Hepatitis C virus (HCV) represents a global health threat. HCV is a blood-borne positive-strand RNA virus belonging to the Flaviviridae family that infects ~160 million people worldwide. About 70% of infected individuals fail to clear the virus and subsequently develop chronic hepatitis, frequently leading to liver cirrhosis and in some cases hepatocellular carcinoma. Therapeutic options for HCV infection are still limited and a protective vaccine is not yet available. Currently available therapies include administration of pegylated alpha interferon in combination with ribavirin. The recently approved protease inhibitors Boceprevir and Telaprevir are also included in the treatment regimen. However, limitations to the treatment with direct-acting antivirals (DAAs) are associated with severe side effects and low sustained virological response (SVR) rates that vary depending on the virus and host genotype. The replication step of the viral life cycle is mostly targeted by majority of DAAs. Recent findings have suggested that a combination of entry inhibitors together with DAAs exhibit a synergistic effect in the treatment of HCV. Therefore, identification of efficient HCV entry inhibitors is of high priority In vitro studies have shown that HCV attachment and subsequent entry into the host cells is mediated by E1 and E2 viral envelope proteins. HCV entry requires interaction with a number of receptors which include CD81, scavenger receptor B1 (SR-B1) and the tight junction proteins, claudin 1 (CLDN1) and occludin (OCLN). Since the E2 glycoprotein is reported to interact directly with cellular receptors, it is an attractive target for neutralisation. The present study focuses on the establishment and characterisation of entry inhibitors as antivirals for HCV. The thesis is presented in three chapters: Chapter 1- ‘Introduction’, provides a brief overview on HCV genotypes, genome organisation, life cycle including details on the entry process and therapies used for the treatment of HCV. Chapter 2 describes the generation of monoclonal antibodies (mAbs) against HCV envelope proteins as potent anti-viral agents for the prevention of HCV infection. Data on the identification and characterization of the neutralizing epitopes of HCV envelope proteins have been presented. Chapter 3 includes isolation of entry inhibitors of HCV from natural sources and identification and characterization of the active components exhibiting antiviral property. A number of studies have reported the role of neutralizing antibodies in the course of HCV infection and emerging data suggest protective effect of antibodies against HCV infection. Most of the ongoing studies are based on HCV genotype 1a which is prevalent globally. However in India, the prevalent genotype is 3a. Therefore, we established a panel of mAbs against HCV-LPs comprising of core-E1-E2 derived from genotype 3a as described in chapter 2. HCV-LP based system has been used in this study since it mimics the biophysical conformation, morphology and antigenic properties of the native virion and represents a model system for studies on viral binding and entry. MAbs were characterised and analyzed for their ability to prevent viral binding and entry into host cells. Three mAbs namely E3D8, H6D3 and A10F2 were identified to recognize the E2 viral glycoprotein which significantly inhibited HCV-LP binding to Huh7 cells in vitro. The neutralizing epitopes corresponding to the mAbs were identified using overlapping truncated fragments and synthetic peptides of the E2 protein. Our experiments suggest that the epitopes recognised by the inhibitory mAbs are unique and different from those reported till now. The synergistic effect of a combination of mAbs on virus neutralization has shown promising results for treatment of viral infections. Since in the present study the epitopes recognised by the mAbs are non-overlapping, we went ahead to determine whether a combination of these mAbs would enhance the ability to block HCV-LP binding. Indeed, flow cytometry and fluorescence microscopy studies revealed that a combination of the antibodies efficiently blocked the binding of HCV-LP to human hepatoma cells. More importantly and of relevance is the observation that the mAbs in combination inhibited viral infection (JFH1 strain) and replication in permissive human hepatocytes as determined by real time RT-PCR. Phytochemicals present in plants have been considered as conducive for prevention of several viral infections and are found to be promising antiviral agents. Natural products which are biologically active disclose drug-like properties since they are small molecules and can be easily metabolised and absorbed by the body. In our study as described in chapter 3, we evaluated extracts from Indian medicinal plants and fruits which are known to have hepato-protective effect, for natural potent attachment and entry inhibitors for HCV. Flow cytometric analysis suggested that the root extract of the herb Boerhavia diffusa and fruit extract of Prunus domestica exhibited high antiviral activity by inhibiting the binding of Hepatitis C virus like particles (HCV-LPs) to the human hepatoma cells. We went on to isolate, identify and confirm the active principles to be Boeravinone H, a dehydrorotenoid, (from Boerhavia diffusa) and Rutin, a flavonoid, (from Prunus domestica) by LC-ESI-MS, NMR, UV and IR spectral analysis. Our study revealed that the compounds block the attachment as well as entry step probably by targeting the viral particle. We also assessed the efficiency of these small molecules (Boeravinone H and Rutin) to inhibit HCV negative strand synthesis post entry by real time RT-PCR. Results suggest significant inhibition of viral entry and infection in the HCV cell culture (ex vivo). To our knowledge it is the first report on Boeravinone H and Rutin as entry inhibitor for HCV. In conclusion, our findings support the potential of employing a cocktail of neutralizing mAbs and antiviral agents from natural source in the management of HCV infection.

Nectine-4 est une molécule d'adhérence membre de la superfamille des immunoglobulines. Elle est localisée au niveau des jonction adhérentes. Exprimée durant l'embryogenèse, nectine-4 n'est pas retrouvée dans les tissus adultes excepté la peau. Des mutations survenant au niveau du gène de la nectine-4 cause le syndrome EDSS affectant le développement de la peau. Nous avons participer à la démonstration que l'expression de nectine-4 est marqueur des carcinomes mammaires,pulmonaires et ovariens. Ainsi, nous avons étudier le role fonctionnel de l'expression de nectine-4 sur la progression tumorale. Les résultats obtenus suggèrent que nectine-4 représente une cible intéressante dans le cadre d'une stratégie d’immunothérapie anti-tumorale.Par l'utilisation d'une méthode multiplex combinant des essais biochimiques, cellulaires et algorithmiques, 5 peptides potentiellement antigéniques ont été identifiés. Toutefois,après génération de lymphocytes cytotoxiques HLA-A*0201 spécifique à partir de PBMC de donneurs sains et la mise en place" de tests de cytotoxicité dirigée; nous avons identifié un nouveau peptide antigénique produit et présenté de façon naturelle à la surface de cellules tumorales. Ce dernier est le peptide nectine-4 N°145 (VLVPPLPSL). En plus de l'identification d'un peptide antigénique, nous avons développé un anticorps monoclonal anti-nectine-4 qui a la capacité de réduire de façon spécifique et significative les capacités métastatiques des cellules tumorales nectine-4 positive.Ainsi, dans cette étude nous avons démontré que nectine-4 qui est un nouveau antigène associé aux tumeurs, affecte la progression tumorale, mais aussi il est possible de cibler cette molécule par des stratégies d'immunothérapie car nous avons pu identifiés un peptide antigénique et un anticorps monoclonal. L'efficacité d'une stratégie d'immunothérapie est en cours de réalisation actuellement. / Nectin-4 is a cell surface adhesion molecule, member of the Ig-superfamily, and is localized at adherens junctions. Nectin4 is expressed during embryogenesis but not in adult tissues, except in the skin. Mutations in nectin-4 gene in humans cause the EDSS syndrome that affects skin development (EctoDermal and Syndactly Syndrome). We and others have recently demonstrated that nectin-4 expression was a tumoral marker of breast, lung and ovarian carcinoma. We thus started to investigate the functional role of nectin-4 overexpression in breast cancer. Using in vitro and in vivo assays, the preliminary results demonstrate that nectin-4 increased the tumorigenicity of malignant cells.Altogether, these results suggest that nectin-4 might be a candidate target forimmunotherapy (vaccination and antibody based therapy). Using a multiplex approachbased on biochemical, cellular and algorithmic assays, five relevant nectin-4 epitopes were identified. Specific cytotoxic T lymphocyte (CTL) populations from healthy donors that recognized and lyzed peptide-pulsed HLA-A*0201 tumor cells were identified. HLAA*0201-restricted CTL that recognized the N4-145 (VLVPPLPSL) nectin-4 epitope was characterized extensively. This CTL kills breast tumor cells that express nectin4, strongly demonstrating that this peptide could be naturally processed and recognized by specific CTL. In parallel, we also tested a blocking monoclonal antibody against the extracellular region of nectin-4. We next demonstrated that this antibody reduced the metastatic capacity of tumors expressing nectin4. To summarize, in this study, we identified nectin-4 as a newcell surface Tumor Associated Antigen and demonstrated its likely implication in cancertumorigenesis. In parallel, we have developed the specific tools required to conduct an effective immunotherapy targeting nectin4 over-expressing cells, which are currently under investigation.

Le système immunitaire adaptatif joue un rôle de premier plan dans la défense contre les infections. La réponse humorale, impliquant la production d'anticorps, est un élément important de la réponse immunitaire adaptative. Au cours d'une infection, des cellules B spécifiques du système immunitaire prolifèrent et libèrent de grandes quantités d'anticorps qui se lient sélectivement à la protéine cible (antigène) trouvée sur le pathogène invasif, induisant la destruction du pathogène.Cependant, le système immunitaire ne répond pas toujours suffisamment efficacement pour détruire les agents pathogènes, et les mécanismes de tolérance empêchent la génération d'anticorps contre les protéines humaines - comme les marqueurs de surface cellulaire sur les cellules cancéreuses ou les cytokines impliquées dans des maladies inflammatoires et auto-immunes - qui pourraient être des cibles thérapeutiques importantes. Par conséquent, il existe un grand intérêt pour la recherche et le développement d'anticorps spécifiques qui peuvent être utilisés pour le traitement des patients par immunothérapie. En raison de leur grande affinité et de leur liaison sélective aux antigènes, les anticorps monoclonaux (mAbs) sont apparus comme des agents thérapeutiques puissants. Les anticorps monoclonaux dérivés de cellules B individuelles ont une séquence unique et présentent une affinité de liaison pour un antigène spécifique. Cependant, jusqu'à maintenant, la découverte des mAbs a été limitée par l'absence de méthodes à haut débit pour le criblage direct et à grande échelle de cellules B primaires non immortalisées pour découvrir les rares cellules B qui produisent des anticorps spécifiques d'intérêt clinique. Ceci est maintenant possible avec l'émergence et l'amélioration des méthodes de compartimentation in vitro pour l'encapsulation et le criblage de cellules uniques dans des gouttelettes picolitriques. Dans mon projet de doctorat, je décris le développement d'immunodosages et de dispositifs microfluidiques pour le criblage phénotypique direct de cellules individuelles à partir de populations de cellules B enrichies. Ce développement a permis une analyse détaillée de la réponse immunitaire humorale, avec une résolution à l’échelle de la cellule unique. C’est aussi un élément essentiel d'un pipeline de détection d'anticorps couplant le criblage phénotypique de cellules individuelles au séquençage d'anticorps sur cellules uniques. Il est maintenant possible, pour la première fois, de cribler des millions de cellules B individuelles en fonction de l'activité de liaison des anticorps sécrétés et de récupérer les séquences d'anticorps / The adaptive immune system plays a leading role in defense against infection. The humoral response, involving the production of antibodies, is an important component of the adaptive immune response. During an infection, specific B cells of the immune system proliferate and release large amounts of antibodies which bind selectively to the target protein (antigen) found on the invading pathogen, inducing destruction of the pathogen. However, the immune system does not always respond efficiently enough to destroy pathogens, and tolerance mechanisms prevent the generation of antibodies against human protein - such as cell surface markers on cancer cells or cytokines involved in inflammatory and autoimmune disease - that could be important therapeutic targets. Hence, there is great interest in research and development of specific antibodies that can be used for immunotherapy of patients. Due to their high affinity and selective binding to antigens, monoclonal antibodies (mAbs) have emerged as powerful therapeutic agents. Monoclonal antibodies derived from single B cells have a unique sequence and display binding affinity for a specific antigen. However, until now, the discovery of mAbs has been limited by the lack of high-throughput methods for the direct and large-scale screening of non-immortalized primary B cells to uncover rare B cells which produce the specific antibodies of clinical interest. This is now becoming possible with the emergence and improvement of in vitro compartmentalization methods for single-cell encapsulation and screening in picoliter droplets. In my PhD project, I describe the development of binding immunoassays and microfluidic devices for the direct phenotypic screening of single-cells from enriched B cell populations. This development has enabled detailed analysis of the humoral immune response, with single-cell resolution and is an essential component of an antibody-discovery pipeline coupling single-cell phenotypic screening to single-cell antibody sequencing. It is now possible, for the first time, to screen millions of single B cells based on the binding activity of the secreted antibodies and to recover the antibody sequences

Human immunodeficiency type 1 (HIV-1) is able to elicit broadly potent neutralizing antibodies in a very small subset of individuals only after several years’ infection and as a result, vaccines that elicit these types of antibodies have been difficult to design. The RV144 trial showed that a moderate protection is possible, which may correlate with antibody dependent cellular cytotoxicity (ADCC) activity. Previous studies in the Lu lab demonstrated that in an HIV-1 vaccine phase I trial, DP6-001, a polyvalent Env DNA prime-protein boost formulation, could elicit potent and broadly reactive, gp120-specific antibodies with positive neutralization activities along with multiple Fc mediated effector functions. I developed a protocol for the production and analysis of HIV-1 Env-specific human monoclonal antibodies (mAbs) isolated from these DP6-001 vaccinees. By utilizing a labeled gp120 bait to isolate Env specific B cells, paired heavy and light chain immunoglobulin (Ig) genes were cloned and allowed for the production of monoclonal antibodies with specificity for gp120. By using this protocol, 13 isolated mAbs from four DP6-001 vaccinees showed broad binding activities to gp120 proteins of diverse subtypes, both autologous and heterologous to vaccine immunogens, with mostly conformational epitopes and a few V3 and C5 specific mAbs. Equally cross-reactive Fc-mediated functional activities, including ADCC and antibody dependent cellular phagocytosis (ADCP), were present with both immune sera and isolated mAbs, confirming the induction of non-neutralizing functional antibodies by the DNA prime- protein boost vaccination. Elicitation of broadly reactive mAbs by vaccination in healthy human volunteers confirms the value of the polyvalent formulation in this HIV-1 vaccine design.

Os estudos de reatividade dos antígenos de líquido hidático de Echinococcus granulosus (Ag LH-Eg) e de líquido vesicular de Taenia crassiceps (Ag LV-Tcra) foram feitos com anticorpos monoclonais (AcMos) anti-E. granulosus e anti-T. crassiceps e amostras humanas por eletroforese em gel de poliacrilamida contendo dodecil sulfato de sódio (SDS-PAGE), Enzyme-Linked Immunosorbent Assay (ELISA) e immunoblot. O SDS-PAGE mostrou um padrão complexo de proteínas entre 97- e 8-kDa do LH-Eg e 97- e 14-kDa do LV-Tcra. A caracterização dos antígenos com os AcMos por ELISA mostrou que todos os AcMoss anti-E . granulosus reagiram com o antígeno LH-Eg e um deles cruzada mente com o antígeno LV-Tcra. Um dos dois AcMo anti-T . crassiceps reagiu também com o LH-¬Eg. A reatividade do LH-Eg com amostras humanas apresentaram melhores resultados com o cut off média mais dois devios-padrão (M+2DP) e na diluição 1:250. As amostras de hidatidose (Hi) mostraram reatividade máxima (100%) nessa diluição. As amostras neurocisticercose (NC) ensaiadas por ELlSA-LH-Eg, apresentaram reatividade cruzada de 66,5%, teníase (T) 46%, controle negativo (CN) 4% e outras parasitoses (OP) 84,5%. O ELlSA-LV-Tcra mostrou 100% de reatividade com as amostras NC na diluição 1 :50 pelo cut off TgRoc. Com as amostras hidatidose, teníase, outras parasitoses e controle negativo a reatividade foi de 73,5; 61,5; 69 e 2%, respectivamente. Todos os AcMos anti-LH-Eg reconheceram as frações 79-,67- e 8-kDa do Ag LH-Eg e as de 24- e 16-kDa pelo AcMo anti¬-antígeno rAgB. No immunoblot, as amostras humanas reconheceram as frações 79-, 67-, 57-, 43-, 38-kDa e também as específicas (24-, 16-e 8-kDa) para o diagnóstico da hidatidose. As frações responsáveis pela reatividade cruzada foram 79-, 67-e 57¬kDa. Nossos estudos mostraram que é necessária uma melhor abordagem incluindo em estudos futuros a obtenção de antígenos recombinantes, específicos de cada um dos parasitos. / Studies to evaluate the reactivity of the hydatic liquid antigens of Echinococcus granulosus (Ag LH-Eg) and of the vesicular liquid antigens of Taenia crassiceps (Ag LV-Tcra) were conducted using anti-E. granulosus and anti-T . crassiceps monoclonal antibodies (MoAbs), and human sample, through SDS-PAGE, ELISA and immunoblot tests. The SDS-PAGE showed a complex standard of proteins from 97¬to 8-kDa of the LH-Eg and from 97-to 14-kDa of the LV-Tcra. The characterization of antigens with the MoAbs through ELISA showed that ali the anti-E . granulosus MoAbs reacted with the LH-Eg antigen and one of them cross-reacted with the LV¬-Tcra antigen. One of the two anti-T. crassiceps MoAb also reacted with the LH-Eg antigen. The reactivity of the LH-Eg with human samples presented better results with the cut off value representing the mean value plus two standard deviations (M+2DP) and with a dilution of 1:250. The hydatidosis samples (Hi) showed maximum reactivity (100%) with this dilution. When evaluated by the ELlSA-LH-Eg, the neurocysticercosis samples (NC) showed cross-reactivity of 66,5%, the taeniasis (T) showed 46%, the negative control (CN) of 4% and 84,5% for other parasitoses (OP). The NC samples, diluted at 1:50, showed 100% of reactivity in ELlSA-LV-Tcra test with the TgRoc cut off value. Concerning the samples of hydatidosis, taeniasis, other parasitoses and the negative control, reactivity was 73,5; 61,5; 69 and 2%, respectively. Ali the anti-LH-Eg MoAbs recognized the fractions 79- and 67-kDa of the Ag LH-Eg and the 24-and 16-kDa through the rAgB anti-antigen MoAb. By immunoblot, the human samples recognized the fractions 79-, 67-, 57-, 43-, 38-kDa and also the specific ones (24-, 16-and 8-kDa) for diagnosing hydatidosis. The fractions, responsible for the cross-reactivity, were 79-, 67-and 57-kDa. Our study showed that further approaches are needed and should include the obtaining of recombinant antigens, specific for each parasite.

Humans have two plasminogen activators (PAs), tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA), which generate plasmin to breakdown fibrin and other barriers to cell migration. Both PAs are used as pharmaceuticals but their efficacies are limited by their rapid clearance from the circulation, predominantly by parenchymal cells of the liver. At the commencement of the work presented here, the hepatic receptors responsible for mediating the catabolism of the PAs were little understood. tPA degradation by hepatic cell lines was known to depend on the formation of binary complexes with the major PA inhibitor, plasminogen activator inhibitor type-1 (PAI-1). Initial studies presented here established that uPA was catabolised in a fashion similar to tPA by the hepatoma cell line, HepG2. Other laboratories around this time found that the major receptor mediating the binding and endocytosis of the PAs is Low Density Lipoprotein Receptor-related Protein (LRP1). LRP1 is a giant 600 kDa protein that binds a range of structurally and functionally diverse ligands including, activated α2 macroglobulin, apolipoproteins, β amyloid precursor protein, and a number of serpin-enzymes complexes, including PA??PAI-1 complexes. Further studies for the work presented here centred on this receptor. By using radiolabelled binding assays, ligand blots, and Western blots on cultured cells, the major findings are that: (1) basal LRP1 expression on HepG2 is low compared to a clone termed, HepG2a16, but appears to increase in long term culture; (2) a soluble form of LRP1, which retains ligand-binding capacity, is present in human circulation; (3) soluble LRP1 is also present in cerebral spinal fluid where its role in neurological disorders such as Alzheimer??s disease is a developing area of interest; and (4) the release of LRP1 is a mechanism conserved in evolution, possibly as distantly as molluscs. The discovery, identification, and characterisation of soluble LRP1 introduces this protein in the human circulation, and presents a possible further level of regulation for its associated receptor system.

Os estudos de reatividade dos antígenos de líquido hidático de Echinococcus granulosus (Ag LH-Eg) e de líquido vesicular de Taenia crassiceps (Ag LV-Tcra) foram feitos com anticorpos monoclonais (AcMos) anti-E. granulosus e anti-T. crassiceps e amostras humanas por eletroforese em gel de poliacrilamida contendo dodecil sulfato de sódio (SDS-PAGE), Enzyme-Linked Immunosorbent Assay (ELISA) e immunoblot. O SDS-PAGE mostrou um padrão complexo de proteínas entre 97- e 8-kDa do LH-Eg e 97- e 14-kDa do LV-Tcra. A caracterização dos antígenos com os AcMos por ELISA mostrou que todos os AcMoss anti-E . granulosus reagiram com o antígeno LH-Eg e um deles cruzada mente com o antígeno LV-Tcra. Um dos dois AcMo anti-T . crassiceps reagiu também com o LH-¬Eg. A reatividade do LH-Eg com amostras humanas apresentaram melhores resultados com o cut off média mais dois devios-padrão (M+2DP) e na diluição 1:250. As amostras de hidatidose (Hi) mostraram reatividade máxima (100%) nessa diluição. As amostras neurocisticercose (NC) ensaiadas por ELlSA-LH-Eg, apresentaram reatividade cruzada de 66,5%, teníase (T) 46%, controle negativo (CN) 4% e outras parasitoses (OP) 84,5%. O ELlSA-LV-Tcra mostrou 100% de reatividade com as amostras NC na diluição 1 :50 pelo cut off TgRoc. Com as amostras hidatidose, teníase, outras parasitoses e controle negativo a reatividade foi de 73,5; 61,5; 69 e 2%, respectivamente. Todos os AcMos anti-LH-Eg reconheceram as frações 79-,67- e 8-kDa do Ag LH-Eg e as de 24- e 16-kDa pelo AcMo anti¬-antígeno rAgB. No immunoblot, as amostras humanas reconheceram as frações 79-, 67-, 57-, 43-, 38-kDa e também as específicas (24-, 16-e 8-kDa) para o diagnóstico da hidatidose. As frações responsáveis pela reatividade cruzada foram 79-, 67-e 57¬kDa. Nossos estudos mostraram que é necessária uma melhor abordagem incluindo em estudos futuros a obtenção de antígenos recombinantes, específicos de cada um dos parasitos. / Studies to evaluate the reactivity of the hydatic liquid antigens of Echinococcus granulosus (Ag LH-Eg) and of the vesicular liquid antigens of Taenia crassiceps (Ag LV-Tcra) were conducted using anti-E. granulosus and anti-T . crassiceps monoclonal antibodies (MoAbs), and human sample, through SDS-PAGE, ELISA and immunoblot tests. The SDS-PAGE showed a complex standard of proteins from 97¬to 8-kDa of the LH-Eg and from 97-to 14-kDa of the LV-Tcra. The characterization of antigens with the MoAbs through ELISA showed that ali the anti-E . granulosus MoAbs reacted with the LH-Eg antigen and one of them cross-reacted with the LV¬-Tcra antigen. One of the two anti-T. crassiceps MoAb also reacted with the LH-Eg antigen. The reactivity of the LH-Eg with human samples presented better results with the cut off value representing the mean value plus two standard deviations (M+2DP) and with a dilution of 1:250. The hydatidosis samples (Hi) showed maximum reactivity (100%) with this dilution. When evaluated by the ELlSA-LH-Eg, the neurocysticercosis samples (NC) showed cross-reactivity of 66,5%, the taeniasis (T) showed 46%, the negative control (CN) of 4% and 84,5% for other parasitoses (OP). The NC samples, diluted at 1:50, showed 100% of reactivity in ELlSA-LV-Tcra test with the TgRoc cut off value. Concerning the samples of hydatidosis, taeniasis, other parasitoses and the negative control, reactivity was 73,5; 61,5; 69 and 2%, respectively. Ali the anti-LH-Eg MoAbs recognized the fractions 79- and 67-kDa of the Ag LH-Eg and the 24-and 16-kDa through the rAgB anti-antigen MoAb. By immunoblot, the human samples recognized the fractions 79-, 67-, 57-, 43-, 38-kDa and also the specific ones (24-, 16-and 8-kDa) for diagnosing hydatidosis. The fractions, responsible for the cross-reactivity, were 79-, 67-and 57-kDa. Our study showed that further approaches are needed and should include the obtaining of recombinant antigens, specific for each parasite.

Integrationen av artificiell intelligens (AI) i bioprocessapplikationer har framträtt som en transformerande metod inom bioteknik- och läkemedelsindustrin, och lovar betydande framsteg i effektivitet, verkan och hållbarhet. Genom att utnyttja avancerade algoritmer, såsom djupinlärning och förstärkningsinlärning, kan AI-system förutsäga och generera nya ligandstrukturer med hög affinitet för sina mål, såsom monoklonala antikroppar (mAbs) i detta projekt. Detta projekt syftar till att utvärdera potentialen hos AI-genererade affinitetsproteiner och validera de datorsimulerade förutsägelserna genom att undersöka bindningseffektiviteten och stabiliteten hos dessa ligander under verkliga förhållanden. Flera våtlabbstekniker användes för att uttrycka och rena de AI-designade proteinerna. Affinitetskromatografi var en teknik som användes för rening, följt av ytplasmonresonans (Biacore) för att studera interaktionen mellan de genererade affinitetsproteinerna och mAbs. Analyseresultat från SDS-PAGE och masspektrometri visade att de flesta proteiner kunde renas med hjälp av affinitetskromatografi. Emellertid visade karaktärisering med Biacore att de flesta proteiner inte interagerade med mAbs, förutom ett designat protein. Cirkulär dikroism (CD) spektrometri som användes för att visualisera sekundärstrukturen i proteiner visade att de flesta proteiner var veckade och bibehöll alfahelixar och betaflak jämfört med det vilda typen proteinet. Sammanfattningsvis ger denna forskning värdefulla insikter i utmaningarna vid utvärdering och karaktärisering av AI-genererade proteiner. Ytterligare forskningsinsatser bör fokusera på att förfina experimentella förhållanden och visualisera sekundärstrukturerna hos de genererade proteinerna för en djupare förståelse av deras stabilitetsproblem. / The integration of artificial intelligence (AI) into bioprocess applications has emerged as a transformative approach in the biotechnology and pharmaceutical industries, promising significant advancements in efficiency, efficacy, and sustainability. By leveraging advanced algorithms, such as deep learning and reinforcement learning, AI systems can predict and generate novel ligand structures with high affinity for their targets, such as monoclonal antibodies(mAbs) in this project. This project aims to evaluate the potential of AI-generated affinity protein ligands and validate the computational predictions by examining the binding efficiency and stability of these ligands in real-world conditions. Several wet lab techniques were employed to express and purify the AI-designed proteins. Affinity chromatography was one technique used for purification, followed by surface plasmon resonance (Biacore) to study the interaction between the generated affinity proteins and mAbs. Analysis results from SDS-PAGE and mass spectrometry showed that most proteins could be purified using affinity chromatography. However, characterization using Biacore revealed that most proteins did not interact with mAbs, except for one designed protein. Circular dichroism (CD) spectrometry used to visualize the secondary structure in proteins showed that most proteins were folded and retained alpha helices and beta sheets when compared to the wild type protein. In conclusion, this research provides valuable insights into the challenges in evaluating and characterizing AI-generated proteins. Further research efforts should focus on refining experimental conditions and visualizing the secondary structures of the generated proteins for a more in-depth understanding of their stability issues.

Antalet monoklonala antikroppar som används i läkemedel ökar kraftigt. Dessa läkemedel är dyra och risken för förfalskning är stor. Behovet att utveckla en metod för snabb och precis identifiering av monoklonala antikroppar är därför brådskande. För identifiering utfördes analyser med Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF-MS), Capillary Gel Electrophoresis (CGE) and Capillary Zone Electrophoresis (CZE) på nio monoklonala antikroppar. Fokuset var att undersöka huruvida signifikanta fysiokemiska egenskaper och unika aminosyrasekvenser var närvarande och kunde urskiljas. Olika analyser med MALDI-ToF-MS användes till att både separera de monoklonala antikropparna baserat på dess fysiokemiska egenskaper, och annotera aminosyrasekvenser innehållande nyckelfragment. Med metoderna baserade på kapillärelektrofores uppnåddes också separation. CZE föredras framför CGE då mängden data som erhålls från CZE är större och provberedningen är enklare. Sammanfattningsvis utformades ett protokoll för identifieringsprocessen, vilket inleds med MALDI-ToF-MS-analyser av monoklonala antikroppar på reducerad form mot kända referenser. Därefter är en hypotes formulerad utifrån vilka antikroppar som ser mest lika ut. Slutligen analyseras dessa med CZE för fastställning av den monoklonala antikroppens identitet. / The number of monoclonal antibodies used in pharmaceuticals is increasing sharply. These medicines are expensive, and the risk of counterfeiting is high. The need to develop a method for rapid and precise identification of monoclonal antibodies is therefore urgent. For identification, analyses were performed with Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF-MS), Capillary Gel Electrophoresis (CGE) and Capillary Zone Electrophoresis (CZE) on nine monoclonal antibodies. The focus was to investigate whether significant physiochemical features and unique amino acid sequences were present and could be distinguished. Various analyses with MALDI-ToF-MS were used to both separate the monoclonal antibodies based on their physicochemical properties and annotate amino acid sequences containing key fragments. With the methods based on capillary electrophoresis, separation was also achieved. CZE is preferred over CGE as the amount of data obtained from CZE is greater and sample preparation is simpler. In summary, an identification process protocol was designed and is initiated with MALDI-ToF-MS analyses of reduced-form monoclonal antibodies against known references. A hypothesis is then formulated based on which antibodies look the most similar. Finally, these are analysed by CZE to determine the identity of the monoclonal antibody.