comparison of this locus with that encoding for rebeccamycin and the gene cluster encoding calicheamicin present an opportunity to study the aminodideoxypentose biosynthesis via comparative genomics. The locus was confirmed via in vitro biochemical characterization of two methyltransferases--one common to AT2433 and rebeccamycin, the other unique to AT2433--as well as via heterologous expression and in vivo bioconversion experiments using the AT2433 N-glycosyltransferase. Preliminary studies of substrate tolerance for these three enzymes reveal the potential to expand upon the enzymatic diversification of indolocarbazoles. Moreover, this work sets the stage for future studies regarding the origins of the indolocarbazole maleimide nitrogen and indolocarbazole asymmetry.     

Two synthetic approaches to rebeccamycin

Two synthetic approaches to a new indolocarbazole antitumor antibiotic, rebeccamycin, were developed. The absolute configuration of rebeccamycin was determined by a total synthesis.     

Calories from carbohydrates: energetic contribution of the carbohydrate moiety of rebeccamycin to DNA binding and the effect of its orientation on topoisomerase I inhibition.

BACKGROUND: Only a few antitumor drugs inhibit the DNA breakage-reunion reaction catalyzed by topoisomerase. One is the camptothecin derivative topotecan that has recently been used clinically. Others are the glycosylated antibiotic rebeccamycin and its synthetic analog NB-506, which is presently in phase I of clinical trials. Unlike the camptothecins, rebeccamycin-type compounds bind to DNA. We set out to elucidate the molecular basis of their interaction with duplex DNA, with particular emphasis on the role of the carbohydrate residue. RESULTS: We compared the DNA-binding and topoisomerase-I-inhibition activities of two isomers of rebeccamycin that contain a galactose residue attached to the indolocarbazole chromophore via an alpha (axial) or a beta (equatorial) glycosidic linkage. The modification of the stereochemistry of the chromophore-sugar linkage results in a marked change of the DNA-binding and topoisomerase-I- poisoning activities. The inverted configuration at the C-1' of the carbohydrate residue abolishes intercalative binding of the drug to DNA thereby drastically reducing the binding affinity. Consequently, the alpha isomer has lost the capacity to induce topoisomerase-I-mediated cleavage of DNA. Comparison with the aglycone allowed us to determine the energetic contribution of the sugar residue. CONCLUSIONS: The optimal interaction of rebeccamycin analogs with DNA is controlled to a large extent by the stereochemistry of the sugar residue. The results clarify the role of carbohydrates in stereospecific drug-DNA interactions and provide valuable information for the rational design of new rebeccamycin-type antitumor agents.     

Facile Chemoenzymatic Strategies for the Synthesis and Utilization of S‐Adenosyl‐L‐Methionine Analogues

A chemoenzymatic platform for the synthesis of S‐adenosyl‐L ‐methionine (SAM) analogues compatible with downstream SAM‐utilizing enzymes is reported. Forty‐four non‐native S/Se‐alkylated Met analogues were synthesized and applied to probing the substrate specificity of five diverse methionine adenosyltransferases (MATs). Human MAT II was among the most permissive of the MATs analyzed and enabled the chemoenzymatic synthesis of 29 non‐native SAM analogues. As a proof of concept for the feasibility of natural product “alkylrandomization”, a small set of differentially‐alkylated indolocarbazole analogues was generated by using a coupled hMAT2–RebM system (RebM is the sugar C4′‐O‐methyltransferase that is involved in rebeccamycin biosynthesis). The ability to couple SAM synthesis and utilization in a single vessel circumvents issues associated with the rapid decomposition of SAM analogues and thereby opens the door for the further interrogation of a wide range of SAM utilizing enzymes.     

An Unusual Role for a Mobile Flavin in StaC-like Indolocarbazole Biosynthetic Enzymes

The indolocarbazole biosynthetic enzymes StaC, InkE, RebC, and AtmC mediate the degree of oxidation of chromopyrrolic acid on route to the natural products staurosporine, K252a, rebeccamycin, and AT2433-A1, respectively. Here, we show that StaC and InkE, which mediate a net 4-electron oxidation, bind FAD with a micromolar K(d), whereas RebC and AtmC, which mediate a net 8-electron oxidation, bind FAD with a nanomolar K(d) while displaying the same FAD redox properties. We further create RebC-10x, a RebC protein with ten StaC-like amino acid substitutions outside of previously characterized FAD-binding motifs and the complementary StaC-10x. We find that these mutations mediate both FAD affinity and product specificity, with RebC-10x displaying higher StaC activity than StaC itself. X-ray structures of this StaC catalyst identify the substrate of StaC as 7-carboxy-K252c and suggest a unique mechanism for this FAD-dependent enzyme.     

Staurosporine and rebeccamycin aglycones are assembled by the oxidative action of StaP, StaC, and RebC on chromopyrrolic acid

In the biosynthesis of the antitumor indolocarbazoles rebeccamycin and staurosporine by streptomycetes, assembly of the aglycones involves a complex set of oxidative condensations. Overall formation of aglycones K252c and arcyriaflavin A from their biosynthetic precursor chromopyrrolic acid involves four- and eight-electron oxidations, respectively. This process is catalyzed by the remarkable enzyme StaP, with StaC and RebC acting to direct the level of oxidation in the newly formed five-membered ring. An aryl-aryl coupling reaction is integral to this transformation as well as oxidative decarboxylation of the dicarboxypyrrole moiety of chromopyrrolic acid. Herein we describe the heterologous expression of staP, staC, and rebC in Escherichia coli and the activity of the corresponding enzymes in constructing the two distinct six-ring scaffolds. StaP is a cytochrome P450 enzyme, requiring dioxygen, ferredoxin, flavodoxin NADP(+)-reductase, and NAD(P)H for activity. StaP on its own converts chromopyrrolic acid into three aglycone products, K252c, arcyriaflavin A, and 7-hydroxy-K252c; in the presence of StaC, K252c is the predominant product, while the presence of RebC directs formation of arcyriaflavin A. (18)O-Labeling studies indicate that the oxygen(s) of the pyrrolinone and maleimide functionalities of the aglycones formed are all derived from dioxygen. This work allowed for the in vitro reconstitution of the full biosynthetic pathway from l-tryptophan to the staurosporine and rebeccamycin aglycones, K252c and 1,11-dichloroarcyriaflavin A.     

蝴蝶霉素及其类似物的化学合成进展

蝴蝶霉素是一种新型的天然抗生素,由于具有特殊的抗肿瘤活性而引起了人们的关注。然而,由于一些不利因素导致蝴蝶霉素无法直接运用于临床。为了寻找活性更好的药物先导化合物,人们对蝴蝶霉素的结构进行修饰和改造,通过生物方法和化学方法,合成了大量的类似物。本文将从化学合成角度出发,立足蝴蝶霉素及其类似物结构构造的关键步骤,对近年来的合成研究进行综述。     

Cloning and characterization of an environmental DNA-derived gene cluster that encodes the biosynthesis of the antitumor substance BE-54017

Soil is predicted to contain thousands of unique bacterial species per gram. Soil DNA libraries represent large reservoirs of biosynthetic diversity from which diverse secondary metabolite gene clusters can be recovered and studied. The screening of an archived soil DNA library using primers designed to target oxytryptophan dimerization genes allowed us to identify and functionally characterize the first indolotryptoline biosynthetic gene cluster. The recovery and heterologous expression of an environmental DNA-derived gene cluster encoding the biosynthesis of the antitumor substance BE-54017 is reported here. Transposon mutagenesis identified two monooxygenases, AbeX1 and AbeX2, as being responsible for the transformation of an indolocarbazole precursor into the indolotryptoline core of BE-54017.     

Indolocarbazole natural products: occurrence, biosynthesis, and biological activity

The indolocarbazole family of natural products, including the biosynthetically related bisindolylmaleimides, is reviewed (with 316 references cited). The isolation of indolocarbazoles from natural sources and the biosynthesis of this class of compounds are thoroughly reviewed, including recent developments in molecular genetics, enzymology and metabolic engineering. The biological activities and underlying modes of action displayed by natural and synthetic indolocarbazoles is also presented, with an emphasis on the development of analogs that have entered clinical trials for its future use against cancer or other diseases.     

Natural product diversification using a non-natural cofactor analogue of S-adenosyl-L-methionine

Adenosine analogues bearing either 5'-aziridine or 5'-N-mustard electrophiles are methyltransferase-dependent DNA alkylating agents. We present here a novel synthetic cofactor bearing a pendant 5'-amino acid N-mustard. Unlike previously studied synthetic cofactors, this material is very efficiently used by the natural product biosynthetic enzyme rebeccamycin methyltransferase (RebM) to generate a number of new rebeccamycin analogues. These data promote the notion that natural product methyltransferases can be used with non-natural cofactors to enhance the molecular diversity of natural product analogues for drug discovery. To our knowledge, this is the first documentation of a biological methyltransferase, other than DNA methyltransferases, that can exploit such synthetic cofactors.     

Synthesis of Arcyriarubin A and Arcyriaflavin A via Cross-Coupling of Indolylboronic Acid with Dibromomaleimides

Arcyriarubin A was first isolated by Steglich in 1980; it is also the key intermediate in the synthesis of indolocarbazole compounds. A new synthetic approach to the natural products arcyriaflavin A and arcyriarubin A is described. The key step is a Suzuki cross-coupling reaction using indolylboronic acid as the starting material. The preparation of arcyriaflavin A was accomplished in eight steps from indole for a total yield of 21%.     

The biochemistry of lower fungi. IX. Synthesis of labeled precursors and biosynthesis of phoenicin and oosporein

The biosynthesis of phoenicine and of oosporeine by intact cells of Penicillium phoeniceum VAN BEYMA and of Chaetomium aureum CHIVERS respectively, has been investigated. Starting from acetic acid, biosynthetic sequences have been proposed; they are based on the incorporation of radioactivity into the two pigments of labelled, biochemically probable precursors. Orsellinic acid appears as a common intermediate, which is converted by multistep processes to 2,3,5-trihydroxytoluene or to 2,3,5,6-tetrahydroxytoluene. Oxidative coupling of two molecules of the triphenol furnishes the reduced form of phoenicine. Similarly, coupling of two molecules of the tetraphenol gives leuco-oosporeine. Both leuco-derivatives are easily dehydrogenated, under physiological conditions, with formation of the diquinones. Coupling occurs when the monophenyl derivatives contain the required number of OH groups in suitable positions.     

Highly convergent synthesis of a rebeccamycin analog with benzothioeno(2,3-a)pyrrolo(3,4-c)carbazole as the aglycone

A highly convergent, scalable synthesis of the rebeccamycin analog 2 was demonstrated in seven steps and 31% overall yield based on the N-protected building block dibromomaleimide 7. The practical synthesis of other two building blocks, 5,6-difluoro-3-benzothiopheneboronic acid 6 and 5,6-difluoroindole 8, is described.     

Synthesis and structures of two novel indolo[3,2-b] carbazole derivatives

Indolocarbazole derivatives have already been reported to be good organic semiconductor candidates. The knowledge of the relationship between the structure and packing of molecules in crystal is indispensable in design of high performance organic semiconductor materials. Two new indolocarbazole derivatives, 2,8-dibromo-5,11-di-[4-(isoindole-1,3-dione-2-yl)butyl]indolo[3,2-b]carbazole (I) and 2,8,6,12-tetrabromo-5,11-di-(4-chlorobutyl)indolo[3,2-b]carbazole (II) have been synthesized and the crystal structures have been studied. The dichloromethane solvate of (I), C₄₂H₃₂Br₂N₄O₄ · 2CH₂Cl₂, is monoclinic, space groups P2₁/n. Unit cell parameters are a = 11.6847(2), b = 12.6942(2), c = 13.7899(2) Å, β = 91.8220(10)°. Unlike other indolo[3,2-b]carbazole derivatives, there is no any π–π stacking between the indolocarbazole backbone of two adjacent molecules in the crystal. Since the isoindole-1,3-dione-2-yl is introduced in 5- and 11-positions in the molecule, the intermolecular short contacts mainly localize in between the pendant groups of the neighboring indolocarbazole molecules. The compound (II) is also monoclinic with P2₁/c space groups. Unit cell parameters are a = 4.6427(9), b = 11.425(2), c = 24.511(4) Å, β = 93.47(1)°. In contrast with compound (I), the molecules of (II) possess strong face-to-face π–π stacking. The crystal structures were studied in detail. It is concluded that linear pedant groups benefit to co-facial π–π interaction. Additionally, the molecule electronic spectra were studied by quantum chemistry theoretical calculation.     

吲哚咔唑异构体的电子结构和光学性质

分别采用密度泛函理论(DFT)和单激发组态相互作用(CIS),在6-31G(d,p)基组水平上优化了5个吲哚咔唑分子的基态和激发态结构.在此结构的基础上,用含时密度泛函理论(TD-DFT)在相同基组水平和极化连续介质模型(PCM)下计算了模型分子的吸收和发射光谱.这几个吲哚咔唑异构体的发射光谱有明显的差别,如异构体5([3,2-b]型)有较大的振子强度,但是相对于其他异构体,其发射能量最小;异构体4([3,2-a]型)的发射能量最大;异构体2([2,3-b]型)的最大振子强度在250-450 nm范围内,与其他几个分子相比为最小.这主要是由分子的激发态几何变化和轨道能级的不同导致的.本文还考察了这类分子的一阶超极化率,结果显示5个分子极化率在同一水平,但静态第一超极化率(β0)有明显差别,异构体2的β0值最大.     

Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids austinol and dehydroaustinol in Aspergillus nidulans

Meroterpenoids are a class of fungal natural products that are produced from polyketide and terpenoid precursors. An understanding of meroterpenoid biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. The filamentous fungus Aspergillus nidulans has previously been found to produce two meroterpenoids, austinol and dehydroaustinol. Using targeted deletions that we created, we have determined that, surprisingly, two separate gene clusters are required for meroterpenoid biosynthesis. One is a cluster of four genes including a polyketide synthase gene, ausA. The second is a cluster of 10 additional genes including a prenyltransferase gene, ausN, located on a separate chromosome. Chemical analysis of mutant extracts enabled us to isolate 3,5-dimethylorsellinic acid and 10 additional meroterpenoids that are either intermediates or shunt products from the biosynthetic pathway. Six of them were identified as novel meroterpenoids in this study. Our data, in aggregate, allow us to propose a complete biosynthetic pathway for the A. nidulans meroterpenoids.     

Comparative metabolomics reveals biogenesis of ascarosides, a modular library of small-molecule signals in C. elegans

In the model organism Caenorhabditis elegans, a family of endogenous small molecules, the ascarosides function as key regulators of developmental timing and behavior that act upstream of conserved signaling pathways. The ascarosides are based on the dideoxysugar ascarylose, which is linked to fatty-acid-like side chains of varying lengths derived from peroxisomal β-oxidation. Despite the importance of ascarosides for many aspects of C. elegans biology, knowledge of their structures, biosynthesis, and homeostasis remains incomplete. We used an MS/MS-based screen to profile ascarosides in C. elegans wild-type and mutant metabolomes, which revealed a much greater structural diversity of ascaroside derivatives than previously reported. Comparison of the metabolomes from wild-type and a series of peroxisomal β-oxidation mutants showed that the enoyl CoA-hydratase MAOC-1 serves an important role in ascaroside biosynthesis and clarified the functions of two other enzymes, ACOX-1 and DHS-28. We show that, following peroxisomal β-oxidation, the ascarosides are selectively derivatized with moieties of varied biogenetic origin and that such modifications can dramatically affect biological activity, producing signaling molecules active at low femtomolar concentrations. Based on these results, the ascarosides appear as a modular library of small-molecule signals, integrating building blocks from three major metabolic pathways: carbohydrate metabolism, peroxisomal β-oxidation of fatty acids, and amino acid catabolism. Our screen further demonstrates that ascaroside biosynthesis is directly affected by nutritional status and that excretion of the final products is highly selective.     

Synthesis of indolo[2,3-a]carbazole glycoside analogs of rebeccamycin: inhibitors of cyclin D1-CDK4

The synthesis and structure-activity relationships of a new series of indolo[2,3-a]carbazole glycosides, analogs of rebeccamycin, derived from the natural sugars (glucose, fucose, mannose, xylose, rhamnose, and galactose) is described.     

An indolocarbazole-bridged macrocyclic porphyrin dimer having homotropic allosterism with inhibitory control

A macrocyclic host, a pair of zinc porphyrins bridged by two anion-acceptable indolocarbazole moieties, has shown strong positive homotropic allosterism upon anionic guest bindings with an inhibitory control mechanism by DABCO addition.