Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-12-18T13:15:58Z No. of bitstreams: 2 Tese - Lívia do Carmo Silva - 2017.pdf: 33507637 bytes, checksum: 4e4e645677db485bad788889218760cd (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-12-18T13:17:23Z (GMT) No. of bitstreams: 2 Tese - Lívia do Carmo Silva - 2017.pdf: 33507637 bytes, checksum: 4e4e645677db485bad788889218760cd (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-12-18T13:17:23Z (GMT). No. of bitstreams: 2 Tese - Lívia do Carmo Silva - 2017.pdf: 33507637 bytes, checksum: 4e4e645677db485bad788889218760cd (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-12-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Paracoccidioidomycosis (PCM) is the cause of several deaths from systemic mycoses. The etiological agents of PCM belong to the genus Paracoccidioides spp., restricted to the regions of Latin America. The infection is acquired by inhaling conidia that primarily settle in the lungs, and can spread to other organs. The treatment of PCM is commonly performed with administration of antifungals such as amphotericin B, itraconazole and co-trimoxazole. The toxicity and side effects of antifungals, added over the long treatment time, has stimulated research for new bioactive compounds. Thus, with the objective of to identify the anti- Paracoccidioides spp. of compounds derived from chalcones and nitrogen heterocycles and to identify the molecular targets and mode of action of argentilactone and RRF-128 in P. brasiliensis were used methodologies such as shape-based virtual screening, minimum inhibitory and fungicidal concentration, cytotoxicity in fibroblast cells, interactions between antifungal, proteomic and chemoproteomics. After the virtual screening, 33 chalcones were proposed as anti-Paracoccidioides molecules, being this activity confirmed by biological assays. Among the compounds, eight aryl and heteroaryl chalcones had selectivity index considered attractive, highlighting Labmol-75 with selectivity index of 64.4 in P. lutzii and 32.2 in P. brasiliensis. In addition, Labmol-75 showed additive interaction with amphotericin B and co-trimoxazole. In relation to nitrogen heterocycles, of the 22 tested compounds, RRF-128 was the most important. RRF-128 showed to inhibit the growth of P. brasiliensis in low concentrations, selectivity index of 64.10, interacting synergistically with itraconazole. In addition, the proteomic analyzes of P. brasiliensis in the presence of the compound provided evidence that the energy metabolism of the fungus is induced to produce acetyl-CoA and that the synthesis of membrane sterols is impaired. In relation to argentilactone, 331 proteins were identified as ligands to this compound in the chemoproteomics assay and after being functionally classified, it was observed that the most representative functional classes are related to amino acid metabolism, energetic and detoxification. The inhibition of the enzymatic activity of malate dehydrogenase, citrate synthase and pyruvate dehydrogenase by argentilactone was confirmed. In addition, argentilactone induced the production of reactive oxygen species, and inhibited chitin and glucan synthesis and arrest of the cell cycle in the G0/G1 phase. From these results, it can be concluded that the compounds Labmol-75, RRF- 128 and argentilactone showed to be promising antifungal agents. / Paracoccidioidomicose (PCM) é a causa de várias mortes por micoses sistêmicas. Os agentes etiológicos da PCM pertencem ao gênero Paracoccidioides spp., restritos às regiões da América Latina. A infecção é adquirida por inalação de conídios que primariamente se instalam nos pulmões, podendo disseminar para outros órgãos. O tratamento da PCM é comumente realizado com a administração de antifúngicos como anfotericina B, itraconazol e co-trimoxazol. A toxidade e efeitos colaterais dos antifúngicos, adicionado ao longo tempo de tratamento, têm impulsionado pesquisas por novos compostos bioativos. Assim, com objetivo de identificar a atividade anti-Paracoccidioides spp. de compostos derivados de chalconas e heterociclos nitrogenados e identificar os alvos moleculares e modo de ação de argentilactona e RRF-128 em P. brasiliensis foram empregadas metodologias como rastreio virtual shape-based, concentração inibitória e fungicida mínima, citotoxicidade em células de fibroblastos, interações entre antifúngicos, proteômica e quimioproteômica. Após o rastreio virtual, 33 chalconas foram propostas como moléculas anti-Paracoccidioides, sendo esta atividade confirmada pelos ensaios biológicos. Dentre os compostos, oito aril e heteroaril chalconas tiveram índices de seletividades considerados promissores, destacando-se Labmol-75 com índice de seletividade de 64,4 em P. lutzii e 32,2 em P. brasiliensis. Além disso, Labmol-75 apresentou interação aditiva com anfotericina B e co-trimoxazol. Dos 22 compostos heterociclos nitrogenados, o RRF-128 apresentou resultados promissor. RRF-128 foi capaz de inibir o crescimento de P. brasiliensis em baixas concentrações e apresentou índice de seletividade de 64,10. Além disso, RRF-128 interagiu de forma sinérgica com itraconazol. As análises proteômicas de P. brasiliensis na presença de RRF-128 forneceram evidências de que o metabolismo energético do fungo é direcionado para produção de acetil-CoA e que a síntese de esteróis de membrana está comprometida. Quanto à argentilactona, 331 proteínas foram identificadas como ligantes a este composto utilizando abordagem quimioproteômica e após serem classificadas funcionalmente, observou-se que as classes funcionais mais representativas são relacionadas ao metabolismo de aminoácidos, energético e detoxificação. A inibição da atividade enzimática de malato desidrogenase, citrato sintase e piruvato desidrogenase por argentilactona foi confirmada. Além disso, argentilactona induziu a produção de espécies reativas de oxigênio, inibiu síntese de quitina e glicana, bem como o aprisionamento do ciclo celular na fase G0/G1. A partir destes resultados, conclui-se que os compostos Labmol-75, RRF-128 e argentilactona são promissores antifúngicos.

No description available.

Post-translationale Modifikationen (PTMs) sind wesentlich für die Regulierung von zellulären Mechanismen. Um diese Prozesse besser zu verstehen, ist es essentiell Methoden für deren Erforschung zu entwickeln. In dieser Arbeit wurden zwei chemoproteomische Ansätze entwickelt, um die PTMs, Proteinphosphorylierung und Proteinpyrophosphorylierung zu untersuchen. Die Proteom-weite Erforschung von Proteinphosphorylierungen beruht gewöhnlich auf der LC-MS/MS-Analyse von enzymatisch verdauten Proteomen und da die Phosphorylierung von niedriger Abundanz ist, wird ein Phosphopeptid-Anreicherungsschritt benötigt. Die Identifizierung von bestimmten Phosphopeptiden ist allerdings abhängig von der gewählten Anreicherungsmethode. Die Entwicklung von neuen Prozeduren ist daher bedeutsam, um neue Phosphorylierungsstellen zu identifizieren. Im ersten Projekt wurde eine milde und selektive Phosphopeptid-Anreicherungsmethode entwickelt und optimiert. Die Methode zeigte die Fähigkeit Phosphopeptide anzureichern und somit das Potential, das Repertoire der vorherigen Methoden zu erweitern, um neue Phosphorylierungsstellen zu identifizieren. Proteinpyrophosphorylierung ist eine unlängst identifizierte PTM, die nicht-enzymatisch an Proteine angefügt wird und es ist nur wenig ist über ihre Funktion bekannt. Vorherige Studien wiesen darauf hin, dass diese Modifikation enzymatisch entfernt wird, allerdings sind die verantwortlichen Enzyme („Proteinpyrophosphatasen“) nicht bekannt. Hier wurde eine Peptidaffinitätsmethode entwickelt, um potentielle Pyrophosphatasen und weitere interagierende Proteine aus humanen Zellen zu identifizieren. Damit wurden 6 Phosphatasen als potentielle Pyrophosphatase-Kandidaten identifiziert und weitere interagierende Proteine gaben Aufschlüsse über die Funktion der Proteinpyrophosphorylierung. Dadurch wurde das Potential der Methode aufgezeigt, interagierende Proteine der Proteinpyrophosphorylierung zu identifizieren, um die zelluläre Rolle zu verstehen. / Post-translational modifications (PTMs) are crucial for the regulation of cellular mechanisms. To better understand these processes, the development of chemical tools to investigate them is of high importance. In this thesis, two chemoproteomics approaches were established to investigate the PTMs protein phosphorylation and protein pyrophosphorylation. The proteome-wide study of protein phosphorylation usually relies on LC-MS/MS analysis of enzymatically digested proteomes, requiring a phosphopeptide enrichment step, due to the low abundance of phosphorylation. However, the identification of certain sets of phosphopeptides is dependend on the choice of enrichment method. Therefore, the development of new workflows is important to identify new phosphorylation sites. In the first project, a mild and selective phosphopeptide enrichment method was developed and optimized. The method was able to enrich phosphopeptides and therefore, showed the potential to complement the repertoire of current methods to identify new phosphorylation sites. Protein pyrophosphorylation is a recently discovered PTM, which is non-enzymatically attached to proteins and there is only sparse knowledge about the function. Previous studies have indicated the enzymatic removal of this modification, but the responsible enzymes (‘protein pyrophosphatases’) are unknown. Here, a peptide affinity capture method was developed to identify potential pyrophosphatases and further interacting proteins from human cells. Therewith, 6 phosphatases were identified as potential pyrophosphatase candidates and further interacting proteins gave insights into the function and mechanisms of protein pyrophosphorylation. Thereby, the potential of this method was demonstrated to identify interacting proteins of protein pyrophosphorylation to understand the cellular role.

La molécule UM171 amplifie les greffons de cellules souches hématopoïétiques. Cela permet l’utilisation de greffons de cellules souches provenant du sang de cordon ombilical pour des greffes chez les patients adultes, notamment dans les cas de cancers du sang. Bien que le mode d’action biologique d’UM171 soit connu, la protéine à laquelle se lie UM171 reste indéterminée. Le but de ce projet est d’identifier cette protéine-cible. Afin d’atteindre cet objectif, cette étude mise sur la conception, la synthèse, puis l’utilisation de sondes d’affinité. Dans ce mémoire, deux types de sonde sont présentées : les sondes d’affinité non covalentes et les sondes d’affinité photoréactives. Dans un premier temps, une sonde non covalente est synthétisée. Cette sonde, très active, est ensuite utilisée dans un essai de chimio-protéomique. Elle permet d’identifier les protéines KBTBD4, RCOR1 et HDAC2 par buvardage de western. Dans un deuxième temps, une sonde photoréactive est conçue, puis synthétisée. Considérant l’hypothèse de la présence d’un acide carboxylique dans le site actif de la protéine-cible, cette sonde exploite une fonctionnalité 2,5-diaryltétrazole comme groupement photoréactif sélectif aux acides carboxyliques. Afin de maximiser l’activité de cette sonde, celle-ci est développée grâce à l’étude de plusieurs analogues, dont la synthèse est également rapportée. Dans un troisième temps, la sonde photoréactive est utilisée dans deux essais de chimio- protéomique. Ces essais ont permis d’identifier la protéine CUL3 par spectrométrie de masse. La protéine CAND1 a également été identifiée, de façon moins significative. / The small molecule UM171 amplifies hematopoietic stem cells grafts. This allows the use of umbilical cord blood stem cells grafts for transplants in adult patients, for example in the case of blood cancer. Although the biological mode of action of UM171 is known, the protein to which UM171 binds remains undetermined. The aim of this project is to identify this target protein. To achieve this goal, this study focuses on the design, synthesis, and use of affinity probes. In this thesis, two types of probes are presented: non-covalent affinity probes and photoreactive affinity probes. First, a non-covalent probe is synthesized. This probe revealed to be very potent and is used in a chemoproteomics assay. The proteins KBTBD4, RCOR1 and HDAC2 are identified by western blotting. Second, a photoreactive probe is designed, and then synthesized. Assuming the presence of a carboxylic acid in the active site of the target protein, this probe exploits a 2,5-diaryltetrazole functionality as its photoreactive group selective to carboxylic acids. To maximize the activity of this probe, it is designed by studying several analogues, the synthesis of which is also reported. Third, the photoreactive probe is used in two chemoproteomics assays. These led to the identification of the protein CUL3 by mass spectrometry. The protein CAND1 was also identified, less significantly.

La leucémie myéloïde aiguë (AML) est une forme agressive du cancer du sang qui est caractérisée par un haut taux de mortalité, tant chez les patients plus jeunes que plus âgés. Le développement de nouveaux traitements est ardu par l’hétérogénéité de cette maladie. Dans cette perspective, les études CCC phénotypiques menées à l’IRIC visent à déceler de nouveaux composés ayant une synergie contre des souches AML primaires de patients en vue de personnaliser les thérapies selon leur profil cytogénétique. Il a été découvert que le MG624, un antagoniste des récepteurs nicotiniques α7-nAChR inhibant la prolifération des cellules cancéreuses dans les SCLC, démontrait une activité spécifique contre la souche AML5. Dans cette recherche, les voies de synthèse des analogues du MG624 sont explorées afin de concevoir une série de sondes permettant d’identifier les cibles potentielles via une approche chimioprotéomique par affinité dans le lysat cellulaire. Cette méthode a permis d’identifier trois cibles potentielles à l’aide d’un essai par compétition et de contrôles négatifs, soit XIAP, NQO2 et U119B, toutes impliquées dans différentes formes de cancer. Ces expériences ont mené à une meilleure compréhension des motifs procurant l’activité du composé chez les cellules leucémiques. La synthèse d’une sonde par photoaffinité a ensuite été élaborée pour éventuellement lier les protéines identifiées de manière covalente dans l’environnement cellulaire natif afin de valider ces cibles. / Acute myeloid leukemia (AML) is an aggressive form of blood cancer characterized by a high mortality rate in both younger and older patients. The development of new treatments is hampered by the heterogeneity of this disease, which has led to the phenotypic CCC studies carried out at IRIC to identify new compounds that exhibit synergies against primary AML patient strains to personalize therapies according to their cytogenetic profile. MG624, an α7-nAChR nicotinic receptor antagonist that inhibits cancer cell proliferation in SCLC, was found to have specific activity against AML5. In this research, the synthetic pathways of MG624 analogues are explored to design a series of probes to identify potential targets via an affinity-based chemoproteomic approach in cell lysate. This method identified three potential targets using a competitive assay and negative controls, namely XIAP, NQO2 and U119B, all implicated in different forms of cancer. These experiments led to a better understanding of the motifs that provide the compound's activity in leukemic cells. A photo-affinity probe synthesis was then developed to covalently bind the identified proteins in the native cellular environment to eventually validate these targets.