La phophomannose isomérase de type I (PMI), une métalloenzyme à zinc, et la phosphoglucose isomérase (PGI), catalysent l’isomérisation réversible du β-D-fructose-6-phosphate (F6P), respectivement en β-D-mannose-6-phosphate (M6P) et en α-D-glucose-6-phosphate (G6P). Ces deux enzymes sont des cibles thérapeutiques potentielles. La phosphoglucose isomérase humaine (hPGI), connu également sous le nom de facteur de motilité autocrine (AMF), stimule, en plus de son activité glycolytique intracellulaire, la migration des cellules in vitro et le développement de métastases in vivo. D'autre part, Candida albicans est la principale levure impliquée en pathologie humaine. Ces dernières années, un problème de résistance du germe aux antifongiques classiques est apparu. En conséquence, la recherche se dirige vers de nouvelles cibles thérapeutiques, dont la PMI de C. albicans (CaPMI) qui joue un rôle important dans la biosynthèse de structures mannosylées nécessaires à la survie du pathogène. Les réactions catalysées par ces deux enzymes mettent en jeu le même intermédiaire de haute énergie (IHE) de type 1,2-cis-ènediolate, sauf qu’il est coordiné au zinc dans le cas de la PMI. La surexpression ainsi que la purification de CaPMI et de hPGI ont été réalisées au laboratoire. Une petite chimiothèque a été créée à partir du 5-phospho-D-arabinono-1,4-lactone (5-PAL) en modulant la partie tête de l’IHE. Un groupe chélatant du zinc (zinc binding group, ZBG) a été introduit dans plusieurs composés dans le but d’inhiber sélectivement CaPMI. De plus, deux composés possédant en partie tête une fonction amine terminale ont été synthétisés pour inhiber spécifiquement la PGI humaine en ciblant un résidu glutamate du site actif de l'enzyme (Glu357). Toutes ces molécules ont d’abord été testées sur la PGI du muscle de lapin et la PMI de E. coli commerciales, et par la suite sur la CaPMI et la hPGI surexprimées. Une série de bons voire très bons inhibiteurs de hPGI, et donc potentiellement anti-métastatiques, a été découverte. Ces composés ne sont cependant pas inhibiteurs de la CaPMI. Deux structures tridimensionnelles à haute résolution de complexes enzyme-inhibiteur ont été obtenues. Au delà des aspects thérapeutiques, mécanistiques et structuraux, un biocapteur électrochimique à base d'un des inhibiteurs synthétisés a été réalisé pour la détection de hPGI qui est un biomarqueur validé de cancers métastatiques. Ce biocapteur a démontré une limite de détection de 43 fM dans du tampon phosphate (PBS). / Phosphoglucose isomerase (PGI) and type I phosphomannose isomerase (PMI), a zinc metalloenzyme, catalyze the reversible isomerization of β-D-fructose 6-phosphate (F6P) to α-D-glucose 6-phosphate (G6P) and β-D-mannose 6-phosphate (M6P), respectively. These two enzymes are potential therapeutic targets. Human PGI (hPGI) often called as AMF-PGI (autocrine motility factor-PGI), in addition to its intracellular glycolytic activity, stimulates cell migration in vitro and metastasis in vivo. Inhibition of its extracellular activity is obviously interesting in oncology. On the other hand, Candida albicans is the main yeast involved in human pathology. During recent years, resistance of this pathogenic fungus to conventional antifungal drugs appeared. Consequently, research is moving towards new therapeutic targets, including C. albicans PMI (CaPMI) that plays an important role in the biosynthesis of mannosylated structures required for pathogen survival. The reactions catalyzed by these two enzymes involve the same high energy intermediate (HEI) type 1,2-cis-enediolate, except that it is coordinated to the zinc active site in the case of PMI. Overexpression and purification of both CaPMI and hPGI were performed in our laboratory. A small chemical library was created from the synthon 5-phospho-D-arabinono-1,4-lactone (5-PAL) by modulating the head part of the HEI. A zinc binding group (ZBG) was introduced in several compounds in order to selectively inhibit the CaPMI enzyme. Moreover, two compounds with a terminal amine function were designed to selectively inhibit hPGI by targeting a glutamate residue of the enzyme (Glu357). All these molecules were first tested on rabbit muscle PGI and PMI from E. coli, and later on CaPMI and hPGI. None of these compounds are good inhibitors of CaPMI. However, a series of strong inhibitors of hPGI, and therefore potentially anti-metastatic drugs, was discovered. High-resolved 3D structures of the two enzymes complexed with inhibitors have been successfully obtained. Beyond the therapeutic, mechanistic and structural aspects, an electrochemical biosensor based on one of the synthesized inhibitors was carried out for the detection of hPGI, which is a validated biomarker of metastatic cancers. This biosensor demonstrated a detection limit of 43 fM in phosphate buffer (PBS).

No description available.

Les anticorps catalytiques (ou abzyme) ont fait l’objet de nombreuses recherches et ont été produits pour réaliser de nombreuses réactions. Ces protéines ont été ensuite découvertes dans le sérum d’individus sains ou atteints de pathologies, dont les pathologies autoimmunes. Les études suggèrent que ces abzymes peuvent avoir des effets bénéfiques ou délétères sur la santé des individus. L’origine des anticorps catalytiques et leur rôle restent ambigus et doivent être approfondis. Nous avons développé une nouvelle stratégie visant à étudier les abzymes, basée sur la technologie du phage display. Nous avons construit 4 banques de fragments d’anticorps, chacune présentant un répertoire immun différent (fond génétique et état d’immunitaire) : saine et naïve, saine et immunisée, autoimmune et naïve, et autoimmune et immunisée. Les stratégies d’amplification et de clonage des régions variables des immunoglobulines ont été conçues afin d’optimiser la taille et la diversité des banques. Nous avons rassemblé les 4 banques en une banque unique élargie contenant 2.7×109 séquences. L’analyse des séquences a mis en évidence des différences dans les profils d’expression des sous-groupes de gènes selon la banque. Nous avons ensuite procédé à la sélection d’abzymes à activité β-lactamase en utilisant deux cibles : un peptide cyclique, et un dérivé de sulfone pénam, inhibiteurs de l’enzyme. Nous avons sélectionné 5 abzymes. Chacun de ces immunoglobulines ont des séquences protéiques propres, incluant un potentiel site actif. Ces résultats montrent que différents motifs peuvent assurer la fonction catalytique de la β-lactamase, confirmant la flexibilité moléculaire de cette enzyme. / Catalytic antibodies (or abzymes) have been the focus numerous studies for some decades and have been produced with the ability to catalyze a wide range of reactions. They have also been discovered naturally in normal physiological and pathological conditions, notably on the background of autoimmune disease. Some have beneficial effects and others are detrimental to individual’s health. Hence, the origin of abzymes and their role in the immune response are ambiguous and must be enhanced. We have developed a novel strategy for the study of abzymes based on the phage display technology. We have constructed 4 libraries representing 4 murine immune repertoires with different genetic backgrounds and immunological states : healthy and naïve, healthy and immunized, autoimmune and naïve , and autoimmune and immunized. The strategies for the amplification and cloning of the immunoglobulin (lg) variable regions have been designed to optimize the size and diversity of the libraries. We have been able to pool the four libraries to create a large repertoire of size 2.7x109. After sequence analysis, we have found a number of statistically significant differences between the libraries. We have then used two strategically chosen targets to select for antibodies endowed with β lactamase activity : a cycle peptide and a penam sulfone, both inhibitors of the enzyme. We have selected for a total of 5 lgs endowed with β lactamase activity. The selected abzymes have different amino acid sequences. 3D modeling has provides insights on potential active sites demonstrating the ability of different structures to maintain the β lactamase activity and confirming the flexibility of the active site.

Le pore de transition de perméabilité mitochondriale (PTPm) joue un rôle majeur dans la mort cellulaire et dans la cardioprotection. Notre hypothèse est que le complexe I de la chaîne respiratoire est impliqué dans la régulation de l’ouverture du PTPm. Sur des mitochondries isolées de cœurs des rongeurs, nous avons pu démontrer que le PTPm est désensibilisé par la cyclosporine A, un inhibiteur de la cyclophiline D (CyP-D), et cet effet est largement amplifié en présence de la roténone, un inhibiteur du complexe I. Ces résultats ont été confirmés chez la souris CyP-D déficiente. L’étude de plusieurs types cellulaires a aussi confirmé l’effet de la roténone dans la régulation du PTPm. Ainsi, nous avons pu montrer que le flux d’électrons travers le complexe I est capable de réagir sur un site de régulation du PTPm cardiaque masqué par la CyP-D. De plus, les analogues de l’ubiquinone, élément de la chaîne respiratoire impliqué dans le transfert d’électrons entre les complexes I, II et III, modulent la susceptibilité du PTPm vis-à-vis du Ca2+. Par ailleurs, dans un modèle de cœur isolé du rat, le postconditionnement par le perindoprilate, un inhibiteur de l’enzyme de conversion, diminue la taille de l’infarctus après l’ischémie-reperfusion d’une façon NO-dépendant. L’ensemble de nos résultats ouvre de nouvelles perspectives thérapeutiques dans la cardioprotection et montre l’importance du complexe I et de la CyP-D comme cibles moléculaires incontournables dans la cardioprotection / The mitochondrial permeability transition pore (mPTP) plays an important role in cell death and cardioprotection. Our hypothesis is that the complex I of mitochondrial respiratory chain regulates the opening of mPTP. We showed that the opening of mPTP was inhibited by Cyclosporin A (CsA), a cyclophilin D (CyP-D) inhibitor, in mitochondria isolated from rodent heart, and this effect was largely amplified by rotenone, a complex I inhibitor. These results were confirmed in mitochondria devoid of CyP-D. A study realised in several cell lines also confirmed the effect of rotenone in mPTP regulation. We concluded that the electron flow through the respiratory chain complex I regulate mPTP opening and the regulatory site is masked by CyP-D in cardiac mitochondria. Moreover, two analogues of ubiquinone, mobile carrier of electrons between complex I, II and complex III, modulate the susceptibility of mPTP. In addition, in a model of isolated rat heart, postconditioning with Perindoprilat, an angiotensin converting enzyme inhibitor, protects the heart from ischemia-reperfusion injury in an NO-dependant manner. The findings of the present work put new therapic perspectives in cardioprotection

La diffraction des rayons X permet d’obtenir des informations sur la structure atomique et même sur la distribution de charges de composés sous forme cristalline, ce qui est d’une importance fondamentale pour la compréhension de leurs propriétés. Accéder expérimentalement à une description de la distribution de charges de systèmes macromoléculaires reste rarement possible malgré les améliorations techniques. Pour pallier cette limite, la transférabilité des paramètres de distributions de charges est un moyen fiable d’obtenir pour ces systèmes un modèle estimé et d’en déduire leurs propriétés électrostatiques. Les résultats présentés dans ce travail de thèse s’intègrent dans une dynamique visant à étendre les méthodes initialement réservées pour l’étude des petites molécules aux systèmes macromoléculaires. Il s’articule autour du développement de la suite de logiciels MoPro et de la banque de données ELMAM (Experimental Library of Multipolar Atom Model) pour l’étude des énergies des interactions électrostatiques au sein du site actif de complexes enzyme-inhibiteur. L’étude du fidarestat, un inhibiteur de l’holoenzyme aldose réductase, réalisée à partir de données obtenues à très haute résolution, est exposée dans ce manuscrit et a servi notamment à l’amélioration de la banque ELMAM en vue de l’étude des complexes holoenzymes aldo-keto réductase. A cette occasion, la légitimité du recours aux modèles transférés de distribution de charges a été discutée pour la première fois par une estimation statistique des incertitudes sur les énergies d’interaction électrostatique entre enzyme et inhibiteur / X-ray diffraction allows to obtain information about atomic structure and charge density distribution of crystal-state compounds, which is of main interest for the understanding of their properties. Reaching experimentally charge density distribution description of macromolecular systems is rarely possible despite technical improvements. To get around this limit, the transferability of charge density distribution parameters is a reliable way to obtain for these systems estimated model and to deduce their electrostatic properties. Works introduced in this PhD thesis manuscript take part in the will of extending methods initially for study of small molecules to macromolecular systems. It is centered on the development of the MoPro software suite and of ELMAM database (Experimental Library of Multipolar Atom Model) for the study of electrostatic interaction energies in enzyme-inhibitor complexes’ active site. The study of fidarestat, an inhibitor of aldose reductase holoenzyme, performed using ultra-high resolution data, is exposed in this manuscript and allowed to improve ELMAM database for the study of electrostatic interaction in aldo-keto reductase holoenzyme complexes. Moreover, the legitimacy of using transferred charge density distribution models was discussed for the first time, thanks to statistical estimation of uncertainties on electrostatic interaction energies between enzyme and inhibitor

A doença de Chagas, causada pelo protozoário flagelado Trypanosoma cruzi, é uma doença tropical que enseja morte/morbidade de milhões de pessoas na América Latina. Por processos migratórios, vem-se estendendo ao sul dos Estados Unidos, Canadá, Europa, Austrália e Japão. Essa doença tem sido considerada super-negligenciada pela indústria farmacêutica, já que os dois fármacos disponíveis para o seu tratamento foram introduzidos há mais de quarenta anos e apresentam baixa eficácia com vários efeitos colaterais severos. Mais recentemente, a Organização Mundial da Saúde considerou a doença de Chagas, dentre outras, como a doença da pobreza! Com esse cenário completamente desfavorável aos portadores da doença, é necessária a descoberta, desenvolvimento e introdução de novos fármacos para o tratamento eficiente e seguro da doença de Chagas. <br />Dentro desse contexto, este trabalho representa uma importante contribuição para o entendimento das razões moleculares da ação farmacológica de substâncias químicas bioativas de interesse à farmacoterapia da doença de Chagas. Ao nível molecular, a enzima pertencente à via de síntese de novo de nucleotídeos de pirimidinas, diidroorotato desidrogenase do Trypanosoma cruzi (TcDHODH), é um alvo promissor para a descoberta e desenvolvimento de candidatos a fármacos de interesse para o tratamento da doença de Chagas. <br />Os conceitos e ferramentas da química medicinal computacional, tais como os ensaios virtuais in silico, foram usados para a identificação de inibidores da TcDHODH. Vinte e seis substâncias inéditas como inibidores da TcDHODH foram adquiridos comercialmente e avaliados experimentalmente através da Calorimetria de Titulação Isotérmica (ITC) para a determinação do mecanismo de inibição e da constante cinética de afinidade (Kiapp). <br />Na etapa de docagem molecular, o objetivo era identificar moléculas que apresentassem uma boa afinidade pelo sítio ativo da enzima TcDHODH. A primeira série de ligantes selecionados dos métodos in silico, apresentou inibição enzimática na concentração de micromolar com eficiência média de ligante de 0,50 kcal mol-1 átomo-1. Devido à baixa massa molecular (aproximadamente 200 kDa) e a alta eficiência de ligante, essa série foi considerada como constituída de excelentes substâncias com elevado poder de reconhecimento biomolecular. Por isso, foram caracterizadas como substâncias passíveis de otimização no processo do-ligante-para-substância matriz. <br />As enzimas TcDHODH e DHODH de Leishmania major (LmDHODH) têm sítios ativos com elevado grau de similaridade. Portanto, usando a enzima LmDHODH como padrão de substituição da TcDHODH é possível fazer a descrição do modo de interação do co-complexo TcDHODH-inibidor. O modo de ação descrito através da resolução da estrutura cristalográfica de raios-X, além de validar ortogonalmente os resultados cinéticos obtidos por ITC - que identificou as substâncias como inibidores competitivos (por interação direta no sítio ativo da enzima TcDHODH), geraram hipóteses farmacofóricas para a busca de novas moléculas (chamadas de segunda geração), agora com padrão superior de reconhecimento molecular do sítio da TcDHODH. Para validar complementarmente a hipótese, foi demonstrado que os inibidores da TcDHODH inibem, similarmente, a LmDHODH. <br />Uma análise cuidadosa da estrutura tridimensional da enzima TcDHODH, demostrou a possibilidade de ocupação do sítio S2 que se estende além da região do sítio catalítico S1, permitindo assim o aumento da afinidade biomolecular com os inibidores. Além disso, o sítio S2 não é encontrado na estrutura da proteína de humanos (HsDHODH), podendo ser uma região passível de seletividade frente à enzima TcDHODH. <br />O emprego adequado dessa hipótese resultou na otimização dos ligantes identificados previamente para substâncias mais potentes que inibiram a enzima de forma competitiva em relação ao substrato diidroorotato (DHO) em valores Kiapp de 121 &plusmn; 14 nM e 190 &plusmn; 10 nM. <br />A técnica de ITC foi fundamental no processo de descoberta de inibidores enzimáticos, pois se mostrou extremamente susceptível à determinação da interação intermolecular enzima-inibidor, permitindo acompanhar a cinética da reação e obter os valores da constante de afinidade de maneira precisa e acurada. Com isso, a taxa de acerto obtida nesta tese foi de 46%, considerando-se apenas as substâncias com valores de Ki app < 100 &micro;M. Esse é um número favoravelmente apreciável, já que na literatura ele gira em torno de 1-10% quando o planejamento in silico é realizado, quando comparado às taxas de acerto dos métodos de ensaio em larga escala (HTS), entre 0-2 %, os resultados alcançados neste trabalho são ainda mais significativos. <br />Além disso, as substâncias químicas selecionadas através da integração de métodos in silico e biocalorimétricos apresentam elevado grau de complexidade no processo biomolecular de interação enzima-ligante, que permite classificá-las para as fases seguintes da gênese planejada de fármacos. / American trypanosomiasis or Chagas disease, caused by the haemoflagellate Trypanosoma cruzi, is a tropical disease that affects millions of people in Latin America. Epidemiology of Chagas disease in non-endemic countries is attained by immigration as the disease also affects people in the United States, Canada, Europe, Australia and Japan. However, the United States are not to be written off as an area of nonendemicity for Chagas disease like Europe or Asia because the southern states have enzootic T. cruzi transmission that involves triatomine species and hosts such as raccoons, opossums, and domestic dogs. Even though, this disease has been considered as a super-neglected from the big Pharma Industry viewpoint since the only available drugs for its treatment were introduced in the market more than forty years ago and worsen is that they have low efficacy and cause various severe side effects. <br />Although the current clinical scenario is of course discouraging and is far from being even a soothing treatment for those who suffer from the disease, it prompt ones to set efforts towards the need of discovering and developing new efficacious and safe drugs to treat Chagas disease. <br />Our research group covers the concept of enzymes acting as targets for the action of drugs. Once T. cruzi has many druggable targets, the dihydroorotate dehydrogenase enzyme (TcDHODH) that belongs to the de novo pyrimidine nucleotide synthetic pathway has been chosen for the search of new inhibitors that may be of use in the treatment of Chagas disease. To accomplish with this and considering that inhibitors are molecules that decrease enzyme activity leading to parasite death, we used the concepts and tools of modern computational medicinal chemistry such as in silico screening of small molecules that bind to the active site of the TcDHODH. <br />After a thoroughly program of virtually screening thousands of compounds, 26 were purchased from commercially available sources and experimentally assayed against the TcDHODH using Isothermal Titration Calorimetry (ITC) in order to determine the mechanism of inhibition and the kinetic affinity constant (Kiapp). <br />The first series of inhibitors selected from our in silico strategy were evaluated by ITC to yield compounds that inhibited the TcDHODH in the micromolar concentration range with an average of 0.50 kcal mol-1 atom-1 ligand efficiency (LE). Because the assayed compounds have low molecular weight (ca. 200 kDa) and high LE, which bring them to the specific bimolecular pattern recognition all of them were considered good inhibitors capable of being selected to enter the hit-to-lead optimization process. <br />The detailed description of the ligand-enzyme mode of binding (MOB) is thoroughly accomplished by solving the X ray crystal structure of the surrogate Leishmania major DHODH enzyme (LmDHODH), which has a high degree of similarity with the enzyme TcDHODH. The MOB credited to be in the active site of the TcDHODH orthogonally validated the ITC kinetic experimental data obtained for all ligands as competitive inhibitors that interact at the active site of the TcDHODH and helped to generate pharmacophoric hypotheses for the search of new second generation molecules acting against the enzyme TcDHODH.  Analyzing the 3D structure of the TcDHODH along with its surrogate LmDHODH, we envisaged the possibility of compounds to extend their side chain beyond the region of the catalytic site (called S1), and interacting in a region called S2, so to increase binding affinity. Moreover, the TcDHODH S2 site that is not found in the 3D protein structure of humans (HsDHODH) is likely to offer new insights for the search of inhibitors whose binding to this S2 site can pave the roads towards the needed structural basis for selective inhibition of TcDHODH. <br />The most potent compounds inhibited the enzyme competitively with respect to the substrate dihydroorotate (DHO) at Kiapp values of 121 &plusmn; 14 nM and 190 &plusmn; 10 nM, which constitutes high affinity TcDHODH inhibitors. The ITC technique was pivotal to this process of enzyme inhibitors discovery, because it proved to be extremely sensitive thus allowing to monitor the kinetics of the reaction and to obtain precise and accurate values of affinity constants. <br />The hit rate obtained in this work, considering only those compounds with Kiapp < 100 &micro;M, was 46%. This is a really high number, since literature values range from 1 to 10% when the planning new inhibitors via in silico methods when compared to the success rates obtained by the methods of testing on large scales (HTS), 0-2 %, the results achieved in this work are even more significant. Moreover, the compounds selected through the integration of in silico and calorimetric methods showed a high degree of complexity in the process of bimolecular enzyme-ligand recognition, which allows to pass them to the next phase of the drug design process.

A doença de Chagas, causada pelo protozoário flagelado Trypanosoma cruzi, é uma doença tropical que enseja morte/morbidade de milhões de pessoas na América Latina. Por processos migratórios, vem-se estendendo ao sul dos Estados Unidos, Canadá, Europa, Austrália e Japão. Essa doença tem sido considerada super-negligenciada pela indústria farmacêutica, já que os dois fármacos disponíveis para o seu tratamento foram introduzidos há mais de quarenta anos e apresentam baixa eficácia com vários efeitos colaterais severos. Mais recentemente, a Organização Mundial da Saúde considerou a doença de Chagas, dentre outras, como a doença da pobreza! Com esse cenário completamente desfavorável aos portadores da doença, é necessária a descoberta, desenvolvimento e introdução de novos fármacos para o tratamento eficiente e seguro da doença de Chagas. <br />Dentro desse contexto, este trabalho representa uma importante contribuição para o entendimento das razões moleculares da ação farmacológica de substâncias químicas bioativas de interesse à farmacoterapia da doença de Chagas. Ao nível molecular, a enzima pertencente à via de síntese de novo de nucleotídeos de pirimidinas, diidroorotato desidrogenase do Trypanosoma cruzi (TcDHODH), é um alvo promissor para a descoberta e desenvolvimento de candidatos a fármacos de interesse para o tratamento da doença de Chagas. <br />Os conceitos e ferramentas da química medicinal computacional, tais como os ensaios virtuais in silico, foram usados para a identificação de inibidores da TcDHODH. Vinte e seis substâncias inéditas como inibidores da TcDHODH foram adquiridos comercialmente e avaliados experimentalmente através da Calorimetria de Titulação Isotérmica (ITC) para a determinação do mecanismo de inibição e da constante cinética de afinidade (Kiapp). <br />Na etapa de docagem molecular, o objetivo era identificar moléculas que apresentassem uma boa afinidade pelo sítio ativo da enzima TcDHODH. A primeira série de ligantes selecionados dos métodos in silico, apresentou inibição enzimática na concentração de micromolar com eficiência média de ligante de 0,50 kcal mol-1 átomo-1. Devido à baixa massa molecular (aproximadamente 200 kDa) e a alta eficiência de ligante, essa série foi considerada como constituída de excelentes substâncias com elevado poder de reconhecimento biomolecular. Por isso, foram caracterizadas como substâncias passíveis de otimização no processo do-ligante-para-substância matriz. <br />As enzimas TcDHODH e DHODH de Leishmania major (LmDHODH) têm sítios ativos com elevado grau de similaridade. Portanto, usando a enzima LmDHODH como padrão de substituição da TcDHODH é possível fazer a descrição do modo de interação do co-complexo TcDHODH-inibidor. O modo de ação descrito através da resolução da estrutura cristalográfica de raios-X, além de validar ortogonalmente os resultados cinéticos obtidos por ITC - que identificou as substâncias como inibidores competitivos (por interação direta no sítio ativo da enzima TcDHODH), geraram hipóteses farmacofóricas para a busca de novas moléculas (chamadas de segunda geração), agora com padrão superior de reconhecimento molecular do sítio da TcDHODH. Para validar complementarmente a hipótese, foi demonstrado que os inibidores da TcDHODH inibem, similarmente, a LmDHODH. <br />Uma análise cuidadosa da estrutura tridimensional da enzima TcDHODH, demostrou a possibilidade de ocupação do sítio S2 que se estende além da região do sítio catalítico S1, permitindo assim o aumento da afinidade biomolecular com os inibidores. Além disso, o sítio S2 não é encontrado na estrutura da proteína de humanos (HsDHODH), podendo ser uma região passível de seletividade frente à enzima TcDHODH. <br />O emprego adequado dessa hipótese resultou na otimização dos ligantes identificados previamente para substâncias mais potentes que inibiram a enzima de forma competitiva em relação ao substrato diidroorotato (DHO) em valores Kiapp de 121 &plusmn; 14 nM e 190 &plusmn; 10 nM. <br />A técnica de ITC foi fundamental no processo de descoberta de inibidores enzimáticos, pois se mostrou extremamente susceptível à determinação da interação intermolecular enzima-inibidor, permitindo acompanhar a cinética da reação e obter os valores da constante de afinidade de maneira precisa e acurada. Com isso, a taxa de acerto obtida nesta tese foi de 46%, considerando-se apenas as substâncias com valores de Ki app < 100 &micro;M. Esse é um número favoravelmente apreciável, já que na literatura ele gira em torno de 1-10% quando o planejamento in silico é realizado, quando comparado às taxas de acerto dos métodos de ensaio em larga escala (HTS), entre 0-2 %, os resultados alcançados neste trabalho são ainda mais significativos. <br />Além disso, as substâncias químicas selecionadas através da integração de métodos in silico e biocalorimétricos apresentam elevado grau de complexidade no processo biomolecular de interação enzima-ligante, que permite classificá-las para as fases seguintes da gênese planejada de fármacos. / American trypanosomiasis or Chagas disease, caused by the haemoflagellate Trypanosoma cruzi, is a tropical disease that affects millions of people in Latin America. Epidemiology of Chagas disease in non-endemic countries is attained by immigration as the disease also affects people in the United States, Canada, Europe, Australia and Japan. However, the United States are not to be written off as an area of nonendemicity for Chagas disease like Europe or Asia because the southern states have enzootic T. cruzi transmission that involves triatomine species and hosts such as raccoons, opossums, and domestic dogs. Even though, this disease has been considered as a super-neglected from the big Pharma Industry viewpoint since the only available drugs for its treatment were introduced in the market more than forty years ago and worsen is that they have low efficacy and cause various severe side effects. <br />Although the current clinical scenario is of course discouraging and is far from being even a soothing treatment for those who suffer from the disease, it prompt ones to set efforts towards the need of discovering and developing new efficacious and safe drugs to treat Chagas disease. <br />Our research group covers the concept of enzymes acting as targets for the action of drugs. Once T. cruzi has many druggable targets, the dihydroorotate dehydrogenase enzyme (TcDHODH) that belongs to the de novo pyrimidine nucleotide synthetic pathway has been chosen for the search of new inhibitors that may be of use in the treatment of Chagas disease. To accomplish with this and considering that inhibitors are molecules that decrease enzyme activity leading to parasite death, we used the concepts and tools of modern computational medicinal chemistry such as in silico screening of small molecules that bind to the active site of the TcDHODH. <br />After a thoroughly program of virtually screening thousands of compounds, 26 were purchased from commercially available sources and experimentally assayed against the TcDHODH using Isothermal Titration Calorimetry (ITC) in order to determine the mechanism of inhibition and the kinetic affinity constant (Kiapp). <br />The first series of inhibitors selected from our in silico strategy were evaluated by ITC to yield compounds that inhibited the TcDHODH in the micromolar concentration range with an average of 0.50 kcal mol-1 atom-1 ligand efficiency (LE). Because the assayed compounds have low molecular weight (ca. 200 kDa) and high LE, which bring them to the specific bimolecular pattern recognition all of them were considered good inhibitors capable of being selected to enter the hit-to-lead optimization process. <br />The detailed description of the ligand-enzyme mode of binding (MOB) is thoroughly accomplished by solving the X ray crystal structure of the surrogate Leishmania major DHODH enzyme (LmDHODH), which has a high degree of similarity with the enzyme TcDHODH. The MOB credited to be in the active site of the TcDHODH orthogonally validated the ITC kinetic experimental data obtained for all ligands as competitive inhibitors that interact at the active site of the TcDHODH and helped to generate pharmacophoric hypotheses for the search of new second generation molecules acting against the enzyme TcDHODH.  Analyzing the 3D structure of the TcDHODH along with its surrogate LmDHODH, we envisaged the possibility of compounds to extend their side chain beyond the region of the catalytic site (called S1), and interacting in a region called S2, so to increase binding affinity. Moreover, the TcDHODH S2 site that is not found in the 3D protein structure of humans (HsDHODH) is likely to offer new insights for the search of inhibitors whose binding to this S2 site can pave the roads towards the needed structural basis for selective inhibition of TcDHODH. <br />The most potent compounds inhibited the enzyme competitively with respect to the substrate dihydroorotate (DHO) at Kiapp values of 121 &plusmn; 14 nM and 190 &plusmn; 10 nM, which constitutes high affinity TcDHODH inhibitors. The ITC technique was pivotal to this process of enzyme inhibitors discovery, because it proved to be extremely sensitive thus allowing to monitor the kinetics of the reaction and to obtain precise and accurate values of affinity constants. <br />The hit rate obtained in this work, considering only those compounds with Kiapp < 100 &micro;M, was 46%. This is a really high number, since literature values range from 1 to 10% when the planning new inhibitors via in silico methods when compared to the success rates obtained by the methods of testing on large scales (HTS), 0-2 %, the results achieved in this work are even more significant. Moreover, the compounds selected through the integration of in silico and calorimetric methods showed a high degree of complexity in the process of bimolecular enzyme-ligand recognition, which allows to pass them to the next phase of the drug design process.

La néphropathie aux plantes chinoises (CHN) est une maladie rénale grave qui a été décrite pour la première fois en 1993 chez des patientes ayant suivi un régime amaigrissant à base d’extraits de plantes chinoises (Aristolochia fangchi) contenant des acides aristolochiques (AA). Cette néphropathie se caractérise par une atrophie tubulaire et une fibrose interstitielle aboutissant à l’urémie terminale et se complique fréquemment de cancers des voies urinaires. Au moment d’initier ce travail, il subsistait toujours un large débat quant au rôle étiologique réel des acides aristolochiques dans la genèse de cette maladie. En effet, les gélules à visée amaigrissante contenaient d’autres substances potentiellement néphrotoxiques. Mais surtout, il n’existait aucune preuve expérimentale que les AA pouvaient induire une fibrose rénale interstitielle.<p>Dans la première partie de ce travail, nous démontrons que l’injection par voie sous-cutanée d’AA à la dose de 10 mg/Kg/jour à des rats Wistar mâles en déplétion sodée entraîne l’apparition au 35ème jour d’une atrophie tubulaire, d’une fibrose interstitielle et d’une insuffisance rénale, reproduisant ainsi les anomalies caractéristiques de la CHN. Nous avons ensuite montré que la dexfenfluramine, substance anorexigène à action de type sérotoninergique prise concomitamment par les patientes atteintes de CHN, ne potentialise pas la toxicité rénale des AA. Enfin, la stimulation du système rénine angiotensine (SRA) par la déplétion sodée ou l’inhibition de celui-ci par un traitement pharmacologique ne modifie pas la fibrose interstitielle ni l’insuffisance rénale induite par les AA.<p>En conclusion, nous avons réussi à développer un modèle in vivo de fibrose rénale interstitielle induite par les AA. Dès lors nous avons apporté la preuve expérimentale de l’implication des AA dans le développement de la CHN. Ce modèle a permis de démontrer que les autres éléments potentiellement néphrotoxiques contenues dans la cure d’amaigrissement (dexfenfluramine, diurétique, laxatif) n’influençaient pas l’évolution de la fibrose interstitielle, ce qui confirme que la prise isolée d’AA suffit à expliquer le développement de la CHN. Cette confirmation à d’importantes implications en santé publique dans la mesure où des plantes contenant des acides aristolochiques font toujours partie des phytothérapies traditionnelles. De plus, il est apparu que, dans ce modèle, les mécanismes de la fibrose rénale interstitielle pouvaient être largement indépendants du SRA. Enfin, de par sa durée limitée et sa grande reproductibilité, ce modèle constitue un outil expérimental d’avenir pour l’étude des mécanismes physiopathologiques de la fibrose rénale interstitielle en général.<p> / Doctorat en sciences médicales / info:eu-repo/semantics/nonPublished

Caractériser la fonction des protéines est crucial pour notre compréhension des mécanismes moléculaires de la vie, des maladies, et aussi pour inspirer de nouvelles applications en bionanotechnologie. Pour y arriver, il est nécessaire de caractériser la structure et la dynamique de chaque état occupé par la protéine durant sa fonction. La caractérisation expérimentale des états transitoires des protéines représente encore un défi majeur parce que les techniques à haute résolution structurelle, telles que la spectroscopie RMN et la cristallographie aux rayons X, peuvent difficilement être appliquées à l’étude des états de courte durée. De plus, les techniques à haute résolution temporelle, telles que la spectroscopie de fluorescence, nécessitent généralement une chimie complexe pour introduire des fluorophores à des endroits spécifiques dans la protéine. Dans cette thèse nous introduisons l’utilisation des nanoantennes fluorescentes en tant que nouvelle stratégie pour détecter et signaler les changements de conformation des protéines via des interactions non covalentes entre des fluorophores spécifiques et la surface de la protéine. En utilisant des expériences et des simulations moléculaires, nous démontrons que des fluorophores chimiquement divers peuvent se lier et être utilisés pour sonder différentes régions d’une enzyme modèle, la phosphatase alcaline (PA). Ces nanoantennes peuvent être fixées directement aux protéines ou utilisées à l'aide du système de fixation simple et modulaire, le complexe biotine-streptavidine (SA), qui permet un criblage rapide et efficace de la nanoantenne optimale tant dans sa composition que sa longueur. Dans le cas de la PA, nous montrons que nos nanoantennes permettent la détection et la caractérisation des conformations distinctes incluant les changements conformationnels nanoscopiques produisant durant la catalyse du substrat. Nous démontrons également que les signaux fluorescents émis par la nanoantenne peuvent également permettre de caractériser la cinétique enzymatique d’une protéine en une seule expérience tout en incluant la détermination des paramètres « Michaelis-Menten » de ses substrats et inhibiteurs. Nous avons également exploré l'universalité de la stratégie ces nanoantennes fluorescentes en utilisant une autre protéine modèle, la Protéine G et son interaction avec les anticorps, et avons démontré son utilité pour mettre au point un essai permettant de détecter les anticorps. Ces nanoantennes simples et faciles à utiliser peuvent être appliquées pour détecter et analyser les changements conformationnels de toutes tailles et nos résultats suggèrent qu'elles pourraient être utilisées pour caractériser n’importe quel type de fonction. / The characterisation of protein function is crucial to understanding the molecular mechanisms of life and disease, and inspires new applications in bionanotechnology. To do so, it is necessary to characterise the structure and dynamics of each state that proteins adopt during their function. Experimental study of protein transient states, however, remains a major challenge because high-structural-resolution techniques, including NMR spectroscopy and X-ray crystallography, can often not be directly applied to study short-lived protein states. On the other hand, high-temporal-resolution techniques, such as fluorescence spectroscopy, typically require complicated site-specific labelling chemistry. This thesis introduces the use of fluorescent nanoantennas as a new strategy for sensing and reporting on protein conformational changes through noncovalent dye-protein interactions driven by a high local concentration. Using experiments and molecular simulations, we first demonstrate that chemically diverse dyes can bind and be used to probe different regions of a model enzyme, intestinal alkaline phosphatase (AP). These nanoantennas can be attached directly to proteins or employed using the simple and modular biotin-streptavidin (SA) attachment system, which enables rapid and efficient screening for high sensitivity by tuning their length and composition. We show that these nanoantennas enable the detection and characterisation of distinct conformational changes of AP, including nanoscale conformational changes that occur during substrate catalysis. We also show that the fluorescent signal emitted by the nanoantenna enables complete characterisation of enzyme kinetics in one experiment, including determination of Michaelis-Menten parameters of substrates and inhibitors of AP. We then explored the universality of the nanoantenna strategy by using a different model protein system. Protein G was shown to interact with antibodies, using a rapid screening strategy for antibody detection. These effective and easy-to-use nanoantennas could potentially be employed to monitor various conformational changes, and our results offer potential for characterising various protein functions.

Dans le monde entier, les infections virales causent des problèmes de santé majeurs et récurrents, engendrant de sérieux problèmes socio-économiques. Notamment, les virus de la famille Flaviviridae qui représentent un fardeau considérable sur la santé mondiale et font partie des domaines prioritaires de la virologie médicale selon le rapport 2016 du ‘Global Virus Network’. Bien que le traitement actuel contre le virus de l’hépatite C (VHC) ait un taux de guérison dépassant 98%, d’autres comme le virus de la dengue (DENV) et le virus zika (ZIKV) n’ont pas encore de traitement spécifique autorisé. En prenant avantage de la grande expertise de notre laboratoire dans l’étude du VHC, nous avons utilisé des données d’une étude de biologie des systèmes visant à identifier l’interactome des différentes protéines virales. Les techniques utilisées ont combiné l’immunoprécipitation des protéines virales suivie de l’identification des protéines interacteurs humaines par spectrométrie de masse. Des études de génomique fonctionnelle par ARN interférent (ARNi) ont permis d’étudier l’effet de la diminution de l’expression des protéines identifiées sur la réplication du VHC. Cette étude a conduit à la découverte de l’interactant spécifique 17-bêta-hydroxystéroïde déshydrogénase de type 12 (HSD17B12 ou DHB12) de la protéine virale Core comme facteur cellulaire requis à la réplication du VHC. HSD17B12 est une enzyme cellulaire dont l’activité catalytique est requise pour l’élongation des acides gras à très longue chaîne (VLCFA) lors de la deuxième des quatre réactions du cycle d’élongation. Dans cette étude, nous avons déterminé que les cycles de réplication du VHC, ZIKV et DENV dépendent de l’expression et de l’activité métabolique du facteur cellulaire HSD17B12. Ainsi, nous avons étudié les effets de l’inhibition de l’expression génique par ARNi et de façon pharmacologique sur la réplication de plusieurs flavivirus dans une approche antivirale à large spectre. Nous avons démontré que le silençage de HSD17B12 diminue significativement la réplication virale, l’expression des protéines virales et la production de particules infectieuses de cellules Huh7.5 infectées par la souche JFH1 du VHC. L'analyse de la localisation cellulaire de HSD17B12 dans des ii cellules infectées suggère une colocalisation avec l'ARN double brin (ARNdb) aux sites de réplication virale, ainsi qu’avec la protéine Core (et les gouttelettes lipidiques) aux des sites d’assemblage du virus. Nous avons également observé que le silençage de HSD17B12 réduit considérablement le nombre et la taille des gouttelettes lipidiques. En accord avec ces données, la diminution de l’expression de HSD17B12 par ARNi réduit significativement l’acide oléique et les espèces lipidiques telles que triglycérides et phosphatidyl-éthanolamine dans l'extrait cellulaire total. Ces travaux suggèrent une contribution de la capacité métabolique de HSD17B12 lors de la réplication du VHC. De même, nous avons démontré que le silençage de HSD17B12 réduit significativement les particules infectieuses de cellules infectées par DENV et ZIKV. Ces études supportent le rôle de HSD17B12 dans l’efficacité des processus de la réplication de l'ARN viral et de l’assemblage de particules virales. De plus, l'inhibiteur spécifique de HSD17B12, INH-12, réduit la réplication du VHC à des concentrations pour lesquelles aucune cytotoxicité notable n'est observée. Le traitement avec 20 μM d'INH-12 réduit jusqu'à 1,000 fois les particules infectieuses produite par des cellules Huh-7.5 infectées par DENV et ZIKV lors de plusieurs cycles de réplication, et bloque complètement l'expression des protéines virales. En conclusion, ces travaux ont conduit à une meilleure compréhension du rôle de HSD17B12 lors de la synthèse de VLCFA et de lipides requise à la réplication du VHC, permettant d’explorer l’inhibition de HSD17B12 et de l’élongation d’acides gras à très longue chaîne comme nouvelle approche thérapeutique pour le traitement à large spectre des infections par les virus de la famille Flaviviridae. / Infections with viruses are major recurrent socio-economical and health problems worldwide. These include infections by viruses of the Flaviviridae family, which present a substantial global health burden and are among the priority areas of medical virology according to the Global Virus Network 2016 report. While the current treatment regimens for hepatitis C virus (HCV) infection have cure rates of more than 98%, other important members of Flaviviridae like dengue virus (DENV) and zika virus (ZIKV) have no specific licensed treatments. By taking advantage of the most-studied HCV, which our lab has developed a vast expertise in the last 20 years, we used proteomics data of an HCV interactome study, combining viral protein immunoprecipitation (IP) coupled to tandem mass spectrometry identification (IP-MS/MS) and functional genomics RNAi screening. The study uncovered the 17-beta-hydroxysteroid dehydrogenase type 12 (HSD17B12, also named DHB12), as a specific host interactor of core that promotes HCV replication. HSD17B12 catalytic activity is involved in the synthesis of very-long-chain fatty acids (VLCFA) upon the second step of the elongation cycle. In this study, taking HCV as a virus model, we elucidated the dependency of HCV, dengue virus (DENV) and zika virus (ZIKV) replication on expression and metabolic capacity of the host factor HSD17B12. We investigated the effects of the inhibition of gene expression by RNAi and of its pharmacological enzymatic inhibition on flavivirus replication in a broad-spectrum antiviral approach. We showed that silencing expression of HSD17B12 decreases viral replication, viral proteins and iv infectious particle production of the JFH1 strain of HCV in Huh7.5 cells. The cellular localization analysis of HSD17B12 showed a co-staining with double-stranded RNA (dsRNA) at viral replication sites and with core protein (and lipid droplets) at virus assembly sites. Furthermore, HSD17B12 gene silencing drastically reduced the number and size of lipid droplets. In association, the reduced expression of HSD17B12 by RNAi decreases oleic acid levels and lipids such as triglycerides (TG) and phosphatidylethanolamine (PE) in whole-cell extract. The data suggested the requirement of the metabolic capacity of HSD17B12 for HCV replication. Similarly, we provide evidence that HSD17B12 silencing significantly reduces DENV and ZIKV infectious particles. The studies support a role of HSD17B12 for effective viral RNA replication and particle assembly processes. Moreover, the specific HSD17B12 inhibitor, INH-12, reduces HCV replication at concentrations for which no appreciable cytotoxicity is observed. The treatment of DENV- and ZIKV-infected Huh- 7.5 cells with 20 μM of INH-12 dramatically reduces production of infectious particles by up to 3-log10 in infection assays, and completely block viral protein expression. In conclusion, these studies extends our understanding of the role of HSD17B12 in VLCFA synthesis required for the replication of HCV, allowing to explore the inhibition of HSD17B12 and elongation of VLCFA as a novel therapeutic approach for the treatment of a broad-spectrum of viruses of the Flaviviridae family.