Catalase-peroxidase (KatG) of Mycobacterium tuberculosis is a bifunctional heme enzyme that has been shown to play an important role in the activation of a first line drug, isoniazid (INH), used in the treatment of tuberculosis infection. Mutations in the katG gene have been found to be associated with INH resistance. The most commonly encountered mutation is the Ser315Thr point mutation. In this dissertation, the x-ray crystallographic structures of MtbKatG and the mutant enzyme KatG[S315T] are presented to explore the molecular basis of the INH activation and resistance. The structure is dimeric and contains a heme cofactor in each subunit of the dimer. The most important change in KatG[S315T] is due to the presence of the methyl group of the threonine 315 side chain, which is located at the narrowest part of the substrate channel. The protruding methyl group effectively constricts the accessibility to the heme by closing down the dimensions of the channel, constraining the substrate entrance. VirB11 of Brucella abortus is a hexameric ATPase that belongs to the type IV secretion system. The crystal structure of BaVirB11 was found to contain six molecules per asymmetric unit. The Walker A (P loop), His box, and Glu box from the C-terminal domain are located at the interface of the N- and C-terminal domain. A large conformational change was found in the linker region when compared with that of HP0525 structure, the VirB11 analogous from H. pylori. To elucidate the functional role of each domain, seven functional mutations were generated and used for biochemical studies. The GER motif and the linker region were found to be crucial for ATP hydrolysis activity of BaVirB11. Mutations in the GER motif (R101Q) and the linker region (R120E) of BaVirB11 completely abolish the ATP hydrolysis activity of the enzyme. The binding affinities of the two mutants to the ATP; however, are similar to that of the wild-type enzyme, indicating that mutation in the GER motif or the linker region has no effect on ATP binding.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / A bactÃria Helicobacter pylori, à um agente etiolÃgico bem estabelecido para o desenvolvimento de lesÃes gÃstricas como gastrite, Ãlcera pÃptica, metaplasia e doenÃas malignas, com alta incidÃncia de infecÃÃo em todo mundo, porÃm cerca de 80% dos indivÃduos infectados permanecem assintomÃticos e apenas uma minoria desenvolve doenÃas a ela relacionadas. Estudos tÃm sido realizados na tentativa de identificar a relaÃÃo de genes determinantes da patogenicidade de H. pylori, entretanto, atà o momento apenas os genes cagA e o alelo de vacA s1m1 sÃo considerados marcadores de virulÃncia para o desenvolvimento de lesÃes gÃstricas mais graves. A bactÃria H. pylori possui uma alta variabilidade genÃtica, sendo que um dos mecanismos propostos para o desenvolvimento de lesÃo seria atravÃs da inflamaÃÃo. DiferenÃas na intensidade de respostas inflamatÃrias poderiam ser decorrentes do perfil genotÃpico da cepa infectante. Recentes trabalhos apontam a importÃncia dos genes cagE, virB11 de H. pylori, em cÃncer gÃstrico. Entretanto, estudos em lesÃes gÃstricas sÃo restritos. Assim, o objetivo deste trabalho foi determinar o perfil genotÃpico das cepas de H. pylori quanto a presenÃa dos genes de virulÃncia cagA, cagE, virB11, vacA e flaA, circulantes no estado do Cearà em 201 casos de lesÃes gÃstricas de diferentes gravidades, coletadas de pacientes dispÃpticos atendidos em trÃs hospitais de Fortaleza-CE. A detecÃÃo de H. pylori foi feita atravÃs da amplificaÃÃo do gene ureC, os genes estudados por amplificaÃÃo de fragmentos especÃficos, usando a tÃcnica de PCR, foram observados em gel de agarose 1% e poliacrilamida a 6% e 8%. Neste estudo houve um predomÃnio do sexo feminino 59% (119/201), principalmente na faixa etÃria (15-44) 30% (61/201), alta taxa de infecÃÃo por H. pylori 97,5% (196/201). A gastrite crÃnica ativa (GCA) foi a lesÃo gÃstrica mais frequente (55,7%;112/201), associada a pacientes na faixa etÃria de 15-44 (36,6% : 41/112) opondo-se à metaplasia intestinal em que, a frequÃncia dos casos aumentou com a idade sendo maior em pacientes mais velhos 46% (16/35), o que concorda com a literatura. O Ãnico caso de displasia ocorreu numa paciente > 65 anos. As lesÃes gÃstricas foram predominantemente localizadas no antro. O gene cagA foi mais frequente na gastrite crÃnica ativa (GCA), estando tambÃm em alta frequÃncia na gastrite atrÃfica (GA) e metaplasia intestinal (MI). Na GCA foi observado tambÃm alta frequÃncia dos genes cagE, virB11, vacAm1 e flaA, com diferenÃa estatÃstica, quando comparada com a gastrite crÃnica inativa (GCI) (cagA - p=0,007 cagE- p=0,000, virB11 - p=0,005, vacAm1- p=0,047 e flaA - p=0,001), sendo que os genes virB11 e flaA foram mais frequentes na GCA do que na Ãlcera. Os alelos s1 e m1 de vacA , bem como a combinaÃÃo s1m1 foram os mais frequentes nas lesÃes gÃstricas. Os casos H. pylori positivos foram agrupados de acordo com a presenÃa dos genes estudados, levando em consideraÃÃo a presenÃa do alelo s1 e os genes da ilha. Nessas anÃlises foi observada maior frequÃncia de cepas contendo os genes vacA s1 e [Ia (cagA+, cagE+ e virB11+ ) + Ib (cagA+ e virB11+; cagE+ e virB11+) ; 47,7% ] na gastrite crÃnica ativa em relaÃÃo a gastrite crÃnica inativa (GCI), esta com maior frequÃncia de cepas dos grupos [Ic (cagA+ ou cagE+ ou virB11+ ou cagA+ e cagE+) +Id (ureC+); 62%]. Adicionalmente, maior frequÃncia de cepas pertencentes aos grupos Ia e Ib foi observada na metaplasia intestinal incompleta, (59%), enquanto que na metaplasia intestinal completa uma maior frequencia de cepas pertencentes aos grupos Ic + Id, (78%) (p=0,027). Todos os casos de gastrite atrÃfica e Ãlcera eram do grupo I, e um Ãnico caso de displasia pertencia ao grupo Ia. Esses dados evidenciam uma associaÃÃo de cepas com genÃtipos mais virulentos em lesÃes com potencialidade de malignizaÃÃo. / A bactÃria Helicobacter pylori à um agente etiolÃgico bem estabelecido para o desenvolvimento de lesÃes gÃstricas como gastrite, Ãlcera pÃptica, metaplasia e doenÃas malignas, com alta incidÃncia de infecÃÃo todo mundo, porÃm cerca de 80% dos indivÃduos infectados permanecem assintomÃticos e apenas uma minoria desenvolve doenÃas a ela relacionadas. Estudos tem sido realizados na tentativa de identificar a relaÃÃo de genes determinantes da patogenicidade de H. pylori, entretanto, atà o momento apenas os genes cagA e o alelo de vacA s1m1 sÃo considerados marcadores de virulÃncia para o desenvolvimento de lesÃes gÃstricas mais graves. A bactÃria H. pylori possui uma alta variabilidade genÃtica sendo que um dos mecanismos propostos para o desenvolvimento de lesÃo seria atravÃs da inflamaÃÃo. DiferenÃas na intensidade de respostas inflamatÃrias poderiam ser decorrentes do perfil genotÃpico da cepa infectante. Recentes estudos apontam a importÃncia dos genes cagE, virB11 de H. pylori, em cÃncer gÃstrico. Entretanto, estudos em lesÃes gÃstricas sÃo restritos. Assim, o objetivo deste trabalho foi determinar o perfil genotÃpico das cepas de H. pylori quanto a presenÃa dos genes de virulÃncia cagA, cagE, virB11, vacA e flaA, circulantes no estado do Cearà em 201 casos de lesÃes gÃstricas de diferentes gravidades, coletadas de pacientes dispÃpticos atendidos em trÃs hospitais de Fortaleza-CE. A detecÃÃo de H. pylori foi feita atravÃs da amplificaÃÃo do gene ureC, e os genes estudados por amplificaÃÃo de fragmentos especÃficos, usando a tÃcnica de PCR, e foram observados em gel de agarose 1% e poliacrilamida a 6% e 8%. Nesse estudo houve um predomÃnio do sexo feminino 59% (119/201), principalmente na faixa etÃria (15-44) 30% (61/201), e alta taxa de infecÃÃo por H. pylori 97,5% (196/201). A gastrite crÃnica ativa (GCA), foi a lesÃo gÃstrica mais frequente (55,7%;112/201), associada a pacientes na faixa etÃria de 15-44 (36,6% : 41/112) opondo-se à metaplasia intestinal onde a frequÃncia dos casos aumentou com a idade sendo maior em pacientes mais velhos 46% (16/35), o que concorda com a literatura. O Ãnico caso de displasia ocorreu numa paciente > 65 anos. As lesÃes gÃstricas foram predominantemente localizadas no antro. O gene cagA foi mais frequente na gastrite crÃnica ativa (GCA), estando tambÃm em alta frequÃncia na gastrite atrÃfica (GA) e metaplasia intestinal (MI). Na GCA foi observado tambÃm alta freqÃÃncias dos genes cagE, virB11, vacAm1 e flaA com diferenÃa estatÃstica quando comparada com a gastrite crÃnica inativa (GCI) (cagA - p=0,007 cagE- p=0,000, virB11 - p=0,005, vacAm1- p=0,047 e flaA - p=0,001), sendo que os genes virB11 e flaA foram mais frequentes na GCA que na Ãlcera. Os alelos s1 e m1 de vacA , bem como a combinaÃÃo s1m1 foram os mais frequentes nas lesÃes gÃstricas. Os casos H. pylori positivos foram agrupados de acordo com a presenÃa dos genes estudados, levando em consideraÃÃo a presenÃa do alelo s1 e os genes da ilha. Nestas anÃlises foi observada maior frequÃncia de cepas contendo os genes vacA s1 e [Ia (cagA+, cagE+ e virB11+ ) + Ib (cagA+ e virB11+; cagE+ e virB11+) ; 47,7% ] na gastrite crÃnica ativa em relaÃÃo a gastrite crÃnica inativa (GCI), esta Ãltima com maior frequÃncia de cepas dos grupos [Ic (cagA+ ou cagE+ ou virB11+ ou cagA+ e cagE+) +Id (ureC+); 62%]. Adicionalmente, maior frequÃncia de cepas pertencentes aos grupos Ia e Ib foi observada na metaplasia intestinal incompleta, (59%), enquanto que na metaplasia intestinal completa uma maior frequencia de cepas pertencentes aos grupos Ic + Id, (78%) (p=0,027). Todos os casos de gastrite atrÃfica e Ãlcera eram do grupo I, e o Ãnico caso de displasia pertencia ao grupo Ia. Esses dados evidenciam uma associaÃÃo de cepas com genÃtipos mais virulentos em lesÃes com potencialidade de malignizaÃÃo. / The bacterium Helicobacter pylori is a well-established etiological factor in the development of gastric lesions such as gastritis, peptic ulcers, metaplasia and malignancy. The incidence of infection by this pathogen is high worldwide, but about 80% of infected individuals remain asymptomatic, and only a minority develops related diseases. Many studies have been conducted in an attempt to identify the involvement of genes in determining the pathogenicity of H. pylori, but so far, only the genes cagA and vacA allele s1m1 are considered virulence markers for the development of the more severe gastric lesions. H. pylori bacteria have a high genetic variability and one of the proposed mechanisms for lesion development is through inflammation. Differences in the intensity of inflammatory responses could be due to the genotypic profile of the infecting strain. Recent studies indicate the importance of the genes cagE and virB11, but mostly involving gastric cancer, while their role in gastric lesions is limited. The objective of this study was to determine the genetic subtypes of H. pylori strains and the presence of the virulence genes cagA, cagE, virB11 and flaA genes and vacA alleles, circulating in Ceara state, Brazil. Samples were collected from 201 cases of gastric lesions of varying severity, in dyspeptic patients treated at three hospitals in Fortaleza, Ceara State. The detection of H. pylori was performed using ureC gene amplification by PCR, and the detection of the genes studied was carried out by amplification of gene-specific fragments separated in 1% agarose gels. The sample was predominantly female (59%, 119/201) and mainly in the age group 15-44 years old (30%, 61/201), and had a high rate of H. pylori infection (97.5%, 196/201). Active chronic gastritis (ACG) was the most common gastric lesion (55.7%, 112/201), associated with patients aged 15-44 (36.6%, 41/112), unlike intestinal metaplasia, in which the frequency of cases increased with age, being higher in older patients (46%, 16/35), which agrees with the literature. A single case of dysplasia occurred in a patient > 65 years. The lesions were predominantly located in the gastric antrum and 30% of the cases had lesions located in the body and antrum simultaneously. The cagA gene was more frequent in ACG, showing a statistically significant correlation (r = 0.220, p = 0.007); it also showed a high frequency in atrophic gastritis and in intestinal metaplasia. In ACG, a high frequency of the genes cagE, virB11, flaA and vacAm1 was also statistically associated when compared to chronic inactive gastritis (ICG) (cagA - p = 0.007, cagE - p = 0.000, virB11 - p = 0.005, vacAm1 p = 0.047 and flaA - p = 0.001), and the genes virB11 and flaA were more frequent in ACG than in ulcer. The vacA alleles s1 and m1, and the combination s1m1, were the most frequent ones in gastric lesions. Considering the genotypes of H. pylori grouped by the presence of the genes studied, we observed a higher frequency of the most virulent strains in the ACG group (Ia + Ib, 47.7%) when compared to ICG, the latter showing a higher frequency of less virulent strains (Ic + Id, 62%). Additionally, a higher frequency of more virulent strains, belonging to groups Ia and Ib, was observed in incomplete intestinal metaplasia (59%), while in complete intestinal metaplasia an increased frequency of less virulent strains, belonging to the groups Ic + Id (78%) (p = 0.027), was found. All cases of atrophic gastritis and ulcer were in group I, and the single case of dysplasia belonged to group Ia (high virulence). These data indicate the important role of more virulent strains in potential malignant lesions.

Helicobacter pylori est une bactérie à Gram négatif qui colonise plus de 50% de la population humaine. Cette bactérie est l'un des pathogènes les plus présents dans la population et la colonisation se fait dans l'enfance et l'adolescence. H. pylori est responsable de l'apparition de maladies gastriques chez l'humain comme des ulcères gastriques, mais aussi des cancers gastriques. Plusieurs mécanismes contribuent aux maladies gastriques dont une infection chronique à long terme ainsi que des facteurs de virulence comme le système de sécrétion de type 4 (SST4). Le SST4 forme une seringue protéique utilisée par la bactérie pour injecter la protéine CagA dans les cellules humaines. Cette protéine a été la première protéine bactérienne classifiée comme une oncoprotéine par sa capacite à interférer et modifier de nombreuses fonctions et signaux métaboliques des cellules épithéliales gastriques. Afin d'éradiquer Helicobacter, une antibiothérapie est utilisée, cependant depuis les 10 dernières années plus de 50% des bactéries isolées de patients ont été identifiés comme étant porteuses de résistances contre aux moins un antibiotique de première ligne. L’utilisation de petites molécules organiques capables d'interférer avec les facteurs de virulence est une alternative intéressante à la thérapie aux antibiotiques. L'utilisation de ces molécules possède des avantages dont la faible pression de sélection de résistance parce qu’elles n’impactent pas des fonctions vitales des bactéries. Le SST4 de H. pylori est composé de nombreuses protéines essentielles qui pourraient être de potentielles cibles pour des molécules inhibitrices. Nous avons choisi la cible Cagα, une ATPase homologue à VirB11 de Agrobacterium tumefaciens. Cette protéine est essentielle pour l’injection de CagA. Précédemment, notre laboratoire a identifié une petite molécule nommée 1G2 qui était capable d’interagir avec Cagα et de diminuer l’induction de l’interleukine 8 produit par les cellules gastriques lors de l’infection par des souches de H. pylori possédant un SST4 fonctionnel. A partir d’une structure cristallographique de Cagα liée à 1G2 et nous avons créé des protéines Cagα avec des mutations aux site de liaison de 1G2. En utilisant la fluorimétrie différentielle à balayage (DSF) nous avons pu identifier les acides aminés qui contribuent à la liaison de 1G2 (K41, R73 et F39). Basé sur cette information nous avons utilisé la chimie médicinale pour créer une librairie de molécules dérivées de 1G2 dans le but d’identifier des inhibiteurs plus puissants. Après avoir éliminé les molécules ayant un effet toxique sur les cellules gastriques et H. pylori, nous avons sélectionné cinq molécules (1313, 1338, 2886, 2889 et 2902) qui inhibent la production d’IL-8 plus que 1G2 dans notre modèle d’infection cellulaire. Nous avons montré par DSF que les molécules interagissent toujours avec Cagα et 1338, 2889 et 2902 sont des inhibiteurs plus puissants de son activité d’ATPase. Avec le modèle d’infection, nous avons déterminé que les cinq molécules n’affectent par la présence de CagA dans le lysat de l’infection. Cependant, nous avons observé par microscopie électronique à balayage que le SST4 pilus n’était pas présent en présence des inhibiteurs. En plus, nous avons testé les effets de 1G2 sur des souches de H. pylori résistantes, à un ou plusieurs antibiotiques de première ligne, isolées de biopsie gastriques de patients. Comme dans le cas de la bactérie modèle de laboratoire, nous avons observé une diminution de l’induction des IL-8 lors de l’infection ainsi qu’une inhibition de la formation du SST4 pilus. Nous avons aussi identifié que le gène de la protéine Cagα d’une des bactéries résistantes à 1G2 (souche #3822) porte un remplacement de R73 à K ce qui pourrait expliquer la résistance à 1G2. Pour conclure, nous avons dans cette étude caractérisé le site de liaison de 1G2 à Cagα et nous avons identifié des molécules qui sont plus puissantes comme inhibiteurs que 1G2. / Helicobacter pylori is a Gram-negative bacterium that colonizes more than 50% of the human population. This bacterium is one of the most common pathogens in the population and colonization occurs in childhood and adolescence. H. pylori is implicated in the manifestation of gastric diseases in humans such as gastric ulcers and also gastric cancer. Several mechanisms are involved in the formation of gastric diseases including long-term chronic infection as well as virulence factors such as the type 4 secretion system (T4SS). The T4SS forms a protein syringe used by the bacteria to inject the protein CagA into mammalian cells. This protein is the first bacterial protein classified as an oncoprotein by its ability to interact with numerous metabolic functions of gastric epithelial cells. To eradicate Helicobacter, antibiotic therapy is used, but for the last 10 years more than 50% of the bacteria isolated from patients have been identified as carrying resistance against at least one first-line antibiotic. The use of small molecules capable of interfering with virulence factors is being studied as an alternative to antibiotic therapy. The use of these molecules has many advantages, and they may cause lower selection pressure for resistance than antibiotics. The H. pylori T4SS is composed of many essential proteins that could be potential targets for inhibitory molecules. We chose the target Cagα, an ATPase homologous to the model VirB11 from Agrobacterium tumefaciens. This protein is essential for the injection of CagA. Previously, our laboratory identified a small molecule coined 1G2 that interacts with Cagα and decreases the induction of interleukin-8 produced by gastric cells upon infection with H. pylori strains with functional T4SS. Based on a crystallographic study of Cagα bound to 1G2, we created Cagα proteins with mutations at the 1G2 binding site. Using differential scanning fluorimetry, we identified amino acids that contribute to 1G2 binding (K41, R73 and F39). Based on these observations, we used medicinal chemistry to create a library of molecules derived from 1G2 to create more potent inhibitors. After eliminating the molecules with a toxic effect on gastric cells and H. pylori growth, we selected five molecules with stronger effects than 1G2 on IL8 induction in our cell infection model (1313, 1338, 2886, 2889 and 2902). We observed by DSF that the molecules interact with Cagα and 1338, 2889 and 2902 are stronger inhibitors of the ATPase 8 activity than 1G2. With our infection model, we determined that the five molecules do not affect the presence of CagA. However, by scanning electron microscopy we observed that the T4SS pilus was not present. In addition to the tests on a laboratory model bacterium, we evaluated 1G2 on resistant strains of H. pylori isolated from gastric biopsy from patients. Similar to the laboratory model bacterium, 1G2 decreased IL-8 induction and inhibited T4SS pilus formation. We have also identified that strain #3822 that is resistant to 1G2 carries a R73 to K mutation in the Cagα gene, which could explain the 1G2 resistance. To conclude, we have here characterized the 1G2 binding site on Cagα and we created inhibitors that are more potent than 1G2.