Thesis (Ph. D. in Biochemistry)--Vanderbilt University, Dec. 2005. / Title from title screen. Includes bibliographical references.

ASSIS JÚNIOR, Eudmar Marcolino de. Efeito protetor da silimarina sobre a esteato-hepatite não alcoólica experimental induzida por irinotecano. 2014. 84 f. Dissertação (Mestrado em Farmacologia) - Universidade Federal do Ceará. Faculdade de Medicina, Fortaleza, 2014. / Submitted by denise santos (denise.santos@ufc.br) on 2014-10-08T14:00:43Z No. of bitstreams: 1 2014_dis_emassisjunior.pdf: 1785225 bytes, checksum: fd28c699a89420b841078e99f342b777 (MD5) / Approved for entry into archive by denise santos(denise.santos@ufc.br) on 2014-10-08T14:01:06Z (GMT) No. of bitstreams: 1 2014_dis_emassisjunior.pdf: 1785225 bytes, checksum: fd28c699a89420b841078e99f342b777 (MD5) / Made available in DSpace on 2014-10-08T14:01:07Z (GMT). No. of bitstreams: 1 2014_dis_emassisjunior.pdf: 1785225 bytes, checksum: fd28c699a89420b841078e99f342b777 (MD5) Previous issue date: 2014 / O câncer coloretal (CRC) é a 3º neoplasia mais prevalente no mundo. O irinotecano (IRI), fármaco de primeira linha para os tratamentos do CRC e sua metástase hepática, tem aumentado a sobrevivência dos pacientes. Contudo, seus efeitos colaterais, incluindo a esteato-hepatite não alcoólica (NASH), podem limitar o curso do tratamento. Os protocolos baseados em irinotecano foram associados com um aumento no risco de NASH de 3,4 vezes. A silimarina (SIL) tem mostrado ser capaz de prevenir doenças do fígado gorduroso no contexto clínico e em modelos de danos hepáticos induzidos quimicamente. Assim, nosso objetivo foi estudar o efeito da SIL na NASH induzida pelo IRI, assim como o mecanismo envolvido. Métodos e Resultados: Camundongos Swiss fêmeas (n=8-10), foram divididos em 6 grupos e injetados com salina (SAL 5ml/kg i.p.), IRI (50 mg/kg i.p.), SIL (150 mg/kg v.o.) ou IRI (50 mg/kg i.p.) + SIL (SIL 1,5, 15, 150 mg/kg v.o.) 3x/semana/7 semanas. Amostras de sangue foram coletadas na sétima semana para determinar a concentração sérica das enzimas hepáticas ALT e AST (U/L). Animais foram mortos para a coleta do fígado para avaliar do dano tecidual (escores de Kleiner), dosagem de lipídeos totais (mg/g de tecido), MDA (nmol/g tecido), NPSH (mg de NPSH/g tecido), IL-6 (pg/mg de tecido), IL-10 (pg/mg de proteína) e IL-1β (pg/mg de tecido), imunomarcação de óxido nítrico sintase induzida (iNOS), 3-Nitrotirosina (Ntyr), e Receptor Toll Like tipo 4 (TLR4), quantificação do fator nuclear kappa B (NFκB) e da α-actina de músculo liso (α-SMA) e expressão do gene RSS. ANOVA/Teste de Newman-Keuls ou Kruskal Wallis/ Teste de Dunn foram utilizados para análise estatística. Foram consideradas diferentes amostras onde o nível descritivo era inferior a 5%. O trabalho foi aprovado pelo comitê de ética em pesquisa animal sob o número de protocolo: 21/12. O IRI aumentou de forma significante as transaminases hepáticas, o infiltrado neutrofílico, o acúmo de lipídeos, o acúmulo de MDA, a expressão de NTyr, a expressão de α-SMA, a expressão de NFκB, a expressão de IL-1β, a expressão de IL-6, a expressão de TLR4 e quantificação de DNA bacteriano, quando comparados ao grupo SAL. SIL (1,5 mg/kg) melhorou esses parâmetros, exceto a infiltração neutrofílica e a quantificação do DNA bacteriano quando comparados ao o grupo IRI (P<0,05). Por outro lado, a dose media de SIL (15 mg/kg) foi efetiva apenas no Infiltrado Neutrofílico, na expressão de NTyr, na expressão de NFκB e na expressão de IL-6. Adicionalmente, essa dose aumentou a expressão hepática de IL-10, a quantificação de DNA bacteriano e a expressão da α-SMA quando comparados com o grupo IRI (p<0,05). Contudo, a expressão de iNOS não foi afetada pelo pré-tratamento com SIL (P<0,05) e a maior dose foi ainda mais deletéria. Conclusões: O pré-tratamento com SIL previne o dano hepático causado pelo IRI provavelmente através da mudança da resposta inflamatória mediada por receptores TLR4 e citocinas IL-1, IL-6, IL-10 e NFκB. O dano observado no grupo de animais tratados com as maiores doses de SIL parece ser dependente da translocação bacteriana do intestido que é associada a ativação do TLR4. Adicionalmente, a silimarina contribui para hepatoproteção por inibir o estresse oxidativo e a nitrosilação proteica, prevenindo a ativação de mecanismos de fibrose hepática

Submitted by Pedro Barros (pedro.silvabarros@ufpe.br) on 2018-07-05T21:06:38Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) DISSERTAÇÃO Catherine de Araújo Crisóstomo Pontes.pdf: 1677040 bytes, checksum: 5592ec2bdcd5a5f303733530bb245427 (MD5) / Made available in DSpace on 2018-07-05T21:06:38Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) DISSERTAÇÃO Catherine de Araújo Crisóstomo Pontes.pdf: 1677040 bytes, checksum: 5592ec2bdcd5a5f303733530bb245427 (MD5) Previous issue date: 2017-01-31 / O câncer cervical é a quarta neoplasia mais diagnosticada em mulheres no mundo e tem como principal agente etiológico a infecção pelo Papillomavirus Humano (HPV), que induz à proliferação descontrolada das células, levando ao acúmulo de mutações ao longo do tempo podendo levar ao câncer. A expressão anormal de proteínas nucleares, como Ki-67 e TOPIIα, indica desregulação do ciclo celular e pode, em conjunto com outros testes, melhorar a acurácia dos programas de rastreamento. Este estudo objetivou avaliar a detecção dos marcadores Ki-67 e TOPIIα, através da técnica de imunocitoquímica, em pacientes com anormalidades cervicais, observando a possibilidade de detectar lesões clinicamente relevantes, melhorando a sensibilidade da citologia. Participaram do estudo 76 mulheres encaminhadas a um Centro de referência por apresentarem alterações em exames anteriores ou mesmo condilomas, que representam a infecção clínica pelo HPV. Observou-se um maior índice de positividade (IP) de Ki-67 e TOPIIα nas pacientes diagnosticadas com anormalidades cervicais detectadas pela citologia (41,6% e 62,5%, respectivamente). O desempenho do Ki-67 foi melhor em pacientes com LSIL (IP igual a 50%), e TOPIIα teve um melhor desempenho em pacientes com HSIL (66,6%). O teste de associação entre a imunocitoquímica e a citologia em base líquida revelou-se estatisticamente significante (p< 0,05) com valor de p=0,0026 para Ki-67 e p=0,0004 para TOPIIα. Os marcadores analisados, Ki-67 e TOPIIα, se mostraram eficientes na detecção de lesões cervicais clinicamente relevantes, dada a forte associação entre a expressão desses marcadores em pacientes diagnosticadas com anormalidades cervicais pela citologia. / Cervical cancer is the fourth most diagnosed neoplasia in women in the world and its main etiological agent is infection by the Human Papillomavirus (HPV), which induces the uncontrolled proliferation of cells, leading to the accumulation of mutations over time and to cancer in some cases. The abnormal expression of nuclear proteins, such as Ki-67 and TOPIIα, indicating dysregulation of the cell cycle and can, in conjunction with other tests, improve the accuracy of screening programs. This study aimed to evaluate the detection of Ki-67 and TOPIIα, through the technique of immunocytochemistry in patients with cervical abnormalities, noting whether they are useful to detect clinically relevant lesions, improving the sensitivity of cytology. 76 women participated in the study referred to a reference centre for presenting changes in previous tests or even Condyloma, representing clinical infection by HPV. It was observed a higher rate of positivity (IP) of Ki-67 and TOPIIα in patients diagnosed with cervical abnormalities detected by cytology (41.6% and 62.5%, respectively). Seventh six women participated in the study referred to a reference centre for presenting changes in previous tests or even condylomas, representing clinical infection by HPV. It was observed a higher rate of positivity (RP) of Ki-67 and TOPIIα in patients diagnosed with cervical abnormalities detected by cytology (41.6% and 62.5%, respectively). The performance of the Ki-67 was better in patients with LSIL (equal to 50%) and TOPIIα had a better performance in patients with HSIL (66.6%). The test of association between the immunocytochemistry and liquid-based cytology proved to be statistically significant (p < 0.05) with value of p = 0.0026 for Ki-67 and p = 0.0004 to TOPIIα. The markers analysed, Ki-67 and TOPIIα, have proven effective in the detection of cervical lesions clinically relevant, given the strong association between the expression of these markers in patients diagnosed with cervical abnormalities for cytology.

A principle challenge of modern biology is to understand how the human genome is organised and regulated within a nucleus. The field of chromatin biology has made significant progress in characterising how protein and DNA modifications reflect transcription and replication state. Recently our lab has shown that the human genome is organised into large domains of altered DNA helical twist, called DNA supercoiling domains, similar to the regulatory domains observed in prokaryotes. In my PhD I have analysed how the maintenance and distribution of DNA supercoiling relates to biological function in human cells. DNA supercoiling domains are set up and maintained by the balanced activity of RNA transcription and topoisomerase enzymes. RNA polymerase twists the DNA, over-winding in front of the polymerase and under-winding behind. In contrast topoisomerases relieve supercoiling from the genome by introducing transient nicks (topoisomerase I) or double strand breaks (topoisomerase II) into the double helix. Topoisomerase activity is critical for cell viability, but the distribution of topoisomerase I, IIα and IIβ in the human genome is not known. Using a chromatin immunoprecipitation (ChIP) approach I have shown that topoisomerases are enriched in large chromosomal domains, with distinct topoisomerase I and topoisomerase II domains. Topoisomerase I is correlated with RNA polymerase II, genes and underwound DNA, whereas topoisomerase IIα and IIβ are associated with each other and over-wound DNA. This indicates that different topoisomerase proteins operate in distinct regions of the genome and can be independently regulated depending on the genomic environment. Transcriptional regulation by DNA supercoiling is believed to occur through changes in gene promoter structure. To investigate DNA supercoiling my lab has developed biotinylated trimethylpsoralen (bTMP) as a DNA structure probe, which preferentially intercalates into under-wound DNA. Using bTMP in conjunction with microarrays my lab identified a transcription and topoisomerase dependent peak of under-wound DNA in a meta-analysis of several hundred genes (Naughton et al. (2013)). In a similar analysis, Kouzine et al. (2013) identified an under-wound promoter structure and proposed a model of topoisomerase distribution for the regulation of promoter DNA supercoiling. To better understand the role of supercoiling and topoisomerases at gene promoters, a much larger-scale analysis of these factors was required. I have analysed the distribution of bTMP at promoters genome wide, confirming a transcription and expression dependent distribution of DNA supercoils. DNA supercoiling is distinct at CpG island and non-CpG island promoters, and I present a model in which over-wound DNA limits transcription from both CpG island promoters and repressed genes. In addition, I have mapped by ChIP topoisomerase I and IIβ at gene promoters on chromosome 11 and identified a different distribution to that proposed by Kouzine et al. (2013), with topoisomerase I maintaining DNA supercoiling at highly expressed genes. This study provides the first comprehensive analysis of DNA supercoiling at promoters and identifies the relationship between supercoiling, topoisomerase distribution and gene expression. In addition to regulating transcription, DNA supercoiling and topoisomerases are important for genome stability. Several studies have suggested a link between DNA supercoiling and instability at common fragile sites (CFSs), which are normal structures in the genome that frequently break under replication stress and cancer. bTMP was used to measure DNA supercoiling across FRA3B and FRA16D CFSs, identifying a transition to a more over-wound DNA structure under conditions that induce chromosome fragility at these regions. Furthermore, topoisomerase I, IIα and IIβ showed a pronounced depletion in the vicinity of the FRA3B and FRA16D CFSs. This provides the first experimental evidence of a role for DNA supercoiling in fragile site formation.

Camptothecin and its analogues (CPTs) represent one of the most potent classes of anticancer drugs used to treat several solid tumors. CPTs bind topoisomerase I during the replication process and cause DNA damage that results in cell death. However, its effectiveness is limited to 13-30 percent of patients. TopoI cuts and re-ligates DNA supercoiling but in the presence of CPT it fails to re-ligate DNA and collision of replication forks leads to DNA double strand break (DNA-DSB) and cell death. However, in resistant cells, due to deregulated kinase cascade, topoI is continually phosphorylated by DNA-PKcs and rapidly degraded by the ubiquitin proteasomal pathway (UPP). It has been found that BRCA1 plays a key role in imparting cellular resistance to topoI inhibitors. Importantly, BRCA1 ubiquitinates topoI in response to CPT. We hypothesize that disruption of BRCA1 binding to phosphorylated topoI would interrupt the resistance mechanism resulting in higher cellular sensitivity of CPT. Based on an in-silico drug screen, we identified a compound that inhibits topoI degradation by blocking BRCA1 binding. Imaging and survival assays findings are consistent with the hypothesis that BRCA1 plays a role in CPT resistance through its co-localization with topoI, and we speculate this role is through UPP degradation. CPTs are commonly used in combination with cytotoxic compounds, but this study focuses on discovering compounds that can overcome resistance without causing further cytotoxicity. / 2019-07-03T00:00:00Z

Fluoroquinolones are broad spectrum antibiotics that have been in use for nearly 50 years. These agents are used to treat a variety of bacterial infections from simple urinary tract infections to tuberculosis. The protein targets of fluoroquinolones are bacterial type II topoisomerases. Fluoroquinolones inhibit the function of these topoisomerases by intercalating in the nick site of the DNA and forming an interaction with helix-4 of the enzyme through a magnesium-water bridge. The binding of a fluoroquinolone stabilizes the DNA-topoisomerase-fluoroquinolone ternary complex. Helix-4 is where some of the most important fluoroquinolone resistance mutations occur. While the fluoroquinolone class of antibiotics has been successful at treating a variety of infections over the past few decades, a number of problems exist. These problems include the inability of many fluoroquinolones to kill non-growing cells, the emergence of fluoroquinolone resistant mutants, and adverse side effects of this antibiotic class. Thus, various aspects of fluoroquinolone structure and activity are explored in this study. The first topic explored is the question of what structural features are necessary for a fluoroquinolone to be able to kill bacteria in the presence and absence of the protein synthesis inhibitor, chloramphenicol (to mimic a dormant, non-growing state of the bacteria). Previous studies have shown that steric bulk at the C-8 position (especially a methoxy group) is necessary to support the ability of a fluoroquinolone to kill non-growing cells. In this study, the N-1 position of a series of C-8 methoxy fluoroquinolones was explored to gain an understanding of what substituents at the N-1 position of C-8 methoxy fluoroquinolones support the ability to rapidly kill bacteria in the presence of a protein synthesis inhibitor. In a second study the N-1 position is further explored, but with different goals. A recent crystal structure of a fluoroquinolone bound in the ternary complex with topoisomerase IV and DNA has revealed that the N-1 position of the fluoroquinolone is near in space to the catalytic tyrosine residue. It was reasoned that new interactions can be made with active site tyrosine residue through the N-1 position of the fluoroquinolone core. A number of N-1 fluoroquinolone derivatives were designed, synthesized, and evaluated for their ability to inhibit the DNA supercoiling activity of DNA gyrase, as well as the poisoning ability of the fluoroquinolones. The advantages of targeting the catalytic tyrosine residue are that this amino acid cannot be mutated without loss of enzyme function, and that by forming a new binding contact to the enzyme, activity can be maintained against helix-4 mutants. Finally, in a step toward the goal of mitigating the tendon related side effects of fluoroquinolones (thought to be due to Ca2+ coordination), the metal binding domain of the fluoroquinolone was altered. These fluoroquinolones were tested for their ability to inhibit and poison DNA gyrase. From the studies described, we have learned that the N-1 position is very sensitive to modification, that novel binding contacts to bacterial topoisomerases can be made through the N-1 position, and that modifying the metal binding domain of fluoroquinolones can lead to retention of activity against DNA gyrase. These accomplishments all push the fluoroquinolone field ahead by introducing a novel binding interaction to optimize (with the goal of creating a fluoroquinolone that is active against current fluoroquinolone resistant mutants) and by showing that fluoroquinolone activity can be retained even when the metal binding domain is altered, thus moving us closer to the goal of reducing tendon-related side effects.

Fluoroquinolones, a class of type-II topoisomerase inhibitors, have successfully been used as antibiotics for the last several decades, beginning with the use of nalidixic acid in urinary tract infections. This led to the broad-spectrum activity of ciprofloxacin in the 1980s. Unfortunately, use of fluoroquinolones has led to the emergence of resistant bacteria. Recently, this has generated new bacteria such as multidrug-resistant and extensive-drug-resistant strains of M. tuberculosis that are also fluoroquinolone-resistant. Infections caused by these bacterial strains are widespread, with high mortality rate in immune-compromised populations such as the elderly, infants, and in AIDS or HIV-positive patients. Fluoroquinolone resistance is acquired through amino acid substitutions of key fluoroquinolone-binding residues of the type-II bacterial topoisomerases DNA Gyrase and Topoisomerase IV, the enzyme targets of fluoroquinolones. Amino acid substitutions that result in fluoroquinolone resistance are located on Helix-4 of these enzymes, which is the site of a magnesium (Mg)-water bridge that is a crucial binding interaction for fluoroquinolones. When certain substitutions to Helix-4 occur, the Mg-water bridge is compromised and no longer available to anchor fluoroquinolones into a ternary complex composed of topoisomerase, fluoroquinolone, and DNA. This results in drug resistance. Herein are described attempts to generate fluoroquinolones that are capable of overcoming this mechanism of resistance. In the first study, attempts were made to generate a series of novel tricyclic fluoroquinolones and diones designed to exploit intercalative or pi-stacking binding interactions with the bacterial DNA in the ternary complex in order to lessen the importance of the Mg-water bridge interaction. Despite numerous attempts, no complete synthetic pathway to these core structures was ever discovered. The second study investigated the utility of a C7-aminomethylpyrrolidine group on the fluoroquinolone structure. This was done in order to explore the mechanistic reasons why previously generated fluoroquinolones possessing this C7-aminomethylpyrrolidine group maintained activity against common Helix-4 mutants. A panel of fluoroquinolones with C7-aminomethylpyrrolidine groups and diverse core structures was synthesized and docking studies with the original C7-aminomethylpyrrolidine fluoroquinolone and other fluoroquinolones were performed. Target compounds were synthesized and evaluated for inhibition/poisoning purified enzyme and for the ability to inhibit growth with wild-type and fluoroquinolone-resistant cells. In a third study, fluoroquinolones possessing structural variations of the C7-aminomethylpyrrolidine were designed and synthesized to explore structural requirements of the aminomethylpyrrolidine group binding and overcoming fluoroquinolone-resistance caused by alterations of Helix-4. This led to further exploration of the binding space around the C7-position of the fluoroquinolones. In both the second and third studies, the new fluoroquinolones were evaluated for the ability to specifically target bacterial topoisomerases over human topoisomerase. The results of these studies have contributed new knowledge to the binding requirements of fluoroquinolones that maintain potency against fluoroquinolone-resistant type-II topoisomerases, and represent a step towards methodology to overcome bacteria resistant to fluoroquinolones.

Bloom syndrome is a rare autosomal recessive disorder that is caused by mutations in the BLM gene. BLM associates with TopoIIIα and RMI1 to form a complex that is essential to maintain genome integrity. This complex catalyzes a dissolution reaction that resolves recombination intermediates containing two Holliday junctions without crossing over of genetic material. Dissolution activity is remarkable because it accounts for the in vivo role of BLM-TopoIIIα-RMI1 in suppressing sister chromatid exchanges. To further understand the biochemical roles that each member of the BLM complex plays in dissolution, I generated single-stranded catenanes that resemble the proposed intermediates at the latest steps of dissolution. Using this substrate, I demonstrated that TopoIIIα is a single-stranded DNA decatenase that is specifically stimulated by BLM and RMI1. Interaction between TopoIIIα and RMI1 is essential for the optimal decatenase activity. Furthermore, binding of RPA to single-stranded DNA substrate inhibits TopoIIIα decatenase activity. However, complex formation between BLM, TopoIIIα and RMI enables TopoIIIα to displace RPA and catalyze decatenation. Since the decatenase activity is presumed to be involved in many aspects of DNA metabolism, I investigated the roles of RMI1 and TopoIIIα in DNA replication in vivo. Using the molecular combing technique, I showed that RMI1 functions downstream of BLM to promote normal replication fork progression. In addition, BLM, TopoIIIα and RMI1 colocalize with one another in response to replication stress. Finally, interaction between TopoIIIα and RMI1 is essential for nuclear localization of the complex and for the complex to promote recovery from replication stress. This work defines molecular functions for RMI1 and TopoIIIα in DNA replication and repair, providing insight into their roles as suppressors of genome instability.

<p>Topoisomerase III&alpha; (Top3&alpha;) is an essential component of the double Holliday junction (dHJ) dissolvasome complex in metazoans. Previous work has shown that Top3&alpha; and Bloom's helicase (Blm) are able to convergently migrate the dHJ to create solely non-crossover products, thus preserving genomic integrity. However, many questions remain about the details of this process. Using a combination of biochemical and genetic tools, including dHJ substrate assays, gel electrophoresis, EMSA, pulldowns, fly crosses, and electron microscopy, this work expands our knowledge of the dissolution reaction. Tail mutants of Top3&alpha; were created and tested in a series of <italic>in vitro</italic> assays. Through these experiments, I discovered that the C-terminus of Top3&alpha; is important for binding Blm, interacting with DNA, conveying RPA stimulation, and <italic>in vivo</italic> functionality. I also observed that dissolution is an extremely processive reaction, with no accumulation of intermediates prior to product formation. When a non-specific topoisomerase was used (Top1, a type IB), accumulation of an intermediate was evident; however, contrary to predicted models, direct observation revealed that this intermediate is not a hemicatenane structure and still requires branch migration. Modifications were also made to the dHJ substrate creation method so that multiple types of HJ substrates could be produced efficiently.</p> / Dissertation

Protein oligomerization provides a way for cells to modulate function in vivo. In this study, self-assembling protein fragments from ParC, DnaX, and proteins of unknown function were used to generate phenotypes in a dominant negative manner. These fragments were expressed as Thioredoxin (TRX) fusions under the control of the inducible araBAD promoter. Fragments chosen contain only the oligomerization domain of the protein, lacking the regions necessary for catalytic function. Fragments of ParC, a subunit of Topoisomerase (Topo) IV, generated fragment-specific phenotypes. Regions that expressed both the oligomerization domain and CTD of ParC (ParC206-752 and ParC332-752) yielded filamentous cells with several different nucleoid segregation phenotypes. Another ParC fragment containing only the oligomerization domain of ParC (ranging from 333-485) yields a recA-dependent septation defect in a subset of the population. This phenotype suggests that Topo IV may be inhibiting chromosome dimer resolution. The overexpression of DnaX247-455, a fragment containing regions of both the tau and gamma subunits of the DNA Polymerase III holoenzyme, led to a severe plating defect. Upon further investigation, this fragment caused filamentation, a nucleoid defect, and induction of sulA, similar to the effects seen with the dnaX temperature-sensitive alleles. The overexpression of the various y-protein fragments yielded a variety of mediaspecific plating defects on over 50% of the proteins tested. The overexpression of the protein fragments yielded effects that were not seen by other overexpression or deletion experiments, even under similar growth conditions. The results presented here show that the overexpression of self-assembling fragments yield a variety of dominant negative phenotypes. Reducing the activity of protein complexes allows for new aspects of the physiological process to be investigated.