Orientador: Renato Sprung / Tese doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica / Made available in DSpace on 2018-08-06T18:06:45Z (GMT). No. of bitstreams: 1 Villanueva_SandraBizarriaLopes_D.pdf: 2768871 bytes, checksum: ec40bbcbf8152a8c34f6d7fdd395af83 (MD5) Previous issue date: 2005 / Resumo: Materiais do tipo hidrotalcita foram sintetizados, calcinados e caracterizados, assim como utilizados na conversão catalítica de etanol. As sínteses foram realizadas com razões molares AI/(AI + Mg) iguais a 0,20; 0,25 e 0,33; em todos os casos os difratogramas de raios-X demonstraram que, efetivamente, fases de hidrotalcitas tinham sido obtidas. Esses materiais apresentaram áreas superficiais BET de cerca de 50 a 70 m2.g-l, à exceção da hidrotalcita sintetizada com agentes precipitantes contendo amônio, em que a área superficial foi de cerca de 7 m2g -I. A quimissorção de CO2 desses materiais revelou que hidrota1citas calcinadas são sólidos básicos e tal basicidade relaciona-se com o teor de magnésio substituído e também com a temperatura de ca1cinação. Os testes catalíticos foram realizados a temperaturas de 3000 C a 4000 C e verificou-se o aumento da taxa de reação com o incremento da temperatura. Os produtos de condensação éter etílico e nbutanol foram obtidos em maior proporção. Hidrotalcitas da série sódio apresentaram maior rendimento de n-butanol independentemente do teor de alumínio presente na amostra. Todas as amostras utilizadas apresentaram, a baixas conversões, quantidades significativas de n-butanol, o que pode indicar que, além da via de condensação aldólica, a formação desse produto também ocorre via condensação direta do etanol, ou seja, sem a dessorção para a fase gasosa da molécula de acetaldeído. Testes catalíticos comparativos realizados com óxido de magnésio e alumínio resultaram principalmente em acetaldeído e etileno, respectivamente. Traços de n-butanol foram identificados no óxido de magnésio quando testado a 4000 C, e éter etílico foi observado em maior quantidade no óxido de alumínio quando testado a 3000 C / Abstract: Hydrotalcites-like materiaIs were prepared, calcined and characterized as well as used in the catalytic reaction of ethanol. The synthesis were perfonned with AI/(AI + Mg) ratios of 0.20; 0.25 and 0.33; in all cases the x-ray showed hydrotalcites phases. These materiaIs resulted in BET areas of 50 at 70 m2.g-1, except for the hydrotalcite synthesized with NH3, that resulted in a BET area 00 m2g-1. The CO2 chemisorption on these materiaIs revealed that calcined hydrotalcites are basic catalysts and their basicity was related to the quantity of substituted magnesium and to the calcination temperature. The catalytic reactions were performed at 300, 350 and 4000 C; the reaction rate increasing with reaction temperature. The main reaction products identified were ether and n-butanol. The hydrotalcite synthesized with cation sodium presented the highest yield of n-butanoI independent of aluminum content present in the samples. The results of Iow conversions showed significant yield of n-butanoI, and this could indicate that the formation of that product occurs by aldoI condensation and aIso by straight condensation of ethanoI molecule, without acetaldehyde desorption to gas fase. Comparative catalytic tests performed with MgO and AI203 showed acetaldehyde and ethylene predominantly as reaction products. Traces of n-butanoI were identified with MgO when the reaction occurred at 4000 C, and ether was identified with AI203 when the reaction occurred at 3000 C / Doutorado / Desenvolvimento de Processos Químicos / Doutor em Engenharia Química

Ce travail de thèse est consacré à la conception de métalloenzymes artificielles. Un tel concept permet de combiner les avantages des catalyseurs enzymatiques et organométalliques, tels que la sélectivité catalytique élevée et l'efficacité des systèmes enzymatiques et la large portée de substrats des catalyseurs des métaux de transition. Notre approche repose sur l’utilisation de complexes de métaux de transition avec un ligand prochiral hémilabile, qui une fois insérés dans la protéine hôte sera forcé d’adopter une configuration spécifique. La chiralité sera ainsi amenée au plus près du centre métallique et permettra d’augmenter l’énantioselectivité des réactions catalysées. Dans cette thèse, nous rapportons la synthèse de nouveaux complexes de palladium à ligands pinces NCN hémilabiles prochiraux et l’étude de leurs propriétés structurales. De plus, l’ancrage supramoléculaire de ces complexes dans la β-lactoglobuline (β-LG) bovine a été étudié expérimentalement et théoriquement par modélisation moléculaire. Ces constructions ont montré une activité catalytique dans la condensation d’aldol dans l’eau, et permettent d’obtenir, dans certains cas, le produit Cis. Cette diastéréosélectivité inhabituelle résulte de la seconde sphère de coordination apportée par l'hôte protéique. Dans une deuxième partie, on rapporte la synthèse de nouveaux complexes semi-sandwich de ruthénium avec des ligands β-aminothioéther hémilabiles, ainsi que l'étude de leur insertion dans la protéine. Les hybrides catalysent l'hydrogénation par transfert d'arylcétones avec une énantiosélectivité élevée. L'amélioration de la sélectivité a été attribuée au transfert de chiralité de la protéine vers le complexe et à son tour vers le produit de réaction. / This PhD work focused on the development of artificial metalloenzymes. Such a concept allows to combine typical advantages of both enzymatic and organometallic catalysts, such as high catalytic selectivity and efficiency of enzymatic systems and wide substrate scope of transition metals catalysts. Our approach consists in the utilization of transition metal complexes with a prochiral hemilabile ligand, once embedded within the protein host, could be forced to adopt a specific stereoconfiguration. This would in turn make possible to bring the chirality centers closer to the catalytic metal center and, therefore, to increase the enantioselectivity of catalyzed reactions.In this thesis, we report the synthesis of new palladium complexes of prochiral hemilabile NCN pincer ligands and the study of their structural properties. Furthermore, the supramolecular anchoring of these complexes to bovine β-lactoglobulin (β-LG) was studied both experimentally and theorically by computational calculation. These constructs were shown to catalyze aldol condensation reactions in aqueous media, affording, in some cases, the less-favorable cis product. This unusual diastereoselectivity was ensued by the second sphere of coordination brought by the protein host. In a second part, the synthesis of new half sandwich ruthenium complexes of prochiral hemilabile β-aminothioether ligands is reported as well as the study of their insertion in the protein. The hybrids catalyzed the transfer hydrogenation of arylketones with high enantioselectivity. The enhancement of selectivity was attributed to chirality.

O dióxido de carbono no estado supercrítico (CO2-SC) tem despertado considerável interesse nos últimos anos como um novo solvente para reações orgânicas. Nesta tese foi investigada a influência do uso de CO2 supercrítico, associado ou não a líquidos iônicos ou cossolventes, como solvente em reações químicas visando à obtenção de precursores quirais. Foram estudadas as reações de condensação Aldólica, de Morita-Baylis-Hillman (MBH) e do tipo adição de Michael, empregando Organocatálise quando conveniente, isto é, catalisadores provenientes de aminoácidos e ácidos carboxílicos. As reações de MBH foram otimizadas através de um planejamento experimental e sua condição ótima se deu a 70°C, 110 bar, com 6 equivalentes de H2O, tempo reacional de 2h30 min e sem a presença de liquido iônico, tendo um rendimento de 84,6%. Para as condensações aldólicas os melhores resultados com acetona e p-nitrobenzaldeido como materiais de partida foram obtidos a 150 bar e 40°C, com a presença de liquido iônico, em 2 horas de tempo reacional com um rendimento de 54,0% e um excesso enantiomérico de 79,0% utilizando o catalisador (2S,4R)-4-(terc-butildimetilsililoxi)pirrolidina-2-ácido carboxílico. Com ciclohexanona como material de partida foram obtidos a 150 bar e 40°C com a presença de um doador de prótons (resina de troca iônica) em 2 horas de tempo reacional com um rendimento de 70,9% e um excesso enantiomérico de 91,2%, utilizando o catalisador (2S,4R)-4-(terc-butildimetilsililoxi)pirrolidina-2-ácido carboxílico. Outros aldeídos e cetonas utilizados como materiais de partida apresentaram rendimentos menores. Estudos de comportamento de fases foram feitos para os materiais de partida, catalisadores e produtos da reação de condensação Aldólica. Os melhores rendimentos foram obtidos em situações em que os materiais de partida e os catalisadores eram solúveis na fase supercrítica, mas os produtos não, formando uma segunda fase. / Supercritical carbon dioxide (sc-CO2) has attracted considerable interest in the last years as a new solvent for organic reactions. In this thesis, the influence of supercritical CO2 use, associated or not to ionic liquids or cosolvents, as a solvent for chemical reactions aiming at the synthesis of chiral precursors was studied. Aldol condensation, Morita-Baylis-Hillman (MBH) and Michael addition reactions were studied, employing organocatalysis when it was convenient, i.e., catalysts derived from aminoacids or carboxylic acids. MBH reactions were optimized through experimental design, resulting in a maximum yield of 84.6% for the optimal condition at 70°C, 110 bar, and 6 equivalents of H2O, reaction time of 2h30 min and the absence of ionic liquids. For the Aldol condensation reactions employing acetone and p-nitrobenzaldehyde, a maximum yield of 54.0%, with an enantiomeric excess of 79.0% was obtained at 150 bar, 40°C, 2h reaction time, in the presence of ionic liquid, using the catalyst (2S,4R)-4-(terc-butyldimethylsililoxy)pirrolidine-2-carboxylic acid. The yields were significantly lower for other aldehydes and ketones. Yields for Michael addition reactions were very low and their study was discontinued. Phase behavior studies were performed with starting materials, catalysts and products for the Aldol condensation reactions. The best yields were obtained for situations where the starting materials and catalysts were soluble in the supercritical phase and the products were not, forming a second phase.

O dióxido de carbono no estado supercrítico (CO2-SC) tem despertado considerável interesse nos últimos anos como um novo solvente para reações orgânicas. Nesta tese foi investigada a influência do uso de CO2 supercrítico, associado ou não a líquidos iônicos ou cossolventes, como solvente em reações químicas visando à obtenção de precursores quirais. Foram estudadas as reações de condensação Aldólica, de Morita-Baylis-Hillman (MBH) e do tipo adição de Michael, empregando Organocatálise quando conveniente, isto é, catalisadores provenientes de aminoácidos e ácidos carboxílicos. As reações de MBH foram otimizadas através de um planejamento experimental e sua condição ótima se deu a 70°C, 110 bar, com 6 equivalentes de H2O, tempo reacional de 2h30 min e sem a presença de liquido iônico, tendo um rendimento de 84,6%. Para as condensações aldólicas os melhores resultados com acetona e p-nitrobenzaldeido como materiais de partida foram obtidos a 150 bar e 40°C, com a presença de liquido iônico, em 2 horas de tempo reacional com um rendimento de 54,0% e um excesso enantiomérico de 79,0% utilizando o catalisador (2S,4R)-4-(terc-butildimetilsililoxi)pirrolidina-2-ácido carboxílico. Com ciclohexanona como material de partida foram obtidos a 150 bar e 40°C com a presença de um doador de prótons (resina de troca iônica) em 2 horas de tempo reacional com um rendimento de 70,9% e um excesso enantiomérico de 91,2%, utilizando o catalisador (2S,4R)-4-(terc-butildimetilsililoxi)pirrolidina-2-ácido carboxílico. Outros aldeídos e cetonas utilizados como materiais de partida apresentaram rendimentos menores. Estudos de comportamento de fases foram feitos para os materiais de partida, catalisadores e produtos da reação de condensação Aldólica. Os melhores rendimentos foram obtidos em situações em que os materiais de partida e os catalisadores eram solúveis na fase supercrítica, mas os produtos não, formando uma segunda fase. / Supercritical carbon dioxide (sc-CO2) has attracted considerable interest in the last years as a new solvent for organic reactions. In this thesis, the influence of supercritical CO2 use, associated or not to ionic liquids or cosolvents, as a solvent for chemical reactions aiming at the synthesis of chiral precursors was studied. Aldol condensation, Morita-Baylis-Hillman (MBH) and Michael addition reactions were studied, employing organocatalysis when it was convenient, i.e., catalysts derived from aminoacids or carboxylic acids. MBH reactions were optimized through experimental design, resulting in a maximum yield of 84.6% for the optimal condition at 70°C, 110 bar, and 6 equivalents of H2O, reaction time of 2h30 min and the absence of ionic liquids. For the Aldol condensation reactions employing acetone and p-nitrobenzaldehyde, a maximum yield of 54.0%, with an enantiomeric excess of 79.0% was obtained at 150 bar, 40°C, 2h reaction time, in the presence of ionic liquid, using the catalyst (2S,4R)-4-(terc-butyldimethylsililoxy)pirrolidine-2-carboxylic acid. The yields were significantly lower for other aldehydes and ketones. Yields for Michael addition reactions were very low and their study was discontinued. Phase behavior studies were performed with starting materials, catalysts and products for the Aldol condensation reactions. The best yields were obtained for situations where the starting materials and catalysts were soluble in the supercritical phase and the products were not, forming a second phase.

Les réactions de métathèse sont des méthodes performantes pour la création de doubles liaisons carbone-carbone et leurs popularités s’expliquent par l’accessibilité des catalyseurs nécessaires à celles-ci et par la facilité de mise en oeuvre de ces réactions. Elles ont par ailleurs trouvé de nombreuses applications dans la synthèse de molécules naturelles.Les aurisides A et B sont des molécules naturelles d’origine marine isolées du lièvre des mers Dolabella Auricularia en 1996. Ces macrolides présentent une activité cytotoxique intéressante contre des lignées de cellules cancéreuses HeLaS3 avec des valeurs d’IC50 de 0,17 et 1,2 μg/mLrespectivement.Nous avons dans un premier temps développé une voie d’accès au fragment C1-C9 des composés naturels en se basant sur la réaction de métathèse croisée des oléfines. Une étude sur le mode formation de la structure macrocylique par un processus séquentiel impliquant une réaction demétathèse cyclisante et une cétalisation transannulaire a ensuite été conduite sur des composés modèles permettant l’obtention de macrolactones analogues. Cette méthodologie a ensuite été appliquée à la synthèse stéréocontrôlée du squelette carboné des aurisides seulement dépourvu de sa chaîne latérale attaché sur l’atome de carbone C13.Enfin la réaction de métathèse croisée a également été exploitée dans un processus tandem avec celle d’hydrogénation pour la synthèse énantiosélective du 6-hydroxydodécanoate de pentadécyle,composant principal de l’huile essentiel Ylang-Ylang, et qui est également utilisé en médecine traditionnelle contre le choléra. / Metatheses are very useful synthetic tool for the formation of carbon-carbon bonds and their popularityis due to the facile access of the required catalyst for those reactions and also to the ease to performthem. So far, these reactions have found many for the total synthesis of natural products.The aurisides A and B are natural products and have been isolated from the sea hare Dolabella Auricularia in 1996. These macrolides have shown significant cytotoxicity with IC50 values againstHeLaS3 cervical cancer cells of 0.17 and 1.2 μg/mL respectively.We have first developed an access to the C1-C9 fragment of these compounds using the crossmetathesis reaction as a key step. A study for the formation of the macrocyclic core of the aurisides,using a sequential ring closing metathesis / transannular ketalization process was then developed. Thismethodology was first performed on unfonctionnalized substrates and allowed the synthesis ofmacrolactone analogs. It was then further applied on a stereocontrolled synthesis of the aurisideswithout the side chain attached on carbon C13.Finally, the cross metathesis reaction was also combined in a tandem process with a hydrogenation reaction for the enantioselective synthesis of pentadecyl-6-hydroxydodecanoate, the major componentof essantial oil Ylang-Ylang, and is also used in traditional medical treatment against cholera.

Résumé anglais uniquement / Nowadays there is an urgent need to develop green chemical processes, where the use and generation of toxic substances can be avoided. Indeed, the lignocellulose feedstock destructuration will produce aqueous solutions of ketones or aldehydes and it would be an important breakthrough to develop solid base catalysts capable to promote the aldol condensation. In this thesis, the main results are shown as follows: Magnesium and rare earth mixed oxides (MgReOx), rare earth modified MgAl-HT catalyst were prepared and were evaluated in liquid phase acetone self-aldolization. Rare earth modified MgAl catalysts show enhanced catalystic activity than MgReOx catalysts. Rehydrated MgAl-HT modified with Y and La, also present a higher water tolerance for aldol reaction. The same catalysts were also applied to acetone gas phase self-condensation reaction. At low temperature, the mesityl oxide is the main product for all the catalysts. At high temperatures, deactivation rate is lowered over MgAlCe(Y)O catalysts, and the presence of trimers (selectivity of IP over 50%) is much more noticeable for the MgAlY(Ce)O catalysts. A good balance between basicity and acidity is proposed to increase the selectivity of IP. In the cross condensation of citral and acetone, the citral conversion and pseudoionone yield were significantly enhanced over Mg3AlaY1-aOx catalysts. A general mechanism of reaction was proposed that the Y modified MgAl mixed oxides undergoes the rehydration by the water formed during the reaction, and the rehydrated catalysts with active Brønsted basic sites are responsible for the significantly improvement of catalytic activity

Ce travail de thèse se focalise sur l'impact des propriétés acido-basiques des catalyseurs (quantité et force des sites) dans la production d’acroléine par couplage oxydant d’alcools en phase gazeuse. L'influence du rapport entre site acides et sites basiques des catalyseurs a été étudiée dans la condensation aldolique de l'acétaldéhyde et du formaldéhyde en acroléine, réalisée en conditions oxydantes. Les données et corrélations obtenues ont donné des informations indispensables à l’identification des paramètres qui doivent être modifiés afin d'améliorer la sélectivité en acroléine. La première réaction du procédé implique l'oxydation du méthanol et de l'éthanol respectivement en formaldéhyde et acétaldéhyde sur un catalyseur rédox de type FeMoOx.Ensuite, l'aldolisation croisée des deux aldéhydes et la déshydratation en acroléine sont effectuées sur des catalyseurs acido-basiques.Les alcools impliqués dans ce procédé pouvant dériver de la biomasse, cette nouvelle voie de production d'acroléine présente un intérêt élevé puisqu'elle peut remplacer la production actuelle d'acroléine basée sur des ressources fossiles (aujourd'hui l’acroléine est produite industriellement par oxydation du propylène).Le catalyseur optimal doit présenter des caractéristiques amphotères avec une quantité similaire de sites basiques et acides. Une présence modérée et équilibrée de sites acides et basiques améliore le rendement en acroléine et déplace à plus haute température la production des oxydes de carbone. Parmi tous les catalyseurs étudiés, et grâce à ses propriétés acido-basiques spécifiques, MgO supporté sur silice a été identifié comme étant le meilleur catalyseur pour la condensation aldolique des aldéhydes en acroléine en conditions oxydantes / The present work focuses on the impact of the amount and strength of acidic and/or basic sites on the yield of acrolein produced by alcohols oxidative coupling in gas phase. The influence of acid/base ratio of catalytic sites has been studied in the aldol condensation of acetaldehyde and formaldehyde to acrolein performed in oxidizing conditions. The obtained data and correlations supplied valuable information to understand which parameters have to be modified to improve the acrolein selectivity. The first reaction of the process implies methanol and ethanol oxidation respectively to formaldehyde and acetaldehyde on a FeMoOx redox catalyst. Then the cross-aldolization of the two aldehydes and the dehydration to acrolein is performed on acid/base catalysts. Because the alcohols involved in this process can be bio-sourced, this new route to produce acrolein presents a very high interest, since it can replace the current fossil-based acrolein production (nowadays industrially produced by oxidation of propylene). The optimal catalyst should present amphoteric features with a similar amount of both basic and acidic sites. A moderate and balanced presence of acidic and basic sites improves the acrolein yield and the production of carbon oxides is significantly increased only at high temperature. Among all studied catalysts, MgO supported on silica has been identified as the best catalyst for aldol-condensation of aldehydes to acrolein in oxidizing conditions thanks to a given ratio of basic to acidic sites

Les fructose-1,6-bisphosphate aldolases (FBPA) sont des enzymes glycolytiques (EC 4.1.2.13) qui catalysent la transformation réversible du fructose-1,6-bisphosphate (FBP) en deux trioses-phosphates, le glycéraldéhyde-3-phosphate (G3P) et le dihydroxyacétone phosphate (DHAP). Il existe deux classes de FBPA qui diffèrent au niveau de leur mécanisme catalytique. Les classes I passent par la formation d’un intermédiaire covalent de type iminium alors que les classes II, métallodépendantes, utilisent généralement un zinc catalytique. Contrairement au mécanisme des classes I qui a été très étudié, de nombreuses interrogations subsistent au sujet de celui des classes II. Nous avons donc entrepris une analyse détaillée de leur mécanisme réactionnel en nous basant principalement sur la résolution de structures cristallographiques. De nombreux complexes à haute résolution furent obtenus et ont permis de détailler le rôle de plusieurs résidus du site actif de l’enzyme. Nous avons ainsi corrigé l’identification du résidu responsable de l’abstraction du proton de l’O4 du FBP, une étape cruciale du mécanisme. Ce rôle, faussement attribué à l’Asp82 (chez Helicobacter pylori), est en fait rempli par l’His180, un des résidus coordonant le zinc. L’Asp82 n’en demeure pas moins essentiel car il oriente, active et stabilise les substrats. Enfin, notre étude met en évidence le caractère dynamique de notre enzyme dont la catalyse nécessite la relocalisation du zinc et de nombreux résidus. La dynamique de la protéine ne permet pas d’étudier tous les aspects du mécanisme uniquement par l’approche cristallographique. En particulier, le résidu effectuant le transfert stéréospécifique du proton pro(S) sur le carbone 3 (C3) du DHAP est situé sur une boucle qui n’est visible dans aucune de nos structures. Nous avons donc développé un protocole de dynamique moléculaire afin d’étudier sa dynamique. Validé par l’étude d’inhibiteurs de la classe I, l’application de notre protocole aux FBPA de classe II a confirmé l’identification du résidu responsable de cette abstraction chez Escherichia coli (Glu182) mais pointe vers un résidu diffèrent chez H. pylori (Glu149 au lieu de Glu142). Nos validations expérimentales confirment ces observations et seront consolidées dans le futur. Les FBPA de classe II sont absentes du protéome humain mais sont retrouvées chez de nombreux pathogènes, pouvant même s'y révéler essentielles. Elles apparaissent donc comme étant une cible idéale pour le développement de nouveaux agents anti-microbiens. L’obtention de nouveaux analogues des substrats pour ces enzymes a donc un double intérêt, obtenir de nouveaux outils d’étude du mécanisme mais aussi développer des molécules à visée pharmacologique. En collaboration avec un groupe de chimistes, nous avons optimisé le seul inhibiteur connu des FBPA de classe II. Les composés obtenus, à la fois plus spécifiques et plus puissants, permettent d’envisager une utilisation pharmacologique. En somme, c’est par l’utilisation de techniques complémentaires que de nouveaux détails moléculaires de la catalyse des FBPA de classe II ont pu être étudiés. Ces techniques permettront d’approfondir la compréhension fine du mécanisme catalytique de l’enzyme et offrent aussi de nouvelles perspectives thérapeutiques. / Fructose-1,6-bisphosphate aldolases (FBPA) are glycolytic enzymes (EC 4.1.2.13) that catalyze the reversible cleavage of fructose-1,6-bisphosphate (FBP) into the triose phosphates, glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP). There are two classes of FBPAs that differ at the level of their mechanism. Class I FBPAs form a covalent iminium intermediate whereas class II FBPAs, being metalloenzymes, generally use a catalytic zinc in their reaction mechanism. In contrast to the mechanism of the class I FBPAs, which has been thoroughly studied, there are several unresolved inquiries as to the mechanism of class II FBPAs. We have therefore pursued a detailed analysis of the reaction mechanism using as a primary tool the elucidation of crystallographic structures. Several high resolution complexes have been resolved and have provided critical evidence to help us suggest the implication and role of several key residues in the active site. Consequently, we have correctly identified the residue which is responsible for the abstraction of the O4 proton from FBP, a vital step in the reaction mechanism. The residue responsible for this abstraction, which had incorrectly been assigned to Asp82 (in Helicobacter pylori), has been appropriately consigned to His180, a residue which is involved in coordinating the zinc molecule. Nevertheless, Asp82 remains an important residue as it orients, activates and stabilizes substrates. Finally, our study brings to evidence the dynamic character of our enzyme in which catalysis entails the relocalization of the catalytic zinc and several residues. The complexity of this reaction, notably one of the proton exchanges in the mechanism, could not be resolved solely by crystallographic means. In fact, the residue responsible for the stereospecific transfer of the pro(S) proton on carbon 3 (C3) of DHAP is situated on a loop that was not resolved in any of our structures. We therefore developed a molecular dynamics approach to study this intricate movement. After preliminary validation by inhibitor studies with class I FBPAs, the protocol was applied to class II FBPAs and several remarkable observations emerged: the residue responsible for this abstraction in Escherichia coli is Glu182 whereas a different residue, Glu149 (instead of Glu142) appears to assume this role in H. pylori. Our preliminary validations have confirmed this observation and shall be further consolidated in the future. Class II FBP aldolases, although absent from the human proteome, are prevalently found in several pathogens, and have further been found to be essential to a number of these organisms. As such, they are ideal targets for the development of novel anti-microbial agents. Developing new analogues of the cognate substrates of these enzymes is therefore not only advantageous for mechanistic studies, but has endless pharmacological potential. In the context of a collaborative effort involving a group of chemists, a compound that initially had an inhibition constant in the millimolar range was optimized and produced a series of compounds that inhibit in the nanomolar range.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

La tagatose-1,6-biphosphate aldolase de Streptococcus pyogenes est une aldolase qui fait preuve d'un remarquable manque de spécificité vis à vis de ses substrats. En effet, elle catalyse le clivage réversible du tagatose-1,6-bisphosphate (TBP), mais également du fructose-1,6-bisphosphate (FBP), du sorbose-1,6-bisphosphate et du psicose-1,6-bisphosphate, quatre stéréoisomères, en dihydroxyacétone phosphate (DHAP) et en glycéraldéhyde-3-phosphate (G3P). Aldolase de classe I, qui donc catalyse sa réaction en formant un intermédiaire covalent obligatoire, ou base de Schiff, avec son susbtrat, la TBP aldolase de S. pyogenes partage 14 % d’identité avec l’enzyme modèle de cette famille, la FBP aldolase de muscle de mammifère. Bien que le mécanime catalytique de la FBP aldolase des mammifères ait été examiné en détails et qu’il soit approprié d’en tirer des renseignements quant à celui de la TBP aldolase, le manque singulier de stéréospécificité de cette dernière tant dans le sens du clivage que celui de la condensation n’est toujours pas éclairci. Afin de mettre à jour les caractéristiques du mécanisme enzymatique, une étude structurale de la TBP aldolase de S. pyogenes, un pathogène humain extrêmement versatile, a été entreprise. Elle a permis la résolution des structures de l’enzyme native et mutée, en complexe avec des subtrats et des inhibiteurs compétitifs, à des résolutions comprises entre 1.8 Å et 2.5 Å. Le trempage des cristaux de TBP aldolase native et mutante dans une solution saturante de FBP ou TBP a en outre permis de piéger un authentique intermédiaire covalent lié à la Lys205, la lysine catalytique. La determination des profils pH de la TBP aldolase native et mutée, entreprise afin d'évaluer l’influence du pH sur la réaction de clivage du FBP et TBP et ìdentifier le(s) résidu(s) impliqué(s), en conjonction avec les données structurales apportées par la cristallographie, ont permis d’identifier sans équivoque Glu163 comme résidu responsable du clivage. En effet, le mode de liaison sensiblement différent des ligands utilisés selon la stéréochimie en leur C3 et C4 permet à Glu163, équivalent à Glu187 dans la FBP aldolase de classe I, d’abstraire le proton sur l’hydroxyle du C4 et ainsi d’amorcer le clivage du lien C3-C4. L’étude du mécanimse inverse, celui de la condensation, grâce par exemple à la structure de l’enzyme native en complexe avec ses substrats à trois carbones le DHAP et le G3P, a en outre permis d’identifier un isomérisme du substrat G3P comme possible cause de la synthèse des isomères en C4 par cette enzyme. Ce résultat, ainsi que la decouverte d’un possible isomérisme cis-trans autour du lien C2-C3 de la base de Schiff formée avec le DHAP, identifié précedemment, permet de cerner presque complètement les particularités du mécanisme de cette enzyme et d’expliquer comment elle est capable de synthétiser les quatres stéréoisomères 3(S/R), 4(S/R). De plus, la résolution de ces structures a permis de mettre en évidence trois régions très mobiles de la protéine, ce qui pourrait être relié au rôle postulé de son isozyme chez S. pyogenes dans la régulation de l’expression génétique et de la virulence de la bactérie. Enfin, la résolution de la structure du mutant Lys229→Met de la FBP aldolase de muscle en complexe avec la forme cyclique du FBP, de même que des études cristallographiques sur le mutant équivalent Lys205→Met de la TBP aldolase de S. pyogenes et des expériences de calorimétrie ont permis d’identifier deux résidus particuliers, Ala31 et Asp33 chez la FBP aldolase, comme possible cause de la discrimination de cette enzyme contre les substrats 3(R) et 4(S), et ce par encombrement stérique des substrats cycliques. La cristallographie par rayons X et la cinétique enzymatique ont ainsi permis d'avancer dans l'élucidation du mécanisme et des propriétés structurales de cette enzyme aux caractéristiques particulières. / Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes is a class I aldolase that shows a lack of stereospecificity that is rare in enzymes in general, and in aldolases in particular. This aldolase catalyzes the reversible cleavage of tagatose-1,6-bisphosphate (TBP), fructose-1,6-bisphosphate (FBP), sorbose-1,6-bisphosphate and psicose-1,6-bisphosphate, four stereoisomers, in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P). A class I aldolase, the aldolase TBP S. pyogenes shares 14 % identity with the model enzyme of this family, mammalian FBP aldolase. Although the catalytic mechanism of the class I FBP aldolase has been examined in detail and it is appropriate to infer information as to the class I TBP aldolase, the singular lack of specificity of the latter enzyme both in the direction of cleavage and condensation is still not elucidated. To better comprehend the characteristics of the enzymatic mechanism, a structural study of the TBP aldolase of S. pyogenes, an extremely versatile human pathogen, has been undertaken. It has allowed the resolution of high resolution structures of the native and mutated enzyme in complex with subtrates and competitive inhibitors. These same structures allowed us to gain information as to the active site of the enzyme in general and the catalytic residues in particular. TBP aldolase native and mutated soaked in a saturated solution of FBP or TBP also trapped an iminium intermediate covalenty bound to Lys205, the Schiff base-forming lysine. The determination of the pH profiles of the native and mutated enzyme, carried out to assess the influence of pH on FBP and TBP cleavage and identify the residue(s) involved, in conjunction with the structural data provided by crystallography, identified unequivocally Glu163, corresponding to Glu187 in FBP aldolase, as the residue responsible for substrate cleavage. The substantially different binding mode of the ligands, according to the stereochemistry of their C3 and C4 carbons, indeed allows Glu163 to abstract the proton in C3-OH and thus initiate C3-C4 bond cleavage. The study of the inverse mechanism, the condensation one, using for instance the crystallographic structure of native TBP aldolase in complex with DHAP and G3P, its three carbons substrates, has led us to believe that a possible isomerism of the G3P substrate was the reason for the synthesis of both C4 isomers by this enzyme. This result, as well as the discovery of a possible cis-trans isomerism around the C2-C3 bond of the Schiff base formed with DHAP, identified previously, almost completely elucidated the features of this enzyme`s mechanism. In addition, these structures have highlighted three highly mobile regions of the protein, which may be related to the role of its isozyme in the regulation of gene expression and virulence in S. pyogenes. Lastly, the resolution of the structure of the FBP aldolase mutant Lys229 → Met in complex with the cyclic form of FBP, as well as crystallographic studies of the corresponding mutant in TBP aldolase, Lys205→Met and ITC experiments, allowed the identification of two particular residues, Ala31 and Asp33 in FBP aldolase, as responsible for this enzyme discrimination against 3(R) 4(S) substrates, by steric hindrance of the cyclic substrates. X-ray crystallography, enzyme kinetics and isothermal calorimetry thus enabled advances in the elucidation of the mechanism and structural properties of this enzyme with singular characteristics.