Human neurocysticercosis (NC) is an important but neglected cause of epilepsy in developing countries where the parasite occurs. Expression of single-chain variable fragment (scFv) antibodies on the surface of bacteriophage is widely used to prepare antibodies with pre-defined specificities. A phage antibody library was selected against peptides displayed on phages coupled to beads and total saline extract of Taenia solium metacestodes immobilized on microtiter plate wells. After two rounds of selection 96 phage clones of each panning were selected, tested for scFv expression and specificity to each target. Specific clones were further analyzed by ELISA (Enzyme-linked immunosorbent assay), Dot-blot, sequencing and immunofluorescence. After selection, three clones were used for antigen capture to characterize its targets for future immunodiagnostic assays development. Total saline extract was fractionated on ion exchange resin diethylaminoethyl (DEAE), and fractions were tested by ELISA to detect sera IgG from: NC, other parasites and health controls (40 each). The fractions with best diagnostic parameters (sensitivity, specificity, area under curve and likelihood ratio, calculated by TG-ROC) were selected and subjected to antigen capture using each purified scFv clone. Each captured fraction was tested by ELISA to detect IgG in 30 serum samples from each group. In immunofluorescence tests, no fluorescence was observed in negative controls, and all clones showed a non-uniform staining profile, and their targets were elucidated through mass spectrometry. After ion exchange fractionation and ELISA tests, DEAE S2 fraction showed to be the best one and was used to capture new antigens. DEAE S2 showed 93.3% specificity. Among all clones, A4 and B6 captured antigens from saline extract and DEAE S2 fraction, respectively, with the best diagnostic parameters. In conclusion, antibody phage display technology is a potential approach for the study of antigen-antibody interactions, which can be used to further elucidate the biology of interaction on neurocysticercosis and to capture new antigens with potential applications in NC diagnosis and therapeutics. / A neurocistocercose humana (NC) é uma doença muito importante, porém negligenciada e é a maior causa de epilepsia em países em desenvolvimento onde a parasitose ocorre. A expressão de fragmentos de cadeia única das regiões variáveis de anticorpo (scFv) na superfície de bacteriófagos é amplamente utilizada para obter anticorpos com especificidades pré-definidas. Uma biblioteca de anticorpos foi utilizada para a seleção de clones específicos à peptídeos expostos em fagos acoplados a beads e ao extrato salino total de Taenia solium (S) imobilizado em placas de microtitulação. Após dois ciclos de seleção, 96 clones de anticorpos foram selecionados contra cada alvo, testados para expressão do scFv e especificidade pelo alvo. Aqueles clones que se mostraram específicos foram melhor analisados por ELISA (Enzyme linked immunosorbent assay), Dot blot, sequenciamento e imunofluorescência. Três clones foram selecionados para serem utilizados na captura antigênica e caracterização do antígeno verdadeiro e para captura de novos antígenos com potencial aplicação em testes diagnósticos. O extrato S foi fracionado em resina de troca iônica diethylaminoethyl (DEAE) para obter frações que foram posteriormente testadas por ELISA para detectar IgG em amostras de soro de pacientes: com NC, outras parasitoses e saudáveis, 40 amostras cada grupo. A fração com melhores parâmetros diagnósticos (sensibilidade, especificidade, área sob a curva e likelihood ratio, calculadas por TG-ROC) foi selecionada e sujeita à captura antigênica usando cada clone de scFv purificado. Cada fração capturada foi testada por ELISA para detectar IgG em 30 amostras de soro de cada grupo. Nos testes de imunofluorescência, nenhuma fluorescência foi observada com os controles negativos e todos os clones mostraram um padrão de marcação não uniforme, seus antígenos alvo foram elucidados por espectrometria de massas. Após fracionamento por troca iônica e ELISA, a fração DEAE S2 se mostrou a melhor e foi utilizada para a captura de novos antígenos. A fração DEAE S2 mostrou especificidade de 93,3%. Dentre todos os clones, o A4 e o B6 capturaram antígenos do extrato S e fração DEAE S2, respectivamente, com os melhores parâmetros diagnósticos. Em conclusão a tecnologia de exposição de anticorpos em fagos é uma técnica potencial para o estudo de interações antígeno-anticorpo utilizadas para melhor elucidar a a biologia da interação na NC e para capturar novos antígenos potencialmente aplicáveis para o diagnóstico da NC. / Doutor em Imunologia e Parasitologia Aplicadas

The Boophilus microplus tick is one of the most important arthropods that can parasitize bovines, causing great damages to the world livestock through direct and indirect effects. The application of chemical products is the principal method of controlling this parasite, but in function of the disadvantages of this practice, the use of vaccines is a good alternative, because they are residue free, specifics and present smaller possibility to develop resistance. With the objective of selecting synthetic peptides expressed in the capsid of phage display bacteriophages, it was produced the serum policlonal in chickens previously sensitized with total larva proteins of the Boophilus microplus tick. The peptides found in larger frequency and with larger antigenic index (bioinformatics and dot blotting with chicken serum) were selected for the immunization of mice and bovines. The initial data infer that the peptides in phagos induced immune response, evaluated by Elisa test, and the more immunogenic are: 2D7 (SNNADYKQSLL), 2E6 (VNWNSWHKTNLS), 2F3 (SIPTYTPDKVTY) and 2E4 (DAWKMRLSQMYD). The sequences selected in the present work introduce the protean motives NxxxKxxL (2D7, 2E6 and 2E4) and the motive TPDKS (2E4). These sequences presented structural similarities with some tick proteins, mainly the calreticulin. Complementary studies are being accomplished to characterize the sensibility and specificity to the selected peptides. / O carrapato Boophilus microplus é um dos mais importantes artrópodes que parasitam os bovinos, causando grandes prejuízos à pecuária mundial pelos seus efeitos diretos e indiretos. A aplicação de produtos químicos é o principal método de controle deste parasita, mas em função das desvantagens desta prática, o uso de vacinas é uma boa alternativa, por serem livres de resíduos, específicas e apresentarem menor possibilidade de desenvolver resistência. Com o objetivo de selecionar peptídeos sintéticos expressos no capsídeo de bacteriófagos phage display produziu-se soro policlonal em galinhas previamente sensibilizadas com proteínas totais de larvas do carrapato Boophilus microplus. Os peptídeos encontrados em maior freqüência e com maior índice antigênico (bioinformática e dot blotting com soro de galinha), foram selecionados para a imunização de camundongos e bovinos. Os dados iniciais inferirem que os peptídeos em fagos induziram resposta imune, avaliada pelo teste de Elisa, sendo os mais imunogênicos o 2D7 (SNNADYKQSLLL), o 2E6 (VNWNSWHKTNLS), o 2F3 (SIPTYTPDKVTY) e o 2E4 (DAWKMRLSQMYD). As seqüências selecionadas no presente trabalho apresentam os motivos protéicos NxxxKxxL (2D7, 2E6 e 2E4) e o motivo TPDKS (2E4). Estas seqüências apresentaram similaridades estruturais com algumas proteínas do carrapato principalmente a calreticulina. Estudos complementares estão sendo realizados para caracterizar a sensibilidade e especificidade aos peptídeos selecionados. / Doutor em Genética e Bioquímica

Les traitements actuels dirigés contre le VIH ne sont que partiellement efficaces en raison de l'apparition de mutations qui confèrent au virus une grande capacité de résistance aux antirétroviraux existants. Un moyen d'améliorer la lutte contre le virus consiste par conséquent à trouver de nouvelles stratégies d'inhibition. Le complexe de reverse transcription est une des principales cibles pour le développement de traitement anti-SIDA, il catalyse une étape obligatoire du cycle de réplication du virus. Cependant, l'ensemble des inhibiteurs de la transcriptase inverse sont limités par l'apparition rapide de souches résistances. Dans ce contexte, mes travaux de thèse ont permis de développer des inhibiteurs ciblant spécifiquement la reverse transcriptase (RT) du VIH-1, basée sur des fragments d'anticorps dérivés des anticorps chaînes lourdes de dromadaire appelés VHHs ou encore Nanobodies. Associé à une stratégie de vectorisation non invasive basée sur l'utilisation de peptides vecteurs pénétrants, les Nanobodies ont été délivré efficacement dans les cellules et par conséquent ils présentent tous une forte activité antivirale de l'ordre du nanomolaire. L'étude du mécanisme d'action du Nanobody leader NbRT20 montre qu'il agit en tant qu'inhibiteur conformationnel. Il interagit avec la forme intermédiaire inactive de la RT et empêche la mobilité du sous-domaine thumb requis pour le positionnement correct de la matrice/amorce sur la RT et inhibant l'incorporation des nucléotides dans la chaîne d'ADN naissante déstabilisant l'enzyme dans une conformation inactive, non processive. Pris ensemble, ces résultats montrent que la plate-forme Nanobody peut être très efficace pour générer des intracorps extrêmement puissants et sélectifs pour neutraliser la RT et la réplication virale.Mots clés : HIV-1, RT, Nanobodies, peptide vecteur pénétrant / The rapid emergence of drug-resistant viruses against all approved HIV clinical drugs together with inaccessible latent virus reservoirs and side effects of currently used compounds have limited the potency of existing anti-HIV-1 therapeutics. Therefore, there is a critical need for new safer drugs, active against resistant viral strains. Reverse transcriptase (RT) plays an essential role in the replication of human immunodeficiency virus type 1 (HIV-1) and remains a primary target of anti-HIV-1 drugs. To develop specific HIV inhibitors, we have elaborated a new strategy based on short antibody fragments derived from the unique Heavy-chain antibodies present in Camelidae called Nanobodies that targets RT-activation. The immunization of dromedaries with RT has lead to the isolation of a panel of Nanobodies that tightly bind the two subunits of RT and inhibit its DNA-dependent DNA polymerase activity at nanomolar range. From that screen we have elaborated an intrabody (cell penetrating anti-RT Nanobody) NbRT20 that constitutes a potential interesting anti-HIV compound.We demonstrated that NbRT20 inhibits RT polymerase activity and exhibiting a potent antiviral activity with a subnanomolar IC50. NbRT20 binds the thumb subdomain and restricts its flexibility and mobility resulting in an inactive/non processive dimeric conformation of the enzyme. From a mechanistic point of view, we have showed that NbRT20 is a conformational inhibitor. it prevents proper binding of primer/template and of dNTP and destabilizes the enzyme in an inactive/non processive dimeric conformation.Taken together, these results demonstrated that, the Nanobody platform may be highly effective at generating extremely potent and selective intrabody to neutralize RT and HIV proliferation.Key words: HIV-1, RT, Nanobodies, cell penetrating peptide

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Established biopharmaceuticals such as antibodies and derivatives thereof are relatively large. In cancer therapy, this creates a steep drug concentration gradient within tumors, leaving cells far from blood vessels effectively untreated. Continuous pseudo treatments should foster the development of drug resistance and might lead to eventual disease relapse. Drug concentration gradients can be operationalized as tissue penetration efficiencies, which are functions of molecular size. However, small particles are also subject to potent renal clearance, collapsing the therapeutic window beyond clinical applications. In this master’s thesis, spatial bispecificity was engineered into a single albumin binding domain (ABD). Resulting ABD derived affinity proteins (ADAPTs) are saved from urinary excretion by the grace of HSA, but in the more static microenvironment of tumors, following HSA dissociation, they are capable of tissue penetration efficiencies bestowed only upon smaller particles. To this end, phage display was used to raise ADAPTs against the cancer associated proteins human epidermal growth factor receptor 2 (HER2) and carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6), but also the inflammation marker C-reactive protein (CRP). Via Sanger sequencing, 9 variants were picked for protein production and characterization, among which two spatially bispecific binders were found. ADAPTs were also evaluated for aggregation tendencies, structural conformity to library design, and thermal stability. One ADAPT, binding HER2, passed all tests of initial characterizations. Deep sequencing was used to analyze selection output, from which many more binders should be screened in future experiments. / Etablerade bioläkemedel liksom antikroppar och deras derivat är relativt stora protein. Som cancerterapeutiska skapar de således branta koncentrationsgradienter utgående från tumörpenetrerande blodkärl. Detta riskerar att lämna vissa cancerceller utanför det terapeutiska fönstret. Det svaga selektionstryck som således verkar i tumörperiferin fostrar cancerceller till att utveckla resistens mot detsamma. Koncentrationsgradienten beror på proteinets vävnadspenetrarande förmåga, vilken är en funktion av proteinets storlek. Mindre proteiner borde därmed lättare ackumuleras i hela tumören och förebygga resistensutveckling. Problemet med små proteiner är deras mycket korta halveringstid i serum, en följd av relativt obehindrad filtrering ut i urinen via njurarna. I det här examensarbetet utvecklades rumsbispecifika bindare av cancerassocierade protein med hjälp av fagdisplayselektioner från ett proteinbibliotek baserat på en enda albuminbindande domän (ABD). Resulterande ABD deriverade affinitetsprotein (ADAPT) undkommer ovan nämnda filtrering tack vare sin naturligt starka interaktion med humant serumalbumin (HSA). I den mer långsamt flödande tumörmikromiljön tillåts ADAPTerna efter albumindissociation sedan utöva en bland bioläkemedel överlägsen vävnadspenetration. Tre parallella selektionsspår utfördes mot de cancerassocierade målproteinerna human epidermal growth factor receptor 2 (HER2) och carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) samt den utsöndrade inflammationsmarkören C-reaktivt protein (CRP). Via Sangersekvensering kunde flera kandidater identifieras. Bland 6 karakteriserade ADAPTer uppvisade samtliga hög HSA-affinitet, tre konstaterades interagera specifikt med sitt målprotein, och två verkade binda även rumsbispecifikt. ADAPTer utvärderades även för sin benägenhet att bilda aggregat, strukturell överensstämmelse med experimentell design, och värmestabilitet. Endast en bindare, mot HER2, klarade sig genom alla prövningar som proteinkarakteriseringen innebar utan underkänt. Även en högparallel sekvensering utav selektionsresultat utfördes, men utanför de tidsramar som tillät ytterligare karakterisering.

Prostate cancer is one of the most common cancer types worldwide. However, current diagnostic approaches and treatments are invasive and unspecific. Prostate-specific membrane antigen (PSMA) is an ideal biomarker for prostate cancer and can act as a target for therapeutic or diagnostic agents. Previous attempts to develop an affibody with affinity towards PSMA have been unsuccessful, therefore this thesis aimed at making the affibody selections against PSMA more efficient. In this thesis HEK293 cells expressing a modified version of PSMA containing a 3C protease cleavage site were generated, to enable extraction of the extracellular domain of PSMA during the selections. However, further analyses must be performed to determine if the extracellular domain can be successfully cleaved off. To develop an affibody that can be used both in vitro and in vivo, selections will be carried out against recombinant PSMA as well. The recombinant PSMA was previously produced incorporating an Avi tag for site-specific biotinylation and immobilization for the selections. To biotinylate the recombinant PSMA, the enzyme BirA that catalyzes the biotinylation of the Avi tag, was produced. A protein yield of 8.95 mg/liter culture was obtained and the site-specific biotinylation was highly efficient. To evaluate the proposed affibody selection strategy the next step is to determine if cleavage of the PSMA expressed on the HEK293 cells is possible, optimize the cleavage conditions and to start initial selections using the generated HEK293 cells and the produced BirA enzyme. / Prostatacancer är en av de mest förekommande cancertyperna över hela världen. Nuvarande diagnostiska metoder och terapeutiska behandlingar är dock invasiva och ospecifika. Prostataspecifikt membranantigen (PSMA) är en idealisk biomarkör för prostatacancer och kan agera som en målmolekyl för terapeutiska eller diagnostiska ändamål. Tidigare försök att utveckla en affibody med affinitet mot PSMA har inte lyckats, därför var målet med detta examensarbete att effektivisera selekteringen av affibodies mot PSMA. I detta projekt har HEK293 celler som uttrycker en modifierad version av PSMA, innehållande ett 3C-proteas- klyvningsställe, genererats för att möjliggöra extraktion av den extracellulära domänen av PSMA under selekteringen. Ytterligare analyser måste dock utföras för att avgöra om den extracellulära domänen kan klyvas av. För att utveckla en affibody som kan användas både in vitro och in vivo kommer selekteringen att utföras även mot rekombinant PSMA. Rekombinant PSMA har producerats tidigare med en Avi tag för specifik biotinylering och immobilisering under selekteringen. För att biotinylera det rekombinanta PSMA producerades enzymet BirA, som katalyserar biotinyleringen av en Avi tag. Ett proteinutbyte av 8,95 mg/liter kultur erhölls och den specifika biotinyleringen var effektiv. För att utvärdera den föreslagna strategin för selektering av affibodies är nästa steg att avgöra om klyvning av PSMA uttryckt av HEK293 cellerna är möjlig, optimera klyvningsförhållandena och starta initiala selektioner med de genererade HEK293-cellerna och det producerade BirA-enzymet.

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