Rozprawy doktorskie na temat „RETROVIRAL PROTEASE”

Introdução: Uma proporção significante de pacientes infectados por HIV-1 (pacientes HIV-1+) tratados com inibidores de protease (IPs) desenvolve mutações de resistência. Estudos recentes têm mostrado que células T CD8+ de pacientes HIV- 1+ reconhecem epitopos de Pol incluindo mutações selecionadas por drogas. Nenhum epitopo CD4+ da protease foi descrito na base de dados de Los Alamos. Objetivo: Considerando que a protease de HIV-1 é alvo de terapia antiretroviral e que essa pressão pode selecionar mutações, nós investigamos se mutações selecionadas por IPs afetariam o reconhecimento de epitopos da protease de HIV-1 por células T CD4+ em pacientes tratados com IPs. Nós investigamos o reconhecimento de três regiões da protease preditas de conter epitopos de células T CD4+ bem como mutações induzidas por IPs por células T CD4+ em pacientes HIV- 1+ tratados com IPs. Materiais e Métodos: Quarenta pacientes HIV-1+ tratados com IPs foram incluídos (30 em uso de Lopinavir/ritonavir, 9 em uso de Atazanavir/Ritonavir e 1 em uso exclusivo de Atazanavir). Para cada paciente determinou-se a seqüência endógena da protease de HIV-1, genotipagem viral e tipagem HLA classe II. Utilizamos o algoritmo TEPITOPE para selecionar peptídeos promíscuos, ligadores de múltiplas moléculas HLA-DR, codificando as três regiões da protease de HIV-1 cepa HXB2 (HXB2 4-23, 45-64, e 76-95) e 32 peptídeos adicionais contidos nas mesmas regiões incorporando as mutações induzidas por IPs mais freqüentes no Brasil. Os 35 peptídeos foram sintetizados. Respostas proliferativas de células T CD4+ e CD8+ aos peptídeos foram determinadas por ensaios de proliferação com diluição do corante CFSE. Ensaios de ligação a alelos HLA classe II foram realizados para confirmar a promiscuidade desses peptídeos e avaliar a habilidade de se ligarem a moléculas HLA presentes em cada paciente. Resultados: Todos os peptídeos foram reconhecidos por pelo menos um paciente e respostas proliferativas de células T CD4+ e CD8+ a pelo menos um peptídeo da protease de HIV-1 foram encontradas em 78% e 75% dos pacientes, respectivamente. A terceira região (Protease 76 95) foi a mais freqüentemente reconhecida. Ao compararmos as respostas de células T às seqüências da protease do HIV-1 endógeno, observamos que a maioria dos pacientes não foi capaz de reconhecer peptídeos idênticos às essas seqüências, porém reconheceram peptídeos variantes diferentes das mesmas regiões. Apenas sete pacientes responderam às seqüências endógenas. Verificamos que diversos peptídeos endógenos que não foram reconhecidos apresentaram ausência de ligação a alelos HLA portados por estes pacientes, sugerindo que mutações selecionadas por pressão imune tenham levado ao escape de apresentação de antígeno e evasão de resposta de linfócitos T CD4+. Alternativamente, isso poderia ser explicado pela presença de um vírus replicante distinto presente no plasma uma vez que somente foram obtidas seqüências provirais. Conclusão: Epitopos selvagens e mutantes da protease do HIV-1 reconhecidos por células T CD4+ foram identificados. Também verificamos que a maior parte dos pacientes não reconheceu as seqüências da protease endógena enquanto que reconheceram seqüências variantes. O reconhecimento de seqüências não-endógenas poderia ser hipoteticamente conseqüência de alvo de populações HIV-1 minoritárias; protease de HERV que contém regiões de similaridade com a protease do HIV-1; ou seqüências de HIV-1 presentes apenas em parceiros virêmicos. A falha de reconhecimento de seqüências endógenas seria mais provável devido ao escape imune, do que ao nível de apresentação ou reconhecimento por células T. Isso implica em uma conseqüência patofisiológica na evasão de respostas de células T contra a protease de HIV-1 e no fato de ser tradicionalmente considerada uma proteína pouco antigênica<br>Introduction: A significant proportion of protease inhibitor (PI)-treated HIV-1 infected (HIV-1+) patients develop resistance mutations. Recent studies have shown that CD8+ T cells from HIV-1 patients can recognize antiretroviral drug-induced mutant Pol epitopes. No HIV-1 protease CD4 epitopes are described in the Los Alamos database. Aims: Given that the protease of HIV-1 is a target of antiretroviral therapy and this pressure may lead to the selection of mutations, we investigated whether PI-induced mutations affect the recognition of HIV-1 protease epitopes by CD4 + T cells in PI-treated patients. We investigated the recognition of three protease regions predicted to harbor CD4+ T cell epitopes as well as PI-induced mutations by CD4+ T cells of PI-treated HIV-1+ patients. Methods: Forty PI-treated HIV-1+ patients were included (30 undergoing Lopinavir/ritonavir, 9 undergoing Atazanavir/ritonavir and 1 undergoing exclusively Atazanavir treatment). For each patients, the endogenous HIV-1 protease sequence, viral genotype and HLA class II typing were determined. We used the TEPITOPE algorithm to select promiscuous, multiple HLA-DR-binding peptides encoding 3 regions of HIV-1 HXB2 strain protease (HXB2 4-23, 45-64, and 76-95) and 32 additional peptides contained in the same regions, but encompassing the most frequent PI-induced mutations in Brazil. The 35 peptides were thus synthesized. Proliferative responses of CD4+ and CD8+ T cells against peptides were determined by the CFSE dilution assay. HLA class II binding assays were made to confirm the promiscuity of these peptides and evaluate their ability to bind the HLA molecules carried by each patient. Results: All tested peptides were recognized by at least one patient and proliferative responses of CD4+ and CD8+ T cells against at least one HIV-1 protease peptide were found in 78% and 75% patients, respectively. The third region (Protease 76-95) was the most frequently recognized. By comparing T-cell responses to HIV-1 endogenous protease sequences, we found that most patients failed to recognize identical peptides of those sequences, but recognized different variant peptides of the same region. Only seven patients responded to endogenous sequences. We found that several endogenous peptides that failed to be recognized showed no binding to the HLA alleles carried by that given patient, suggesting that mutations selected by immune pressure have led to escape of antigen presentation, as well as direct escape of the CD4+ T cell response. Alternatively, it could have been due to the presence of a different replicating virus in the plasma-since we only obtained proviral sequences. Conclusion: Wild-type and mutant HIV-1 protease epitopes recognized by CD4+ T cells were identified. We also found that most patients failed to recognize their endogenous protease sequences, while they recognized variant sequences. The recognition of non-endogenous sequences could hypothetically be a consequence of targeting a minor HIV-1 population; HERV protease, that contains regions of similarity with HIV-1 protease; or HIV-1 sequences present only in viremic partners. The failure to recognize endogenous sequences is most likely due to immune escape, either at the level of presentation or direct T cell recognition. This may have a pathophysiological consequence on evasion of T cell responses against protease and the fact that it has been considered traditionally a poorly antigenic HIV-1 protein.

Viruses are a major threat to humans due to their unique adaptability, evolvability and  capability to control their hosts as parasites and genetic elements. HIV/AIDS is the third largest cause of death by infectious diseases in the world, and drug resistance due to the viral mutations is still the leading cause of treatment failure. The flaviviruses, such as Dengue virus (DEN) and Japanese encephalitis virus (JEV), represent other major cause of morbidity and mortality, and the areas where these viruses are endemic are spreading rapidly. No curative therapy for any flavivirus could be made available as yet. The first part of this thesis focuses on the HIV-1 drug resistance caused by mutations in a major HIV drug target, the HIV-1 reverse transcriptase (RT) as a response to the largest class of clinically used anti-retrovirals, the NRTIs. A robust proteochemometric model was created to analyse the complex mutation patterns in RT drug resistance. The model identified more than ten frequently-occurring mutations, each conferring at least two-fold decrease in susceptibility for one or several NRTIs. Using our prediction server (hivdrc.org), the model can be applied to propose optimum combination therapy for patients harbouring mutated HIV variants. The second part of the thesis encompasses studies on a promising drug target, the NS2B(H)-NS3pro, in two flaviviruses, namely the dengue virus (DEN) and Japanese encephalitis virus (JEV). Functional determinants of DEN NS2B(H)-NS3pro were identified by site-directed mutagenesis. Further, peptide inhibitors were designed using proteochemometrics (PCM) and statistical molecular design (SMD), synthesized and assayed on DEN proteases, which resulted in some novel peptides with low micromolar or sub-micromolar inhibitor activity. The very poorly characterised JEV NS2B(H)-NS3pro  was cloned, purified and the kinetic parameters of this attractive drug target were determined for a series of model substrates and inhibitor. The results identified the role in target-ligand interaction of different residues on specific positions in the target (NS2B(H)-NS3pro) and ligands (substrates/inhibitors). Overall, the findings in this thesis contribute to rational antiviral drug discovery and therapy.

This work is primarily concerned with the expression, purification, and characterisation of aspartic proteases from three retroviruses of the lentivirus subgroup, specifically the Human Immunodeficiency Viruses types 1 and 2, and the Simian Immunodeficiency Virus isolated from the African Green Monkey (HIV-1 PR, HIV-2 PR, SIVagm PR respectively). These viruses cause immunodeficiency syndromes within their respective hosts, and understanding their molecular biology would facilitate development of Acquired Immunodeficiency Syndrome (AIDS) treatments in man. The proteases are essential to viral maturation and infection and are of great interest with respect to the development of new antivirals. This thesis describes attempts to develop improved methods for the over-expression and purification of these cytotoxic proteins for use in structural and biochemical studies. The development of a system for expression and purification of active, crystallisable HIV-1 PR is described, followed by a preliminary analysis of two compounds intended to act as irreversible "suicide inhibitors" of HIV-1 PR. The expression, purification, crystallisation, and preliminary crystallographic data for the native HIV-2 PR using the same expression system are also reported. Mutagenesis of the HIV-2 protease is described, whereby the conserved active site aspartic acids of the native homodimer were changed to histidine and cysteine, with the intention of modifying the enzyme's mechanism, whilst maintaining its native substrate specificity and overall structure. Finally the production of an insoluble, non-toxic, histidine tagged fusion of mutant E.coli Uracil DNA Glycosylase (UDG) and the SIVagm PR is reported. This was intended to produce high levels of a non-toxic fusion protein, allow one-step affinity purification, and provide native soluble protease following autocatalytic cleavage from the fusion protein. The effects of protease toxicity and codon usage on yields are discussed in light of the results presented.

La proteine p27 de groupe des retrovirus aviaires a ete purifiee a partir du virus exogene amv(mav)b, par electrophorese preparative et electroelution. Les caracterisations biochimiques et immunologiques de cette proteine ont confirme le polymorphisme structural que presente ce constituant majeur de la capside virale. Une collection de 320 anticorps monoclonaux diriges contre cette proteine a ete isolee et l'etude de la distinction entre les virus exogenes et endogenes de leucoses aviaires a l'aide de ces anticorps a ete effectuee. L'un d'entre eux reagit specifiquement avec les virus exogenes et presente une affinite suffisante pour la detection de la proteine p27 exogene. Une cartographie epitopique de la proteine p27 exogene a l'aide d'anticorps monoclonaux a ete realisee par clivage chimique de l'antigene et identification des fragments peptidiques, ainsi qu'avec un systeme bia-core base sur l'analyse des interactions biospecifiques par resonance plasmonique de surface. Nous avons determine respectivement huit et onze epitopes differents a l'aide de ces deux methodes. En particulier, deux anticorps monoclonaux sont diriges contre une region de la proteine p27 presentant une epitope specifique de la forme exogene et un epitope specifique du virus amv(mav)b. A l'aide de programmes de predictions d'epitopes, un oligopeptide de 25 acides amines situe dans la region cooh-terminale de la proteine a ete synthetise et les resultats montrent qu'il comporte plusieurs epitopes, dont l'epitope discriminant les formes exogenes et endogenes de proteine p27. Ces travaux ont apporte des donnees relatives a l'antigenicite de la proteine p27 exogene et des outils de detection des retrovirus aviaires exogenes

Innerhalb der Retroviren unterscheiden sich die Foamyviren (FV) bezüglich ihrer Proteinexpression, der Partikelmorphogenese und ihres Reproduktionszyklus deutlich von den Orthoretroviren. Im Rahmen dieser Arbeit wurden zwei exklusive Merkmale der Foamyviren, die ungewöhnliche Struktur des Gag-Proteins und die Gag unabhängige Pol-Expression, in ihrer Auswirkung auf Morphogenese und Zusammensetzung foamyviraler Partikel untersucht. Für die Morphogenese infektiöser Partikel sind sehr unterschiedliche Mengen der Genprodukte eines Retrovirus nötig. Im Gegensatz zu den Orthoretroviren wird bei Foamyviren das Produkt des pro/pol-ORFs von einer eigenen, gespleißten mRNA translatiert. Der Gag/Pro/Pol-Gehalt in den Viruspartikeln kann folglich nicht wie bei Orthoretroviren über eine gekoppelte Translation und Inkorporation von Gag- und Gag/Pro/Pol-Fusionsproteinen reguliert werden. In dieser Arbeit wurde der Frage nach dem molekularem Verhältnis von Gag- und Pro/Pol-Proteinen in foamyviralen Partikeln nachgegangen. In den isolierten PFV Partikeln war der relative Gehalt an dem Gag-Prozessierungsprodukt p68 viermal höher als der Gehalt an dem Gag-Vorläuferprotein p71. Das Gag-Prozessierungsprodukt p68 bildet somit das Hauptstrukturelement der PFV Kapside. Weiterhin ergab sich ein Verhältnis von 16 Gag-Molekülen zu einem p85PR/RT-Molekül sowie 10 Gag-Molekülen pro p40IN-Molekül. Damit entsprach die Gag/Pol-Zusammensetzung von PFV Partikeln den stöchiometrischen Verhältnissen in orthoretroviralen Partikeln von 10 - 20 Gag-Molekülen pro Pol-Molekül. Dieses Ergebnis ist in Hinsicht auf die unterschiedlichen Synthesestrategien von Gag und Pol bei Orthoretro- und Foamyviren bemerkenswert. Basierend auf diesen Ergebnissen stellt sich für weiterführende Untersuchungen nun die Frage nach der Regulation der Gag- und Pol-Synthese bei Foamyviren. Bei Orthoretroviren setzt sich in einem Prozess der Selbstorganisation das Strukturprotein Gag autonom zu virusähnlichen Partikeln zusammen, die auch in Abwesenheit weiterer viraler Komponenten aus der Wirtszelle freigesetzt werden. Foamyviren dagegen benötigen für die Freisetzung ihrer Viruspartikel neben dem Strukturprotein obligat die Koexpression ihres Glykoproteins. Im zweiten Teil dieser Arbeit wurden funktionelle Abschnitte im PFV Gag-Protein eingegrenzt und charakterisiert, die eine Rolle bei der Bildung und Freisetzung der viralen Partikel spielen. Eine schrittweise Deletion des PFV Gag-Proteins vom C-Terminus her zeigte, dass die N-terminalen 300 As von PFV Gag ausreichend für die Freisetzung von partikulärem viralem Proteinmaterial sind. Die Analyse weiterer Deletionsmutanten innerhalb des N-Terminus des PFV Gag-Proteins belegte, dass die As 6 - 200 für die Bildung viraler Kapside entbehrlich sind, aber für die Interaktion mit dem viralen Glykoprotein und für eine Freisetzung der viralen Partikel aus der Wirtszelle essentiell sind. Die Substitution einzelner konservierter Aminosäuren durch Alanin zwischen As 40 - 60 blockierte die Partikelmorphogenese. Die Aminosäureabfolge dieses Proteinabschnittes zeigte eine große Ähnlichkeit mit einem zellulären Transportsignal, dass in den Gag-Proteinen von Retroviren des Typ-D-Morphogeneseweges entdeckt worden ist. Eine parallele Mutationsanalyse des FFV Gag-Proteins ließ vermuten, dass dieses Motiv wohl universell in allen FV Gag-Proteinen vorhanden ist. Weiterhin konnten Aminosäureabschnitte am unmittelbaren N-Terminus des PFV Gag-Proteins sowie zwischen As 130 - 200 eingegrenzt werden, die essentiell für die Struktur des Proteins sind und eventuell eine wichtige Funktion bei der Partikelmorphogenese erfüllen. Weitere Untersuchungen und insbesondere eine Strukturaufklärung des PFV Gag-Proteins sind nötig, um die genaue Funktion der einzelnen Proteinabschnitte zu charakterisieren.

L'element gypsy est un retrovirus endogene de drosophile. Sa mobilite est controlee par le gene flamenco au niveau de la transcription de gypsy. Ce gene a un effet maternel, car gypsy ne transpose que chez les descendants de femelles homozygotes pour l'allele permissif de flamenco. Afin d'etablir un protocole experimental permettant de suivre gypsy au cours de son cycle de replication, des lignees transgeniques de drosophile, contenant un element marque dans le gene env, ont ete obtenues. Leurs etudes indiquent que, meme si le clone de l'element gypsy utilise n'est pas autonome pour sa transposition, l'epitope marqueur n'affecte ni les etapes de maturation des arn ni la localisation et l'expression de la proteine env marquee. Afin de tester la fonction de la proteine de l'orf3 de gypsy, nous avons produit un vecteur retroviral de type momlv enveloppe par cette proteine. Les tests d'infection sur des cellules de d. Melanogaster ont montre que ces particules sont infectieuses, prouvant que cette proteine a une fonction d'enveloppe retrovirale. La mesure du taux de transposition d'un element gypsy defectif pour le gene env a revele qu'il est capable d'effectuer un cycle de transposition de maniere autonome. Les evenements de transposition de gypsy dans la lignee germinale de femelles permissives ne requierent apparemment donc pas une etape d'infection, mais feraient intervenir un processus passif, encore indetermine. L'obtention de femelles ayant un germen flamenco permissif et un soma flamenco restrictif ou ayant un soma permissif et un germen restrictif indique que la presence d'un soma permissif est necessaire et suffisant pour que l'element gypsy puisse transposer. La capacite de gypsy a etre transfere du soma au germen, sans necessiter la presence d'une proteine env fonctionnelle, fait de l'element gypsy un element a la croisee des retrotransposons et des retrovirus.

Innerhalb der Retroviren unterscheiden sich die Foamyviren (FV) bezüglich ihrer Proteinexpression, der Partikelmorphogenese und ihres Reproduktionszyklus deutlich von den Orthoretroviren. Im Rahmen dieser Arbeit wurden zwei exklusive Merkmale der Foamyviren, die ungewöhnliche Struktur des Gag-Proteins und die Gag unabhängige Pol-Expression, in ihrer Auswirkung auf Morphogenese und Zusammensetzung foamyviraler Partikel untersucht. Für die Morphogenese infektiöser Partikel sind sehr unterschiedliche Mengen der Genprodukte eines Retrovirus nötig. Im Gegensatz zu den Orthoretroviren wird bei Foamyviren das Produkt des pro/pol-ORFs von einer eigenen, gespleißten mRNA translatiert. Der Gag/Pro/Pol-Gehalt in den Viruspartikeln kann folglich nicht wie bei Orthoretroviren über eine gekoppelte Translation und Inkorporation von Gag- und Gag/Pro/Pol-Fusionsproteinen reguliert werden. In dieser Arbeit wurde der Frage nach dem molekularem Verhältnis von Gag- und Pro/Pol-Proteinen in foamyviralen Partikeln nachgegangen. In den isolierten PFV Partikeln war der relative Gehalt an dem Gag-Prozessierungsprodukt p68 viermal höher als der Gehalt an dem Gag-Vorläuferprotein p71. Das Gag-Prozessierungsprodukt p68 bildet somit das Hauptstrukturelement der PFV Kapside. Weiterhin ergab sich ein Verhältnis von 16 Gag-Molekülen zu einem p85PR/RT-Molekül sowie 10 Gag-Molekülen pro p40IN-Molekül. Damit entsprach die Gag/Pol-Zusammensetzung von PFV Partikeln den stöchiometrischen Verhältnissen in orthoretroviralen Partikeln von 10 - 20 Gag-Molekülen pro Pol-Molekül. Dieses Ergebnis ist in Hinsicht auf die unterschiedlichen Synthesestrategien von Gag und Pol bei Orthoretro- und Foamyviren bemerkenswert. Basierend auf diesen Ergebnissen stellt sich für weiterführende Untersuchungen nun die Frage nach der Regulation der Gag- und Pol-Synthese bei Foamyviren. Bei Orthoretroviren setzt sich in einem Prozess der Selbstorganisation das Strukturprotein Gag autonom zu virusähnlichen Partikeln zusammen, die auch in Abwesenheit weiterer viraler Komponenten aus der Wirtszelle freigesetzt werden. Foamyviren dagegen benötigen für die Freisetzung ihrer Viruspartikel neben dem Strukturprotein obligat die Koexpression ihres Glykoproteins. Im zweiten Teil dieser Arbeit wurden funktionelle Abschnitte im PFV Gag-Protein eingegrenzt und charakterisiert, die eine Rolle bei der Bildung und Freisetzung der viralen Partikel spielen. Eine schrittweise Deletion des PFV Gag-Proteins vom C-Terminus her zeigte, dass die N-terminalen 300 As von PFV Gag ausreichend für die Freisetzung von partikulärem viralem Proteinmaterial sind. Die Analyse weiterer Deletionsmutanten innerhalb des N-Terminus des PFV Gag-Proteins belegte, dass die As 6 - 200 für die Bildung viraler Kapside entbehrlich sind, aber für die Interaktion mit dem viralen Glykoprotein und für eine Freisetzung der viralen Partikel aus der Wirtszelle essentiell sind. Die Substitution einzelner konservierter Aminosäuren durch Alanin zwischen As 40 - 60 blockierte die Partikelmorphogenese. Die Aminosäureabfolge dieses Proteinabschnittes zeigte eine große Ähnlichkeit mit einem zellulären Transportsignal, dass in den Gag-Proteinen von Retroviren des Typ-D-Morphogeneseweges entdeckt worden ist. Eine parallele Mutationsanalyse des FFV Gag-Proteins ließ vermuten, dass dieses Motiv wohl universell in allen FV Gag-Proteinen vorhanden ist. Weiterhin konnten Aminosäureabschnitte am unmittelbaren N-Terminus des PFV Gag-Proteins sowie zwischen As 130 - 200 eingegrenzt werden, die essentiell für die Struktur des Proteins sind und eventuell eine wichtige Funktion bei der Partikelmorphogenese erfüllen. Weitere Untersuchungen und insbesondere eine Strukturaufklärung des PFV Gag-Proteins sind nötig, um die genaue Funktion der einzelnen Proteinabschnitte zu charakterisieren.

A enzima Paraoxonase-1 (PON1) possui atividades paraoxonase, arilestearase e lactonase, entre outras. É a mais estuda da família das PONs que é composta pela PON1, PON2 e PON3. Sugere-se, que todas atuam inibindo o processo de peroxidação lipídica de moléculas como a lipoproteína de baixa densidade (LDL) e alta densidade (HDL), caracterizando assim um possível papel anti-aterogênico. O gene da PON1 apresenta dois sítios polimórficos, com a troca de uma Gln192Arg (Q/R) e Met55Leu, que estão associados com diferenças na atividade e concentrações séricas da enzima. Por sua vez, indivíduos soropositivos para o HIV-1 apresentam alterações do metabolismo lipídico, que poderiam estar associados a alterações na atividade da PON1 e a terapia antirretroviral (TARV) com inibidores de protease (IP). O objetivo do estudo foi determinar as atividades séricas da PON1 e da arilestearase (ARE), e as freqüências alélicas dos polimorfismos genéticos da PON1 192QR e 55LM, e ainda, avaliar a correlação destes parâmetros com as alterações lipídicas em indivíduos soropositivos para o HIV-1 tratados com IP. No período de Setembro de 2009 até Junho de 2012, 174 indivíduos soropositivos e 46 soronegativos para o HIV-1 foram estudados. Foi realizada a genotipagem dos polimorfismos da PON1 192QR e 55LM através de PCR-RFLP. A atividade sérica da PON1/ARE foi avaliada por espectrofotometria empregando-se como substratos o paraoxon e o fenilacetato, respectivamente. O RNA-HIV-1 foi quantificado pelo método NASBA, e os linfócitos T-CD4+ e T-CD8+ por citometria de fluxo. Os níveis séricos de colesterol total, HDL, LDL, triglicérides (TG), ApoA1 e ApoB100 foram determinados e os anticorpos IgG anti-oxLDL por ELISA. A atividade sérica da PON1 foi inferior nos grupos de soropositivos, p<0,05, porém, a atividade ARE não apresentou diferenças entre os grupos estudados, p>0,05. Ambas as atividades não apresentaram relação com os genótipos PON1 192QR e 55LM, e estes genótipos apresentaram uma freqüência alélica semelhante ao grupo de soronegativos. Os níveis séricos de TG foram superiores nos grupos de soropositivos com TARV, p<0,05, enquanto o grupo tratado com IP apresentou níveis séricos de HDL e Apo-A1 inferiores aos demais grupos, p<0,05. Níveis séricos de Apo-B100, IgG anti-oxLDL, e o índice de risco aterogênico foram superiores no grupo tratado com IP, p<0,05. Concluí-se, que indivíduos soropositivos para o HIV-1 apresentaram alterações no metabolismo lipídico, principalmente nos tratados com IP, que adicionalmente apresentaram um maior índice de risco aterogênico e maiores níveis de anticorpos IgG anti-oxLDL. Estas alterações não apresentaram relação com os polimorfismos PON1 192QR e 55LM da PON1, e demonstraram que a atividade da enzima PON-1 esta diminuída em indivíduos soropositivos para o HIV-1<br>The enzyme Paraoxonase-1 (PON1) has paraoxonase (PON), arylesterase (ARE) and lactonase activities, among others. It is the most studied member of PON family which is composed of PON1, PON2 and PON3. It is suggested that all members acts by inhibiting the peroxidation of lipid molecules as the low-density lipoprotein (LDL) and high-density lipoprotein (HDL), characterizing a potential anti-atherogenic effect. The PON1 gene has two mainly polymorphic sites, with an exchange of Gln192Arg (Q/R) and Met55Leu (L/M), which are associated with differences in activity and serum concentrations of the enzyme. In turn, seropositive individuals for HIV-1 show changes in lipid metabolism, which could be associated with changes in the activity of PON1 and highly active antiretroviral therapy (HAART) with protease inhibitors (PI). The aim of this study was to determinate the serum PON and ARE activities of PON1, the allele frequencies of PON1 192QR and PON1 55LM genetic polymorphisms and evaluate the correlation between these parameters and lipid abnormalities in seropositive patients for HIV-1 treated with IP. In the period from September 2009 until June 2012, 174 seropositive individuals and 46 soronegative individuals for HIV-1 were studied. We performed PON1 192QR and 55LM genotyping by PCR-RFLP. Serum activities PON and ARE of PON1 were evaluated by spectrophotometry using paraoxon and phenylacetate, respectively, as substrates. The HIV-1-RNA was quantified by the NASBA method, and lymphocytes T-CD4+ and T-CD8+, by flow cytometry. Serum levels of total cholesterol, HDL, LDL, triglycerides (TG), apoA1 and ApoB100 were determined. IgG anti-oxLDL antibodies were quantified by ELISA. The serum PON1 activity was lower in the seropositive group, p<0.05, however, ARE activity did not differ between groups, p>0.05. Both activities had no relation with the PON1 192QR and PON1 55LM genotype, and these individuals showed an allele frequency similar to the seronegative group. Serum levels of TG were higher in groups of HIV-positive with HAART, p<0.05, while the IP-treated group showed serum levels of HDL and ApoA1 lower than other groups, p <0.05. Serum levels of ApoB100, IgG anti-oxLDL antibodies, and atherogenic risk indices were higher in the group treated with PI, p<0.05. It was concluded that individuals HIV-1-infected showed changes in lipid metabolism, especially in those treated with IP, which additionally showed a higher rate of atherogenic risk and higher levels of IgG anti-oxLDL antibodies. These changes did not correlated with PON1 192QR and 55LM polymorphisms and demonstrated that the activity of PON1enzyme is decreased in individuals seropositive for HIV-1

La proteine de regulation vpr du retrovirus vih-1 est une petite proteine basique de 96 acides amines, 14 kda, hautement conservee chez vih-1, vih-2 et siv, et presente dans le virus en quantite importante, comparable a celles de gag. Vpr est impliquee dans un grand nombre d'etape de l'infection virale via des interactions avec des partenaires cellulaires ou viraux. Ainsi elle influence la transcription inverse, regule la replication virale, intervient dans la translocation nucleaire du complexe de preintegration, forme des canaux ioniques dans les membranes lipidiques, stimule la transcription du long terminal repeat et d'autres promoteurs, induit l'arret du cycle cellulaire de la cellule hote, et regule les phenomenes d'apoptose. Nous avons alors entrepris l'etude de la proteine par rmn homonucleaire et heteronucleaire (15n, 13c), filtration sur gel, dichroisme circulaire, modelisation moleculaire sous contraintes rmn et relaxation, afin de determiner la structure 3d de cette proteine, et d'apprehender son mecanisme d'action, et les modes de reconnaissance avec ces differentes cibles. Au vu de la taille de la proteine de regulation vpr, ce projet a ete subdivise en trois etudes : le fragment n-terminal (1-51), puis le fragment c-terminal (52-96) et enfin l'etude de la proteine entiere (1-96). Nous avons ainsi pu determiner la structure du domaine n-terminal qui presente un domaine 1-13 flexible, suivi par un motif coude-helice -coude -helice -coude. Le domaine c-terminal, quant a lui, s'organise autour d'une helice (53-78), suivie d'une region flexible (79-96). La proteine entiere, est constituee : d'une region n-terminale tres flexible (1-13), d'un motif coude-helice -coude, d'une deuxieme helice , d'une boucle, d'une helice (55-83) et d'un domaine flexible (84-96). Ainsi, via la determination structurale de ces deux fragments et de la proteine entiere vpr(1-96), nous avons ete en mesure d'expliquer un certain nombre de mecanismes impliquant vpr.

Encapsulation d'adn dans des liposomes contenant du lactosylceramide dont le sucre terminal est reconnu specifiquement par des recepteurs presents sur la membrane plasmique des cellules visees, c. A. D. , les hepatocytes et les cellules endotheliales du foie et egalement les lymphocytes de la rate. Injection par voie intraveineuse des liposomes. Role de l'endocytose, dans leur internalisation. Modele genetique constitue du gene de la preproinsuline i de rat insere dans des vecteurs retroviraux permettant l'expression du gene dans des celules non insulogenes

Today, it is estimated that 35 million people are living with human immunodeficiency virus (HIV). Since its initial discovery in 1981, researchers and medical providers have worked endless hours to understand the pathology, transmission, and medical management of HIV. In the early days of HIV, life expectancy after diagnosis was 10 years. However, after the development of zidovudine (AZT) in 1987, life expectancy of HIV patients began to slowly increase, albeit still lower than that of the general population. The development of AZT opened the door for more antiretroviral drugs and more drug classes. Now, patients undergo a triple drug regimen to manage HIV. These patients are able to maintain viral suppression and are no longer experiencing opportunistic infection or other AIDS-related conditions. While HIV is medically managed, this is a chronic condition and to-date, not cured. As opposed to opportunistic infections and other AIDS-related conditions, patients are succumbing to non-AIDs related conditions such as renal, neurological, bone disorders, and liver complications. The leading non-AIDs related condition is cardiovascular disease (CVD). Even with viral suppression, HIV infection itself contributes to the pathology and development of atherosclerosis and CVD. It is clear that chronic immune activation, HIV proteins, and dyslipidemia appear to be key factors in CVD development. Since the life expectancy of HIV patients has increased, physicians are now seeing an older generation of HIV patients. Medical providers are shifting focus toward understanding the long-term effects of not just HIV, but antiretroviral therapy (ART) as well. It appears that drug interactions and long-term toxicity augment CVD development. Protease inhibitors (PIs), compared to other ART drug classes, appear to increase the risk of atherosclerosis, especially through dyslipidemia. Due to management of HIV being life-long, compliance is difficult because of high pill burden, drug-drug interactions, and drug side effects. This can result in drug failure leading HIV patients to switch to second-line ART regimens. PIs are a common component of second-line ART regimens. Compared to other ART drugs, PIs have a high genetic barrier to resistance. However, PIs have a low bioavailability requiring high dosage and/or boosting with ritonavir (RTV). Lopinavir (LPV) boosted with RTV (LPV/r) is a favorable PI as it is used in a combination pill and is the most cost effective. However, multiple studies have shown LPV/r correlates more to CVD compared to other PIs. Patients on LPV/r exhibit an increased intima-medial thickening, a hallmark characteristic of atherosclerosis and an increased risk for myocardial infarction. Unfortunately, researchers are greatly conflicted as to why this is and in general why PIs increase the risk of CVD. Future medical treatment for HIV is complex and requires long-term medical management. In recent years, integrase inhibitors (IIs) have exhibited promise to provide better lipid profiles while maintaining viral suppression. However, as this drug class is relatively new and expensive, the financial burden on HIV patients is high. The next step toward addressing the global health issue of HIV is understanding the exact mechanism of how PIs contribute to CVD. This will not only increase the life expectancy of HIV patients, but reduce drug toxicity, non-AIDS related conditions, and increase adherence and viral suppression. It is clear that future research must be focused on understanding the role PIs have in CVD development. Physicians are seeing an older generation of HIV patients, and a vast majority are on second-line regimens. By understanding this relationship, researchers could design alternative drugs to manage CVD risk, by modifying current PIs or designing entirely new drugs.

Structural and functional investigations on DNA-damage inducible protein1 (Ddi1) from Entamoeba histolytica, Trypanosoma cruzi and Toxoplasma gondii have been carried out. Ddi1 belongs to the ubiquitin receptor family of proteins. One of its domains is similar to the retroviral aspartic proteinases. It has been shown that this domain is the target of HIV-protease inhibitors that were being used in the treatment of AIDS and it was observed that these drugs reduced the infection caused by many parasitic protozoa such as Trypanosoma and Leishmania species that are responsible for prevalent opportunistic diseases in AIDS patients. The retroviral protease-like domain (RVP) present in Ddi1 proteins of these organisms was identified as the target of these drugs. The binding of the RVP domain of Ddi1 from E. histolytica, T. cruzi and T. gondii with HIV protease inhibitors; and the binding of ubiquitin and K48-linked diubiquitin with the ubiquitin associated domain (UBA) have been established by Biolayer Interferometry (BLI). The crystal structure of the RVP domain of Ddi1 from T. gondii (ToxoDdi1-RVP) shows that it forms a homodimer similar to that observed in HIV protease and the reported structures of the same domain from S. cerevisiae, L. major and human. The ‘flap’ regions in ToxoDdi1-RVP are similar to the flaps of HIV protease which close-in upon substrate/inhibitor binding. Both the ‘flap’ regions are clearly visible in the electron density maps. Though the native form of the domain shows an open dimeric structure, normal mode analysis reveals that it can take up a closed conformation resulting from relative movements of the subunits. Comparison of the structure of ToxoDdi1-RVP with the available crystal structures of Ddi1-RVP from other organisms revealed that the active site architecture is conserved in all the proteins with differences in the back β-sheet topology and the size of the binding cavity.

Few studies have assessed the optimum second line highly active anti-retroviral therapy (HAART) regimen in patients who had failed on the first-line HAART in resource-limited settings. This study aimed to compare the Protease inhibitor (PI)-based second line HAART regimens used in one clinic in Trinidad by comparing immunological, virological and clinical outcomes of patients on the different second line HAART regimens. The records of 35 treatment-experienced patients, over 21years of age and on PI-based regimens for at least six months, were analysed using SPSS version 20. The regimen containing TDF/FTC/AZT/LPV/r proved to produce superior outcomes compared to the other second line regimens. Due the small number of usable patients’ records, the findings cannot be generalised but indicate directions for future studies attempting to compare the treatment outcomes of different second line HAART regimens<br>Health Studies<br>M. A. (Public Health)

Structuraj investigations on the Ddi1 (DNA-damage inducible protein 1) of Leishmania major and on the rotavirus nonstructural protein NSP4 were carried out. Ddi1 belongs to the ubiquitin receptor family of proteins. One of its domains is similar to the retroviral aspartic proteinases. It has been shown that this domain is the target of HIV-protease inhibitors that were being used in the treatment of AIDS and it was observed that these drugs effectively controlled opportunistic diseases caused by many parasitic protozoa such as Leishmania and Plasmodium species. The retroviral protease-like domains present in Ddi1 proteins of these organisms were identified as the targets of these drugs. Structural studies on Ddi1 from L. major have been carried out, in an attempt to provide a platform for the design of anti-protozoal compounds. Rotavirus NSP4, the first viral enterotoxin to be identified, is a multifunctional glycoprotein that plays critical roles in viral pathogenesis and morphogenesis. As part of an ongoing project on the structural characterization of NSP4, we determined the structure of the diarrhea-inducing region of this protein from the rotavirus strain MF66. Chapter 1 presents an overview of Ddi1 and NSP4 of the rotavirus with an emphasis on their structural features. The methods employed during the course of the present work are described in Chapter 2. Structural studies on the retroviral protease-like domain of Ddi1 (Ddi1-RVP) of L. major is presented in Chapter 3. Apart from this domain, Ddi1 of L. major also has a ubiquitin-associated and ubiquitin-like domains whereas P. falciparum has only the ubiquitin-associated domain. Activity of the full length Ddi1 of L. major and the retroviral protease domain of P. falciparum using an HIV protease substrate was shown to be inhibited by an HIV protease inhibitor, saquinavir. Binding of saquinavir to the proteins was also confirmed by Biolayer Interferometry studies. The crystal structure of the retroviral protease domain of L. major Ddi1 has been determined. It forms a homodimeric structure similar to that of HIV protease and the reported structure of the same domain from Saccharomyces cerevisiae. The loops in Ddi1-RVP are similar to the 'flap' regions of the HIV protease which close-in upon substrate/inhibitor binding; they are visible in the electron density maps, unlike the case of the S. cerevisiae protein. Though the native form of the domain shows an open dimeric structure, normal mode analysis reveals that it can take up a closed conformation resulting from relative movements of the subunits. The present structure of Ddi1-RVP of L. major with the defined 'flap'-like loops will be helpful in the design of effective drugs against protozoal diseases, starting with HIV protease inhibitors as the lead compounds. Chapter 4 describes the structural investigations carried out on the diarrhea-inducing region of the nonstructural protein NSP4 of the rotavirus strain MF66 which forms an α-helical coiled-coil structure. Crystal structures of a synthetic peptide and of two recombinant proteins spanning this region showed parallel tetrameric organization of this domain with a bound Ca2+ ion at the core. Subsequently, we determined the structure of NSP4 from a different strain as a pentamer without the bound Ca2+ ion. This new structure provides more insights into understanding some of the functions of NSP4 such as the release of ions into the cytoplasm and binding to the double-layered particle (DLP). We also established conditions responsible for these structural transitions. The crystal structure of the coiled-coil domain of NSP4 presented in this chapter shows an entirely different structure which is an antiparallel tetramer. This explains our failure to determine the structure by the molecular replacement method using known oligomers. The structure was solved by the Sulphur-SAD method using diffraction data collected with Cr Ka radiation. The study reveals that the structural diversity of NSP4 is not limited. We could relate sequence variations and pH conditions to the differences in oligomeric assemblies. Surface properties of the domain suggest that the new form is likely to interact with different sets of proteins compared to those that interact with the parallel tetramers or pentamers. Further investigations are needed to establish this property.

Structuraj investigations on the Ddi1 (DNA-damage inducible protein 1) of Leishmania major and on the rotavirus nonstructural protein NSP4 were carried out. Ddi1 belongs to the ubiquitin receptor family of proteins. One of its domains is similar to the retroviral aspartic proteinases. It has been shown that this domain is the target of HIV-protease inhibitors that were being used in the treatment of AIDS and it was observed that these drugs effectively controlled opportunistic diseases caused by many parasitic protozoa such as Leishmania and Plasmodium species. The retroviral protease-like domains present in Ddi1 proteins of these organisms were identified as the targets of these drugs. Structural studies on Ddi1 from L. major have been carried out, in an attempt to provide a platform for the design of anti-protozoal compounds. Rotavirus NSP4, the first viral enterotoxin to be identified, is a multifunctional glycoprotein that plays critical roles in viral pathogenesis and morphogenesis. As part of an ongoing project on the structural characterization of NSP4, we determined the structure of the diarrhea-inducing region of this protein from the rotavirus strain MF66. Chapter 1 presents an overview of Ddi1 and NSP4 of the rotavirus with an emphasis on their structural features. The methods employed during the course of the present work are described in Chapter 2. Structural studies on the retroviral protease-like domain of Ddi1 (Ddi1-RVP) of L. major is presented in Chapter 3. Apart from this domain, Ddi1 of L. major also has a ubiquitin-associated and ubiquitin-like domains whereas P. falciparum has only the ubiquitin-associated domain. Activity of the full length Ddi1 of L. major and the retroviral protease domain of P. falciparum using an HIV protease substrate was shown to be inhibited by an HIV protease inhibitor, saquinavir. Binding of saquinavir to the proteins was also confirmed by Biolayer Interferometry studies. The crystal structure of the retroviral protease domain of L. major Ddi1 has been determined. It forms a homodimeric structure similar to that of HIV protease and the reported structure of the same domain from Saccharomyces cerevisiae. The loops in Ddi1-RVP are similar to the 'flap' regions of the HIV protease which close-in upon substrate/inhibitor binding; they are visible in the electron density maps, unlike the case of the S. cerevisiae protein. Though the native form of the domain shows an open dimeric structure, normal mode analysis reveals that it can take up a closed conformation resulting from relative movements of the subunits. The present structure of Ddi1-RVP of L. major with the defined 'flap'-like loops will be helpful in the design of effective drugs against protozoal diseases, starting with HIV protease inhibitors as the lead compounds. Chapter 4 describes the structural investigations carried out on the diarrhea-inducing region of the nonstructural protein NSP4 of the rotavirus strain MF66 which forms an α-helical coiled-coil structure. Crystal structures of a synthetic peptide and of two recombinant proteins spanning this region showed parallel tetrameric organization of this domain with a bound Ca2+ ion at the core. Subsequently, we determined the structure of NSP4 from a different strain as a pentamer without the bound Ca2+ ion. This new structure provides more insights into understanding some of the functions of NSP4 such as the release of ions into the cytoplasm and binding to the double-layered particle (DLP). We also established conditions responsible for these structural transitions. The crystal structure of the coiled-coil domain of NSP4 presented in this chapter shows an entirely different structure which is an antiparallel tetramer. This explains our failure to determine the structure by the molecular replacement method using known oligomers. The structure was solved by the Sulphur-SAD method using diffraction data collected with Cr Ka radiation. The study reveals that the structural diversity of NSP4 is not limited. We could relate sequence variations and pH conditions to the differences in oligomeric assemblies. Surface properties of the domain suggest that the new form is likely to interact with different sets of proteins compared to those that interact with the parallel tetramers or pentamers. Further investigations are needed to establish this property.

Tese de doutoramento em Bioquímica, na especialidade de Tecnologia Bioquímica, apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra<br>Os membros do género Rickettsia são bactérias intracelulares obrigatórias do tipo gram-negativas, cuja transmissão a mamíferos pode ocorrer através de vetores artrópodes como carraças, pulgas ou piolhos. Entre as várias espécies identificadas, muitas são patogénicas para o Homem causando doenças infeciosas agudas das quais se destacam o tifo epidémico (Rickettsia prowazekii), a febre maculosa das montanhas rochosas (Rickettsia rickettsii) e a febre escaro-nodular (Rickettsia conorii). A elevada patogenicidade e o caráter emergente destas doenças, associados à inexistência de vacinas eficazes para a sua prevenção, reforçam inequivocamente a necessidade de identificar novos fatores proteicos para o desenvolvimento de terapêuticas inovadoras. Neste sentido, tem-se assistido nas últimas décadas a avanços significativos na compreensão dos mecanismos de patogénese e de resposta imunitária às rickettsioses. Contudo, a validação da função biológica de genes de Rickettsia tem sido amplamente limitada pela natureza estritamente intracelular destes organismos que dificulta a sua manipulação. Por conseguinte, a comparação entre os múltiplos genomas disponíveis de Rickettsia tem revelado ser o método mais expedito para a identificação de novos fatores proteicos potencialmente implicados na patogenicidade destes micro-organismos. Este trabalho descreve a identificação e caracterização de uma nova protease membranar do tipo retropepsina, altamente conservada em 55 genomas de Rickettsia. Apesar da baixa similaridade na sequência de aminoácidos relativamente a outras retropepsinas, demonstrámos que a proteína codificada pelo gene homólogo RC1339 de R. conorii Malish 7, designada por APRc para protease aspártica de Rickettsia conorii, é uma enzima ativa com propriedades altamente reminiscentes desta família de proteases aspárticas. Entre outras, destacam-se a atividade autolítica comprometida pela mutação do aspartato catalítico, a acumulação na forma dimérica, uma atividade ótima a pH de 6 e a inibição por inibidores específicos da protease do vírus da imunodeficiência humana do tipo 1. Além disso, utilizando uma abordagem de mapeamento de especificidade de alto débito, foi possível confirmar que os determinantes de especificidade da APRc são semelhantes aos de outras proteases aspárticas de ambos os tipos, retropepsina e pepsina. Neste trabalho, demonstrámos também que o gene codificante da APRc é transcrito e traduzido em pelo menos duas espécies patogénicas de Rickettsia (R. conorii e R. rickettsii), e que esta proteína é integrada na membrana externa de ambas. Ao explorar as potenciais funções biológicas da APRc, verificámos que esta protease catalisa o processamento in vitro de dois membros da família das proteínas autotransportadoras envolvidas na adesão e invasão de Rickettsia: Sca5/rOmpB e Sca0/rOmpA. Estes resultados apontam assim para a participação da APRc numa via proteolítica relevante para a virulência destes micro-organismos, surgindo esta protease como um alvo interessante para a intervenção terapêutica contra as rickettsioses. Por fim, ao demonstrar que a APRc é um novo membro da família das proteases aspárticas do tipo retropepsina, provamos simultaneamente que estas enzimas estão efetivamente presentes em bactérias gram-negativas intracelulares, pelo que poderão representar uma forma ancestral desta classe de proteases.<br>Members of the genus Rickettsia are obligate intracellular, gram-negative, arthropod-borne pathogens of humans and other mammals, causing severe infections including epidemic typhus (Rickettsia prowazekii), Rocky Mountain spotted fever (Rickettsia rickettsii), and Mediterranean spotted fever (Rickettsia conorii). The life-threatening character of diseases caused by many Rickettsia spp. and the lack of reliable protective vaccine against rickettsioses strengthens the importance of identifying new protein factors for the potential development of innovative therapeutic tools. However, progress in correlating rickettsial genes and gene functions has been greatly hampered by the intrinsic difficulty in working with these obligate intracellular bacteria, despite the increasing insights into the mechanisms of pathogenesis of and the immune response to rickettsioses. Therefore, comparison of the multiple available genomes of Rickettsia is proving to be the most practical method to identify new factors that may play a role in pathogenicity. The present work reports the identification and characterization of a novel membrane-embedded retropepsin-like homologue, highly conserved in 55 Rickettsia genomes. Using R. conorii Malish 7 gene homologue RC1339 as our working model we demonstrate that, despite the low overall sequence similarity to retropepsins, the gene product of RC1339 APRc (for Aspartic Protease from Rickettsia conorii) is an active enzyme with features highly reminiscent of this family of aspartic proteases, such as autolytic activity impaired by mutation of the catalytic aspartate, accumulation in the dimeric form, optimal activity at pH 6, and inhibition by specific HIV-1 protease inhibitors. Moreover, specificity preferences determined by a high-throughput profiling approach confirmed common preferences between this novel rickettsial enzyme and other aspartic proteases, both retropepsin and pepsin-like enzymes. Additionally, we have also shown that APRc is transcribed and translated by at least two pathogenic rickettsial species, R. conorii and R. rickettsii, and is integrated into the outer membrane of both species. By further exploring one of its putative biological roles, we have demonstrated that APRc is sufficient to catalyze the in vitro processing of two conserved high molecular weight autotransporter adhesin/invasion proteins, Sca5/rOmpB and Sca0/rOmpA, thereby suggesting the participation of this enzyme in a relevant proteolytic pathway in rickettsial virulence. As a novel bona fide member of the retropepsin family of aspartic proteases, APRc emerges as an intriguing target for therapeutic intervention against fatal rickettsioses. Finally, with this work we demonstrate that retropepsin-type aspartic proteases are indeed present in gram-negative intracellular bacteria such as Rickettsia, suggesting that these enzymes may represent an ancestral form of this class of proteases.<br>FCT - SFRH/BD/47638/2008

Molecular modelling and simulation are powerful methods in providing important in-formation on different biological systems to elucidate their structural and functional proper-ties, which cannot be determined in experiment. These methods are applied to analyse versa-tile biological systems: lipid membrane bilayers stabilized by an intercalated single wall carbon nanotube and retroviral proteins such as HIV protease and integrase. HIV-1 integrase has nuclear localization signals (NLS) which play a crucial role in nuclear import of viral preintegration complex (PIC). However, the detailed mechanisms of PIC formation and its nuclear transport are not known. Previously it was shown that NLSs bind to the cell transport machinery e.g. proteins of nuclear pore complex such as transportins. I investigated the interaction of this viral protein HIV-1 integrase with proteins of the nuclear pore complex such as transportin-SR2 (Shityakov et al., 2010). I showed that the transportin-SR2 in nuclear import is required due to its interaction with the HIV-1 integrase. I analyzed key domain interaction, and hydrogen bond formation in transportin-SR2. These results were discussed in comparison to other retroviral species such as foamy viruses to better understand this specific and efficient retroviral trafficking route. The retroviral nuclear import was next analyzed in experiments regarding the retroviral ability to infect nondividing cells. To accomplish the gene transfer task successfully, ret-roviruses must efficiently transduce different cell cultures at different phases of cell cycle. However, promising and safe foamy viral vectors used for gene transfer are unable to effi-ciently infect quiescent cells. This drawback was due to their inability to create a preintegra-tion complex (PIC) for nuclear import of retroviral DNA. On the contrary, the lentiviral vec-tors are not dependant on cell cycle. In the course of reverse transcription the polypurine tract (PPT) is believed to be crucial for PIC formation. In this thesis, I compared the transduction frequencies of PPT modified FV vectors with lentiviral vectors in nondividing and dividing alveolar basal epithelial cells from human adenocarcinoma (A549) by using molecular cloning, transfection and transduction techniques and several other methods. In contrast to lentiviral vectors, FV vectors were not able to effi-ciently transduce nondividing cell (Shityakov and Rethwilm, unpublished data). Despite the findings, which support the use of FV vectors as a safe and efficient alternative to lentiviral vectors, major limitation in terms of foamy-based retroviral vector gene transfer in quiescent cells still remains. Many attempts have been made recently to search for the potential molecules as pos-sible drug candidates to treat HIV infection for over decades now. These molecules can be retrieved from chemical libraries or can be designed on a computer screen and then synthe-sized in a laboratory. Most notably, one could use the computerized structure as a reference to determine the types of molecules that might block the enzyme. Such structure-based drug design strategies have the potential to save off years and millions of dollars compared to a more traditional trial-and-error drug development process. After the crystal structure of the HIV-encoded protease enzyme had been elucidated, computer-aided drug design played a pivotal role in the development of new compounds that inhibit this enzyme which is responsible for HIV maturation and infectivity. Promising repre-sentatives of these compounds have recently found their way to patients. Protease inhibitors show a powerful sustained suppression of HIV-1 replication, especially when used in combi-nation therapy regimens. However, these drugs are becoming less effective to more resistant HIV strains due to multiple mutations in the retroviral proteases. In computational drug design I used molecular modelling methods such as lead ex-pansion algorithm (Tripos®) to create a virtual library of compounds with different binding affinities to protease binding site. In addition, I heavily applied computer assisted combinato-rial chemistry approaches to design and optimize virtual libraries of protease inhibitors and performed in silico screening and pharmacophore-similarity scoring of these drug candidates. Further computational analyses revealed one unique compound with different protease bind-ing ability from the initial hit and its role for possible new class of protease inhibitors is dis-cussed (Shityakov and Dandekar, 2009). A number of atomistic models were developed to elucidate the nanotube behaviour in lipid bilayers. However, none of them provided useful information for CNT effect upon the lipid membrane bilayer for implementing all-atom models that will allow us to calculate the deviations of lipid molecules from CNT with atomistic precision. Unfortunately, the direct experimental investigation of nanotube behaviour in lipid bilayer remains quite a tricky prob-lem opening the door before the molecular simulation techniques. In this regard, more de-tailed multi-scale simulations are needed to clearly understand the stabilization characteristics of CNTs in hydrophobic environment. The phenomenon of an intercalated single-wall carbon nanotube in the center of lipid membrane was extensively studied and analyzed. The root mean square deviation and root mean square fluctuation functions were calculated in order to measure stability of lipid mem-branes. The results indicated that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics (Shityakov and Dandekar, 2011). On the other hand, different lipid membranes may have dissimilarities due to the differing abilities to create a bridge formation between the adherent lipid molecules. The results derived from this thesis will help to develop stable nanobiocom-posites for construction of novel biomaterials and delivery of various biomolecules for medi-cine and biology<br>Molekulare Modellierung und Simulationen sind leistungsstarke Methoden, um wich-tige Informationen von verschiedenen biologischen Systemen, welche nicht durch Experi-mente erschlossen werden können, darzustellen, und deren strukturelle und funktionelle Ei-genschaften aufzuklären. Diese Arbeit untersucht in Simulationen Interaktionen viraler Proteinen sowie von Kohlenstoffenanoröhren mit Membranen und Proteinen. Die HIV-1 Integrase besitzt Kernlokalisierungssignale („nuclear localization signals [NLS]“), welche eine entscheidende Rolle beim Import des viralen Präintegrationskomplexes („preintegration complex [PIC]“) in den Zellkern spielen. Die Ausbildung des PIC und sein Import in den Zellkern sind im Detail noch nicht bekannt. Es wurde bereits gezeigt, dass die NLS an Moleküle des Zelltransportsystems binden, wie z.B. an Transportinkernporen. Im Rahmen meiner Arbeit untersuchte ich die Interaktionen der viralen HIV-1 Integrase mit Proteinen der Kernporen wie dem Transportin-SR2 Protein (Shityakov et al., 2010). Hierbei wurden die möglichen Interaktionen des Transportin-SR2 Protein mit der HIV-1-Integrase und die Bedeutung dieser Interaktionen mit dem Import in den Kern aufgezeigt. Zudem wur-den die Interaktionen der Schlüsseldomänen und die Ausbildung von Wasserstoffbrücken-bindungen im dem Transportin-SR2 Protein untersucht. Die Ergebnisse wurden mit Protein-komplexen andere retroviralen Spezies, wie z.B. dem humanen Spumaretrovirus („human foamy virus [HFV]“), verglichen, um diesen spezifischen und sehr effizienten retroviralen Transportweg in die Wirtszelle zu entschlüsseln. Der experimentelle Teil dieser Arbeit beschäftigte sich damit, den retroviralen Kern-import zu untersuchen, um die Fähigkeit des Retrovirus, nicht teilende Zellen zu infizieren, besser zu verstehen verstanden wird. Um dies zu bewerkstelligen, müssen Retroviren Zellkul-turen in verschiedenen Stadien des Zellzyklus effizient transduzieren. Vielversprechende und sichere- HFV- Vektoren, welche in der Gentherapie eingesetzt werden könnten, sind nicht in der Lage, diese Effizienz bei ruhenden Zellen zu gewährleisten. Dies rührte daher, dass diese nicht in der Lage waren, einen PIC für den Transport der retroviralen DNA auszubilden. Lentivirale Vektoren sind dagegen nicht auf einen bestimmten Zellzyklus angewiesen. Für die reverse Transkription ist der Polypurinteil („polypurine tract [PPT]“) essentiell für die Ausbildung der PIC. In dieser Doktorarbeit vergleiche ich die Transduktionsfrequenz von PPT-modifizierten HFV-Vektoren mit denen von lentiviralen Vektoren in nichtteilenden und tei-lenden Lungenkarzinomepithelzellen. Hierbei wurden Methoden wie Klonierung, Transfektion, und Transduktion (wie auch weitere Methoden) angewendet. Im Gegensatz zu lentiviralen Vektoren konnten HFV-Vektoren sich nicht teilende Zellen in meinen Versuchen nicht effizient transduzieren (Shityakov und Rethwiln, unveröffentlicht). Trotz der Befunde, dass HFV-Vektoren sichere und effiziente Alternativen zu lentiviralen Vektoren darstellen, bestehen immer noch große Einschränkungen, diese HFV-basierten, retroviralen Vektoren für Gentherapien bei ruhenden Zellen einzusetzen. Viele Versuche wurden unternommen, um mögliche, vielversprechende Moleküle, welche als Wirkstoffe für eine HIV-Therapie eingesetzt werden könnten, zu finden. Diese Moleküle können aus chemischen Substanzbibliotheken bezogen werden oder am Computer in silico entworfen und dann synthetisiert werden. Digitalisierte Strukturen können als Refe-renzen benutzt werden, um besser herauszufinden, wie diese Moleküle Typen diverse Enzy-me blokieren könnten. Strukturbasiertes Wirkstoffdesign hat das Potential, viele Jahre und Geld an Entwicklungskosten einzusparen. Nachdem die Kristallstruktur der HIV-kodierten Proteasen aufgeklärt war, spielte das computergestützte Wirkstoffdesign eine zentrale Rolle bei der Entwicklung neuer Wirkstoffe gegen die Protease. Vielversprechende Vertreter dieser Wirkstoffklasse werden seit kurzem nun auch für die Behandlung von Patienten eingesetzt. Proteaseinhibitoren zeigen eine wir-kungsvolle und langanhaltende Inhibition der HIV-1-Replikation; besonders dann, wenn sie in Kombinationstherapien eingesetzt werden. Aber diese Wirkstoffe werden immer weniger effektiv, je resistenter die HIV-Stämme durch Mutationen in den retroviralen Proteasen wer-den. Im Rahmen meiner Arbeit mit computergestütztem Wirkstoffdesign nutzte ich Model-lierungsmethoden wie den „lead expansion algorithm“ (Tripos®) um virtuelle Wirkstoffbibli-otheken mit verschiedenen Affinitäten zur Proteasebindungsstelle zu erstellen. Zusätzlich wandte ich Verfahren der computergestützten, kombinatorischen Chemie an, um virtuelle Bibliotheken von Proteaseinhibitoren zu designen, und zu verbessern. Parallel dazu wurde eine in silico Selektion sowie eine Einteilung nach Pharmakophorähnlichkeiten für diese Kandidaten vorgenommen. Weiterführende computergestützte Analysen förderten einen ein-zigartigen Wirkstoff zu Tage, welcher neuartige Proteasebindungseigenschaften aufweist, und dessen Rolle für eine potentiell neuartige Klasse von Proteaseinhibitoren schon beschrieben wurde (Shityakov und Dandekar, 2009). Eine Reihe von Modellen mit atomarer Auflösung wurden bereits entwickelt, um das Verhalten von Nanoröhren in Lipid-Doppelschichten aufzuklären. Die Auswirkungen auf die molekular Dynamik einer einschichtigen Karbonnanoröhre, welche in das Zentrum einer Lipid-Doppelschicht eingefügt wurde, wurden intensiv studiert und analysiert. Die Normalabweichung und Fluktuationen wurden berechnet, um eine Aussage über die Stabilität der Lipid-Doppelschichten treffen zu können. Die Ergebnisse weisen darauf hin, dass eine eingefügte Karbonnanoröhre die Freiheit für Konformationsänderungen bei nahegelegenen Lipiden einschränkt und dadurch einen Einfluss auf die Membranstabilität hat (Shityakov und Dandekar, 2011). Es kann aber außer-dem sein, dass verschiedene Lipid-Doppelschichten Unterschiede in ihrer Fähigkeit, Brücken zwischen benachbarten Lipiden auszubilden, aufweisen. Viren und Karbonnanoröhren werden damit in verschiedenen dynamischen Simulati-onen untersucht, um mehr über ihre Interaktionen mit Proteinen und Membranen zu erfahren

Tese de mestrado, Doenças Infecciosas Emergentes, Faculdade de Medicina, Universidade de Lisboa, 2009<br>The lipid profile of individuals infected with HIV-1 is characterized with high levels of total cholesterol, LDL cholesterol and triglycerides e low levels of HDL cholesterol. The regimens based in atazanavir (ATV) revealed improved metabolic and lipid profile in comparison with other protease inhibitors, with identical viral suppression. The objectives of this study were to analyse the efficacy and safety of boosted ATV as part of combination antiretroviral therapy in HIV-1 infected patients. Study sample consisted of patients medicated with ATV/RTV at least for 6 months. Patients were recruited at the Infectious Diseases Department of Santa Maria Hospital in Lisbon. Clinical files were analyzed, including demographic, clinical, and laboratory data, as well as history of present and past therapy. Data from 190 patients was collected and analyzed in five different moments: before treatment with ATV/RTV, and at month 6, 12, 18, and 24. Safety of ATV/RTV was evaluated in terms of lipid and metabolic profile improvements, whereas the efficacy was established through HIV-1 viral load, and levels of T CD4+ cells. The use of ATV/RTV therapy was associated with no alteration in metabolic and lipid profile, meaning that this therapy does not increase the levels of total cholesterol, LDL, triglycerides and glycemia. The improved lipid and metabolic profile can reduce the cardiovascular risk and the metabolic complications of the patients doing this type of therapy. The efficacy was accomplished with a statistical significant reduction in viral load and a significant increase in CD4+ T cell counts.<br>Resumo alargado em português