Desde a descoberta da cisplatina várias tentativas têm sido feitas com o objetivo de desenvolver novos quimioterápicos com menor toxicidade e efeitos colaterais melhorados para tratar o câncer. Complexos de coordenação com metais de transição variados vêm sendo estudados buscando melhoras na biodisponibilidade, seletividade e efeitos adversos. Neste sentido, o presente trabalho consiste na síntese e caracterização estrutural de complexos de PdII e PtII com ligantes derivados de tiossemicarbazidas contendo o grupo fluoróforo pireno visando a obtenção de potenciais agentes antitumorais. Os agentes quelantes foram preparados a partir de reações de condensação entre o pirenocarboxaldeído e a tiossemicarbazida desejada resultando em compostos 1-pirenocarboxaldeído-N(3)-R-tiossemicarbazona, H2PrR, onde R = etil ou ciclohexil, Pr = pireno. A partir dos ligantes H2PrR foram realizadas as reações de complexação com os íons metálicos PdII e PtII, sendo possível obter duas classes de complexos com diferentes características: complexos monoméricos contendo ligantes clorido e trifenilfosfano do tipo [MCl(PPh3)(HPrR)] e complexos tetraméricos do tipo [M4(μ-S-PrR-κ3-C,N,S)4], onde M = PdII ou PtII, R = etil ou ciclohexil. Nas duas primeiras séries, o grupo R foi modificado por etil e ciclohexil para investigar a correlação entre lipoficilidade e atividade antiproliferativa, enquanto que o grupamento pireno foi incluído pensando que um maior número de unidades aromáticas possivelmente melhoraria a intercalação com o DNA e/ou ser utilizado como um marcador celular. A caracterização dos complexos envolveu técnicas como: análise elementar, espectroscopia na região do infravermelho e do UV-Vis, condutimetria, ressonância magnética nuclear (1H e 13C RMN) e difração de raios X em monocristal. As análises mostraram que os agentes complexantes podem atuar em diferentes modos coordenação tanto com relação à denticidade quanto à carga. A atividade antiproliferativa dos novos compostos de PdII e PtII foi determinada, sendo que vários deles apresentaram IC50 promissores contra células de câncer de ovário e, em muitos casos, as atividades observadas foram melhores do que a da cisplatina. Os dados obtidos indicam efeitos diferentes nos resultados de atividade biológica para os centros metálicos (Pd vs Pt) e ligantes utilizados (Etil vs Ciclohexil). Estudos de captação e distribuição celular mostraram que o complexo [PdCl(PPh3)(HPrCh)] atinge o núcleo celular. Com o intuito de verificar possíveis alvos biológicos, testes de interação com o DNA, ciclo celular e inibição da enzima Top IB foram realizados para os compostos. Os resultados do ciclo celular, mostraram uma maior inibição nos estádios S e G2/M para os complexos do tipo [PdCl(PPh3)(HPrR)]. Diante dos resultados obtidos, verificou-se que a Top IB é um dos alvos moleculares para os complexos do tipo [MCl(PPh3)(HPrR)], um mecanismo diferente da cisplatina. Estes resultados preliminares são bastante promissores e mostram que alguns dos complexos estudados neste trabalho apresentam-se como potenciais agentes para serem usados na terapia do câncer em combinação com os demais fármacos em uso clínico. / Since the discovery of cisplatin, many attepemts have been made to prepare new drugs with less cytotoxicity and side effects. Coordination complexes based on a variety of transition metals have been developed in the search for improved bioavailability, selectivity and reduced adverse side-effects. This work consists on the synthesis and structural characterization of PdII and PtII complexes with chelating compounds derived from thiosemicarbazides containing the pyrene fluorophore group aiming to obtain potential antitumor compounds. The chelating agents were prepared from condensation reactions between the pyrenocarboxaldehyde and the desired thiosemicarbazide resulting in 1-pyrenocarboxaldehyde-N (3) -R-thiosemicarbazone compounds, H2PrR, where R = ethyl or cyclohexyl. Complexation reactions with the metal ions PdII and PtII were carried out with the H2PrR ligands. It was possible to obtain two main classes of complexes with different characteristics: i) monomeric complexes containing chlorido and triphenylphosphane ligands of the type [MCl(PPh3)(HPrR)] and (ii) tetramer complexes of the type [{M(PrR)}4], where M = PdII or PtII and R = etyl ou cyclohexyl. In both series the R group was modified by ethyl and cyclohexyl in order to investigate the correlation between lipophilicity and antiproliferative activity, while the pyrene group was attached to the ligands with the belief that a higher number of aromatic units would improve DNA intercalation and/or to be used as an intracellular probe. The characterization of the complexes involved techniques such as: elemental analysis, infrared and UV-Vis spectroscopy, conductimetry, nuclear magnetic resonance (1H and 13C NMR) and single crystal X-ray diffraction. The antiproliferative activity of the novel PdII and PtII compounds have been determined, several of them showed promising IC50 against ovarian cancer cells, and in many cases the observed activities are better than that of cisplatin. The data obtained indicate different effects for the metal centers (Pd vs Pt) and the ligands used (ethyl vs cyclohexyl). Uptake and cellular distribution studies proved that the palladium complex [PdCl(PPh3)(HPrCh)] achieved the cell nucleus. In order to verify possible biological targets, interaction with DNA, cell cycle and inhibition experiments of the topoisomerase IB (Top IB) enzyme were performed for some compounds. Cell cycle results showed an inhibition at the S and G2/M stages for the complexes [PdCl(PPh3)(HPrR)]. Overall, the results indicated the Top IB enzyme as one of the targets of the complexes. These preliminary results are quite promising and show that some of the complexes studied here can be used in cancer therapy in combination with other anticancer drugs.

Le cancer est aujourd’hui un problème de santé majeur et fait l’objet de multiples recherches. De nombreuses molécules ont été synthétisées dans l’optique de trouver des médicaments plus efficaces, plus sélectifs et surtout présentant moins d’effets secondaire. Parmi ces molécules se trouvent les lamellarines. Les lamellarines sont des composés naturels d’origine marine ayant été isolés à partir du mollusque posobranche « Lamellaria ». Actuellement, plus de 35 lamellarines ont été isolées et identifiées et certaines d’entre-elles présentent des activités biologiques intéressantes. Parmi elles certaines sont efficaces contre des cellules cancéreuses de type MDR (Multi-Drug-Resistant). Dans le cadre de la recherche de nouveaux agents cytotoxiques et d’inhibiteurs de kinase toujours plus sélectifs, la structure des lamellarines a été simplifiée par réduction du nombre de cycles et par introduction de l’indole comme coeur de la molécule. Les activités biologiques, particulièrement intéressantes, sont également rapportées dans le document. / Cancer is nowadays a major problem of public health and is the subject of many researches. Numerous molecules have been synthetized with the aim of finding more efficient and selective drugs with less secondary effects. The lamellarins can be found among these molecules. Lamellarins are a family of marine alkaloids, isolated from the prosobranch mollusk « Lamellaria ». More than 35 lamellarins have been isolated to date and only a few show interesting bioactive properties. Moreover, these compounds have been reported for their efficiency in the treatement of multi-drug resistant (MDR). In the course to design original active products, the structure of lamellarins was simplified by reduction of the number of rings and the introduction of an indol as the core of the molecule. The biological activities are reported in the document and analysed.

Submitted by Haroudo Xavier Filho (haroudo.xavierfo@ufpe.br) on 2016-04-05T17:59:08Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE_SINARA MONICA VITALINO DE ALMEIDA_FINAL UNIFICADO BIBLIOTECA.pdf: 9803056 bytes, checksum: 68bd08234fdac2b45bf400b3ebd62957 (MD5) / Made available in DSpace on 2016-04-05T17:59:08Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE_SINARA MONICA VITALINO DE ALMEIDA_FINAL UNIFICADO BIBLIOTECA.pdf: 9803056 bytes, checksum: 68bd08234fdac2b45bf400b3ebd62957 (MD5) Previous issue date: 2015-07-23 / CAPES, CNPq / O câncer é, sem sombra de dúvidas, a doença mais temida pela população, em razão da sua alta incidência e elevadas taxas de mortalidade para determinados tipos da doença. Nas últimas décadas, os pesquisadores têm obtido avanços significativos no entendimento da patogênese, nas características e nas terapias do câncer. A quimioterapia é frequentemente o tratamento escolhido para muitos tipos de câncer e por este motivo a pesquisa por novos agentes quimioterápicos constitui um dos alicerces na luta contra o câncer. Os intercaladores orgânicos são compostos poliaromáticos que podem se inserir entre pares de bases adjacentes da dupla fita de DNA e inibir a síntese de ácido nucléico in vivo, essa propriedade é comumente observada em drogas anticâncer usadas na terapia clínica. Por isto, a descoberta de novos intercaladores do DNA tem sido considerada uma abordagem prática e um número expressivo de moléculas tem sido avaliado quanto às suas propriedades intercaladoras. Neste trabalho foram sintetizados novos agentes anticâncer tendo como molécula de partida o anel acridina. Foram sintetizados e caracterizados oito novos derivados da série 2-acridin-9-il-metileno-N-fenil-hidrazina-carbotioamida (3a-3h) com diferentes substituintes na porção fenil (não substituídos ou com substituintes elétrondoadores ou elétron-retiradores) e dois novos derivados da série 3-(acridin-9-il)-n-benzilideno-2- cianoacrilohidrazidas (AMTAC-01 e AMTAC-02). Os compostos foram avaliados quanto às suas propriedades intercaladoras ao ctDNA in vitro e atividades antiproliferativas contra linhagens de células tumorais de mama (MCF-7), ovário resistente a múltiplas drogas (NCI-ADR/RES), pulmão (NCI-H460), próstata (PC-3), cólon (HT29), ovário (OVCAR-03), rim (786-0), leucemia (K562) e glioma (U251). Foram investigadas alterações morfológicas induzidas por tratamento de células MCF-7 com o composto mais ativo da série 2-acridin-9-il-metileno-N-fenil-hidrazinacarbotioamida (3a) através de microscopias eletrônicas de transmissão, varredura e da análise de exposição de fosfatidilserina e fragmentação de DNA. Além disso, a atividade de inibição da topoisomerase IIa dos derivados 3-(acridin-9-il)-n-benzilideno-2-cianoacrilohidrazidas foi verificada e a ligação com ctDNA foi estudada por meio de espectroscopia de absorção em fluorescência. Todos os derivados produzidos das duas séries apresentaram interação com o DNA. Após o contato com DNA foram verificados efeitos hipercrômicos e hipocrômicos, bem como mudanças para o vermelho ou azul nos espectros de absorbância. Essas modificações são preditivas de formação de complexo entre DNA e derivado. As constantes de ligação calculadas estão entre 1.74 x 104 e 1.0 x 106 M-1 para os derivados 3a-3h e entre 2.3-2.5 x 106 M-1 para os AMTAC’s. Estes valores indicam alta afinidade pelos pares de base do DNA. Da série 2-acridin- 9-il-metileno-N-fenil-hidrazina-carbotioamida o composto mais eficiente para ligação in vitro com o DNA foi o derivado cloro-substituído (3f), enquanto o composto mais ativo no teste antiproliferativo foi o derivado não substituído na porção tiossemicarbazona (3a). Os valores de concentração letal para 50 % do número inicial de células para o derivado 3a contra as linhagens NCI-H460, MCF-7, U251, NCI-ADR/RES, HT-29 e PC-3 foram 43.41, 60.26, 68.93, 70.2, 70.24 e 72.95 μM, respectivamente. As análises por microscopias eletrônicas de varredura e transmissão de células MCF-7 tratadas com 60 μM do derivado 3a demonstraram alterações ultramorfológicas indicativas de autofagia: vacúolos com dupla membrana. Além disso, os derivados AMTAC-01 e AMTAC-02 foram mais ativos contra as linhagens tumorais de próstata e melanoma, respectivamente. Ambos os derivados apresentaram atividade inibidora topoisomerase IIa na concentração de 50 μM. Os resultados indicam que uma ligação eficiente ao DNA é uma condição necessária para atividade antitumoral e que os novos derivados híbridos de acridina apresentaram promissoras atividades antiproliferativa, ligadora do DNA e inibição da topoisomerase. / People fear cancer more than any other serious illness which can be explained by the high incidence and mortality rates for some types of cancer. In the last decades, significant advances were obtained regarding cancer pathogenesis, features and therapies. Chemotherapy is often the treatment of choice for many types of cancer and the search for new chemotherapeutic agents still plays a major role in the fight against cancer. Organic intercalators are poliaromatic compounds that are able to insert into DNA double strands and inhibit in vivo acid nucleic synthesis. This characteristic is, in general, observed in anticancer drugs, hence the discovery and development of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. In this work, new anticancer agents were synthetized based on acridine nucleus for structural modification using substituted thiosemicarbazide moieties. It were synthetized eight new (Z)-2-(acridin-9- ylmethylene)-N-phenylhydrazinecarbothioamide derivatives (3a-3h) presenting different substituents on phenyl ring (non-substituted and electron-donating or -withdrawing) and two new 3-(acridin-9-yl)-N-benzylidene-2-cyanoacrilohydrazide derivatives (AMTAC-01 and AMTAC-02). In vitro ctDNA interaction was assayed and antiproliferative activity was evaluated against cancer cell lines of glioma (U251), breast (MCF-7), ovary expressing phenotype multiple drugs resistance (NCI-ADR/RES), kidney (786–0), lung (NCI-H460), prostate, (PC-3), ovary (OVCAR-03), colon adenocarcinoma (HT-29) and chronic myeloid leukemia (K-562). It was investigated ultramorphological changes induced by 3a treatment on MCF-7 cells by transmission and scanning electron microscopies, besides the evaluation of phosphatidylserine externalization and DNA fragmentation. Topoisomerase IIa inhibitory activity of AMTAC’s was evaluated. ctDNA binding properties were performed with calf thymus DNA (ctDNA) by electronic absorption and fluorescence spectroscopies. Both hyperchromic and hypochromic effects, as well as red or blue shifts were demonstrated by addition of ctDNA to the derivatives. These spectroscopic alterations indicated formation of derivative-DNA complex. The calculated binding constants ranged from 1.74 x 104 to 1.0 x 106 M-1 for 3a-3h derivatives and 2.3-2.5 x 106 M-1 for AMTAC’s compounds. These values mean that the new acridine derivatives have high affinity to ctDNA. From (Z)-2-(acridin-9- ylmethylene)-N-phenylhydrazinecarbothioamide serie, the most efficient compound in in vitro binding to ctDNA was 3f, while the most active compound in antiproliferative assay was 3a. Regarding lethal concentration (LC50), compound 3a was lethal to NCI-H460, MCF-7, U251, NCI-ADR/RES, HT-29 and PC-3 cells on the respective concentrations: 43.41, 60.26, 68.93, 70.2, 70.24 and 72.95 μM. Scanning and transmission electron microscopies revealed that treatment with 60 μM of 3a induces morphological changes in MCF-7 cells indicating autophagy, such as vacuole with double membrane. On the other hand, antiproliferative assay demonstrated that AMTAC-01 and AMTAC-02 were most active against prostate and melanoma tumor cell lines, respectively. Both derivatives displayed potent topoisomerase IIα inhibitory activity at 50 μM. Taking together, these results indicates that an efficient binding is a necessary condition for antiproliferative activity. The new acridine hybrid derivatives showed promising DNA binding, antiproliferative against cancer cells and inhibitory topoisomerase activity.

Desde a descoberta da cisplatina várias tentativas têm sido feitas com o objetivo de desenvolver novos quimioterápicos com menor toxicidade e efeitos colaterais melhorados para tratar o câncer. Complexos de coordenação com metais de transição variados vêm sendo estudados buscando melhoras na biodisponibilidade, seletividade e efeitos adversos. Neste sentido, o presente trabalho consiste na síntese e caracterização estrutural de complexos de PdII e PtII com ligantes derivados de tiossemicarbazidas contendo o grupo fluoróforo pireno visando a obtenção de potenciais agentes antitumorais. Os agentes quelantes foram preparados a partir de reações de condensação entre o pirenocarboxaldeído e a tiossemicarbazida desejada resultando em compostos 1-pirenocarboxaldeído-N(3)-R-tiossemicarbazona, H2PrR, onde R = etil ou ciclohexil, Pr = pireno. A partir dos ligantes H2PrR foram realizadas as reações de complexação com os íons metálicos PdII e PtII, sendo possível obter duas classes de complexos com diferentes características: complexos monoméricos contendo ligantes clorido e trifenilfosfano do tipo [MCl(PPh3)(HPrR)] e complexos tetraméricos do tipo [M4(μ-S-PrR-κ3-C,N,S)4], onde M = PdII ou PtII, R = etil ou ciclohexil. Nas duas primeiras séries, o grupo R foi modificado por etil e ciclohexil para investigar a correlação entre lipoficilidade e atividade antiproliferativa, enquanto que o grupamento pireno foi incluído pensando que um maior número de unidades aromáticas possivelmente melhoraria a intercalação com o DNA e/ou ser utilizado como um marcador celular. A caracterização dos complexos envolveu técnicas como: análise elementar, espectroscopia na região do infravermelho e do UV-Vis, condutimetria, ressonância magnética nuclear (1H e 13C RMN) e difração de raios X em monocristal. As análises mostraram que os agentes complexantes podem atuar em diferentes modos coordenação tanto com relação à denticidade quanto à carga. A atividade antiproliferativa dos novos compostos de PdII e PtII foi determinada, sendo que vários deles apresentaram IC50 promissores contra células de câncer de ovário e, em muitos casos, as atividades observadas foram melhores do que a da cisplatina. Os dados obtidos indicam efeitos diferentes nos resultados de atividade biológica para os centros metálicos (Pd vs Pt) e ligantes utilizados (Etil vs Ciclohexil). Estudos de captação e distribuição celular mostraram que o complexo [PdCl(PPh3)(HPrCh)] atinge o núcleo celular. Com o intuito de verificar possíveis alvos biológicos, testes de interação com o DNA, ciclo celular e inibição da enzima Top IB foram realizados para os compostos. Os resultados do ciclo celular, mostraram uma maior inibição nos estádios S e G2/M para os complexos do tipo [PdCl(PPh3)(HPrR)]. Diante dos resultados obtidos, verificou-se que a Top IB é um dos alvos moleculares para os complexos do tipo [MCl(PPh3)(HPrR)], um mecanismo diferente da cisplatina. Estes resultados preliminares são bastante promissores e mostram que alguns dos complexos estudados neste trabalho apresentam-se como potenciais agentes para serem usados na terapia do câncer em combinação com os demais fármacos em uso clínico. / Since the discovery of cisplatin, many attepemts have been made to prepare new drugs with less cytotoxicity and side effects. Coordination complexes based on a variety of transition metals have been developed in the search for improved bioavailability, selectivity and reduced adverse side-effects. This work consists on the synthesis and structural characterization of PdII and PtII complexes with chelating compounds derived from thiosemicarbazides containing the pyrene fluorophore group aiming to obtain potential antitumor compounds. The chelating agents were prepared from condensation reactions between the pyrenocarboxaldehyde and the desired thiosemicarbazide resulting in 1-pyrenocarboxaldehyde-N (3) -R-thiosemicarbazone compounds, H2PrR, where R = ethyl or cyclohexyl. Complexation reactions with the metal ions PdII and PtII were carried out with the H2PrR ligands. It was possible to obtain two main classes of complexes with different characteristics: i) monomeric complexes containing chlorido and triphenylphosphane ligands of the type [MCl(PPh3)(HPrR)] and (ii) tetramer complexes of the type [{M(PrR)}4], where M = PdII or PtII and R = etyl ou cyclohexyl. In both series the R group was modified by ethyl and cyclohexyl in order to investigate the correlation between lipophilicity and antiproliferative activity, while the pyrene group was attached to the ligands with the belief that a higher number of aromatic units would improve DNA intercalation and/or to be used as an intracellular probe. The characterization of the complexes involved techniques such as: elemental analysis, infrared and UV-Vis spectroscopy, conductimetry, nuclear magnetic resonance (1H and 13C NMR) and single crystal X-ray diffraction. The antiproliferative activity of the novel PdII and PtII compounds have been determined, several of them showed promising IC50 against ovarian cancer cells, and in many cases the observed activities are better than that of cisplatin. The data obtained indicate different effects for the metal centers (Pd vs Pt) and the ligands used (ethyl vs cyclohexyl). Uptake and cellular distribution studies proved that the palladium complex [PdCl(PPh3)(HPrCh)] achieved the cell nucleus. In order to verify possible biological targets, interaction with DNA, cell cycle and inhibition experiments of the topoisomerase IB (Top IB) enzyme were performed for some compounds. Cell cycle results showed an inhibition at the S and G2/M stages for the complexes [PdCl(PPh3)(HPrR)]. Overall, the results indicated the Top IB enzyme as one of the targets of the complexes. These preliminary results are quite promising and show that some of the complexes studied here can be used in cancer therapy in combination with other anticancer drugs.

The eubacterial genome is maintained in a negatively supercoiled state which facilitates its compaction and storage in a small cellular space. Genome supercoiling can potentially influence various DNA transaction processes such as DNA replication, transcription, recombination, chromosome segregation and gene expression. Alterations in the genome supercoiling have global impact on the gene expression and cell growth. Inside the cell, the genome supercoiling is maintained judiciously by DNA topoisomerases to optimize DNA transaction processes. These enzymes solve the problems associated with the DNA topology by cutting and rejoining the DNA. Due to their essential cellular functions and global regulatory roles, DNA topoisomerases are fascinating candidates for the study of the effect of topology perturbation on a global scale. Genus Mycobacterium includes a large number of species including the well-studied Mycobacterium smegmatis (Msm) as well as various pathogens–Mycobacterium leprae, Mycobacterium abscessus and Mycobacterium tuberculosis (Mtb), the last one being the causative agent of the deadly disease Tuberculosis (TB), which claims millions of lives worldwide annually. The organism combats various stresses and alterations in its environment during the pathogenesis and virulence. During such adaptation, various metabolic pathways and transcriptional networks are reconfigured. Considering their global regulatory role, DNA topoisomerases and genome supercoiling may have an influence on the mycobacterial survival and adaptation. Biochemical studies from our laboratory have revealed several distinctive characteristics of mycobacterial DNA gyrase and topoisomerase I. DNA gyrase has been shown to be a strong decatenase apart from its characteristic supercoiling activity. Similarly, the mycobacterial topoisomerase I exhibits several distinct features such as the ability to bind both single- as well as double-stranded DNA, site specific DNA binding and absence of Zn2+ fingers required for DNA relaxation activity in other Type I enzymes. Although, efforts have been made to understand the biochemistry and mechanism of mycobacterial topoisomerases, in vivo significance and regulatory roles remain to be explored. The present study is aimed at understanding the mechanism, in vivo functions, regulation and genome wide distribution of mycobacterial topoisomerases. Chapter 1 of the thesis provides introduction on DNA topology, genome supercoiling and DNA topoisomerases. The importance of genome supercoiling and its regulatory roles has been discussed. Further, the regulation of topoisomerase activity and the role in the virulence gene regulation is described. Finally, a brief overview of Mtb genome, disease epidemiology, and pathogenesis is presented along with the description of the work on mycobacterial topoisomerases. In Chapter 2, the studies are directed to understand the DNA relaxation mechanism of mycobacterial Type IA topoisomerase which lack Zn2+ fingers. The N-terminal domain (NTD) of the Type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli TopoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial TopoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. It is elucidated that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the strand passage step of the catalysis. It is hypothesized that the loss of Zn2+ fingers from the mycobacterial TopoI could be associated with Zn2+ export and homeostasis. In Chapter 3, the studies have been carried out to understand the regulation of mycobacterial TopoI. Identification of Transcription Start Site (TSS) suggested the presence of multiple promoters which were found to be sensitive to genome supercoiling. The promoter activity was found to be specific to mycobacteria as the promoter(s) did not show activity in E. coli. Analysis of the putative promoter elements suggested the non-optimal spacing of the putative -35 and -10 promoter elements indicating the involvement of supercoiling for the optimal alignment during the transcription. Moreover, upon genome relaxation, the occupancy of RNA polymerase was decreased on the promoter region of topoI gene implicating the role of DNA topology in the Supercoiling Sensitive Transcription (SST) of TopoI gene from mycobacteria. The involvement of intrinsic promoter elements in such regulation has been proposed. In Chapter 4, the importance of TopoI for the Mtb growth and survival has been validated. Mtb contains only one Type IA topoisomerase (Rv3646c), a sole DNA relaxase in the cell, and hence a candidate drug target. To validate the essentiality of Mtb topoisomerase I for bacterial growth and survival, conditionally regulated strain of topoI in Mtb was generated. The conditional knockdown mutant exhibited delayed growth on agar plate and in liquid culture the growth was drastically impaired when TopoI expression was suppressed. Additionally, novobiocin and isoniazid showed enhanced inhibitory potential against the conditional mutant. Analysis of the nucleoid revealed its altered architecture upon TopoI depletion. These studies establish the essentiality of TopoI for the Mtb growth and open up new avenues for targeting the enzyme. In Chapter 5, the influence of perturbation of TopoI activity on the Msm growth and physiology has been studied. Notably, Msm contains an additional DNA relaxation enzyme– an atypical Type II topoisomerase TopoNM. The TopoI depleted strain exhibited slow growth and drastic change in phenotypic characters. Moreover, the genome architecture was disturbed upon depletion of TopoI. Further, the proteomic and transcript analysis indicated the altered expression of the genes involved in central metabolic pathways and core DNA transaction processes in the mutant. The study suggests the importance of TopoI in the maintenance of cellular phenotype and growth characteristics of fast growing mycobacteria having additional topoisomerases. In Chapter 6, the ChIP-Seq method is used to decipher the genome wide distribution of the DNA gyrase, topoisomerase I (TopoI) and RNA polymerase (RNAP). Analysis of the ChIP-Seq data revealed the genome wide distribution of topoisomerases along with RNAP. Importantly, the signals of topoisomerases and RNAP was found to be co-localized on the genome suggesting their functional association in the twin supercoiled domain model, originally proposed by J. C. Wang. Closer inspection of the occupancy profile of topoisomerases and RNAP on transcription units (TUs) revealed their co-existence validating the topoisomerases occupancy within the twin supercoiled domains. On the genomic scale, the distribution of topoisomerases was found to be more at the ori domains compared to the ter domain which appeared to be an attribute of higher torsional stress at ori. The reappearance of gyrase binding at the ter domain (and the lack of it in the ter domain of E. coli) suggests a role for Mtb gyrase in the decatenation of the daughter chromosomes at the end of replication. The eubacterial genome is maintained in a negatively supercoiled state which facilitates its compaction and storage in a small cellular space. Genome supercoiling can potentially influence various DNA transaction processes such as DNA replication, transcription, recombination, chromosome segregation and gene expression. Alterations in the genome supercoiling have global impact on the gene expression and cell growth. Inside the cell, the genome supercoiling is maintained judiciously by DNA topoisomerases to optimize DNA transaction processes. These enzymes solve the problems associated with the DNA topology by cutting and rejoining the DNA. Due to their essential cellular functions and global regulatory roles, DNA topoisomerases are fascinating candidates for the study of the effect of topology perturbation on a global scale. Genus Mycobacterium includes a large number of species including the well-studied Mycobacterium smegmatis (Msm) as well as various pathogens–Mycobacterium leprae, Mycobacterium abscessus and Mycobacterium tuberculosis (Mtb), the last one being the causative agent of the deadly disease Tuberculosis (TB), which claims millions of lives worldwide annually. The organism combats various stresses and alterations in its environment during the pathogenesis and virulence. During such adaptation, various metabolic pathways and transcriptional networks are reconfigured. Considering their global regulatory role, DNA topoisomerases and genome supercoiling may have an influence on the mycobacterial survival and adaptation. Biochemical studies from our laboratory have revealed several distinctive characteristics of mycobacterial DNA gyrase and topoisomerase I. DNA gyrase has been shown to be a strong decatenase apart from its characteristic supercoiling activity. Similarly, the mycobacterial topoisomerase I exhibits several distinct features such as the ability to bind both single- as well as double-stranded DNA, site specific DNA binding and absence of Zn2+ fingers required for DNA relaxation activity in other Type I enzymes. Although, efforts have been made to understand the biochemistry and mechanism of mycobacterial topoisomerases, in vivo significance and regulatory roles remain to be explored. The present study is aimed at understanding the mechanism, in vivo functions, regulation and genome wide distribution of mycobacterial topoisomerases. Chapter 1 of the thesis provides introduction on DNA topology, genome supercoiling and DNA topoisomerases. The importance of genome supercoiling and its regulatory roles has been discussed. Further, the regulation of topoisomerase activity and the role in the virulence gene regulation is described. Finally, a brief overview of Mtb genome, disease epidemiology, and pathogenesis is presented along with the description of the work on mycobacterial topoisomerases. In Chapter 2, the studies are directed to understand the DNA relaxation mechanism of mycobacterial Type IA topoisomerase which lack Zn2+ fingers. The N-terminal domain (NTD) of the Type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli TopoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial TopoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. It is elucidated that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the strand passage step of the catalysis. It is hypothesized that the loss of Zn2+ fingers from the mycobacterial TopoI could be associated with Zn2+ export and homeostasis. In Chapter 3, the studies have been carried out to understand the regulation of mycobacterial TopoI. Identification of Transcription Start Site (TSS) suggested the presence of multiple promoters which were found to be sensitive to genome supercoiling. The promoter activity was found to be specific to mycobacteria as the promoter(s) did not show activity in E. coli. Analysis of the putative promoter elements suggested the non-optimal spacing of the putative -35 and -10 promoter elements indicating the involvement of supercoiling for the optimal alignment during the transcription. Moreover, upon genome relaxation, the occupancy of RNA polymerase was decreased on the promoter region of topoI gene implicating the role of DNA topology in the Supercoiling Sensitive Transcription (SST) of TopoI gene from mycobacteria. The involvement of intrinsic promoter elements in such regulation has been proposed. In Chapter 4, the importance of TopoI for the Mtb growth and survival has been validated. Mtb contains only one Type IA topoisomerase (Rv3646c), a sole DNA relaxase in the cell, and hence a candidate drug target. To validate the essentiality of Mtb topoisomerase I for bacterial growth and survival, conditionally regulated strain of topoI in Mtb was generated. The conditional knockdown mutant exhibited delayed growth on agar plate and in liquid culture the growth was drastically impaired when TopoI expression was suppressed. Additionally, novobiocin and isoniazid showed enhanced inhibitory potential against the conditional mutant. Analysis of the nucleoid revealed its altered architecture upon TopoI depletion. These studies establish the essentiality of TopoI for the Mtb growth and open up new avenues for targeting the enzyme. In Chapter 5, the influence of perturbation of TopoI activity on the Msm growth and physiology has been studied. Notably, Msm contains an additional DNA relaxation enzyme– an atypical Type II topoisomerase TopoNM. The TopoI depleted strain exhibited slow growth and drastic change in phenotypic characters. Moreover, the genome architecture was disturbed upon depletion of TopoI. Further, the proteomic and transcript analysis indicated the altered expression of the genes involved in central metabolic pathways and core DNA transaction processes in the mutant. The study suggests the importance of TopoI in the maintenance of cellular phenotype and growth characteristics of fast growing mycobacteria having additional topoisomerases. In Chapter 6, the ChIP-Seq method is used to decipher the genome wide distribution of the DNA gyrase, topoisomerase I (TopoI) and RNA polymerase (RNAP). Analysis of the ChIP-Seq data revealed the genome wide distribution of topoisomerases along with RNAP. Importantly, the signals of topoisomerases and RNAP was found to be co-localized on the genome suggesting their functional association in the twin supercoiled domain model, originally proposed by J. C. Wang. Closer inspection of the occupancy profile of topoisomerases and RNAP on transcription units (TUs) revealed their co-existence validating the topoisomerases occupancy within the twin supercoiled domains. On the genomic scale, the distribution of topoisomerases was found to be more at the ori domains compared to the ter domain which appeared to be an attribute of higher torsional stress at ori. The reappearance of gyrase binding at the ter domain (and the lack of it in the ter domain of E. coli) suggests a role for Mtb gyrase in the decatenation of the daughter chromosomes at the end of replication.

This report combines a series of papers to trace progression in the area of type-2 topoisomerase research. First, Deibler et al. show that knotted DNA is harmful to cells. Knots can block both transcription and replication, and can also act as a catalyst for mutation. Despite the fact that type-2 topoisomerases perform the important functions of unknotting and decatenating DNA, the mechanism by which they accomplish this task is still unknown. Buck and Zechiedrich propose a model in which the enzyme uses local geometry to infer global topology, and thus where to perform segment passage in order to obtain the desired results. In two articles, Liu et al. evaluate this theory quantitatively for the decatenation and unknotting problems. In both cases it is shown that the presence of certain juxtapositions is strongly correlated with global topology. This correlation is not enough, however, and Liu et al. go on to show that when segment passage operations designed to mimic type-2 topoisomerase action are performed at hooked juxtapositions, the overwhelming tendency is towards unknotting and decatenation. / text

<p>Topoisomerase 1 (Top1), a Type IB topoisomerase, functions to relieve transcription- and replication-associated torsional stress in DNA. Top1 cleaves one strand of DNA, covalently associates with the 3’ end of the nick to form a Top1-cleavage complex (Top1cc), passes the intact strand through the nick and finally re-ligates the broken strand. The chemotherapeutic drug, Camptothecin, intercalates at a Top1cc and prevents the crucial re-ligation reaction that is mediated by Top1, resulting in the conversion of a nick to a toxic double-strand break during DNA replication or the accumulation of Top1cc. This mechanism of action preferentially targets rapidly dividing tumor cells, but can also affect non-tumor cells when patients undergo treatment. Additionally, Top1 is found to be elevated in numerous tumor tissues making it an attractive target for anticancer therapies. We investigated the effects of Top1 on genome stability, effects of persistent Top1-cleavage complexes and elevated Top1 levels, in Saccharomyces cerevisiae. We found that increased levels of the Top1cc resulted in a five- to ten-fold increase in reciprocal crossovers, three- to fifteen fold increase in mutagenesis and greatly increased instability within the rDNA and CUP1 tandem arrays. Increased Top1 levels resulted in a fifteen- to twenty-two fold increase in mutagenesis and increased instability in rDNA locus. These results have important implications for understanding the effects of CPT and elevated Top1 levels as a chemotherapeutic agent.</p> / Dissertation

Orientadores: Luiz Carlos Teixeira, Marcelo Alvarenga / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-09-11T21:07:48Z (GMT). No. of bitstreams: 1 Manna_ElizaDelFiol_M.pdf: 877307 bytes, checksum: 7ee78365634d93a3ce0c44565891f5ee (MD5) Previous issue date: 2005 / Resumo: Objetivo: O objetivo deste estudo foi avaliar a associação entre a expressão imunoistoquímica da topoisomerase IIa, HER2 e receptores hormonais e a resposta à quimioterapia primária baseada em antraciclina em carcinoma invasivo de mama. Materiais e Métodos: Analisamos 109 prontuários de pacientes tratadas com quimioterapia primária baseada em antraciclina no Centro Atenção Integral à Saúde da Mulher da Universidade Estadual de Campinas, no período de 1996 a 2004. As respostas clínica e patológica à quimioterapia primária foram associadas com a superexpressão da topoisomerase IIa e do HER2 e com a negatividade dos receptores hormonais. A análise estatística foi realizada através do teste qui-quadrado ou teste exato de Fisher. Resultados: A freqüência da superexpressão da topoisomerase IIa foi de 41%. Não houve associação estatística entre a resposta clínica e a superexpressão da topoisomerase IIa, do HER2 e negatividade dos receptores hormonais. Entretanto, houve associação entre a resposta completa patológica e a negatividade dos receptores hormonais (p=0,0289). Conclusões: O presente estudo sugere que esses marcadores não deveriam ser considerados fatores preditivos de resposta à quimioterapia primária com antraciclina, sendo necessários estudos prospectivos desenhados para esse propósito / Abstract: Background: The aim of this study was to evaluate the association between immunohistochemical expression of topoisomerase IIa, HER2 and hormonal receptors and response to primary anthracyclin-based chemotherapy in invasive breast carcinoma. Materials and Methods: We analyzed 109 medical charts of patients treated with primary anthracyclin-based chemotherapy in Women¿s Integral Health Care Center of State University of Campinas from 1996 to 2004. The clinical and pathological response to primary chemotherapy was associated with overexpression of topoisomerase IIa and HER2 and hormonal receptor negativity. Statistical analysis was performed using Chi-square or Fisher¿s Exact Test. Results: The frequency of topoisomerase IIa overexpression was 41%. No statistical association between clinical response and overexpression of topoisomerase IIa, HER2 and hormonal receptor negativity was found. However, there was an association between complete pathological response and hormonal receptor negativity (p=0.0289). Conclusions: The present study suggested that these markers should not be considered predictors of response to primary anthracyclin-based chemotherapy, and prospective studies must be designed for this purpose / Mestrado / Ciencias Biomedicas / Mestre em Tocoginecologia

Multi-drug resistance in bacterial pathogens has become a global health crisis. Each year, millions of people worldwide are infected with bacterial strains that are resistant to currently available antibiotics. Diseases such as tuberculosis, pneumonia, and gonorrhea have become increasingly more difficult to treat. It is essential that novel drugs and cellular targets be identified in order to treat this resistance. Bacterial topoisomerase IA is a novel drug target that is essential for cellular growth. As it has never been targeted by existing antibiotics, it is an attractive target. Topoisomerase IA is responsible for relieving torsional strain on DNA by relaxing supercoiled DNA following processes such as replication and transcription. The aim of this study is to find novel compounds that can be developed as leads for antibiotics targeting bacterial type IA topoisomerase. Various approaches were used in order to screen thousands of compounds against bacterial type IA topoisomerases, including mixture-based screening and virtual screening. In the mixture-based screen, scaffold mixtures were tested against the M. tuberculosis topoisomerase I enzyme and subsequently optimized for maximum potency and selectivity. The optimized compounds were effective at inhibiting the enzyme at low micromolar concentrations, as well as killing the tuberculosis bacteria. In a virtual screen, libraries with hundreds of thousands of compounds were screened against the E. coli and M. tuberculosis topoisomerase I crystal structures in order to find new classes of drugs. The top hits were effective at inhibiting the enzymes, as well as preventing the growth of M. smegmatis cells in the presence of efflux pump inhibitors. Organometallic complexes containing Cu(II) or Co(III) were tested as well against various topoisomerases in order to determine their selectivity. We discovered a poison for human type II topoisomerase that has utility as an anticancer agent, as it killed even very resistant cell lines of breast and colon cancer. The Co(III) complexes were found to inhibit the bacterial topoisomerase I very selectively over other topoisomerases. The various methods of drug discovery utilized here have been successful at identifying new classes of compounds that may be further developed into antibiotic drugs that specifically target bacterial type IA topoisomerases.

The modification of proteins by xenobiotic and endogenous electrophilic species produced in cells undergoing oxidative stress contributes to cellular toxicity and disease processes. Many xenobiotics are themselves reactive electrophiles; however non-reactive compounds may become reactive towards proteins and DNA following metabolism. Identifying actual sites of adduction on target proteins is critical for determining the structural and functional consequences associated with the modification. 1,4-benzoquinone (BQ) is a reactive quinone and environmental toxicant, formed from oxidative metabolism of benzene, an aromatic hydrocarbon found in gasoline and other fuels. Although environmental and occupational exposure to benzene is associated with the development of aplastic anemia and leukemia, the mechanism of toxicity remains elusive. Due to the electrophilic nature of BQ, it reacts with glutathione to form quinol-thioether (QT) conjugates that retain the ability to redox cycle between the reduced (HQ) and oxidized (BQ) forms. BQ and its QT metabolites are reactive, and can produce cellular necrosis through oxidative stress and protein modification. One further consequence of oxidative stress is the elevation of cellular membrane lipid peroxidation, resulting in the formation of reactive lipid-aldehydes such as 4-hydroxynonenal (4HNE). Adduction of critical amino acid residues in target bone marrow proteins by 4HNE and QTs following exposure to benzene could contribute to its hematotoxic effects. This dissertation builds upon the foundation of proteins targeted by electrophilic adduction by outlining techniques to pinpoint the specific amino acids targeted and furthermore predict the functional releavance of adduction. For the first time, protein targets of reactive endogenous lipid aldehydes are reported in the bone marrow of chemically treated rats. Furthermore, novel sites of adduction by aldehydes and benzene-glutathione conjugates are reported within functional regions of topoisomerase II. Inhibition of bone marrow DNA topoisomerase II by benzene metabolites is implicated as a potential mechanism of benzene-induced hematotoxicity and acute-myeloid leukemia. The strong inhibitory effect of these compounds on topoisomerase II activity suggests that their presence in the bone marrow may play a role in benzene-induced myelotoxicity.