Les liposomes sont des structures sphériques formés par l'auto-assemblage de molécules amphiphiles sous forme d'une bicouche. Cette bicouche sépare le volume intérieur du liposome du milieu extérieur, de la même manière que les membranes cellulaires. Les liposomes sont donc des modèles de membranes cellulaires et sont formulés pour étudier les processus biologiques qui font intervenir la membrane (transport de molécules à travers la membrane, effets des charges en surface, interactions entre la matrice lipidique et d'autres molécules, etc.). Parce qu'ils peuvent encapsuler une solution aqueuse en leur volume intérieur, ils sont aussi utilisés aujourd'hui comme nanovecteurs de principes actifs. Nous avons formulé des liposomes non-phospholipidiques riches en stérol que nous avons appelés stérosomes. Ces stérosomes sont composés d'environ 30 % d'amphiphiles monoalkylés et d'environ 70 % de stérols (cholestérol, Chol, et/ou sulfate de cholestérol, Schol). Quand certaines conditions sont respectées, ces mélanges sont capables de former une phase liquide ordonnée (Lo) pour donner, par extrusion, des vésicules unilamellaires. Certaines de ces nouvelles formulations ont été fonctionnalisées de manière à libérer leur contenu en réponse à un stimulus externe. En incorporant des acides gras dérivés de l’acide palmitique possédant différents pKa, nous avons pu contrôler le pH auquel la libération débute. Un modèle mathématique a été proposé afin de cerner les paramètres régissant leur comportement de libération. En incorporant un amphiphile sensible à la lumière (un dérivé de l’azobenzène), les liposomes formés semblent répondre à une radiation lumineuse. Pour ce système, il serait probablement nécessaire de tracer le diagramme de phase du mélange afin de contrôler la photo-libération de l’agent encapsulé. Nous avons aussi formulé des liposomes contenant un amphiphile cationique (le chlorure de cétylpyridinium). En tant que nanovecteurs, ces stérosomes montrent un potentiel intéressant pour la libération passive ou contrôlée de principes actifs. Pour ces systèmes, nous avons développé un modèle pour déterminer l’orientation des différentes molécules dans la bicouche. La formation de ces nouveaux systèmes a aussi apporté de nouvelles connaissances dans le domaine des interactions détergents-lipides. Aux nombreux effets du cholestérol (Chol) sur les systèmes biologiques, il faut ajouter maintenant que les stérols sont aussi capables de forcer les amphiphiles monoalkylés à former des bicouches. Cette nouvelle propriété peut avoir des répercussions sur notre compréhension du fonctionnement des systèmes biologiques. Enfin, les amphiphiles monoalkylés peuvent interagir avec la membrane et avoir des répercussions importantes sur son fonctionnement. Par exemple, l'effet antibactérien de détergents est supposé être dû à leur insertion dans la membrane. Cette insertion est régie par l'affinité existant entre le détergent et cette dernière. Dans ce cadre, nous avons voulu développer une nouvelle méthode permettant d'étudier ces affinités. Nous avons choisi la spectroscopie Raman exaltée de surface (SERS) pour sa sensibilité. Les hypothèses permettant de déterminer cette constante d’affinité se basent sur l’incapacité du détergent à exalter le signal SERS lorsque le détergent est inséré dans la membrane. Les résultats ont été comparés à ceux obtenus par titration calorimétrique isotherme (ITC). Les résultats ont montré des différences. Ces différences ont été discutées. / Liposomes are spherical structures formed by the self-assembly of amphiphilic molecules to form bilayers. The bilayer separates the interior volume of the liposome from the external milieu, as do cellular membranes. Liposomes are cellular membrane models and are used to study biological processes that occur in relation with the membrane (molecular transport across the membrane, surface charge effects, interactions between the lipid matrix and other molecules, etc.). Because they can encapsulate an aqueous solution in their interior volume, they are also used as nanovectors of active agents. We have formulated non-phospholipid liposomes enriched in sterol that we have named sterosomes. These sterosomes are composed of approximately 30 % of monoalkylated amphiphiles and around 70 % of sterols (cholesterol, Chol, and/or cholesterol sulfate, Schol). Under certain conditions, these mixtures are able to form a liquid ordered phase (Lo) and unilamellar vesicles by extrusion. Some of these new formulations were functionalized in order to release their content in response to an external stimulus. By incorporating fatty acids (palmitic acid derivatives) with different pKas, we were able to control the pH at which the release starts. A mathematical model has been proposed in order to get insights on the parameters that control their release behavior. By incorporating a light-sensitive amphiphile (an azobezene derivative), liposomes seem to respond to an irradiation. For this system, it is probably necessary to plot the phase diagram of the mixture in order to control the photo-release of the encapsulated agent. We also have formulated liposomes containing a cationic amphiphile (cetylpyridinium chloride). As nanovectors, these sterosomes show an interesting potential for passive or active agent controlled release. For these systems, a model has been developed in order to study the orientation of the different molecules in the bilayer. The formation of these new formulations has also contributed to new knowledge in the detergent-lipid interaction field. Added to the numerous known effects of cholesterol (Chol) on biological systems, we must now add that sterols are also able to force monoalkylated amphiphiles to form bilayers. This new property can have an impact on our comprehension of biological system functioning. Finally, monoalkykated amphiphiles can interact with the membrane and have a negative impact on its functioning. For example, the antibactericidal effect of detergents is supposed to be due to their insertion in the membrane. This insertion is related to the affinity between the detergent and the membrane. Within this field, we wanted to develop a new method to investigate detergent-membrane affinities. We chose surface enhanced Raman Spectroscopy (SERS) due to its sensitivity. Hypotheses allowing the determination of affinity constants are based on the incapability of the detergent to enhance the SERS signal when the detergent is inserted in the membrane. Results were compared to those obtanined bi isothermal titration calorimetry (ITC). Differences were found and are discussed.

No description available.

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.

Submitted by Jorge Dias (jorge.dias@gvmail.br) on 2013-04-19T05:24:34Z No. of bitstreams: 1 dissertacaorevisada.pdf: 2278867 bytes, checksum: f8f1e3424e247a608b0f0ecaa72e886b (MD5) / Approved for entry into archive by Suzinei Teles Garcia Garcia (suzinei.garcia@fgv.br) on 2013-04-19T13:57:46Z (GMT) No. of bitstreams: 1 dissertacaorevisada.pdf: 2278867 bytes, checksum: f8f1e3424e247a608b0f0ecaa72e886b (MD5) / Made available in DSpace on 2013-04-19T14:00:02Z (GMT). No. of bitstreams: 1 dissertacaorevisada.pdf: 2278867 bytes, checksum: f8f1e3424e247a608b0f0ecaa72e886b (MD5) Previous issue date: 2013-04-02 / The increasing use of computing and communication resources in the companies, looking for modernization, agility, cost reduction and others, has brought many benefits, but has also become a huge problem for the planeta. The amount of electronic waste (e-waste) generated by computer and communication equipment has doubled every five years, becoming a major focus of attention in recent years. The volume of electronic waste generated by the disposal of computer equipment and communication technologies (ITC), has grown to 50 million tonnes per year, equivalent to eight times the total waste of São Paulo city. The total Brasilian electronics market is considered the fifth in the world after China, the U.S., Japan and Russia. The total production of electronic waste in Brazil in 2011 was one million tonnes and partially with respect to ITC equipment was estimated at 98 000 tonnes. Considering this context, this study aims to contribute to the expansion of knowledge in green supply chain management (GSCM) applied to the Brazilian ITC business reality. Specifically intend to identify which factors influence the process of adoption and implementation of green ITC management in large companies using ITC in Brazil, from the models proposed by Molla (2008) and Coopers and Molla (2008). Thus we sought to answer the following research question: what factors influence large companies, users of information technology and communication (ITC) at Brazil, in the adoption of green IT management concepts? A case study was conducted in six major companies, all leaders in their sectors, representing major areas of services and manufacturing. As a final result, we propose a new analytical model, which seemed more appropriate to the service sector. The study also identified that the management of green ITC in manufacturing companies have different priorities of service companies. Often their operational challenges are more critical to sustainability than the management of green ITC itself. Moreover, the study of the services provided by the public sector despite large annual budgets, pointed restrictions concerning legal aspects of disability and qualification and training of its employees as limiting factors for the implementation of green management programs more extensively. / A crescente utilização de recursos de informática e comunicação nas empresas, visando modernização, agilidade, redução de custos e outros, tem trazido diversos benefícios, mas tem também se tornado um enorme problema para o planeta. A quantidade de lixo eletrônico (e-waste) gerada pelos equipamentos de informática e comunicação tem dobrado a cada cinco anos, se tornando um dos principais focos de atenção nos últimos anos. O volume de lixo eletrônico gerado pelo descarte de equipamentos de informática e comunicação (TIC), já ultrapassa a marca de 50 milhões de toneladas por ano, o que equivale a oito vezes a produção total de resíduos da cidade de São Paulo. O mercado brasileiro total de eletrônicos é considerado o quinto do mundo, depois da China, Estados Unidos, Japão e Rússia. A produção total de lixo eletrônico no Brasil em 2011 foi de um milhão de toneladas e a parte referente a equipamentos de TIC foi estimada em 98 mil toneladas. Frente a este contexto este estudo visa contribuir para a expansão do conhecimento na gestão verde da cadeia de suprimentos (GSCM) aplicado à realidade empresarial brasileira de TIC. Especificamente pretende-se identificar quais fatores influenciam o processo de adoção e aplicação da gestão verde de TIC, em grandes empresas usuárias de TIC no Brasil, a partir dos modelos propostos por Molla (2008) e Molla e Coopers (2008). Desta forma buscou-se responder ao seguinte problema de pesquisa: quais fatores influenciam grandes empresas usuárias de tecnologia da informação e comunicação (TIC) no Brasil na adoção de conceitos de gestão de verde? Para isto, foi realizado estudo de caso em seis grandes empresas, todas lideres em seus setores, representando grandes áreas de serviços e manufatura. Como resultado final, foi proposto um novo modelo analítico, que pareceu mais adequado ao setor de serviços. O estudo também identificou que na gestão verde de TIC empresas manufatureiras tem prioridades diferentes das de serviço. Muitas vezes seus desafios operacionais são mais críticos em relação à sustentabilidade, que a gestão verde de TIC em si. Por outro lado, o estudo dos serviços prestados pelo setor público apesar dos grandes orçamentos anuais, apontou restrições quanto aos aspectos legais e deficiência de qualificação e capacitação de seus colaboradores como fatores limitantes para a implantação de programas de gestão verde mais abrangentes.

La protéine NS5A est essentielle pour la réplication et l'assemblage du virus de l'hépatite C (VHC), et elle constitue une cible thérapeutique prometteuse pour le développement d'antiviraux. Cependant, aucune fonction claire n'a encore été décrite pour NS5A, et les connaissances structurales restent limitées. Ainsi, nous avons caractérisé l'état intrinsèquement désordonné des domaines D2 et D3 de NS5A en décrivant leurs espaces conformationnels et leurs potentialités de repliement en combinant différentes méthodes biophysiques. Nous avons aussi mis en évidence la variabilité structurale du domaine D2 au sein des génotypes du VHC, ce qui pourrait être en rapport avec les différences de pathogénie et d'efficacité des thérapies observées selon les génotypes. L'interaction de D2 et D3 avec la cyclophiline humaine A (CypA) a été étudiée par résonance plasmonique de surface (SPR). Bien que des mutations au sein du domaine D2 rendent la réplication du VHC moins dépendante de la présence de CypA, ces mutations n'empêchent pas la liaison entre D2 et CypA. En revanche, elles induisent des perturbations structurales qui pourraient affecter la cinétique d'interconversion des conformères de D2. Nous avons montré par SPR que D2 et D3 interagissent avec le domaine de fixation à l'ADN du récepteur nucléaire FXR. Cette interaction pourrait inhiber la fixation de FXR sur sa cible ADN, suggérant une implication de NS5A dans la modulation de l'activité transcriptionnelle de ce récepteur nucléaire. L'ensemble de ces informations, nous a permis de proposer un modèle de la structure globale de NS5A permettant une meilleure compréhension des propriétés structurales et fonctionnelles de cette protéine énigmatique / NS5A is essential for HCV replication and particle assembly, and constitutes a very promising drug target. However, no clear function has yet been described for NS5A, and structural knowledge remains limited. We characterized the intrinsically disordered nature of NS5A domains D2 and D3, and describe their folding propensity and their overall conformational behaviour by combining different biophysical methods. We also highlighted the structural variability of D2 domain in HCV genotypes, which might be correlated with the disparities observed between genotypes in terms of pathogenesis and efficiency of therapies. The interactions between D2 and D3 with human cyclophilin A (CypA) was analysed by surface plasmon resonance (SPR). We showed that mutations in the D2 domain conferring resistance of HCV replication to CypA inhibitors did not prevent the interaction between D2 and CypA. However, they induce structural perturbations that may affect the kinetics of conformers interconversion of D2. We also showed by SPR that D2 and D3 interact with the of DNA-binding domain of the nuclear receptor FXR (farnesoid X receptor alpha). This interaction reduce the binding of FXR to its DNA target, suggesting an involvement of NS5A in the modulation of the transcriptional activity of FXR. All this data led us to propose a model of the overall structure of NS5A, which provides a useful template for a better understanding of structural and functional properties of this enigmatic protein

Im Rahmen der vorliegenden Arbeit wurden die Wechselwirkungen im System Bakterium –Tensid – Schadstoff mittels kalorimetrischer Untersuchungen (ITC, DSC) sowie mit XPS-Analysen und durch Zeta-Potential-Messungen an Bakterienoberflächen charakterisiert. Für die Untersuchungen wurden zwei Gram-positive Rhodococcus-Stämme und ein Gram-negativer Pseudomonas putida-Stamm verwendet. Als Biotenside wurden das Rhamnolipid JBR 425 und der von Rhodococcus erythropolis B7g produzierte Trehalosetetraester (THL-4) ausgewählt. Das synthetische Tensid SDS diente als Referenzsubstanz. Aus den kalorimetrischen Experimenten konnte eine starke Wechselwirkung zwischen den Tensiden und den aktiven Bakterienkulturen abgeleitet werden. THL-4 führte beim Wachstum der Rhodococcen auf n-Hexadecan zur Verkürzung der lag-Phase. SDS wies hingegen eine toxische Wirkung für die Bakterienstämme auf. Thermodynamische Betrachtungen ergaben, dass Wechselwirkungen des SDS mit den Bakterienzellen gegenüber der Mizellbildung bevorzugt werden.

Neuromodulation, such as spinal cord stimulation (SCS) and deep brain stimulation (DBS), has been shown to modulate pathophysiological brain activity and provide symptomatic therapy for several neurological disorders, including Parkinson’s Disease. The effectiveness of this therapy could likely be further improved by neuromodulation that is adaptive, delivering stimulation more selectively, by monitoring a biomarker in recorded brain signals, which indicates the presence of a pathological state. In the treatment of Parkinson’s Disease, the most commonly proposed solutions for adaptive neuromodulation are relying on excessive beta-band oscillatory activity as a biomarker, which is however often highly variable between patients during movement and in conjunction with neuromodulatory treatment, such as levodopa. These limitations hinder broader use of this biomarker and prompts further research for alternative solutions. In this work, we instead present the use of a novel feature of evoked electrophysiological activity, which utilizes the inter-trial phase coherence between stimulation pulses, to classify parkinsonian brain states in 6-OHDA lesioned rats. We developed a method, which relates to the rate of decay in inter-tral phase coherence, evoked by single SCS or DBS pulses, that is able to statistically separate experimental conditions recorded from a dopaminergic depleted hemisphere from conditions a non-depleted hemisphere, while also being able to separate conditions with levodopa treatment from conditions without treatment. For animals undergoing SCS we can classify phase decay measurements from pharmacologically treated or untreated parkinsonian states, using a Bayesian model, with a high accuracy and strong classifier performance for a single channel (AUC 0.85 – 0.99) in the motor cortex and striatum. In ongoing experiments, similar implementation of adaptive DBS is being evaluated. Our results support the implementation of our feature in a protocol aimed at performing closed-loop neuromodulation in the 6-OHDA rat model of Parkinon’s Disease, that can serve as the basis for further studies. / Neuromodulering, såsom ryggmärgsstimulering (SCS) och djup hjärnstimulering (DBS), har visat sig kunna modulera patofysiologisk hjärnaktivitet och ge symtomatisk behandling av flera neurologiska sjukdomar, inklusive Parkinsons sjukdom. Effekten av denna behandling skulle sannolikt kunna förbättras ytterligare genom neuromodulering som är adaptiv och ger stimulering mer selektivt, genom övervakning av en biomarkör i registrerade hjärnsignaler, som indikerar förekomsten av ett patologiskt tillstånd. Vid behandling av Parkinsons sjukdom förlitar sig de vanligaste lösningarna för adaptiv neuromodulering på överdriven beta-bands oscillatorisk aktivitet som en biomarkör som dock ofta är mycket varierande mellan patienter, under rörelse och i samband med behandling så som levodopa. Dessa begränsningar hindrar en bredare användning av denna biomarkör och ytterligare forskning krävs för att hitta alternativa lösningar. I detta arbete presenterar vi istället en ny egenskap hos väckt elektrofysiologisk aktivitet, som utnyttjar faskoherens mellan stimuleringspulser för att klassificera parkinsonistiska hjärntillstånd hos 6-OHDA-lesionerade råttor. Vi har utvecklat en metod som relaterar till avklingningshastigheten i faskoherens, framkallad av enstaka SCS- eller DBS-pulser, som kan statistiskt särskilja de experimentella tillstånden i en dopaminergiskt utarmad hemisfär från liknande tillstånd, fast i en icke utarmad hemisfär. Den kan även statistiskt särskilja tillstånd med levodopabehandling från tillstånd utan behandling. För djur som genomgår SCS kan vi klassificera fasförfallsmätningar från farmakologiskt behandlade eller obehandlade parkinsontillstånd, med hjälp av en Bayesiansk modell, med hög noggrannhet och stark klassificeringsprestanda för en enda kanal (AUC 0,85 - 0,99) i motorcortex och striatum. I pågående experiment utvärderas en liknande implementering av adaptiv DBS. Våra resultat stöder implementeringen av vår funktion i ett protokoll som syftar till att utföra sluten neuromodulering i 6-OHDA-råttmodellen för Parkinons sjukdom, som kan tjäna som grund för ytterligare studier.

Tuberculosis affects millions of people worldwide every year. The current treatment for TB is divided into a regimen of both first- and second-line drugs, where first-line treatments are more tolerated and require shorter treatment lengths. With rising levels of resistance, alternative treatment regimes are urgently needed to fight this disease. Ethionamide, a second-line drug is administered as a prodrug which is activated in vivo by the enzyme EthA, which is in turn regulated by EthR. The disruption of the action of EthR could lead to novel therapeutics which could enhance the efficacy of ethionamide, and raise it to a first-line treatment. The work reported in this thesis examines the elaboration of three chemical scaffolds using fragment-based approaches to develop novel inhibitors capable of disrupting the EthR-DNA interaction. The first scaffold, 5-(furan-2-yl)isoxazole was investigated by fragment-merging approaches and produced compounds with the best of these having a KD of 7.4 uM. The second scaffold, an aryl sulfone was elaborated using fragment-merging strategies. This led to several modifications of the fragment, leading to several variants with KDs around 20 uM. With both of these series the affinity could not be improved below 10 uM and due to the synthetic complexity a further scaffold was prioritised. The third scaffold was explored was a 4-(4-(trifluoromethyl)phenyl)piperazine using fragmentgrowing from the NH of the piperazine to probe deeper into the EthR binding pocket. In addition to this, SAR around the 4-(trifluoromethyl)phenyl group was assessed to explore the interactions with EthR. These modifications led to compounds with nanomolar IC50s. A range of compounds were then screened by REMAssay to determine the boosting effect on ethionamide, and this identified compounds with up to 30 times boosting in the ethionamide MIC. The final chapter examines a concept where compounds were designed to exploit the dimeric nature of EthR by linking two chemical warheads with a flexible linker. These compounds are examined using mass spectrometry to investigate the stoichiometry of the interaction to provide insight into the binding of these extended compounds and exploring an alternative strategy to inhibit EthR. The work in this thesis demonstrated the successful use of fragment-based approaches for development of novel EthR inhibitors which showed significant ethionamide boosting effects.

Le RXP470.1 est l’un des premiers inhibiteurs puissants de la MMP-12, une métalloprotéase à zinc impliquée dans de nombreuses pathologies comme l’athéroclérose et la bronchopneumopathie obstructive chronique (BPCO). Pour comprendre les bases moléculaires contrôlant l’interaction de cet inhibiteur avec sa cible, des approches pluridisciplinaires associant des relations structure-activité, avec des études de cristallographie de complexes enzymes inhibiteurs et d’études de microcalorimétrie, décrivant les contributions enthalpiques et entropiques impliquées dans la formation des complexes, ont été réalisées dans ce travail de thèse. Les affinités de trois analogues du RXP470.1 ont été tout d’abord déterminées. Puis quatre structures cristallographiques de complexes enzyme/inhibiteur décrivant le mode d’interaction duRXP470.1 et de ces trois analogues ont été obtenues avec des résolutions de 1.15 Å, 1.50 Å, 1.50Å et 1.30 Å, respectivement. Parallèlement les études de microcalorimétrie ont été menées pour étudier les facteurs énergétiques contrôlant l’interaction du RXP470.1 avec la MMP-12. Les résultats indiquent que la présence d’une chaîne latérale très longue et hydrophobe en position P1’de l’inhibiteur s’insérant dans la cavité S1’ de la MMP-12 est essentielle à la très bonne affinité de cet inhibiteur pour la MMP-12. Cette interaction met essentiellement en jeu un effet entropique très important de - 4 kcal/mol. L’interaction du RXP470.1 est aussi essentiellement dirigée par une forte augmentation d’entropie (-TDS= -10 kal/mol) et une composante enthalpique beaucoup plus faible (DH= -2.5 kcal/mol), et ce malgré l’observation dans le cristal de nombreuses interactions entre l’inhibiteur et le site actif de la MMP-12. L’étude de microcalorimétrie met aussi en lumière la prise d’un proton au cours de la formation du complexe enzyme inhibiteur impliquant deux résidus chargés négativement en solution, le résidu catalytique Glu219 et le groupe phosphoryle chélatant du zinc dans l’inhibiteur. Cette étude révèle aussi que si le groupe phosphoryle est considéré comme un chélatant faible de l’atome de zinc, il impose néanmoins des contraintes directionnelles très importantes qui ont un impact sur le positionnement des autres parties de l’inhibiteur dans le site actif de l’enzyme. Ce dernier effet pourrait expliquer pourquoi un certain nombre d’interactions entre l’inhibiteur et l’enzyme ne sont pas optimisées et pourquoi la variation d’enthalpie pour former le complexe reste relativement faible. Cette étude ouvre maintenant la voie à d’autres études en plaçant au centre des futurs travaux le rôle du groupe chélatant dans la conception des inhibiteurs de MMP, ainsi de nouveaux inhibiteurs puissants et sélectifs d’autres MMP devraient voir le jour grâce à ce travail et aux résultats obtenus. / RXP470.1 is one of the first highly potent and selective inhibitor of MMP-12, a zinc protease involved in several human diseases such as atherosclerosis and chronic obstructive pulmonary disease (COPD). To understand the molecular determinants controlling the interaction of RXP470.1 with MMP-12 active site, a multidisciplinary approach combining structure-activity data, crystallography and microcalorimetry have been performed on RXP470.1 and its three analogues. The affinities of the three RXP470.1 analogues have been determined. Then, fourcrystal structures of MMP-12 in interaction with these inhibitors have beendetermined at high resolution, 1.15 Å, 1.50 Å, 1.50 Å et 1.30 Å, respectively. These data have indicated that the presence of a long hydrophobic side chain in the P1’ position of the RXP470.1, which enters deeply inside the S1’ cavity of MMP-12, is playing a key role in the inhibitor affinity. The contribution of this side chain is mostly entropic (-TDS - 4 kcal/mol). The interaction of RXP470.1 with MMP-12 is also mostly driven by a sizeable entropy increase (-TDS= -10 kal/mol) and a more modest enthalpy contribution (DH= -2.5 kcal/mol), despite the observation in the crystal structure of several contacts between inhibitor and MMP-12 active site. Furthermore, this study reveals that the binding of RXP470.1 to MMP-12 is linked to a proton uptake involving two negatively charged residues, the catalytic Glu219 and the phosphoryl group of the inhibitor. Furthermore, despite that the phosphoryl group is considered as a weak zincbinding group, this study highlights that the interactions of this group with the active site zinc atom involved strong directionality between these two groups. This effect has strong impact on the positioning of the other parts of the inhibitor in the MMP-12 active site. This last effect could be responsible for the modest enthalpy increase associated with the binding of RXP470.1 to MMP-12, by preventing the optimization of several interactions between the inhibitor and the enzyme. The results indicate that the role of the zinc-binding group should be better consider in the future. Finally this study opens a new vision in this field and should allow the design of new selective inhibitors of other MMPs.

Les traitements pharmacologiques symptomatiques de la maladie d’Alzheimer (MA) actuellement commercialisés ont un effet modeste sur le fonctionnement cognitif. De plus, le développement clinique de nouveaux composés plus efficaces est freiné par l’absence de critères prédictifs pour juger précocement de leur efficacité clinique.Dans ce contexte, l’électroencéphalographie (EEG) pourrait constituer un bio-marqueur suffisamment sensible pour identifier précocement (Phase I) le potentiel thérapeutique d’une nouvelle molécule sur le fonctionnement cognitif. De plus, la difficulté pour détecter des améliorations subtiles dans les performances cognitives en Phase I (i.e. chez des sujets sains) pourrait être palliée par le développement de paradigmes expérimentaux, tels que la privation de sommeil (PS), visant à induire des déficits cognitifs réversibles chez le sujet sain.Ainsi, l’EEG et l’EEG couplée à la privation de sommeil (PS) seraient des stratégies innovantes et pertinentes pour juger et prédire l’efficacité clinique d’une molécule en Phase I.Dans ce travail, nous tentons de juger de la pertinence de telles stratégies en identifiant, chez des sujets sains, des marqueurs EEG du fonctionnement cognitif liés soit (1) à la prise d’un médicament ayant un effet sur la cognition, (2) soit à l’induction d’un déclin cognitif réversible, (3) soit à l’effet concomitant des deux paramètres. Pour y parvenir, deux études ont été réalisées.Dans une première étude, l’effet du donepezil sur l’activité électrique corticale a été étudié chez 30 volontaires adultes, jeunes et sains. Ces volontaires ont été traités par donepezil (5 mg/jour per os) (vs. placebo) pendant 15 jours suivant une procédure en double aveugle, randomisée et en cross-over. _x000D_A la fin de la période de traitement, un EEG (58 voies) a été réalisé au cours de deux tâches attentionnelles (auditive et visuelle). Les potentiels évoqués cognitifs (PEC), la cohérence de phase inter-essais (ITC) et la perturbation spectrale liée à l’événement (ERSP) ont ensuite été calculés.Dans une deuxième étude, l’effet d’une PS a été étudié chez 36 volontaires adultes, jeunes et sains. De plus, l’effet d’un médicament ayant un effet bien connu sur la cognition (en particulier sur la vigilance), le modafinil, a également été étudié sur cette PS.Suite à une PS de 24 h, les participants se sont vus administrés une dose de modafinil (200 mg en prise unique) (vs. placebo) suivant une procédure en double aveugle, randomisée et en cross-over. Un EEG (25 voies) a été réalisé au cours d’une tâche attentionnelle auditive (identique à celle de l’étude I) avant et après la PS. Les PEC, l’ITC et l’ERSP ont ensuite été calculés.Grâce à ces deux études, nous avons identifié, à l’échelle de groupe, des marqueurs EEG de la cognition liés soit à l’induction d’un déclin cognitif (induit par une PS), soit à l’intervention pharmacologique ciblant le système cholinergique (donepezil) ou différents neurotransmetteurs (modafinil). L’ensemble de ces marqueurs porterait sur la modulation de l’activité corticale au sein du réseau fronto-pariétal ventral, connu pour régir les processus attentionnels et exécutifs. Nous avons également confirmé que ce réseau serait sous-tendu par des activités oscillatoires δ/θ et α. L’efficience cognitive serait le reflet de l’intégrité de ce réseau.Nous avons conclu que l’EEG est un outil suffisamment sensible pour détecter des changements subtils dans les processus neurocognitifs de participants adultes, jeunes et sains suivant l’administration d’un traitement de la MA et de manière plus générale suivant l’administration d’un médicament ayant un effet sur la cognition lorsqu’un déclin cognitif est provoqué (PS).Sous réserve de réplication des résultats et d’analyses complémentaires, l’EEG ainsi que l’EEG couplée à la PS pourraient constituer des outils additionnels à l’évaluation cognitive pour prédire l’efficacité de nouveaux candidat médicaments de la MA. / Symptomatic pharmacological treatments currently marketed for Alzheimer’s disease (AD) have a modest effect on cognitive functioning. In addition, the clinical development of new and more effective compounds is hampered by the lack of predictive criteria to judge their early clinical efficacy.In this context, electroencephalography (EEG) could be a sufficiently sensitive biomarker to identify in an early stage (i.e. Phase I) the therapeutic potential of a new molecule on cognitive functioning. In addition, the difficulty to detect subtle improvements in cognitive performance in Phase I (i.e. in healthy subjects) could be overcome by the development of experimental paradigms such as sleep deprivation (SD), to induce cognitive deficits, still reversible in healthy subjects.EEG and EEG coupled with sleep deprivation (SD) would be innovative and relevant strategies to determine and predict the clinical effectiveness of a molecule in Phase I.In this work, we try to determine the relevance of such strategies by identifying, in healthy subjects, EEG markers of cognitive functioning related to (1) either the taking of a cognitive drug, (2) or the induction of a reversible cognitive decline, (3) or concomitant effects of the two parameters. In order to do that, two studies were performed.In a first study, the effect of donepezil on cortical electrical activity was studied in 30 young, healthy adult volunteers. These volunteers were treated with donepezil (5 mg/day orally) (vs. placebo) for 15 days following a double-blind, randomized, cross-over trial.At the end of the treatment period, an EEG (58 electrodes) was performed during two attentional tasks (auditory and visual). Event-related potentials (ERP), the inter-trial coherence (ITC) and the event-related spectral perturbation (ERSP) were then calculated.In a second study, the effect of SD was studied in 36 young, healthy adult volunteers. In addition, the effect of a cognitive drug (involving high alertness), the modafinil was also studied on this SD._x000D_Following a SD of 24 h, the participants were administered a dose of modafinil (200 mg in a single dose) (vs. placebo) in a double-blind, randomized, cross-over trial. An EEG (25 electrodes) was performed in a hearing attentional task (identical to that of Study 1) before and after the PS. The ERP, ITC and ERSP were then calculated.Through these two studies, we have found, at the group level, cognitive EEG markers related either to the induction of cognitive decline (SD) or pharmacological intervention targeting cholinergic system (donepezil) or several neurotransmitters (modafinil). All these markers would concern the modulation of cortical activity in the ventral frontoparietal network, known to regulate attentional and executive processes. We also confirmed that the network is underlying by δ/θ and α oscillatory activities. The cognitive efficiency would reflect the integrity of the network.We conclude that EEG is a sufficiently sensitive tool to detect subtle changes in neurocognitive processes of young, healthy adult volunteers, following the administration of a treatment of AD and more generally following the administration of a drug having an effect on cognition when cognitive decline is caused (SD).EEG and EEG coupled with SD could constitute additional tools to the current cognitive assessment for predicting the efficacy of new drug candidates for AD before initiation Phases II/III clinical trials. However, the present works needs to be replicated so that the EEG markers described here can be validated so as to be used in drug trials.