El virus de la hepatitis G (GBV-C/HGV) es un virus ARN perteneciente a la familia Flaviviridae. Su prevalencia, basada en la positividad del ARN, oscila entre el 1 y el 4% en la población general. Sin embargo este porcentaje aumenta hasta el 20-30% en los individuos expuestos a sangre o sus derivados, en individuos infectados por el virus de la hepatitis C o por el virus de la inmunodeficiencia humana (HIV), hecho que indica que se transmite principalmente por vía parenteral. Aunque no está claro su potencial patogénico, los estudios más recientes sugieren que la infección por este virus reduce la mortalidad en los pacientes infectados por el HIV, de ahí el interés en disponer de una herramienta que permita el diagnóstico de la infección por GBV-C/HGV de un modo rápido y sencillo. Desde hace años, los péptidos sintéticos se vienen utilizando en sistemas de diagnóstico para muchas enfermedades, sin embargo, los péptidos lineales que mimetizan epítopos B son débilmente reconocidos por los anticuerpos, y por ello, existe la tendencia de utilizar combinaciones más complejas que permitan mejorar tanto la sensibilidad como la especificidad de los ensayos.En esta tesis se han diseñado y sintetizado, utilizando la metodología de síntesis en fase sólida, construcciones peptídicas en las que se combinan regiones de proteínas de envoltura y no estructurales. Se han sintetizado tanto péptidos quiméricos, que contienen más de un epítopo (lineales y ramificados), como péptidos cíclicos en los que los epítopos sufren restricción de movilidad. La capacidad antigénica de las construcciones sintéticas se ha evaluado utilizando principalmente la técnica del enzimoinmunoensayo (ELISA) aunque también se ha investigado la utilidad de la técnica de la resonancia del plasmón de superficie (SPR) para detectar la presencia de anticuerpos anti-GBV-C/HGV en muestras de suero de individuos pertenecientes tanto a los grupos de riesgo como en la población sana. Además, se ha realizado un estudio conformacional con la finalidad de establecer una correlación entre la estructura secundaria adoptada por los péptidos y su capacidad antigénica. Finalmente, se ha estudiado la capacidad inmunogénica de las construcciones peptídicas en animales de experimentación. Los resultados obtenidos muestran, por un lado, que las construcciones en las que se combinan varios epítopos son las que presentan una mejor precisión diagnóstica, y por otro lado, que la introducción de restricción de movilidad permite incrementar la sensibilidad mostrada por la molécula precursora lineal. / "Design and synthesis of peptides for serodiagnose of the hepatitis G virus (GBV-C/HGV) infection". The GB virus C, so called hepatitis G virus (GBV-C/HGV), is a single-strand RNA virus belonging to the Flaviviridae family. The prevalence rate of GBV-C/HGV in healthy blood donors is 1-4% in worldwide and about 20-35% in high risk populations, thus indicating that this virus is transmitted via the parenteral route. Although controversial data exit concerning the potential to cause hepatitis in humans recent studies suggest that coinfection with HIV is associated with prolonged survival. For this reason it would be interesting to find an easy tool to diagnose this apparently non-pathogenic virus. In recent years, synthetic peptides that mimic specific epitopes of infectious agents have been used in diagnostic systems for various diseases. The main drawback of this approach is that peptides representing topographic B-cell epitopes are poorly recognised by antibodies. There is a tendency toward using chimeric to avoid those problems and to improve the sensitivity and specificity of the assays.In this thesis, new putative epitopes located both in envelope and in nonstructural proteins of GBV-C/HGV were synthesized using solid-phase chemistry. The corresponding synthetic peptides, obtained in linear, multimeric and cyclic forms, were used as antigens in ELISA and in real-time bioespecific interaction measurements (SPR) to detect GBV-C/HGV-specific antibodies in different panels of human sera. Furthermore, CD and FT-IR have been used in conjunction to characterize the conformational changes therein with synthetic constructs that could explain their different antigenicity.The results obtained showed, on one hand, that the combination of different antigens seems to be necessary to ensure good sensitivity and more specificity and, on the other hand, that cyclic compounds show higher ability to recognize anti-GBV-C/HGV antibodies than its parent peptide. Our results offer a new approach to develop new diagnostic peptide based biosensors for serodiagnosis of GBV-C/HGV infection.

Submitted by Nuzia Santos (nuzia@cpqrr.fiocruz.br) on 2016-04-12T19:03:42Z No. of bitstreams: 1 Dissertacao_BCM_EmersondeCastroBarbosa.pdf: 6431092 bytes, checksum: 15243f7b5580193cfc7b7ad5b935a77a (MD5) / Approved for entry into archive by Nuzia Santos (nuzia@cpqrr.fiocruz.br) on 2016-04-12T19:06:13Z (GMT) No. of bitstreams: 1 Dissertacao_BCM_EmersondeCastroBarbosa.pdf: 6431092 bytes, checksum: 15243f7b5580193cfc7b7ad5b935a77a (MD5) / Made available in DSpace on 2016-04-12T19:06:13Z (GMT). No. of bitstreams: 1 Dissertacao_BCM_EmersondeCastroBarbosa.pdf: 6431092 bytes, checksum: 15243f7b5580193cfc7b7ad5b935a77a (MD5) Previous issue date: 2015 / Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Belo Horizonte, MG, Brasil / Produtos naturais são potenciais fontes alternativas para o desenvolvimento de antivirais para o tratamento da dengue, assim como de outras doenças causadas por vírus da família Flaviviridae ou mesmo para um amplo espectro de viroses. Neste estudo foi feita a triagem da atividade in vitro contra o Dengue virus 2 (DENV-2) de 3101 extratos, provenientes de plantas e de fungos da Coleção de Amostras para Bioensaios da Fiocruz. Para tal, células BHK-21 foram infectadas com DENV-2 e tratadas simultaneamente com 25 μg/mL de extrato sendo o resultado analisado por dois métodos: observação do grau de inibição do efeito citopático (ECP) por microscopia óptica e análise da viabilidade celular pelo ensaio colorimétrico do MTT. Dentre os 3101 extratos testados, 115 extratos apresentaram atividade antiviral contra DENV-2 e foram selecionados para a determinação da respectiva concentração efetiva 50 (CE 50). Cinquenta e cinco destes extratos foram obtidos de plantas pertencentes a 20 famílias distintas: Amaryllidaceae (3), Annonaceae (1), Asteraceae (5), Begoniaceae (1), Clusiaceae (1), Combretaceae (1), Erythroxylaceae (1), Fabaceae 4), Lythraceae (2), Malpighiaceae (8), Malvaceae (1), Melastomataceae (2), Melochia (1), Myrtaceae (3), Rubiaceae (8), Sapindaceae (9), Ochnaceae(1), Primulaceae (1), Vitaceae (1), Vochysiaceae (1). Os demais extratos (60) foram obtidos de culturas de fungos endofíticos coletados no Brasil, no continente Antártico e no Deserto do Atacama, ainda não identificados. Até o momento, os extratos vegetais mais promissores foram obtidos de plantas da família Amaryllidaceae (IS = 32,15) e da família Fabaceae (IS = 20,47) e (IS = 24,47). Vinte extratos fúngicos apresentaram valores de CE 50 que variaram entre 3,1 a 12,5 μg/mL e sem citotoxicidade aparente até a concentração de 100 μg/mL. Nossos resultados mostram que tais plantas e fungos são fontes promissoras de substâncias com ação antiviral contra DENV. / Natural products are potential alternat ive sources for the development of antiviral drugs for dengue treatment of, as well as for other diseases caused by viruses of the Flaviviridae family or even caused by a br oad spectrum of viruses. In this study, were performed an in vitro screening for activity against Dengue virus (DENV-2) of 3101 extracts fr om plants and fungi belonging to Fiocruz Minas extract sample collection. To this end, BHK-21 cells infected with DENV-2 were simultaneously treated with 25 μg/mL of extract and t he results analyzed by two methods: observing the degree of inhibiti on of DENV cytopathic effect (CPE) by optical microscopy and also by analysis of cell viability MTT colorimetric assay. Among the 3101 extracts tested, 115 extrac ts showed antiviral activity against DENV-2 and were selected for determination of its half maximal effective concentration (EC 50 ). Fifty-five of these extracts ar e taken from plants belonging to 20 different families: Amaryllidaceae (3), Annonaceae (1), Asteraceae (5), Begoniaceae (1), Clusiaceae (1), Combretaceae (1), Erythroxylaceae (1), Fabaceae (4), Lythraceae (2), Malpighiaceae (8), Malvaceae (1), Melastomataceae (2), Melochia (1), Myrtaceae (3), Rubiaceae (8), Sapindaceae (9), Ochnaceae (1), Primulaceae (1) Vitaceae (1), Vochysiaceae (1). The other extracts (60) were obtained from endophytic fungal cu ltures collected in Brazil, from Antarctic and the Atacama Desert soils, not identified yet. To date, the most promis ing plant extracts were obtained from plants of the Amaryllidaceae family (IS = 32.15) and Fabaceae (IS = 20.47) and (IS = 24.47). Twent y fungal extracts showed EC 50 values ranging from 3.1 to 12.5 mg/mL without any apparent cyt otoxicity up to the concentration of 100 μg/mL. Our results show that these pl ants and fungi are prom ising sources of substances with antiviral action against Dengue virus.

Mosquito-borne viruses, such as dengue virus (DENV), Zika virus (ZIKV), chikungunya virus (CHIKV), yellow fever virus (YFV), Japanese encephalitis virus (JEV), and West Nile virus (WNV) are major threats to global public health resulting in millions of infections and hundreds of thousands of deaths annually. The presence of these viruses and their increasing emergence/spread continues to escalate. Notably, Usutu virus (USUV; Genus: Flavivirus; Family: Flaviviridae) is one such pathogen currently causing mass die-offs of avian hosts throughout Europe. USUV is categorized in the Japanese Encephalitis virus (JEV) antigenic complex and thus shares many antigenic and pathologic characteristics with fellow members, such as JEV and WNV. Respective to human infections, USUV cases are generally asymptomatic; nonetheless, acute cases have been reported. These acute cases typically cause mild symptoms, such as fevers and rashes; however, more severe cases can result in neurologic diseases, such as encephalitis and/or meningoencephalitis. In addition to these pathologic similarities, USUV shares several ecological and geographical traits with WNV, a pathogen responsible for several outbreaks during its spread from Africa, to Europe, and eventually the United States. Currently, WNV is considered endemic in areas across the United States due to its transmission via Culex spp.; mosquitoes that are ubiquitous in the United States. These parallels suggest the possible emergence of USUV into the United States and therefore, it is imperative to broaden our knowledge of USUV and assess its potential to become a major global health concern. The overall goal of this thesis was to characterize USUV and evaluate its emergence potential in the United States by: (1) developing infectious clones of recent European and African USUV isolates as tools for characterization and analysis of USUV and (2) assessing the transmission potential of several species of North American mosquitoes. In Aim 1, we show that the aforementioned infectious clones infect and replicate similarly to their parental strains in vitro in both vertebrate and invertebrate models, as well as in transiently immunocompromised CD-1 and IFNAR-/- murine models, and thus serve as useful tools for future molecular studies focusing on USUV. Furthermore, in Aim 2, we describe the ability of field-caught (Southwest Virginia, USA) Culex spp. and Aedes spp. mosquitoes to become infected with a recent European isolate of USUV; although, we report an overall limited potential for these species to transmit this virus. Altogether, these studies form a foundation for understanding the potential emergence of USUV in the United States as well as provide necessary tools needed to aid future research on USUV emergence, transmission, and pathogenesis. / Master of Science / Usutu virus (USUV) is an emerging mosquito-borne virus that was first isolated from a mosquito in 1959 in South Africa, and since then, has become a major problem throughout Africa and Europe causing acute to severe infection in dozens of patients. Additionally, this virus is causing massive die-offs in Eurasian blackbird populations. This is particularly problematic because birds play a critical role in ecosystems as they act as forms of pest control, pollinators, and seed dispersers. Depletion of these species could lead to an imbalance and, eventually, collapse of our natural ecosystem. Additionally, there is a growing concern of USUV making its way into the United States, following a similar track of emergence to WNV's introduction in New York in 1999 and its subsequent spread throughout the states. WNV's introduction to the United States was detrimental to native bird populations and humans, and has caused tens of thousands of infections and thousands of deaths since this introduction. Research has shown USUV causes similar disease symptoms to WNV. The self-limiting illness from these viruses typically includes fever and rashes but some infections can result in more severe cases causing inflammation of the brain and surrounding areas. Like many other prominent mosquito-borne viruses, there is no specific treatment or vaccine for WNV or USUV. Because USUV is so closely related to WNV, and their similar characteristics may point towards similar emergence in the United States, it is essential to garner more information on USUV. The overall goal of this thesis was to establish a reliable tool(s) for further characterization of USUV and demonstrate the potential for USUV emergence in the United States. We first developed molecular tools, known as viral clones, that are valuable to the scientific community which allows the manipulation of USUV genetic material to perform further downstream studies. Our objective for this initial study was to create a molecular tool that would behave similarly to their natural, or "parental", virus. The results from this study suggest we have successfully produced these tools. Furthermore, we sought to determine the potential for field-caught mosquitoes from Southwest Virginia, USA to transmit a recently isolated strain of USUV. These data suggest that while these mosquitoes do have the ability to become infected with USUV, they have a limited potential to transmit this virus to animal hosts. Altogether, these studies have allowed us to expand our knowledge on USUV's potential emergence in the United States and develop powerful tools to continue this essential research.

A dengue é uma doença viral infecciosa predominante de regiões tropicais e subtropicais que atinge cerca de 400 milhões de pessoas anualmente. Possui quatro sorotipos diferentes do vírus (DEN.I-IV), de modo que a reinfecção por um novo sorotipo pode causar um quadro mais grave da doença: a dengue hemorrágica e a síndrome do choque da dengue. Durante o processo de infecção o vírus passa por duas etapas importantes: a primeira é a entrada dentro da célula hospedeira; a segunda etapa, é a fusão da bicamada lipídica viral com a membrana do endossomo. Ambas as etapas são mediadas pela Glicoproteína E, e é nessa proteína que se encontra o peptídeo putativo de fusão. O peptídeo possui elevado grau de homologia entre todos os membros de Flaviviridae. Neste trabalho, avaliamos a interação entre o peptídeo de fusão da dengue II, modificado, e membranas modelo através da combinação de técnicas experimentais (Fluorescência, SAXS, DSC e Cryo-TEM) e simulações por Dinâmica Molecular. Avaliamos a capacidade do peptídeo DEN.II 88-123 em induzir a fusão de vesículas de DMPC, DMPC:DMPG (4:1), bem como de alterar as propriedades das bicamadas lipídicas. Buscamos ainda compreender como sua estrutura secundária é afetada pela interação com as bicamadas lipídicas e qual o posicionamento dele em relação à membrana. Conseguimos mostrar que o peptídeo é capaz de alterar a cooperatividade lipídica das membranas conforme a composição lipídica e isso pode ser relacionado a capacidade de induzir fusão entre vesículas. Entretanto, os resultados de dinâmica molecular revelaram que o peptídeo não foi capaz de induzir mudanças em parâmetros estruturais tais como: área por lipídio, espessura e parâmetro de ordem da bicamada. Durante a interação o peptídeo ficou preferencialmente na superfície da bicamada, com inserção do resíduo hidrofóbico triptofano entre as cadeias alifáticas. O peptídeo não apresentou uma conformação estrutural preferencial, embora tenha apresentado pequenas proporções de formação de folha- e -hélice. Em conjunto, esses resultados podem auxiliar na compreensão do modo de ação dos peptídeos de fusão. / Dengue fever is viral infectious disease widespread in tropical and subtropical areas that infects nearly 400 million people annually. There are four different virus serotypes (DEN.I-IV) so that a reinfection by a different serotype may lead to a more severe case of the disease: dengue hemorrhagic fever and the dengue shock syndrome. During the infection cycle, the virus has two important steps: the first one is the entry in the host cell; the second one, is the fusion between the viral lipid bilayer and the endosomal membrane. Both steps are mediated by the E Glycoprotein, that is the host of the putative fusion peptide. The fusion peptide has a high degree of homology among the members of the Flaviviridae. In this work, we evaluated the interaction between modified dengue fusion peptide and model membranes through the combination of experiments (fluorescence, SAXS, DSC and Cryo-TEM), and Molecular Dynamics simulations. We evaluated the capacity of the DEN.II 88-123 peptide to promote fusion between vesicles composed by DMPC, DMPC:DMPG (4:1), as well as the ability to perturb the lipid bilayer properties. Moreover, we seek to understand how the secondary structure is affected by interaction with the model membranes and the peptide position in the membrane. We showed that the peptide is able to change the membrane lipid cooperativity depending on the lipid composition and it may be related to the capacity of fusion induction between vesicles. However, the results revealed that the peptide does not induce changes in the structural parameters such as area per lipid, thickness and bilayer order parameter. The peptide binds to the surface of the lipid bilayer with the insertion of the tryptophan residue into the region of aliphatic chains. The peptide did not have a preferential secondary structure, although it presented a low percentage of -sheet and -helice conformation. Together, these results may help to understand the mode of action of fusion peptides.

A dengue é uma doença viral infecciosa predominante de regiões tropicais e subtropicais que atinge cerca de 400 milhões de pessoas anualmente. Possui quatro sorotipos diferentes do vírus (DEN.I-IV), de modo que a reinfecção por um novo sorotipo pode causar um quadro mais grave da doença: a dengue hemorrágica e a síndrome do choque da dengue. Durante o processo de infecção o vírus passa por duas etapas importantes: a primeira é a entrada dentro da célula hospedeira; a segunda etapa, é a fusão da bicamada lipídica viral com a membrana do endossomo. Ambas as etapas são mediadas pela Glicoproteína E, e é nessa proteína que se encontra o peptídeo putativo de fusão. O peptídeo possui elevado grau de homologia entre todos os membros de Flaviviridae. Neste trabalho, avaliamos a interação entre o peptídeo de fusão da dengue II, modificado, e membranas modelo através da combinação de técnicas experimentais (Fluorescência, SAXS, DSC e Cryo-TEM) e simulações por Dinâmica Molecular. Avaliamos a capacidade do peptídeo DEN.II 88-123 em induzir a fusão de vesículas de DMPC, DMPC:DMPG (4:1), bem como de alterar as propriedades das bicamadas lipídicas. Buscamos ainda compreender como sua estrutura secundária é afetada pela interação com as bicamadas lipídicas e qual o posicionamento dele em relação à membrana. Conseguimos mostrar que o peptídeo é capaz de alterar a cooperatividade lipídica das membranas conforme a composição lipídica e isso pode ser relacionado a capacidade de induzir fusão entre vesículas. Entretanto, os resultados de dinâmica molecular revelaram que o peptídeo não foi capaz de induzir mudanças em parâmetros estruturais tais como: área por lipídio, espessura e parâmetro de ordem da bicamada. Durante a interação o peptídeo ficou preferencialmente na superfície da bicamada, com inserção do resíduo hidrofóbico triptofano entre as cadeias alifáticas. O peptídeo não apresentou uma conformação estrutural preferencial, embora tenha apresentado pequenas proporções de formação de folha- e -hélice. Em conjunto, esses resultados podem auxiliar na compreensão do modo de ação dos peptídeos de fusão. / Dengue fever is viral infectious disease widespread in tropical and subtropical areas that infects nearly 400 million people annually. There are four different virus serotypes (DEN.I-IV) so that a reinfection by a different serotype may lead to a more severe case of the disease: dengue hemorrhagic fever and the dengue shock syndrome. During the infection cycle, the virus has two important steps: the first one is the entry in the host cell; the second one, is the fusion between the viral lipid bilayer and the endosomal membrane. Both steps are mediated by the E Glycoprotein, that is the host of the putative fusion peptide. The fusion peptide has a high degree of homology among the members of the Flaviviridae. In this work, we evaluated the interaction between modified dengue fusion peptide and model membranes through the combination of experiments (fluorescence, SAXS, DSC and Cryo-TEM), and Molecular Dynamics simulations. We evaluated the capacity of the DEN.II 88-123 peptide to promote fusion between vesicles composed by DMPC, DMPC:DMPG (4:1), as well as the ability to perturb the lipid bilayer properties. Moreover, we seek to understand how the secondary structure is affected by interaction with the model membranes and the peptide position in the membrane. We showed that the peptide is able to change the membrane lipid cooperativity depending on the lipid composition and it may be related to the capacity of fusion induction between vesicles. However, the results revealed that the peptide does not induce changes in the structural parameters such as area per lipid, thickness and bilayer order parameter. The peptide binds to the surface of the lipid bilayer with the insertion of the tryptophan residue into the region of aliphatic chains. The peptide did not have a preferential secondary structure, although it presented a low percentage of -sheet and -helice conformation. Together, these results may help to understand the mode of action of fusion peptides.

Submitted by Cleide Dantas (cleidedantas@ufpa.br) on 2014-02-10T12:10:12Z No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_CaracterizacaoMolecularCepasVirus.pdf: 1867488 bytes, checksum: d9b8346d11c562383d6eacefda707681 (MD5) / Approved for entry into archive by Ana Rosa Silva (arosa@ufpa.br) on 2014-04-07T16:31:46Z (GMT) No. of bitstreams: 2 Dissertacao_CaracterizacaoMolecularCepasVirus.pdf: 1867488 bytes, checksum: d9b8346d11c562383d6eacefda707681 (MD5) license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) / Made available in DSpace on 2014-04-07T16:31:46Z (GMT). No. of bitstreams: 2 Dissertacao_CaracterizacaoMolecularCepasVirus.pdf: 1867488 bytes, checksum: d9b8346d11c562383d6eacefda707681 (MD5) license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Previous issue date: 2009 / A febre do dengue é uma das mais importantes arboviroses distribuída por todas as áreas tropicais do mundo. O vírus dengue (VDEN) é transmitido principalmente pela picada do mosquito Aedes aegypti infectado. A dispersão do vetor e o aumento do fluxo migratório entre países possibilitaram a ocorrência de grandes epidemias e manifestações clínicas severas, como febre hemorrágica do dengue (FHD) e Síndrome do choque do dengue (SCD). O objetivo deste trabalho foi realizar a caracterização molecular de isolados do VDEN sorotipo 1 (VDEN-1) no Brasil ao nível dos genes estruturais C/prM/M/E de 29 cepas isoladas durante epidemias ocorridas no Brasil no período de 1994 a 2008. A identidade nucleotídica entre as cepas de VDEN-1 do estudo em relação às outras isoladas no Brasil variou de 96,1% a 100%, enquanto o percentual de identidade de aminoácidos foi determinado entre 98,4% a 100%. As diferenças de aminoácidos entre as cepas do estudo, quando comparadas com a cepa FGA/89 (Guiana Francesa), mostraram a presença de importantes substituições não-sinônimas com mudança de caráter bioquímico, tais como os resíduos E297 (Met Tre) e E338 (Ser Leu), sendo necessário estudos para verificar se essas alterações podem ou não estar relacionadas à virulência. A análise filogenética para a proteína E, realizada por meio do método de máxima verossimilhança para as cepas do estudo e outras cepas selecionadas do banco de dados do Genbank, mostraram que as cepas de VDEN-1 isoladas no Brasil desde 1982 pertencem ao genótipo V, corroborando com os resultados publicados anteriormente. O tempo de divergência do VDEN-1, estimado através da hipótese de relógio molecular, mostrou que este vírus teve sua origem a partir de uma linhagem ancestral, há aproximadamente, 113 anos e observou-se ainda que as cepas de VDEN-1 circulantes no Brasil e as provenientes da África possuem um ancestral comum, sendo necessário estudos de filogeografia que mostrem as possíveis rotas de entrada do VDEN-1 no Brasil. / Dengue fever is one of the most important arboviral disease distributed to all tropical areas of the world. Dengue virus (DENV) is transmitted mainly by the bite of infected Aedes aegypti mosquitoes. The dispersion of the vector and the increase of migration between countries caused the occurrence of major epidemics and severe clinical manifestations, such as the dengue hemorrhagic fever (DHF) and the dengue shock syndrome (DSS). The objective of this study was the molecular characterization of isolates of DENV-1 in Brazil at the level of structural genes C / prM / M / E of 29 strains isolated during outbreaks occurred in Brazil between 1994 and 2008. The nucleotide identity among strains of this DENV-1 study compared with other strains isolated in Brazil ranged from 96.1% to 100%, while the percentage of amino acid identity was determined between 98.4% to 100%. The amino acid differences between strains of the study, compared with the strain FGA/89 (French Guiana) showed the presence of important non-synonymous substitutions change of the amino acid biochemical character, such as the E297 residue (Met Thr) and E338 (Ser Leu), more detailed studies are needed to investigate if any of them may be related to DENV-1 virulence. The phylogenetic analysis of the E gene, performed using the maximum likelihood method for the studied strains and other strains selected from the database of GenBank showed that the DENV-1 isolates from Brazil since 1982 belonged to genotype V, confirming previously published data. The time of divergence of DENV-1, estimated by molecular clock method, showed that this virus was originated from an ancestral lineage, there are approximately 113 years and it was also observed that DENV-1 strains circulating in Brazil and those from Africa have a common ancestor, and finally it is necessary phylogeographic studies to show the possible routes of entry of DENV-1 in Brazil.

La virologie bénéficie de plus en plus du développement de la bioinformatique. Mon projet de thèse recouvre la gestion de séquences de protéines se rapportant aux virus à ARN simple brin, de polarité négative et positive. J'ai mis en place une base de données VaZyMolO, qui gère les informations structurales et fonctionnelles des protéines, en définissant et en classant des modules. Cette approche a permis l'identification d'un domaine méthyltransférase sur la protéine L des Mononegavirales, et la définition de la modularité des protéines N et P des Paramyxoviridae. La cartographie du génome du virus du Syndrome Respiratoire Aigue Sévère réalisée à l'aide de VaZyMolO, a contribué à la résolution structurale de la protéine nsp9 de ce virus. Enfin, je présente une étude incluant évolution et analyse structurale des polymérases des Flaviviridae. Dans cette dernière, je propose un modèle de la polymérase du virus GBV-C et un mécanisme d'initiation de la synthèse d'ARN.

Submitted by Ubirajara Cruz (ubirajara.cruz@gmail.com) on 2017-06-07T15:21:51Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Clarissa Caetano de Castro.pdf: 1512780 bytes, checksum: 8bb13b97653dff0e33b2ee2f520be9f0 (MD5) / Approved for entry into archive by Aline Batista (alinehb.ufpel@gmail.com) on 2017-06-08T13:02:14Z (GMT) No. of bitstreams: 2 Clarissa Caetano de Castro.pdf: 1512780 bytes, checksum: 8bb13b97653dff0e33b2ee2f520be9f0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-06-08T13:02:14Z (GMT). No. of bitstreams: 2 Clarissa Caetano de Castro.pdf: 1512780 bytes, checksum: 8bb13b97653dff0e33b2ee2f520be9f0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-03-24 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / A busca de novas substâncias com atividade antiviral levou este estudo a investigar a ação do peptídeo antimicrobiano P34, produzido pelo Bacillus sp. P34, frente ao herpesvírus bovino tipo 1 (BoHV-1) e de moléculas sintetizadas da 2-picolilamina e 2-aminoetilpiperidina derivadas da classe da 4-tiazolidinona denominadas V19 (2a), V20 (2b), V23 (2c), V28 (2d), V29 (2e), AK11 (1a), AK16 (1d), AK17 (1e), AK18 (1b) e AK20 (1c) frente a diversos vírus que infectam animais. Inicialmente foram determinadas as concentrações não citotóxicas dos diferentes compostos, em diferentes linhagens celulares, através dos métodos MTT e vermelho neutro. A seguir a atividade antiviral foi avaliada mediante um ensaio de inibição do efeito citopático. Em todos os testes, o título viral em cultivo celular foi comparado ao título viral na presença de cada composto para a determinação do percentual de inibição (PI). O P34 demonstrou um PI de 99,94% e alto índice de seletividade (SI de 22,9). Os testes para identificar o modo de ação indicaram que o peptídeo P34 não atua sobre as células MDBK, ou receptores celulares. Em concentrações citotóxicas o P34 obteve efeito virucida e 100% de inibição viral nos ensaios de redução viral e de penetração. Foi evidenciada total inibição na produção das partículas de BoHV-1 quando as células foram tratadas com o P34 posterior a 8 h de infecção. Houve redução significativa (p< 0.01) do título do BoHV-1 na presença do P34 após 8 h de infecção (PI de 90%), chegando a 99,9% de PI após 18 h de tratamento pós-infecção. O P34 inibiu o BoHV-1 tanto no meio extracelular, inibindo a infecção celular, quanto no meio intracelular, após a infecção, impedindo o egresso. Com relação às moléculas derivadas da 4-tiazolidinona a menos tóxica foi a AK 16 (157 μg/mL) nas quatro linhagens de células (RK13, MDCK, CRFK e MDBK) e as mais tóxicas foram as AK11, AK18 e AK20 (19 μg/mL). O PI da molécula AK16 foi de 96,9%, 90,1% e 90,1% contra o EAV, FCV e CPV-2, respectivamente. O composto AK17 mostrou PI de 90,1% contra o EAV, a V20 de 78% contra BVDV, a V28 de 94,4% contra EIV e 78% contra BVDV e a V29 de 94,4% contra CPV-2. As moléculas V20 e V28 foram escolhidas para dar continuidade ao estudo frente ao BVDV. Foram determinados para V20 um SI de 16,8 e de 14,73 para V28. Nos ensaios de inibição da produção de partículas virais, adsorção, competição com receptores celulares, penetração viral e efeito virucida não foram observadas diferenças significativas entre os títulos do BVDV com e sem tratamentos com as moléculas. A associação das moléculas V20 e V28 aumentou de 78 para 82% o PI, não sendo verificada alteração no PI quando as moléculas foram associadas com os antivirais interferon-α 2b ou ribavirina. Através da determinação da curva de crescimento do BVDV foi evidenciada atuação no período entre 1 a 5 h pós-infecção com o BVDV, sugerindo ação posterior à entrada viral, mas antes do egresso, provavelmente no período de síntese do RNA e enzimas virais. Os resultados demonstram que o peptídeo P34 e os compostos V20 e V28 derivados da 4-tiazolidinona podem ser considerados promissores antivirais contra BoHV-1 e BVDV. / The search for new substances with antiviral activity has led this study to investigate the action of the antimicrobial peptide P34, produced by Bacillus sp. P34 against bovine herpesvirus type 1 (BoHV-1) and of the synthetic molecules 2-picolylamine and 2-aminoethylpiperidine, which are derived from the class of thiazolidin-4-one named V19 (2a), V20 (2b), V23 (2c), V28 (2d), V29 (2e), AK11 (1a), AK16 (1d), AK17 (1e), AK18 (1b) and AK20 (1c) in opposition to several viruses that infect animals. Initially non-cytotoxic concentrations of the different compounds were determined, in different cell lines, through the MTT and neutral red methods. Then, the antiviral activity was evaluated by an assay of the cytopathic effect inhibition. In all tests, the viral titer in cell culture was compared to the viral titer in the presence of each compound to determine the percentage of inhibition (PI). The P34 demonstrated a PI of 99.94% and high selectivity index (SI 22.9). Tests to identify the mode of action indicated that the peptide P34 has no effect on MDBK cells, or cell receptors. In cytotoxic concentrations P34 obtained virucidal effect and 100% inhibition in viral reduction viral and penetration assays. Total inhibition was observed in the production of the BoHV-1 particles when cells were treated with P34 after 8 h of infection. There was a significant reduction (p <0.01) in BoHV-1 titer in the presence of P34 after 8 h of infection (PI 90%), reaching 99.9% PI after 18 h post-infection treatment. P34 inhibited BoHV-1 as extracellularly, inhibiting cell infection, as intracellularly, after infection, preventing its egress. Regarding molecules derived from thiazolidin-4-one the less toxic was AK16 (157 μg/mL) in the four cell lines (RK13, MDCK, CRFK and MDBK), and the most toxics were AK11, AK18 and AK20 (19 μg/mL). The PI of AK16 molecule was 96.9%, 90.1% and 90.1% against EAV, FCV and CPV-2, respectively. The compound AK17 showed PI of 90.1% against EAV, V20 of 78% against BVDV, V28 of 94.4% against EIV and 78% against BVDV and the V29 of 94.4% against CPV-2. V20 and V28 molecules were chosen to continue the study against BVDV. To V20 and V28 molecules, were determined SI of 16.8 and 14.73, respectively. In assays of inhibition of production of viral particles, adsorption, competing with cellular receptors, viral penetration and virucidal effect no significant differences were observed between titers the BVDV with and without treatment with the molecules. The association of V20 and V28 molecules increased the PI from 78 to 82%, and changes in the PI were not verified when the molecules were associated with antiviral interferon-α 2b and ribavirin. Through the determination of BVDV growth curve, was observed activity in the period between 1 to 5 h post-infection with BVDV, suggesting further action on viral entry, but probably, before the egress, in the period of RNA synthesis and viral enzymes. The results demonstrate that peptide P34 and compounds V20 and V28 derived from thiazolidin-4-one can be considered as promising antiviral against BoHV-1 and BVDV.

L’hépatite C est une maladie affectant aujourd’hui 170 millions d’individus dans le monde. Cette maladie est causée par le virus de l'hépatite C (VHC). Les nouveaux traitements récemment mis sur le marché, visant à soigner l’hépatite C, sont très onéreux et donc inaccessibles pour les pays du Sud. De plus, l’utilisation de ces nouvelles molécules engendre l’apparition de mutation de résistance virale responsable de l’échec des traitements pour 5 à 10% des patients. La découverte de nouveaux antiviraux est donc toujours indispensable. Les plantes utilisées en médecine traditionnelle depuis des siècles sont une source de composés bio-actifs très intéressante. L’utilisation de ces plantes ou de composés naturels en complément des molécules utilisées en thérapie classique, permettrait de réduire significativement le coût de ces traitements et de les rendre accessibles à davantage de patients.L’epigallocatéchine-3-gallate (EGCG) et la delphinidine sont des molécules naturelles issues respectivement du thé vert et des fruits rouges. Ces deux molécules inhibent l’étape d’entrée du VHC dans les cellules hépatocytaires. Nous avons montré que l'EGCG et la delphinidine inhibent cette étape virale dans les hépatocytes en déformant les particules et bloquant ainsi leur attachement à la surface cellulaire. Nous nous sommes ensuite intéressés au processus engendrant cette déformation qui est probablement lié à l’agrégation des glycoprotéines d’enveloppe virale.Nous avons procédé au criblage d’extraits bruts de plantes extrêmophiles tunisiennes et mis en évidence que l’extrait brut de rhizome de Juncus maritimus inhibait l’étape de réplication du VHC. Le J. maritimus est une plante fortement présente dans les sols arides en Tunisie mais également sur les côtes françaises. En collaboration avec le laboratoire de Pharmacognosie de Lille et grâce à un fractionnement bioguidé, le principe actif a pu être isolé. Il s’agit du déhydrojuncusol qui inhibe la réplication virale avec une concentration effective médiane de 1,31 µM. De plus, nous avons montré que le déhydrojuncusol pouvait inhiber la réplication de virus présentant des mutations de résistance aux traitements actuels ciblant la protéine virale NS5A. Nous avons cherché à identifier la cible virale du déhydrojuncusol et il semblerait que ce soit également la protéine NS5A.Les résultats obtenus dans cette thèse confortent l’hypothèse que des molécules naturelles pourraient être utilisées dans le traitement de l’hépatite C. / Hepatitis C is a liver disease affecting 170 million people worldwide. This disease is caused by hepatitis C virus (HCV). New treatments, recently marketed, against HCV are very expensive and not really accessible for most-infected patients especially in low-income countries. Moreover, the use of these new molecules generates the emergence of HCV resistant variants responsible for treatment failure for 5 to 10% of the patients. Therefore, the discovery of new antiviral molecules is always needed. Since centuries, plants are used in traditional medicine. They are a very attractive source of bio-active compounds. Plant extracts or natural molecules used in combination with actual therapy, could significantly reduce the cost of these new treatments and render them accessible to more patients.Epigallocatechin-3-gallate (EGCG) and delphinidin are natural molecules derived respectively from green tea and red berries. These two molecules inhibit HCV entry into hepatocyte cells. We have shown that this inhibition is due to a deformation of viral particles by the molecules inducing a blockade of virus attachment to the cell surface. We further investigated the process leading to this deformation, and conclude that it might be related to aggregation of viral envelope glycoproteins.We screened extracts of extremophile plants from Tunisia and showed that the crude extract of Juncus maritimus rhizome inhibited HCV replication step. J. maritimus is a plant present in arid soils in Tunisia but also in French coasts. In collaboration with the Pharmacognosy laboratory of Lille and thanks to a bioguided fractionation, the active compound present in this plant could be isolated. It was identified as dehydrojuncusol, which inhibits viral replication with a half maximal effective concentration of 1.31 &#956;M. We have also shown that dehydrojuncusol is able to inhibit replication of viruses with resistance mutations to current treatments targeting the viral protein NS5A. We have also tried to identify the viral target of dehydrojuncusol, and it seems that the target might also be the NS5A protein.The results obtained in this thesis confirm the hypothesis that natural molecules could be used in the treatment of hepatitis C.

Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: the genus Flavivirus, with its type I cap structure at the 5′ untranslated region (UTR) and a highly structured 3′ UTR, and the remaining three groups, which exhibit translation control by means of an internal ribosomal entry site (IRES) in the 5′ UTR and a much shorter less-structured 3′ UTR. The main findings of this survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C/hepatitis G virus in addition to the flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3′ UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.