Pseudomonas aeruginosa (PA) est la troisième bactérie impliquée dans les maladies nosocomiales et est la principale cause de mortalité des patients atteints de la mucoviscidose. PA est résistante à la plupart des traitements antibiotiques. Trouver de nouvelles stratégies thérapeutiques est devenu un enjeu majeur de santé publique, l’une d’entre elles est l’inhibition de facteurs de virulence. Parmi ceux-ci, les lectines sont des protéines impliquées dans l’adhésion et la formation de biofilm via des interactions avec des sucres (PA-IL, PA- IIL, FliC, FliD, PilA, PilY1 et CupB6).Le but de ce travail est donc de trouver des leurres moléculaires ayant une forte affinité pour ces lectines. Ceux-ci sont des motifs saccharidiques présentés de façon multivalente : glycoclusters. De part leur grande diversité structurale et leur faible quantité, un outil de criblage innovant a été développé qui consiste en une lame de verre microstructurée : le glycocluster-microarray. Les glycoclusters sont immobilisés de manière ordonnée par DNA Directed Immobilization (DDI). Deux méthodes de criblage ont été développées grâce à cet outils : 1) le criblage en solution et par compétition d’une bibliothèque de motifs saccharidiques et 2) le criblage d’une bibliothèque de glycoclusters immobilisés sur le microarray. Avec cet outil, des protocoles de mesures d’IC50 et de Kd ont aussi été fiabilisés pour caractériser les meilleurs candidats inhibiteurs des lectines. Le glycocluster- microarray présente l’avantage de n’utiliser qu’une très faible quantité de matériel (quelques picomoles) et permet de réaliser diverses analyses en parallèle.Afin de valider cet outil, une étude sur l’impact de la densité de surface en glycocluster a été menée. Le criblage de plus de 150 motifs saccharidiques a permis de sélectionner ceux ayant une forte affinité pour les lectines. L’analyse sur microarray complétée par de la modélisation moléculaire d’une bibliothèque de glycoclusters, possédant ces motifs et différentes topologies, valences et propriétés (aromaticité, charge,…), a permis d’identifier les paramètres clés dirigeant les relations structure-affinité. Une activité anti-biofilm chez PA a été démontrée avec les meilleurs glycoclusters ciblant PA-IL.Tester l’activité in vivo, chez l’animal, des meilleurs candidats est une voie à explorer. Cibler d’autres lectines comme celles présentes sur le flagelle et les pili de PA et notamment impliquées dans son adhésion précoce est aussi une voie à développer. Pour cela, des tests préliminaires ont été présentés et d’autres sont en cours faisant appel à l’utilisation de bactéries entières ainsi qu’à une détection sans marquage des lectines. / Summary: Pseudomonas aeruginosa (PA) is the third pathogen involved in nosocomial diseases and the major cause of mortality of cystic fibrosis patients. PA develops resistance to antibiotics treatments. And so, developing new therapeutic strategies is a public health issue. One of the promising strategies is to inhibit virulence factors involved in the adhesion and the biofilm formation of PA. Some of these virulence factors are lectins which interact with sugars (PA-IL, PA-IIL, FliC, FliD, PilA, PilY1 and CupB6).The goal of this work is to find molecular decoys which have a strong affinity for these lectins. These are saccharidic units with a multivalent display: glycoclusters. An innovative screening tool has been developed: the glycocluster-microarray, to study lectin/glycocluster interactions. It is a microstructured glass slide where glycoclusters are immobilized by DNA Directed Immobilization (DDI). Two screening methods have been developed with this microarray: 1) the screening in solution and by competition of a saccharidic units library and2) the screening of a glycoclusters library immobilized on the microarray. Protocols of IC50 and Kd measurements have also been developed with this tool to characterize the best lectins inhibitors. This tool allows to use few amount of material (few picomoles) and to do parallel analysis.To validate the microarray, a study of the impact of glycoclusters surface density has been done. The screening of more than 150 saccharidic units allowed the selection of the ones that display the best affinity forlectins. The analysis, on microarray and molecular simulations, of the glycoclusters library displaying thesesaccharidic units and several topologies, valences and properties (aromaticity, charge,…) enable to identify key parameters of structure-affinity relationships. An anti-biofilm activity has been observed for the best glycoclusters targeting PA-IL.Testing in vivo activity of these best candidates will be explored. Targeting others lectins such as the ones on the flagella and pili of PA and involved in the early adhesion needs also to be developed. To this end, preliminary tests have been showed and some are in progress.

A ciclodextrina glicosiltransferase (CGTase) é a única enzima capaz de catalisar a reação de ciclização a partir do amido e, assim, formar oligossacarídeos cíclicos conhecidos como ciclodextrinas (CDs). Através desta reação é produzida uma mistura de α-, β- e γ-CD que, respectivamente, contém 6, 7 e 8 resíduos de glicose. As CDs têm atraído enorme atenção devido ao seu grande potencial de aplicação em diversas áreas da indústria. Potencial este proporcionado por sua estrutura cônica, com interior hidrofóbico, capaz de encapsular sólidos, líquidos e gases, conferindo propriedades importantes e protegendo-os. Neste trabalho foi estudada a imobilização de uma CGTase em sílica mesoporosa de forma direcionada às cisteínas presentes em sua superfície, alterando a exposição do sítio ativo. A ligação via cisteínas nativas da proteína aumentou em quatro vezes a eficiência da imobilização, quando comparada a ligação via grupamento amino. Esta, no entanto, apresentou maior atividade enzimática em faixas mais amplas de temperatura e pH, além de maior estabilidade operacional, mantendo 100 % de sua atividade após 200 h de reação contínua a 60 °C e pH 4. Ainda que apresentando menor estabilidade da ligação, o derivado obtido por ligação dissulfeto manteve 40 % da atividade inicial durante 200 h e então, o suporte pôde ser recarregado e reutilizado por igual período. Os suportes desenvolvidos apresentaram estabilidade satisfatória, possibilitando o uso do derivado imobilizado em reator de leito fixo operado de forma contínua. Quando avaliado em relação a produção das três ciclodextrinas principais, o derivado cuja imobilização da enzima ocorreu via grupamento amino, evidenciou a possibilidade de modulação da produção apenas variando as condições de reação. α- e β-CD foram produzidas preferencialmente em pH 8,0 e 2 min (3,44 mg mL-1 e 3,51 mg mL-1, respectivamente), enquanto que pH mais ácido (4,0) e maior tempo de reação (141 min) favoreceram a formação de γ-CD (3,35 mg mL-1), com baixa formação α-CD (0,75 mg mL-1). Por fim, os resultados deste estudo evidenciam a importância da imobilização da CGTase para a estabilização de sua estrutura a fim de aplicá-la em sistemas contínuos de produção de CDs onde é possível modular o perfil dos produtos gerados em função das condições de reação, aumentando assim a produtividade do biocatalisador. / Cyclodextrin glycosyltransferase (CGTase) is the only enzyme capable of catalyzing the cyclization reaction from the starch and thus forming cyclic oligosaccharides known as cyclodextrins (CDs). Through this reaction, is produced a mixture of α-, β- and γ-CD containing, 6, 7 and 8 glucose residues respectively. Cyclodextrins (CD) have been attracting considerable attention because of its great potential for application in various areas of industry. This potential is provided by its conical structure with hydrophobic interior, capable of encapsulating solids, liquids and gases, changing important features and protecting them. In this work, the immobilization of CGTase in mesoporous silica was studied in a way directed to cysteines present on its surface, altering the exposure of the active site. The connection via native cysteine of the protein increased by four times the efficiency of immobilization compared to amino groups connection. The binding of amino groups, however, showed greater enzymatic activity in wider ranges of temperature and pH, and higher operational stability, while maintaining 100 % of its activity after 200 h of continuous reaction at 60 °C and pH 4. Although showing less stable connection, the derivative obtained by disulfide bond retained 40 % of the initial activity for 200 h and then, the support could be reloaded and reused for the same period. Developed supports showed satisfactory stability, enabling the use of the derivative assets in a packed bed reactor and operated continuously. It was demonstrated the possibility of modulating the CDs production just varying the reaction conditions, using the derivative of which the enzyme immobilization occurred via amino group, to evaluate the production of three main cyclodextrins. α- and β-CD were produced preferentially at pH 8.0 and 2 min (3.44 mg mL-1 and 3.51 mg mL-1, respectively), whereas the more acid pH (4.0) and longer reaction (141 min) favored the formation of γ-CD (3.35 mg mL-1 and 0.75 mg mL-1 of α-CD). Finally, the results of this study show the importance of the immobilization of CGTase to the stabilization of its structure in order to apply it in continuous CD production systems, where it is possible to modulate the profile of the products generated as a function of the reaction conditions, thus increasing the productivity of the biocatalyst.

A ciclodextrina glicosiltransferase (CGTase) é a única enzima capaz de catalisar a reação de ciclização a partir do amido e, assim, formar oligossacarídeos cíclicos conhecidos como ciclodextrinas (CDs). Através desta reação é produzida uma mistura de α-, β- e γ-CD que, respectivamente, contém 6, 7 e 8 resíduos de glicose. As CDs têm atraído enorme atenção devido ao seu grande potencial de aplicação em diversas áreas da indústria. Potencial este proporcionado por sua estrutura cônica, com interior hidrofóbico, capaz de encapsular sólidos, líquidos e gases, conferindo propriedades importantes e protegendo-os. Neste trabalho foi estudada a imobilização de uma CGTase em sílica mesoporosa de forma direcionada às cisteínas presentes em sua superfície, alterando a exposição do sítio ativo. A ligação via cisteínas nativas da proteína aumentou em quatro vezes a eficiência da imobilização, quando comparada a ligação via grupamento amino. Esta, no entanto, apresentou maior atividade enzimática em faixas mais amplas de temperatura e pH, além de maior estabilidade operacional, mantendo 100 % de sua atividade após 200 h de reação contínua a 60 °C e pH 4. Ainda que apresentando menor estabilidade da ligação, o derivado obtido por ligação dissulfeto manteve 40 % da atividade inicial durante 200 h e então, o suporte pôde ser recarregado e reutilizado por igual período. Os suportes desenvolvidos apresentaram estabilidade satisfatória, possibilitando o uso do derivado imobilizado em reator de leito fixo operado de forma contínua. Quando avaliado em relação a produção das três ciclodextrinas principais, o derivado cuja imobilização da enzima ocorreu via grupamento amino, evidenciou a possibilidade de modulação da produção apenas variando as condições de reação. α- e β-CD foram produzidas preferencialmente em pH 8,0 e 2 min (3,44 mg mL-1 e 3,51 mg mL-1, respectivamente), enquanto que pH mais ácido (4,0) e maior tempo de reação (141 min) favoreceram a formação de γ-CD (3,35 mg mL-1), com baixa formação α-CD (0,75 mg mL-1). Por fim, os resultados deste estudo evidenciam a importância da imobilização da CGTase para a estabilização de sua estrutura a fim de aplicá-la em sistemas contínuos de produção de CDs onde é possível modular o perfil dos produtos gerados em função das condições de reação, aumentando assim a produtividade do biocatalisador. / Cyclodextrin glycosyltransferase (CGTase) is the only enzyme capable of catalyzing the cyclization reaction from the starch and thus forming cyclic oligosaccharides known as cyclodextrins (CDs). Through this reaction, is produced a mixture of α-, β- and γ-CD containing, 6, 7 and 8 glucose residues respectively. Cyclodextrins (CD) have been attracting considerable attention because of its great potential for application in various areas of industry. This potential is provided by its conical structure with hydrophobic interior, capable of encapsulating solids, liquids and gases, changing important features and protecting them. In this work, the immobilization of CGTase in mesoporous silica was studied in a way directed to cysteines present on its surface, altering the exposure of the active site. The connection via native cysteine of the protein increased by four times the efficiency of immobilization compared to amino groups connection. The binding of amino groups, however, showed greater enzymatic activity in wider ranges of temperature and pH, and higher operational stability, while maintaining 100 % of its activity after 200 h of continuous reaction at 60 °C and pH 4. Although showing less stable connection, the derivative obtained by disulfide bond retained 40 % of the initial activity for 200 h and then, the support could be reloaded and reused for the same period. Developed supports showed satisfactory stability, enabling the use of the derivative assets in a packed bed reactor and operated continuously. It was demonstrated the possibility of modulating the CDs production just varying the reaction conditions, using the derivative of which the enzyme immobilization occurred via amino group, to evaluate the production of three main cyclodextrins. α- and β-CD were produced preferentially at pH 8.0 and 2 min (3.44 mg mL-1 and 3.51 mg mL-1, respectively), whereas the more acid pH (4.0) and longer reaction (141 min) favored the formation of γ-CD (3.35 mg mL-1 and 0.75 mg mL-1 of α-CD). Finally, the results of this study show the importance of the immobilization of CGTase to the stabilization of its structure in order to apply it in continuous CD production systems, where it is possible to modulate the profile of the products generated as a function of the reaction conditions, thus increasing the productivity of the biocatalyst.

A ciclodextrina glicosiltransferase (CGTase) é a única enzima capaz de catalisar a reação de ciclização a partir do amido e, assim, formar oligossacarídeos cíclicos conhecidos como ciclodextrinas (CDs). Através desta reação é produzida uma mistura de α-, β- e γ-CD que, respectivamente, contém 6, 7 e 8 resíduos de glicose. As CDs têm atraído enorme atenção devido ao seu grande potencial de aplicação em diversas áreas da indústria. Potencial este proporcionado por sua estrutura cônica, com interior hidrofóbico, capaz de encapsular sólidos, líquidos e gases, conferindo propriedades importantes e protegendo-os. Neste trabalho foi estudada a imobilização de uma CGTase em sílica mesoporosa de forma direcionada às cisteínas presentes em sua superfície, alterando a exposição do sítio ativo. A ligação via cisteínas nativas da proteína aumentou em quatro vezes a eficiência da imobilização, quando comparada a ligação via grupamento amino. Esta, no entanto, apresentou maior atividade enzimática em faixas mais amplas de temperatura e pH, além de maior estabilidade operacional, mantendo 100 % de sua atividade após 200 h de reação contínua a 60 °C e pH 4. Ainda que apresentando menor estabilidade da ligação, o derivado obtido por ligação dissulfeto manteve 40 % da atividade inicial durante 200 h e então, o suporte pôde ser recarregado e reutilizado por igual período. Os suportes desenvolvidos apresentaram estabilidade satisfatória, possibilitando o uso do derivado imobilizado em reator de leito fixo operado de forma contínua. Quando avaliado em relação a produção das três ciclodextrinas principais, o derivado cuja imobilização da enzima ocorreu via grupamento amino, evidenciou a possibilidade de modulação da produção apenas variando as condições de reação. α- e β-CD foram produzidas preferencialmente em pH 8,0 e 2 min (3,44 mg mL-1 e 3,51 mg mL-1, respectivamente), enquanto que pH mais ácido (4,0) e maior tempo de reação (141 min) favoreceram a formação de γ-CD (3,35 mg mL-1), com baixa formação α-CD (0,75 mg mL-1). Por fim, os resultados deste estudo evidenciam a importância da imobilização da CGTase para a estabilização de sua estrutura a fim de aplicá-la em sistemas contínuos de produção de CDs onde é possível modular o perfil dos produtos gerados em função das condições de reação, aumentando assim a produtividade do biocatalisador. / Cyclodextrin glycosyltransferase (CGTase) is the only enzyme capable of catalyzing the cyclization reaction from the starch and thus forming cyclic oligosaccharides known as cyclodextrins (CDs). Through this reaction, is produced a mixture of α-, β- and γ-CD containing, 6, 7 and 8 glucose residues respectively. Cyclodextrins (CD) have been attracting considerable attention because of its great potential for application in various areas of industry. This potential is provided by its conical structure with hydrophobic interior, capable of encapsulating solids, liquids and gases, changing important features and protecting them. In this work, the immobilization of CGTase in mesoporous silica was studied in a way directed to cysteines present on its surface, altering the exposure of the active site. The connection via native cysteine of the protein increased by four times the efficiency of immobilization compared to amino groups connection. The binding of amino groups, however, showed greater enzymatic activity in wider ranges of temperature and pH, and higher operational stability, while maintaining 100 % of its activity after 200 h of continuous reaction at 60 °C and pH 4. Although showing less stable connection, the derivative obtained by disulfide bond retained 40 % of the initial activity for 200 h and then, the support could be reloaded and reused for the same period. Developed supports showed satisfactory stability, enabling the use of the derivative assets in a packed bed reactor and operated continuously. It was demonstrated the possibility of modulating the CDs production just varying the reaction conditions, using the derivative of which the enzyme immobilization occurred via amino group, to evaluate the production of three main cyclodextrins. α- and β-CD were produced preferentially at pH 8.0 and 2 min (3.44 mg mL-1 and 3.51 mg mL-1, respectively), whereas the more acid pH (4.0) and longer reaction (141 min) favored the formation of γ-CD (3.35 mg mL-1 and 0.75 mg mL-1 of α-CD). Finally, the results of this study show the importance of the immobilization of CGTase to the stabilization of its structure in order to apply it in continuous CD production systems, where it is possible to modulate the profile of the products generated as a function of the reaction conditions, thus increasing the productivity of the biocatalyst.

Pseudomonas aeruginosa (PA) est l’un des principaux germes impliqués dans les maladies nosocomiales et est aussi la principale cause de mortalité et morbidité des patients atteints de la mucoviscidose malgré l’utilisation massive d’antibiotiques. Dans la lutte contre PA, une alternative aux antibiotiques est l’inhibition de ses facteurs de virulence notamment ceux impliqués dans l’adhésion et la formation du biofilm via des interactions de type sucres/protéines. Ces protéines sont appelées lectines (PA-IL, PA-IIL, FliD). L’objectif de ce travail est la recherche de molécules inhibitrices (glycoclusters) de ces lectines impliquées dans la virulence de PA. Compte tenu du grand nombre de glycoclusters à tester et des faibles quantités de matériels biologiques disponibles, un outil de criblage innovant a été développé (glycoarray) à partir d’une lame de verre microstructurée et fonctionnalisée chimiquement afin d’immobiliser de manière organisée et ordonnée les glycoclusters. La méthode d’immobilisation choisie est la méthode d’immobilisation spécifique par hybridation de l’ADN appelée DDI : DNA Directed Immobilization. Sur ces glycoarrays, 3 méthodes indépendantes (lecture de fluorescence directe, IC50 et Kd) de mesure des interactions glycoclusters/lectines ont été mises au point et validées par une étude comparative donnant un classement similaire des glycoclusters pour leur affinité vis-à-vis des lectines Il faut noter que ces mesures faites sur glycoarrays ne consomment que quelques picomoles de glycoclusters comparées aux méthodes classiques (ITC, ELLA, RMN, …) qui nécessitent des micromoles de produits. A l’aide de ces glycoarrays, un criblage d’une bibliothèque d’une centaine de glycoclusters multivalents, de différentes topologies, charges et linkers a permis d’identifier deux structures montrant une très forte affinité vis-à-vis des lectines de PA. Ces glycoclusters sont actuellement en test in vitro et in vivo. Ces études d’interactions sur DDI-glycoarray ont été étendues à d’autres agents pathogènes tels que les bactéries Burkholderia ambifaria, Viscum album ou contre le virus de la grippe. Dans le futur, pour mieux appréhender les mécanismes d’interactions sucres/protéines, il serait intéressant de pouvoir suivre en temps réel ces interactions en utilisant des systèmes de détection sans marquage tel que, par exemple, la résonance plasmonique de surface. Aussi, le dernier chapitre donne les prémices d’une adaptation de la méthode DDI sur glycoarray sur surface d’or. / Pseudomonas aeruginosa (PA) is one of the predominant bacterium encountered in nosocomial infections. PA infections often lead to chronic inflammation and eventually to death despite aggressive antibiotic therapy. A promising approach is to inhibit the virulence factors of PA such as PA-IL, PA-IIL, FliD (lectins). Therefore, there is a great interest for studying carbohydrate/lectin interactions in order to design new treatments. The goal of this work is the research for inhibitory molecules (glycoclusters ) of these lectins involved in the virulence of PA. An innovative screening tool for studying carbohydrate/lectin interactions has been developed (glycoarray). Glycoarray are microstructured glass-slides, chemically functionalized in order to immobilize, organized and orderly, glycoclusters at the surface. The immobilization method is the specific immobilization method based on DNA hybridization called DDI (DNA Directed Immobilization). This miniaturized analytical biosystem allows multiplex test performed in one single microwell. Moreover, three independent methods of affinity measurement (direct fluorescence read-out, IC50 and Kd) have been developed and validated by a comparative study giving a similar ranking of glycoclusters for their affinity towards PA-IL. These measurements on glycoarrays consume only a few picomoles glycoclusters compared to conventional methods (ITC, ELLA...) that require micromoles of products. Using these glycoarrays, the screening of a library of hundreds of glycoclusters presenting different topologies, multivalencies, charges and linkers led to the identification of two structures showing a very strong affinity for PA lectins. These glycoclusters are currently in vitro assay and in vivo. These interaction studies on DDI-glycoarray were extended to other pathogens such as Burkholderia ambifaria bacteria, Viscum album or against the influenza virus. In the future, to better understand the mechanisms of sugar / protein interactions, it would be interesting to monitor in real time the interactions using label-free detection systems such as, for example, the surface plasmon resonance (SPR). Also, the last chapter gives the beginnings of an adaptation of the method of DDI glycoarray on gold surface