Ongoing advances in tissue engineering with the goal to address the clinical shortage of donor organs have encouraged the design and development of biomaterials to be used in tissue-engineered scaffolds. Furthermore, biomaterials have been used as delivery vehicles for vaccines that aim to enhance the protective immunity against pathogenic agents. These tissue-engineered constructs or vaccines are usually combination products that combine biomaterial and biological (e.g. cells, proteins, and/or DNA) components. Upon introduction into the body, the host response towards these products will be a combination of both a non-specific inflammatory response towards the biomaterial and an antigen-specific immune response towards the biological component(s). Recently, the biomaterial component was shown to influence the immune response towards a co-delivered antigen. Specifically, poly(lactic-co-glycolic acid) (PLGA), but not agarose, scaffolds or microparticles (MPs) enhanced the humoral response to a model antigen, ovalbumin. This in vivo result echoed with the in vitro study that PLGA, but not agarose, supported a mature phenotype of dendritic cells (DCs), the most potent antigen-presenting cells. Therefore, it is hypothesized that the effect of biomaterials on DC phenotype may influence the adaptive immunity against a co-delivered antigen. Understanding how biomaterials affect DC response will facilitate the selection and design of biomaterials that direct a desired immune response for tissue engineering or vaccine delivery applications. The objectives of this research were to elucidate the correlations between material properties and DC phenotype, develop predictive models for DC response based on material properties, and uncover the molecular basis for DC response to biomaterials. Well-defined biomaterial systems, including clinical titanium (Ti) substrates and two polymer libraries, were chosen to study induced DC phenotype. Due to the time-consuming nature of conventional methods for assessing DC phenotype, a high-throughput (HTP) method was first developed to screen for DC maturation based on surface marker expression (CHAPTER 4). A 96-well filter plate-based HTP methodology was developed and validated for the assessment of DC response to biomaterials. A "maturation factor", defined as CD86/DC-SIGN and measured by immunostaining, was found to be a cell number-independent metric for DC maturation and could be adapted to screen for DC maturation in a microplate format. This methodology was shown to reproducibly yield similar results of DC maturation in response to biomaterial treatment as compared to the conventional flow cytometric method upon DC treatment in 6-well plates. In addition, the supernatants from each treatment could easily be collected for cytotoxicity assessment using glucose-6-phosphate dehydrogenase (G6PD)-based assay and cytokine profiling using multiplex technology. In other words, the 96-well filter plate-based methodology can generate three outcomes from one single cell culture: 1) maturation marker expression, 2) cytotoxicity, and 3) cytokine profile. To examine which material properties were critical in determining DC phenotype, a set of three clinical titanium (Ti) substrates with well-defined surfaces was used to treat DCs (CHAPTER 5). These Ti substrates included pretreatment (PT), sand-blasted and acid-etched (SLA), and modified SLA (modSLA), with different roughness and surface energy. DCs responded differentially to these substrates. Specifically, PT and SLA induced a mature DC (mDC) phenotype, while modSLA-treated DCs remained immature based on surface marker expression, cytokine production profiles and cell morphology. Both PT and SLA induced higher CD86 expression as compared to iDC control, while modSLA maintained CD86 expression at a level similar to iDC. PT- or SLA-treated DCs exhibited dendritic processes associated with a mDC phenotype, while modSLA-treated DCs were rounded, a morphology associated with an iDC phenotype. Furthermore, PT induced increased secretion of MCP-1 by DCs compared to iDCs, indicating that PT promoted a pro-inflammatory environment. SLA induced higher IL-16 production, which is a pleiotropic cytokine, by DCs, most likely as a pro-inflammatory response due to the enhanced maturation of DCs induced by SLA. In contrast, modSLA did not induced enhanced production of any cytokines examined. Principal component analysis (PCA) were used to reduce the multi-dimensional data space and confirmed these experimental results, and it also indicated that the non-stimulating property of modSLA co-varied with certain surface properties, such as high surface hydrophilicity, % oxygen and % titanium of the substrates. In contrast, high surface % carbon and % nitrogen were more associated with a mDC phenotype. Furthermore, PCA also suggested that surface line roughness (Ra) did not contribute to the expression of CD86, an important maturation marker, suggesting that roughness had little impact on DC response (CHAPTER 5). DC response-material property relationships were also derived using more complex materials from a combinatorial library of polymethacrylates (pMAs) (CHAPTER 6). Twelve pMAs were selected and were found to induce differential DC response using the HTP method described in CHAPTER 4. These pMAs resulted in a trend of increasing DC maturation represented by the metric CD86/DC-SIGN, which was consistent with the trends of the production of pro-inflammatory cytokine, TNF-α, and chemokine, IL-8. Interestingly, this set of pMAs induced an opposite trend of IL-16 production, which is most likely released as an anti-inflammatory cytokine in this situation. These polymers were characterized extensively for a number of material properties, including surface chemical composition, glass transition temperature (Tg), air-water contact angle, line roughness (Ra), surface roughness (Sa), and surface area. Similar to the results from the Ti study, PCA determined that surface carbon correlated with enhanced DC maturation, while surface oxygen was associated with an iDC phenotype. In addition, Tg, Ra, and surface area were unimportant in determining DC response. Partial square linear regression (PLSR), a multivariate modeling approach, was implemented using the pMAs as the training set and a separate polymer library, which contained methacrylate- and acrylate-based terpolymers, as the prediction set. This model successfully predicted DC phenotype in terms of surface marker expression with R2prediction = 0.76. Furthermore, prediction of DC phenotype was effective based on only theoretical chemical composition of the bulk polymers with R2prediction = 0.80 (CHAPTER 6). Nonetheless, one should note that a predictive model can be only as good as what it is trained on and cannot be used to predict the DC response induced by a type of materials different from the training set. Also, this model might not contain all the important material properties such as polymer swelling and cannot predict specific types of immune responses. However, these results demonstrated that a generalized immune cell response can be predicted from biomaterial properties, and computational models will expedite future biomaterial design and selection (CHAPTER 6). From the pMA library, pMAs that induced the two extremes of DC phenotype (mature or immature) were identified for elucidating the mechanistic basis of biomaterial-induced DC responses (CHAPTER 7). Two pMAs, polyhydroxyethylmethacrylate (pHEMA) and poly(isobutyl-co-benzyl-co-terahydrofurfuryl)methacrylate (pIBTMA), were selected because they induced the least and the most mature DC phenotype, respectively. These pMAs were used to elucidate the activation profiles of transcription factors in DCs after biomaterial treatment and were compared to the iDC and mDC controls. In addition, a combined treatment of pHEMA and LPS was also included to determine if pHEMA could maintain an iDC phenotype in the presence of LPS. Interestingly, pIBTMA induced DC maturation primarily through the activation of NF-κB, while pHEMA mediated suppression of DC maturation through multiple TFs, including the activation of ISRE, E2F-1, GR-PR, NFAT, and HSF. GR-PR and E2F-1 have been shown to be associated with the suppression of DC maturation; ISRE, E2F-1, and NFAT are linked to apoptosis induction; HSF regulates the production of heat shock proteins (HSPs) that induce DC maturation and inhibit apoptosis. The activation of HSF by pHEMA was most likely a natural defensive mechanism against the other apoptotic signals. Therefore, pHEMA suppressed DC maturation through the induction of apoptosis. Surprisingly, in the presence of pHEMA, the effect of LPS was completely eliminated, suggesting that biomaterials can override the effect of soluble factors. The morphology and surface marker expression of DCs treated with these different biomaterials or controls were consistent with TF activation profiles (CHAPTER 7). Overall, this research illustrates that biomaterial properties, within the chosen biomaterial space, can be correlated to DC phenotype and more importantly, can be used as predictors for relative levels of DC phenotype. Furthermore, the differential responses induced by different biomaterials were mediated through the distinct activation profiles of transcription factors. Together, these findings are expected to facilitate the design and selection of biomaterials that direct desired immune responses.

The rapid development of the gene engineering techniques, especially methods for in vitro directed evolution and combinatorial mutagenesis, has triggered the generation of new binding agents to almost any antigen of interest as an alternative to broadly used antibodies. These so-called non-Ig scaffolds are often derived from proteins with useful biophysical properties. While the therapeutic market is still dominated by monoclonal antibodies, the easy option of desired customization of non-Ig binders by conventional methods of gene engineering predestine them largely for the use in the diagnostic area. The ABD scaffold, derived from a three-helix bundle of albumin-binding domain of streptococcal protein G, represents one of the small non-Ig scaffolds. In our laboratory, we have established a highly complex combinatorial library developed on the ABD scaffold. This ABD scaffold-derived library was used to generate unique binders of human prostate cancer (PCa) biomarkers PSP94, KLK2, KLK11 for the more precise diagnosis of PCa. The second part of the thesis describes the generation of ABD-derived binders selectively recognizing different phenotypes of circulating tumor cells as a binding component of the cell capture zone of microfluidic chip for lung adenocarcinoma diagnosis. Beside this already...

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Fast and precise quantification of circulating tumour cells (CTC) in lung adenocarcinoma is a pivotal step in acceleration of diagnosis, selection of early therapy and estimation of treatment prognosis. Development of a new type of microfluidic device based on detection and quantification of epithelial- and mesenchymal-type CTC by high-affinity and cell-type specific protein binders anchored to a microfluidic chip surface represents a highly innovative approach. In this work, we used EpCAM membrane glycoprotein as a target for generation of epithelial cell-specific protein binders by a directed evolution of proteins selected from highly complex combinatorial libraries derived from albumin-binding domain scaffold (ABD) or human muscle protein domain-derived "Myomedin" scaffold. Collections of EpCAM-binding candidates from the both used libraries were generated and particular binding variants were further characterized by DNA sequencing, biochemically and by functional cell-surface binding assays. The best candidates might serve as robust anchor proteins of a microfludic chip. Key words: epithelial cell, EpCAM, protein binder, ribosome display, combinatorial library, protein scaffold

The bacterium Escherichia coli (E. coli) is in many situations an ideal host for production of recombinant proteins, since it generally provides a rapid and economical means to achieve sufficiently high product quantities. However, there are several factors that may limit this host’s ability to produce large amounts of heterologous proteins in a soluble and native form. For many applications a high purity of the recombinant protein is demanded, which implies a purification strategy where the product efficiently can be isolated from the complex milieu of host cell contaminants. In this thesis, different strategies based on both rational and combinatorial genetic engineering principles have been investigated, aiming at improving and facilitating recombinant E. coli protein production and purification. One objective was to improve the PEG/salt aqueous two-phase system (ATPS) purification process of the lipase cutinase, by increasing the selectivity of the protein for the system top-phase. Peptide tags, with varying properties, were designed and genetically fused to the C-terminal end of ZZ-cutinase. Greatly increased partitioning values were observed for purified protein variants fused to tryptophan containing peptide tags, particularly a (WP)4 peptide. The partitioning properties of the ZZ-cutinase-(WP)4 protein were also retained when added to the ATPS directly from an E. coli total cell disintegrate, emphasizing the applicability of this genetic engineering strategy for primary protein purification in ATPSs. Further on, a combinatorial library approach using phage display technology was investigated as a tool for identification of peptide tags capable of improving partitioning properties of ZZ-cutinase in an ATPS. Repeated ATPS-based partitioning-selection cycles of a large phagemid (pVIII) peptide library, resulted in isolation of phage particles preferentially decorated with peptides rich in tyrosine and proline residues. Both a peptide corresponding to a phage library derived peptide sequence as well as peptides designed based on information of amino acid appearance frequencies in later selection rounds, were shown to improve partitioning several-fold when genetically fused to the C-terminal end of ZZ-cutinase. From the two- to four–fold increased production yields observed for these fusion proteins compared to ZZ-cutinase-(WP)4, it was concluded that the selection system used allowed for selection of desired peptide properties related to both partitioning and E. coli protein production parameters. Bacterial protein production is affected by several different mRNA and protein sequence-related features. Attempts to address single parameters in this respect are difficult due to the inter-dependence of many features, for example between codon optimization and mRNA secondary structure effects. Two combinatorial expression vector libraries (ExLib1 and ExLib2) were constructed using a randomization strategy that potentially could lead to variations in many of these sequence-related features and which would allow a pragmatic search of vector variants showing positive net effects on the level of soluble protein production. ExLib1 was constructed to encode all possible synonymous codons of an eight amino acid N-terminal extension of protein Z, fused to the N-terminal of an enhanced green fluorescent reporter protein (EGFP). In ExLib2, the same eight positions were randomized using an (NNG/T) degeneracy code, which could lead to various effects on both the nucleotide and protein level, through the introduction of nucleotide sequences functional as e.g. alternative ribosome binding or translation initiation sites or as translated codons for an Nterminal extension of the target protein by a peptide sequence. Flow cytometric analyses and sorting of library cell cultures resulted in isolation of clones displaying several-fold increases in whole cell fluorescence compared to a reference clone. SDS-PAGE and western blot analyses verified that this was a result of increases (up to 24-fold) in soluble intracellular ZEGFP product protein content. Both position specific codon bias effects and the appearance of new ribosomal binding sites in the library sequences were concluded to have influenced the protein production. To explore the possibility of applying the same combinatorial library strategy for improving soluble intracellular production of heterologous proteins proven difficult to express in E. coli, three proteins with either bacterial (a transcriptional regulator (DntR)) or human (progesterone receptor ligand binding domain (PRLBD) and 11-β Hydroxysteroid dehydrogenase type I (11-β)) origin, were cloned into the ExLib2 library. Flow cytometric sorting of libraries resulted in isolation of DntR library clones showing increased soluble protein production levels and PR-LBD library clones with up to ten-fold increases in whole cell fluorescence, although the product under these conditions co-separated with the insoluble cell material. / QC 20100623

L'aplicació de mètodes de cribatge virtual adquireix cada vegada més importància en el procés de descobriment de fàrmacs, complementant a les tècniques de High-throughput screening per tal de facilitar i contribuir a la comprensió dels mecanismes bioquímics d'actuació dels fàrmacs, donar agilitat i reduir el cost del procés.Pel que fa a la present tesi, l'interès farmacològic és la inhibició de receptors de tirosina cinases. Aquests enzims participen en múltiples processos de senyalització cel·lular, fet que fa que tant la disfunció de les mateixes o el seu paper privilegiat en els mecanismes del cicle cel·lular les converteixin en diana farmacològica de malalties com el càncer i altres relacionades amb desordres hiperproliferatius, migratoris, del desenvolupament embrionari i malalties vasculars. Una de las estratègies d'inhibició més usuals és el bloqueig del lloc d'unió de l'ATP a través de molècules orgàniques com les piridopirimidines, heterocicles especialment interessants per al grup d'investigació en el qual es desenvolupa aquest treball per la seva àmplia experiència sintètica en aquests sistemes.En la present tesi s'exploren i validen gran part de les tècniques de cribatge virtual amb l'objectiu d'establir una seqüència jerarquitzada de filtres que permetin avaluar aquells compostos candidats a ser sintetitzats. Els successius passos de filtrat inclouen la selecció de compostos d'una quimioteca virtual a partir de la diversitat o representativitat de l'espai químic, l'aplicació de recerques de similitud i models farmacofòrics construïts a partir d'inhibidors coneguts, un filtrat mitjançant docking o acoblament dels inhibidors a la cavitat d'unió d'aquestes proteïnes i mètodes de predicció de l'afinitat d'unió d'una sèrie de lligands. La jerarquia d'aquestes etapes s'imposa a partir de la diferència de recursos computacionals que requereix cadascuna d'elles, sent aquests cada vegada superiors. Els mètodes han estat validats retrospectivament en bases de dades formades per compostos actius recopilades de la bibliografia. Una vegada validades, han permès la caracterització prospectiva dels candidats sintètics.S'ha dissenyat un fingerprint d'interacció estructural proteïna-lligand basat en el concepte de parells atòmics (IFbAP) destinat a facilitar el postprocessat dels resultats de docking, aplicant-se com a filtre en un cribatge virtual. La seva capacitat per a discriminar entre compostos actius e inactius s'analitza per a tres dianes: el receptor d'estrogen, el receptor del factor de creixement de fibroblasts i la transcriptasa reversa del HIV.Paral·lelament, s'ha seguit amb el desenvolupament del programa PRALINS (Program for Rational Analysis of Libraries in Silico), programa dirigit al disseny de quimioteques combinatòries virtuals que incorpora els principals criteris de selecció basats en diversitat. En el context de les quimioteques combinatòries focalitzades, es proposa un nou mètode (Direct), la capacitat de focalització del qual s'ha testat front als mètodes tradicionals, també implementats a PRALINS. Així mateix s'incorporen i analitzen mètodes d'avaluació de diversitat, suggerint-se un mètode (cell-integral-diversity criterion) destinat a superar els desavantatges dels mètodes tradicionals. S'incorporen els algoritmes genètics a PRALINS com a tècnica d'optimització, tant d'un únic criteri de diversitat/similitud com per a realitzar optimitzacions multiobjetiu.En l'àmbit d'una altra línia d'investigació del grup dirigida cap al desenvolupament d'inhibidors del procés de fusió del HIV, s'estudia el mode d'unió de dos antagonistes de CXCR4 i CCR5, receptors cel·lulars de la família de les GPCRs implicats en aquesta etapa del cicle del virus. / La aplicación de métodos de cribado virtual cobra cada vez más importancia en el proceso de descubrimiento de fármacos, complementando a las técnicas de High-throughput screening con el fin de facilitar y contribuir a la comprensión de los mecanismos bioquímicos de actuación de los fármacos, agilizar y reducir el coste del proceso.En particular, el interés farmacológico de la presente tesis es la inhibición de receptores de tirosina quinasas. Estos enzimas participan en múltiples procesos de señalización celular, por lo que tanto la disfunción de las mismas o su papel privilegiado en los mecanismos del ciclo celular las convierten en diana farmacológica de enfermedades como el cáncer y otras relacionadas con desórdenes hiperproliferativos, migratorios, del desarrollo embrionario y enfermedades vasculares. Una de las estrategias de inhibición más usuales es el bloqueo del sitio de unión del ATP a través de moléculas orgánicas como las piridopirimidinas, heterociclos especialmente interesantes para el grupo de investigación en el que se desarrolla este trabajo por su amplia experiencia sintética en dichos sistemas.En la presente tesis se exploran y validan gran parte de las técnicas de cribado virtual con el objetivo de establecer una secuencia jerarquizada de filtros que permitan evaluar aquellos compuestos candidatos a ser sintetizados. Los sucesivos pasos de filtrado incluyen la selección de compuestos de una quimioteca virtual a partir de la diversidad o representatividad del espacio químico, la aplicación de búsquedas de similitud y modelos farmacofóricos construidos a partir de inhibidores conocidos, un filtrado mediante docking o acoplamiento de los inhibidores en la cavidad de unión de estas proteínas y métodos de predicción de la afinidad de unión de una serie de ligandos. La jerarquía de estas etapas se impone a partir de la diferencia de recursos computacionales que requiere cada una de ellas, siendo éstos cada vez superiores. Los métodos han sido validados retrospectivamente en bases de datos formadas por compuestos activos recopilados de la bibliografía. Una vez validadas, han permitido la caracterización prospectiva de los candidatos sintéticos.Se ha diseñado un fingerprint de interacción estructural proteína-ligando basado en el concepto de pares atómicos (IFbAP) destinado a facilitar el postprocesado de los resultados de docking, aplicándose como filtro en un cribado virtual. Su capacidad para discriminar entre compuestos activos e inactivos se analiza para tres dianas: el receptor de estrógeno, el receptor del factor de crecimiento de fibroblastos y la transcriptasa reversa del HIV.Paralelamente, se ha continuado con el desarrollo del programa PRALINS (Program for Rational Analysis of Libraries in Silico), programa dirigido al diseño de quimiotecas combinatorias virtuales que incorpora los principales criterios de selección basados en diversidad. En el contexto de las quimiotecas combinatorias focalizadas, se propone un nuevo método (Direct), cuya capacidad de focalización se ha testado frente a los métodos tradicionales, también implementados en PRALINS. Asimismo se incorporan y analizan métodos de evaluación de diversidad, sugiriéndose un método (cell-integral-diversity criterion) destinado a superar las desventajas de los métodos tradicionales. Se incorporan los algoritmos genéticos en PRALINS como técnica de optimización, tanto de un único criterio de diversidad/similitud como para realizar optimizaciones multiobjetivo.En el ámbito de otra línea de investigación del grupo dirigida hacia el desarrollo de inhibidores del proceso de fusión del HIV, se estudia el modo de unión de dos antagonistas de CXCR4 y CCR5, receptores celulares de la familia de las GPCRs implicados en dicha etapa del ciclo del virus. / Virtual screening is progressively gaining importance in the drug discovery process, complementing high-throughput screening in order to facilitate and contribute to the understanding of the action mechanism of drugs, while expediting and reducing the cost of the process.The pharmacological focus of this thesis lies in the inhibition of tyrosine kinase receptors. These enzymes are the critical components of signalling pathways, so both their dysfunction and their privileged role in the cell cycle pathways make them pharmacological targets in diseases such as cancer and others related to hyperproliferative disorders, migratory disorders, embryonic development and vascular pathologies. One of the most common strategies of inhibition is the blockage of the ATP binding site by small organic molecules such as pyridopyrimidines, which are of particular interest for the research group where this project was carried out due to our wide experience in the synthesis of these heterocycles.In the present thesis, most of the techniques currently employed in virtual screening are explored and validated with the aim of establishing a hierarchical database of screening to be used in the evaluation of drug candidates to be synthesized. The successive filtering steps include compound selection from a combinatorial library based on diversity or representativity of the chemical space, pharmacophore similarity searches, docking and affinity predictions for a series of ligands. The different strategies have been retrospectively validated in databases containing active compounds compiled from literature. After validation, they have been applied in the prospective characterization of the synthetic candidates.A structural interaction fingerprint has been designed, based on the concept of atomic pairs (IFbAP), for the post processing of docking outputs as a filter step in virtual screening. Its ability to discern between active and inactive compounds has been analysed for three targets: estrogen receptor, fibroblast growth factor receptor and HIV reverse transcriptase.We have also continued developing the PRALINS program (Program for Rational Analysis of Libraries in Silico), a program for the design of combinatorial libraries, which incorporates the main diversity selection criteria. In the context of focused combinatorial libraries, we propose a new method (Direct), whose ability to focalise has been compared to the traditional methodologies also implemented in PRALINS. Moreover, different diversity evaluation criteria have been compared, introducing a new method (cell-integral-diversity criterion) aimed at surpassing the disadvantages of traditional techniques. We have implemented genetic algorithms as optimisation techniques, both for unique diversity/similarity criterion and for carrying out multiobjective optimisations.Within another research area of interest for the group, directed towards the development of inhibitors of the HIV fusion process, we study the binding mode for CXCR4 and CCR5 antagonists.

Millions of years of evolution have resulted in an immense number of different proteins, which participate in virtually every process within cells and thus are of utmost importance for allknown forms of life. In addition, there are several examples of natural proteins which have found use in applications outside their natural environment, such as the use of enzymes infood industry and washing powders or the use of antibodies in diagnostic, bioseparation or therapeutic applications. To improve the performance of proteins in such applications, anumber of techniques, all collectively referred to as ‘protein engineering’, are performed in thelaboratory.Traditionally, methods involving ‘rational design’, where a few alterations are introduced atspecific protein locations to hopefully result in expected improvements have been applied.However, the use of more recent techniques involving a simultaneous construction of a large number of candidate variants (protein libraries) by various diversification principles, fromwhich rare clones showing enhanced properties can be isolated have contributed greatly to thefield of protein engineering.In the present thesis, different protein traits of biotechnological importance have beenaddressed for improvements by the use of such methods, in which there is a crucial need tomaintain a clonal link between the genotype and the phenotype to allow an identification of protein library members isolated by virtue of their functional properties. In all protein library investigations included in this thesis this coupling has been obtained by Escherichia coli bacterialcell-membrane compartmental confinement.In a first study, a combination of error prone PCR and gene-shuffling was applied to the Tobacco Etch Virus (TEV)-protease gene in order to produce collections from which genesencoding variants showing an enhanced soluble expression of the enzyme frequently used inbiotechnology to cleave fusion proteins were identified. Using Green Fluorescence Protein(GFP)-based cell fluorescence analysis, a clone with a five-fold increase in the yield of solubly produced protein was successfully isolated. In a second study, a novel and different GFPbased selection system, in addition also involving targeted in vivo protein degradation principles,was employed for investigations of the substrate sequence space of the same protease. In two additional studies, a selection system denoted Protein Fragment Complementation Assay(PCA), based on the affinity driven structural complementation of a genetically split β-lactamase enzyme was used to identify variants having desired target protein binding abilities,including both specificity and affinity. Using Darwinian principles concerning clonal growth advantages, affibody binding proteins showing sub-nanomolar dissociation constants to thehuman cytokine TNF-α were isolated. Taken together, these studies have shown that the bacterial format is very well suited for use in various aspects of protein library selection. / QC 20100729

Les Acides Peptido-nucléiques (PNA) sont des analogues synthétiques d’oligonucleotides naturels, ils sont constitués d’une répétition d’unités N-(2-aminoethyl)-glycine reliées par une liaison peptidique. Leur stabilité chimique et biologique en font une alternative intéressante pour les assemblages supramoléculaires ayant une application biologique tels que l’encodage de chimiothèques combinatoires de petites molécules et des réactions engendrées par hybridation. Ce travail de thèse avait pour objectif la synthèse d’acides peptido-nucléiques modifiés dans le but d’améliorer leur hybridation, leurs propriétés physico-chimiques ainsi que la synthèse des chimiothèques combinatoires. / Peptide nucleic acids (PNA) are structural analogs of natural nucleic acids composed of repeating units of N-(2-aminoethyl)-glycine residues linked by peptide bonds. Their chemical and biological stability makes them very suitable for supramolecular assemblies with biological applications such as encoding combinatorial libraries of small molecules and for performing templated reactions. This phD project aimed at the synthesis of modified peptide nucleic acids to enhance their physicochemical and hybridization properties as well as for construction of combinatorial libraries.

Fast and precise quantification of circulating tumour cells (CTC) in lung adenocarcinoma is a pivotal step in acceleration of diagnosis, selection of early therapy and estimation of treatment prognosis. Development of a new type of microfluidic device based on detection and quantification of epithelial- and mesenchymal-type CTC by high-affinity and cell-type specific protein binders anchored to a microfluidic chip surface represents a highly innovative approach. In this work, we used EpCAM membrane glycoprotein as a target for generation of epithelial cell- specific protein binders by a directed evolution of proteins selected from highly complex combinatorial libraries derived from albumin-binding domain scaffold (ABD) or human muscle protein domain-derived "Myomedin" scaffold. Collections of EpCAM-binding candidates from the both used libraries were generated and particular binding variants were further characterized by DNA sequencing, biochemically and by functional cell-surface binding assays. The best candidates might serve as robust anchor proteins of a microfludic chip. Key words: epithelial cell, EpCAM, protein binder, ribosome display, combinatorial library, protein scaffold

For three decades, the ongoing HIV pandemic has taken the lives of tens of millions of people. Still, more tens of millions are fighting this incurable disease today. Current failures in combating this global problem are caused mainly by the virus's extreme ability of mutation, its very effective molecular shield which repels the immune system's attacks, and its immense variability. A breakthrough, achieved relatively recently, is the discovery of the so-called broadly neutralizing antibodies against HIV-1, which carry a very efficient and broad neutralizing response. So far, it's not known how to elucidate the production of these antibodies in the infected hosts to quell or altogether eliminate the virus. This work deals with experimental results, which led to both in vivo and in vitro proof-of-concept of the so-called protein mimetics, the ability to imitate viral surface epitopes, and therefore stimulate an efficient immune response carried by targeted broadly neutralizing antibodies. This effect is mediated by recombinant binding proteins, based on the Myomedin scaffold. This work describes the selection and characterization of these binding proteins mimicking the epitopes of one of the most effective broadly neutralizing antibodies, 10E8. It shows that the binding affinities of selected...