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Ben Shen - One of the best experts on this subject based on the ideXlab platform.
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genome mining of micromonospora yangpuensis dsm 45577 as a producer of an anthraquinone fused Enediyne
Organic Letters, 2017Co-Authors: Xiaohui Yan, Chin-yuan Chang, Dong Yang, Jianjun Chen, Ajeeth Adhikari, Ivana Crnovcic, Nan Wang, Christoph Rader, Ben ShenAbstract:A new anthraquinone-fused Enediyne, yangpumicin A (YPM A, 1), along with four Bergman cyclization congeners (YPM B–E, 2–5), was isolated from Micromonospora yangpuensis DSM 45577 after mining Enediyne biosynthetic gene clusters from public actinobacterial genome databases and prioritizing the hits by an Enediyne genome neighborhood network analysis for discovery. YPM A is potent against a broad spectrum of human cancer cell lines. The discovery of 1 provides new opportunities for the functionalization of Enediynes to develop new conjugation chemistries for antibody–drug conjugates.
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Predictive Model for Epoxide Hydrolase-Generated Stereochemistry in the Biosynthesis of Nine-Membered Enediyne Antitumor Antibiotics
2016Co-Authors: Geoffrey P. Horsman, Anna Lechner, Yasuo Ohnishi, Bradley S. Moore, Ben ShenAbstract:Nine-membered Enediyne antitumor antibiotics C-1027, neocarzinostatin (NCS), and kedarcidin (KED) possess Enediyne cores to which activity-modulating peripheral moieties are attached via (R)- or (S)-vicinal diols. We have previously shown that this stereochemical difference arises from hydrolysis of epoxide precursors by epoxide hydrolases (EHs) with different regioselectivities. The inverting EHs, such as SgcF, hydrolyze an (S)-epoxide substrate to yield an (R)-diol in C-1027 biosynthesis, whereas the retaining EHs, such as NcsF2 and KedF, hydrolyze an (S)-epoxide substrate to yield an (S)-diol in NCS and KED biosynthesis. We now report the characterization of a series of EH mutants and provide a predictive model for EH regioselectivity in the biosynthesis of the nine-membered Enediyne antitumor antibiotics. A W236Y mutation in SgcF increased the retaining activity toward (S)-styrene oxide by 3-fold, and a W236Y/Q237M double mutation in SgcF, mimicking NcsF2 and KedF, resulted in a 20-fold increase in the retaining activity. To test the predictive utility of these mutations, two putative Enediyne biosynthesis-associated EHs were identified by genome mining and confirmed as inverting enzymes, SpoF from Salinospora tropica CNB-440 and SgrF (SGR_625) from Streptomyces griseus IFO 13350. Finally, phylogenetic analysis of EHs revealed a familial classification according to inverting versus retaining activity. Taken together, these results provide a predictive model for vicinal diol stereochemistry in Enediyne biosynthesis and set the stage for further elucidating the origins of EH regioselectivity
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Enediynes exploration of microbial genomics to discover new anticancer drug leads
Bioorganic & Medicinal Chemistry Letters, 2015Co-Authors: Ben Shen, Tingting Huang, Jeffrey D. Rudolf, Xiaohui Yan, Dong Yang, Qihui Teng, Jeremy R LohmanAbstract:The Enediyne natural products have been explored for their phenomenal cytotoxicity. The development of Enediynes into anticancer drugs has been successfully achieved through the utilization of polymer- and antibody–drug conjugates (ADCs) as drug delivery systems. An increasing inventory of Enediynes would benefit current application of ADCs in many oncology programs. Innovations in expanding the Enediyne inventory should take advantage of the current knowledge of Enediyne biosynthesis and post-genomics technologies. Bioinformatics analysis of microbial genomes reveals that Enediynes are underexplored, in particular from Actinomycetales. This digest highlights the emerging opportunities to explore microbial genomics for the discovery of novel Enediyne natural products.
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cloning and sequencing of the kedarcidin biosynthetic gene cluster from streptoalloteichus sp atcc 53650 revealing new insights into biosynthesis of the Enediyne family of antitumor antibiotics
Molecular BioSystems, 2013Co-Authors: Jeremy R Lohman, Shengxiong Huang, Geoffrey P Horsman, Paul E Dilfer, Yihua Chen, Evelyn Wendtpienkowski, Tingting Huang, Ben ShenAbstract:Enediyne natural product biosynthesis is characterized by a convergence of multiple pathways, generating unique peripheral moieties that are appended onto the distinctive Enediyne core. Kedarcidin (KED) possesses two unique peripheral moieties, a (R)-2-aza-3-chloro-β-tyrosine and an iso-propoxy-bearing 2-naphthonate moiety, as well as two deoxysugars. The appendage pattern of these peripheral moieties to the Enediyne core in KED differs from the other Enediynes studied to date with respect to stereochemical configuration. To investigate the biosynthesis of these moieties and expand our understanding of Enediyne core formation, the biosynthetic gene cluster for KED was cloned from Streptoalloteichus sp. ATCC 53650 and sequenced. Bioinformatics analysis of the ked cluster revealed the presence of the conserved genes encoding for Enediyne core biosynthesis, type I and type II polyketide synthase loci likely responsible for 2-aza-L-tyrosine and 3,6,8-trihydroxy-2-naphthonate formation, and enzymes known for deoxysugar biosynthesis. Genes homologous to those responsible for the biosynthesis, activation, and coupling of the L-tyrosine-derived moieties from C-1027 and maduropeptin and of the naphthonate moiety from neocarzinostatin are present in the ked cluster, supporting 2-aza-L-tyrosine and 3,6,8-trihydroxy-2-naphthoic acid as precursors, respectively, for the (R)-2-aza-3-chloro-β-tyrosine and the 2-naphthonate moieties in KED biosynthesis.
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polyketide synthase chemistry does not direct biosynthetic divergence between 9 and 10 membered Enediynes
Proceedings of the National Academy of Sciences of the United States of America, 2010Co-Authors: Geoffrey P Horsman, Yihua Chen, Ben ShenAbstract:Enediynes are potent antitumor antibiotics that are classified as 9- or 10-membered according to the size of the Enediyne core structure. However, almost nothing is known about Enediyne core biosynthesis, and the determinants of 9- versus 10-membered Enediyne core biosynthetic divergence remain elusive. Previous work identified Enediyne-specific polyketide synthases (PKSEs) that can be phylogenetically distinguished as being involved in 9- versus 10-membered Enediyne biosynthesis, suggesting that biosynthetic divergence might originate from differing PKSE chemistries. Recent in vitro studies have identified several compounds produced by the PKSE and associated thioesterase (TE), but condition-dependent product profiles make it difficult to ascertain a true catalytic difference between 9- and 10-membered PKSE-TE systems. Here we report that PKSE chemistry does not direct 9- versus 10-membered Enediyne core biosynthetic divergence as revealed by comparing the products from three 9-membered and two 10-membered PKSE-TE systems under identical conditions using robust in vivo assays. Three independent experiments support a common catalytic function for 9- and 10-membered PKSEs by the production of a heptaene metabolite from: (i) all five cognate PKSE-TE pairs in Escherichia coli; (ii) the C-1027 and calicheamicin cognate PKSE-TEs in Streptomyces lividans K4-114; and (iii) selected native producers of both 9- and 10-membered Enediynes. Furthermore, PKSEs and TEs from different 9- and 10-membered Enediyne biosynthetic machineries are freely interchangeable, revealing that 9- versus 10-membered Enediyne core biosynthetic divergence occurs beyond the PKSE-TE level. These findings establish a starting point for determining the origins of this biosynthetic divergence.
Jeremy R Lohman - One of the best experts on this subject based on the ideXlab platform.
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Structural Insights into the Free-Standing Condensation Enzyme SgcC5 Catalyzing Ester-Bond Formation in the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027.
Biochemistry, 2018Co-Authors: Chin-yuan Chang, Jeremy R Lohman, Tingting Huang, Karolina Michalska, Lance Bigelow, Jeffrey D. Rudolf, Robert Jedrzejczak, Xiaohui Yan, Gyorgy BabniggAbstract:C-1027 is a chromoprotein Enediyne antitumor antibiotic, consisting of the CagA apoprotein and the C-1027 chromophore. The C-1027 chromophore features a nine-membered Enediyne core appended with three peripheral moieties, including an (S)-3-chloro-5-hydroxy-β-tyrosine. In a convergent biosynthesis of the C-1027 chromophore, the (S)-3-chloro-5-hydroxy-β-tyrosine moiety is appended to the Enediyne core by the free-standing condensation enzyme SgcC5. Unlike canonical condensation domains from the modular nonribosomal peptide synthetases that catalyze amide-bond formation, SgcC5 catalyzes ester-bond formation, as demonstrated in vitro, between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the Enediyne core as an acceptor substrate. Here, we report that (i) genes encoding SgcC5 homologues are widespread among both experimentally confirmed and bioinformatically predicted Enediyne biosynthetic gene clusters, forming a new clade of condensation enzymes, (ii) SgcC5 sh...
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Structural Insights into the Free-Standing Condensation Enzyme SgcC5 Catalyzing Ester-Bond Formation in the Biosynthesis of the Enediyne Antitumor Antibiotic C‑1027
2018Co-Authors: Chin-yuan Chang, Jeremy R Lohman, Tingting Huang, Karolina Michalska, Lance Bigelow, Jeffrey D. Rudolf, Robert Jedrzejczak, Xiaohui Yan, Gyorgy BabniggAbstract:C-1027 is a chromoprotein Enediyne antitumor antibiotic, consisting of the CagA apoprotein and the C-1027 chromophore. The C-1027 chromophore features a nine-membered Enediyne core appended with three peripheral moieties, including an (S)-3-chloro-5-hydroxy-β-tyrosine. In a convergent biosynthesis of the C-1027 chromophore, the (S)-3-chloro-5-hydroxy-β-tyrosine moiety is appended to the Enediyne core by the free-standing condensation enzyme SgcC5. Unlike canonical condensation domains from the modular nonribosomal peptide synthetases that catalyze amide-bond formation, SgcC5 catalyzes ester-bond formation, as demonstrated in vitro, between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the Enediyne core as an acceptor substrate. Here, we report that (i) genes encoding SgcC5 homologues are widespread among both experimentally confirmed and bioinformatically predicted Enediyne biosynthetic gene clusters, forming a new clade of condensation enzymes, (ii) SgcC5 shares a similar overall structure with the canonical condensation domains but forms a homodimer in solution, the active site of which is located in a cavity rather than a tunnel typically seen in condensation domains, and (iii) the catalytic histidine of SgcC5 activates the 2-hydroxyl group, while a hydrogen-bond network in SgcC5 prefers the R-enantiomer of the acceptor substrate, accounting for the regio- and stereospecific ester-bond formation between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol upon acid–base catalysis. These findings expand the catalytic repertoire and reveal new insights into the structure and mechanism of condensation enzymes
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Crystal Structure of Thioesterase SgcE10 Supporting Common Polyene Intermediates in 9- and 10-Membered Enediyne Core Biosynthesis
2017Co-Authors: Thibault Annaval, Jeremy R Lohman, Chin-yuan Chang, Lance Bigelow, Jeffrey D. Rudolf, Robert Jedrzejczak, Gyorgy Babnigg, Youngchang Kim, Andrzej Joachimiak, George N. PhillipsAbstract:Enediynes are potent natural product anticancer antibiotics, and are classified as 9- or 10-membered according to the size of their Enediyne core carbon skeleton. Both 9- and 10-membered Enediyne cores are biosynthesized by the Enediyne polyketide synthase (PKSE), thioesterase (TE), and PKSE-associated enzymes. Although the divergence between 9- and 10-membered Enediyne core biosynthesis remains unclear, it has been observed that nascent polyketide intermediates, tethered to the acyl carrier protein (ACP) domain of PKSE, could be released by TE in the absence of the PKSE-associated enzymes. In this study, we determined the crystal structure of SgcE10, the TE that participates in the biosynthesis of the 9-membered Enediyne C-1027. Structural comparison of SgcE10 with CalE7 and DynE7, two TEs that participate in the biosynthesis of the 10-membered Enediynes calicheamicin and dynemicin, respectively, revealed that they share a common α/β hot-dog fold. The amino acids involved in both substrate binding and catalysis are conserved among SgcE10, CalE7, and DynE7. The volume and the shape of the substrate-binding channel and active site in SgcE10, CalE7, and DynE7 confirm that TEs from both 9- and 10-membered Enediyne biosynthetic machineries bind the linear form of similar ACP-tethered polyene intermediates. Taken together, these findings further support the proposal that the divergence between 9- and 10-membered Enediyne core biosynthesis occurs beyond PKSE and TE catalysis
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Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered Enediyne antitumor antibiotic C-1027
The Journal of Antibiotics, 2016Co-Authors: Tingting Huang, Jeremy R Lohman, Chin-yuan Chang, Jeffrey D. Rudolf, Xiaohui Yan, Dong Yang, Ivana Crnovcic, Youngchang Kim, Changsoo Chang, Lance BigelowAbstract:Comparative analysis of the Enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the Enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into Enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus . SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other Enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered Enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered Enediyne core biosynthesis.
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Strain Prioritization and Genome Mining for Enediyne Natural Products
American Society for Microbiology, 2016Co-Authors: Xiaohui Yan, Tingting Huang, Jeffrey D. Rudolf, Dong Yang, Qihui Teng, Ivana Crnovčičć, Jeremy R LohmanAbstract:The Enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 Enediynes have been structurally characterized to date. Here we report a genome survey of 3,400 actinomycetes, identifying 81 strains that harbor genes encoding the Enediyne polyketide synthase cassettes that could be grouped into 28 distinct clades based on phylogenetic analysis. Genome sequencing of 31 representative strains confirmed that each clade harbors a distinct Enediyne biosynthetic gene cluster. A genome neighborhood network allows prediction of new structural features and biosynthetic insights that could be exploited for Enediyne discovery. We confirmed one clade as new C-1027 producers, with a significantly higher C-1027 titer than the original producer, and discovered a new family of Enediyne natural products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a broad spectrum of cancer cell lines. Our results demonstrate the feasibility of rapid discovery of new Enediynes from a large strain collection
Mauro G. Da Silva - One of the best experts on this subject based on the ideXlab platform.
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Synthesis and evaluation of cytotoxic activity derived 2,3-diyne-1,4-naphthoquinones
Universidade Federal de Mato Grosso do Sul, 2012Co-Authors: Mauro G. Da Silva, Tania M. S. Silva, Celso De A. Camara, Anderson C. S. Feitosa, Claudia Do Ó PessoaAbstract:In the present study ten 2,3-diyne-1,4-naphthoquinone derivatives (3a-j) were synthesized by Sonogashira coupling reaction between the 2,3-dibromo-1,4-naphthoquinone (2) and several functionalized terminal alkynes using a catalytic complex of palladium (II) and CuI. Alkynes are among phenylacetylene, 1-ethyl-4-methoxybenzene, 2-methyl-3-butyn-2-ol, 1-ethynyl-1-cyclohexanol, 4-pentyn-2-ol, 4-pentyn-1-ol, 1-pentyne, 1-hexyne, 1-decyne and 1-octyne. The yields of products obtained ranged 15 to 55%. The Enediynes having hydroxyl groups, in their structures such as 2,3-di(3-hydroxy-3-methylbut-1-in-1-yl)-, 2,3-di[(1-hydroxycyclohexyl)ethynyl]- and 2,3-di(5-hydroxypent-1-yl)-1,4-naphthoquinone were subjected to acetylation reaction using acetic anhydride and montmorillonite clay K-10 under sonication, thereby obtaining three new Enediyne derivatives (3c’, d’ and f’) with yields ranging from 56 to 71%. The compounds were all characterized by 1H NMR and 13C NMR spectra, IR and MS-LC. These compounds containing the 1,4-naphthoquinone nucleus and acetylenic substituents in the quinonoid ring form a Enediyne system (Z-3-ene-1,5-diyne) highly reactive, possibly subject to Bergman cycloaromatization, with potential antitumor activity. The Enediynes underwent evaluation of the cytotoxic potential against three tumor cell lines, OVCAR-8 (ovarian adenocarcinoma - human), PC-3M (metastatic prostate cancer - human), NCI-H358M (bronchoalveolar lung carcinoma - human), presenting, in general, satisfactory results for inhibition of cell growth. The compound 2,3-di(3-hydroxy-3-methylbut-1-in-yl)-1,4-naphthoquinone (3c) where said among the substances analyzed by presenting a lower IC50 (˂ 2 µg/mL) for three cell lines tested, which is characterized as a potent cytotoxic agent.
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Síntese de derivados 2,3-diino-1,4-naftoquinonas usando a reação de Sonogashira e avaliação da atividade citotóxica.
Universidade Federal Rural de Pernambuco, 2012Co-Authors: Mauro G. Da SilvaAbstract:No presente trabalho foram obtidos dez derivados 2,3-diino-1,4- naftoquinonas, entre estes sete são inéditos na literatura, empregando a reação de acoplamento de Sonogashira entre o 2,3-dibromo-1,4-naftoquinona e diversos alquinos terminais funcionalizados, utilizando um complexo catalítico de paládio (II) e CuI. Entre os alquinos estão o fenilacetileno, o 4-metoxifenilacetileno, o 2-metil-3- butin-2-ol, o 1-etinil-1-cicloexanol, o 4-pentin-2-ol, o 4-pentin-1-ol, o 1-pentino, o 1- hexino, o 1-octino e o 1-decino. Os rendimentos dos produtos obtidos variaram entre 15-55%. Os enediinos que possuem grupos hidroxilas presentes em suas estruturas, como o 2,3-di(3-hidroxi-3-metilbut-1-in-il)-, o 2,3-di[(1-hidroxicicloexil)etinil]- e o 2,3- di(5-hidroxipent-1-il)-1,4-naftoquinona, foram submetidos à reação de acetilação utilizando anidrido acético e argila montmorillonita K-10 em ultrassom, obtendo assim, três novos derivados enediinos com rendimentos que variaram de 56-71%. Os compostos obtidos foram todos caracterizados por espectros de RMN 1H e RMN 13C, LC-MS e IV. Estes compostos contendo o núcleo 1,4-naftoquinona e substituintes acetilênicos no anel quinônico formam um sistema enediino (Z-3-eno-1,5-diino) altamente reativo, possivelmente sujeito a cicloaromatização de Bergman, com potencial atividade antitumoral. Os enediinos foram submetidos à avaliação do potencial citotóxico em três linhagens de células tumorais, OVCAR-8 (adenocarcinoma de ovário humano), PC-3M (carcinoma de próstata metastático humano), NCI-H358M (carcinoma bronquioalveolar de pulmão humano, apresentando, no geral, resultados satisfatórios para inibição do crescimento celular. O composto 2,3-di(3-hidroxi-3-metilbut-1-in-1-il)-1,4-naftoquinona se destacou dentre as substâncias analisadas por apresentar menor CI50 (˂ 2 μg/mL) para as três linhagens de células testadas, o que o caracteriza como potente agente citotóxico.In the present study ten 2,3-diyne-1,4-naphthoquinone derivatives were synthesized by Sonogashira coupling reaction between the 2,3-dibromo-1,4- naphthoquinone and several functionalized terminal alkynes using a catalytic complex of palladium (II) and CuI. Alkynes are among phenylacetylene, 1-ethyl-4- methoxybenzene, 2-methyl-3-butyn-2-ol, 1-ethynyl-1-cyclohexanol, 4-pentyn-2-ol, 4- pentyn-1-ol, 1-pentyne, 1-hexyne, 1-octyne and 1-decyne. The yields of products obtained ranged 15 to 55%. The Enediynes having hydroxyl groups, in their structures such as 2,3-di(3-hydroxy-3-methylbut-1-yn-1-yl)-, 2,3-di[(1- hydroxycyclohexyl)ethynyl]- and 2,3-di(5-hydroxypent-1-yl)-1,4-naphthoquinone were subjected to acetylation reaction using acetic anhydride and montmorillonite clay K- 10 under sonication, thereby obtaining three new Enediyne derivatives with yields ranging from 56 to 71%. The compounds were all characterized by 1H NMR and 13C NMR spectra, IR and MS-LC. These compounds containing the 1,4-naphthoquinone nucleus and acetylenic substituents in the quinonoid ring form a Enediyne system (Z-3-ene-1,5-diyne) highly reactive, possibly subject to Bergman cycloaromatization, with potential antitumor activity. The Enediynes underwent evaluation of the cytotoxic potential against three tumor cell lines, OVCAR-8 (ovarian adenocarcinoma - human), PC-3M (metastatic prostate cancer - human), NCI-H358M (bronchoalveolar lung carcinoma - human), presenting, in general, satisfactory results for inhibition of cell growth. The compound 2,3-di(3-hydroxy-3-methylbut-1-yn-yl)-1,4-naphthoquinone where said among the substances analyzed by presenting a lower IC50 (˂ 2 μg/mL) for three cell lines tested, which is characterized as a potent cytotoxic agent
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Síntese de derivados 2,3-diino-1,4-naftoquinonas usando a reação de Sonogashira e avaliação da atividade citotóxica
Programa de Pós-Graduação em Química, 2012Co-Authors: Mauro G. Da SilvaAbstract:No presente trabalho foram obtidos dez derivados 2,3-diino-1,4- naftoquinonas, entre estes sete são inéditos na literatura, empregando a reação de acoplamento de Sonogashira entre o 2,3-dibromo-1,4-naftoquinona e diversos alquinos terminais funcionalizados, utilizando um complexo catalítico de paládio (II) e CuI. Entre os alquinos estão o fenilacetileno, o 4-metoxifenilacetileno, o 2-metil-3- butin-2-ol, o 1-etinil-1-cicloexanol, o 4-pentin-2-ol, o 4-pentin-1-ol, o 1-pentino, o 1- hexino, o 1-octino e o 1-decino. Os rendimentos dos produtos obtidos variaram entre 15-55%. Os enediinos que possuem grupos hidroxilas presentes em suas estruturas, como o 2,3-di(3-hidroxi-3-metilbut-1-in-il)-, o 2,3-di[(1-hidroxicicloexil)etinil]- e o 2,3- di(5-hidroxipent-1-il)-1,4-naftoquinona, foram submetidos à reação de acetilação utilizando anidrido acético e argila montmorillonita K-10 em ultrassom, obtendo assim, três novos derivados enediinos com rendimentos que variaram de 56-71%. Os compostos obtidos foram todos caracterizados por espectros de RMN 1H e RMN 13C, LC-MS e IV. Estes compostos contendo o núcleo 1,4-naftoquinona e substituintes acetilênicos no anel quinônico formam um sistema enediino (Z-3-eno-1,5-diino) altamente reativo, possivelmente sujeito a cicloaromatização de Bergman, com potencial atividade antitumoral. Os enediinos foram submetidos à avaliação do potencial citotóxico em três linhagens de células tumorais, OVCAR-8 (adenocarcinoma de ovário – humano), PC-3M (carcinoma de próstata metastático – humano), NCI-H358M (carcinoma bronquioalveolar de pulmão – humano, apresentando, no geral, resultados satisfatórios para inibição do crescimento celular. O composto 2,3-di(3-hidroxi-3-metilbut-1-in-1-il)-1,4-naftoquinona se destacou dentre as substâncias analisadas por apresentar menor CI50 (˂ 2 μg/mL) para as três linhagens de células testadas, o que o caracteriza como potente agente citotóxico.In the present study ten 2,3-diyne-1,4-naphthoquinone derivatives were synthesized by Sonogashira coupling reaction between the 2,3-dibromo-1,4- naphthoquinone and several functionalized terminal alkynes using a catalytic complex of palladium (II) and CuI. Alkynes are among phenylacetylene, 1-ethyl-4- methoxybenzene, 2-methyl-3-butyn-2-ol, 1-ethynyl-1-cyclohexanol, 4-pentyn-2-ol, 4- pentyn-1-ol, 1-pentyne, 1-hexyne, 1-octyne and 1-decyne. The yields of products obtained ranged 15 to 55%. The Enediynes having hydroxyl groups, in their structures such as 2,3-di(3-hydroxy-3-methylbut-1-yn-1-yl)-, 2,3-di[(1- hydroxycyclohexyl)ethynyl]- and 2,3-di(5-hydroxypent-1-yl)-1,4-naphthoquinone were subjected to acetylation reaction using acetic anhydride and montmorillonite clay K- 10 under sonication, thereby obtaining three new Enediyne derivatives with yields ranging from 56 to 71%. The compounds were all characterized by 1H NMR and 13C NMR spectra, IR and MS-LC. These compounds containing the 1,4-naphthoquinone nucleus and acetylenic substituents in the quinonoid ring form a Enediyne system (Z-3-ene-1,5-diyne) highly reactive, possibly subject to Bergman cycloaromatization, with potential antitumor activity. The Enediynes underwent evaluation of the cytotoxic potential against three tumor cell lines, OVCAR-8 (ovarian adenocarcinoma - human), PC-3M (metastatic prostate cancer - human), NCI-H358M (bronchoalveolar lung carcinoma - human), presenting, in general, satisfactory results for inhibition of cell growth. The compound 2,3-di(3-hydroxy-3-methylbut-1-yn-yl)-1,4-naphthoquinone where said among the substances analyzed by presenting a lower IC50 (˂ 2 μg/mL) for three cell lines tested, which is characterized as a potent cytotoxic agent.Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNP
Chin-yuan Chang - One of the best experts on this subject based on the ideXlab platform.
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Structural Insights into the Free-Standing Condensation Enzyme SgcC5 Catalyzing Ester-Bond Formation in the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027.
Biochemistry, 2018Co-Authors: Chin-yuan Chang, Jeremy R Lohman, Tingting Huang, Karolina Michalska, Lance Bigelow, Jeffrey D. Rudolf, Robert Jedrzejczak, Xiaohui Yan, Gyorgy BabniggAbstract:C-1027 is a chromoprotein Enediyne antitumor antibiotic, consisting of the CagA apoprotein and the C-1027 chromophore. The C-1027 chromophore features a nine-membered Enediyne core appended with three peripheral moieties, including an (S)-3-chloro-5-hydroxy-β-tyrosine. In a convergent biosynthesis of the C-1027 chromophore, the (S)-3-chloro-5-hydroxy-β-tyrosine moiety is appended to the Enediyne core by the free-standing condensation enzyme SgcC5. Unlike canonical condensation domains from the modular nonribosomal peptide synthetases that catalyze amide-bond formation, SgcC5 catalyzes ester-bond formation, as demonstrated in vitro, between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the Enediyne core as an acceptor substrate. Here, we report that (i) genes encoding SgcC5 homologues are widespread among both experimentally confirmed and bioinformatically predicted Enediyne biosynthetic gene clusters, forming a new clade of condensation enzymes, (ii) SgcC5 sh...
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Structural Insights into the Free-Standing Condensation Enzyme SgcC5 Catalyzing Ester-Bond Formation in the Biosynthesis of the Enediyne Antitumor Antibiotic C‑1027
2018Co-Authors: Chin-yuan Chang, Jeremy R Lohman, Tingting Huang, Karolina Michalska, Lance Bigelow, Jeffrey D. Rudolf, Robert Jedrzejczak, Xiaohui Yan, Gyorgy BabniggAbstract:C-1027 is a chromoprotein Enediyne antitumor antibiotic, consisting of the CagA apoprotein and the C-1027 chromophore. The C-1027 chromophore features a nine-membered Enediyne core appended with three peripheral moieties, including an (S)-3-chloro-5-hydroxy-β-tyrosine. In a convergent biosynthesis of the C-1027 chromophore, the (S)-3-chloro-5-hydroxy-β-tyrosine moiety is appended to the Enediyne core by the free-standing condensation enzyme SgcC5. Unlike canonical condensation domains from the modular nonribosomal peptide synthetases that catalyze amide-bond formation, SgcC5 catalyzes ester-bond formation, as demonstrated in vitro, between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the Enediyne core as an acceptor substrate. Here, we report that (i) genes encoding SgcC5 homologues are widespread among both experimentally confirmed and bioinformatically predicted Enediyne biosynthetic gene clusters, forming a new clade of condensation enzymes, (ii) SgcC5 shares a similar overall structure with the canonical condensation domains but forms a homodimer in solution, the active site of which is located in a cavity rather than a tunnel typically seen in condensation domains, and (iii) the catalytic histidine of SgcC5 activates the 2-hydroxyl group, while a hydrogen-bond network in SgcC5 prefers the R-enantiomer of the acceptor substrate, accounting for the regio- and stereospecific ester-bond formation between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol upon acid–base catalysis. These findings expand the catalytic repertoire and reveal new insights into the structure and mechanism of condensation enzymes
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genome mining of micromonospora yangpuensis dsm 45577 as a producer of an anthraquinone fused Enediyne
Organic Letters, 2017Co-Authors: Xiaohui Yan, Chin-yuan Chang, Dong Yang, Jianjun Chen, Ajeeth Adhikari, Ivana Crnovcic, Nan Wang, Christoph Rader, Ben ShenAbstract:A new anthraquinone-fused Enediyne, yangpumicin A (YPM A, 1), along with four Bergman cyclization congeners (YPM B–E, 2–5), was isolated from Micromonospora yangpuensis DSM 45577 after mining Enediyne biosynthetic gene clusters from public actinobacterial genome databases and prioritizing the hits by an Enediyne genome neighborhood network analysis for discovery. YPM A is potent against a broad spectrum of human cancer cell lines. The discovery of 1 provides new opportunities for the functionalization of Enediynes to develop new conjugation chemistries for antibody–drug conjugates.
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Crystal Structure of Thioesterase SgcE10 Supporting Common Polyene Intermediates in 9- and 10-Membered Enediyne Core Biosynthesis
2017Co-Authors: Thibault Annaval, Jeremy R Lohman, Chin-yuan Chang, Lance Bigelow, Jeffrey D. Rudolf, Robert Jedrzejczak, Gyorgy Babnigg, Youngchang Kim, Andrzej Joachimiak, George N. PhillipsAbstract:Enediynes are potent natural product anticancer antibiotics, and are classified as 9- or 10-membered according to the size of their Enediyne core carbon skeleton. Both 9- and 10-membered Enediyne cores are biosynthesized by the Enediyne polyketide synthase (PKSE), thioesterase (TE), and PKSE-associated enzymes. Although the divergence between 9- and 10-membered Enediyne core biosynthesis remains unclear, it has been observed that nascent polyketide intermediates, tethered to the acyl carrier protein (ACP) domain of PKSE, could be released by TE in the absence of the PKSE-associated enzymes. In this study, we determined the crystal structure of SgcE10, the TE that participates in the biosynthesis of the 9-membered Enediyne C-1027. Structural comparison of SgcE10 with CalE7 and DynE7, two TEs that participate in the biosynthesis of the 10-membered Enediynes calicheamicin and dynemicin, respectively, revealed that they share a common α/β hot-dog fold. The amino acids involved in both substrate binding and catalysis are conserved among SgcE10, CalE7, and DynE7. The volume and the shape of the substrate-binding channel and active site in SgcE10, CalE7, and DynE7 confirm that TEs from both 9- and 10-membered Enediyne biosynthetic machineries bind the linear form of similar ACP-tethered polyene intermediates. Taken together, these findings further support the proposal that the divergence between 9- and 10-membered Enediyne core biosynthesis occurs beyond PKSE and TE catalysis
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Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered Enediyne antitumor antibiotic C-1027
The Journal of Antibiotics, 2016Co-Authors: Tingting Huang, Jeremy R Lohman, Chin-yuan Chang, Jeffrey D. Rudolf, Xiaohui Yan, Dong Yang, Ivana Crnovcic, Youngchang Kim, Changsoo Chang, Lance BigelowAbstract:Comparative analysis of the Enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the Enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into Enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus . SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other Enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered Enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered Enediyne core biosynthesis.
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internal amide triggered cycloaromatization of maduropeptin like nine membered Enediyne
Chemical Communications, 2008Co-Authors: Yutaro Norizuki, Kazuo Komano, Itaru Sato, Masahiro HiramaAbstract:In the Masamune–Bergman cyclization of a nine-membered non-conjugated Enediyne with an internal, maduropeptin-like nucleophile, the exocyclic alkene migrated to form the nine-membered conjugated Enediyne, triggered by the intramolecular addition of the amide group; final aromatized products showed up to 85% yield.
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photochemical cycloaromatization of non benzenoid Enediynes
Angewandte Chemie, 1999Co-Authors: Toshio Kaneko, Miki Takahashi, Masahiro HiramaAbstract:An efficient photo-Bergman reaction of aliphatic Enediynes has been realized. Photolysis of 1 results in the formation of 4 in good yields along with [D2 ]3. Enediyne 4, which has never been isolated in the thermal reaction of 1, arises here by a retro-Bergman reaction of the diradical intermediate 2.
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Synthesis and chemistry of chromoprotein antitumor antibiotics: Nine-membered Enediynes are equilibrated with p-benzyne type biradicals
Pure and Applied Chemistry, 1997Co-Authors: Masahiro HiramaAbstract:The recent discovery of nine-membered cyclic Enediyne chromophores (1 for the antitumor antibiotics (2-1027; 2 for kedarcidin) stabilized by specific apoproteins prompted us to synthesize a highly strained carbocyclic core structure to elucidate the specific mechanism which prevents their spontaneous aromatization. We have achieved successful synthesis of Enediynes 10 and 14 as models of 1 and 2, respectively, and found the remarkable solvent dependence of the rate of cycloaromatization of 14. The kinetic data and the ESR spectra strongly indicate that the hydrogen abstraction rate of p- benzyne biradical 17 is slower than that of phenyl radical by a factor of 100, and that the equilibrium is virtually reached between 14 and 17 in CH3CN and CD2C12 at ambient temperature, which suggests a hypothesis that the chromophores 1 and 2 may also be equilibrated with their p-benzyne forms and are stabilized kinetically by specific apoproteins. Thus, those molecules may exist indefinitely if they remain free of hydrogen donor(s) in the holoprotein complex. The kinetics and energetics of Bergman cycloaromatization as well as our endeavours toward the total syntheses of 1 and 2 are disclosed.