Ce projet illustre cinq études, mettant l'emphase sur le développement d'une nouvelle approche diagnostique cardiovasculaire afin d'évaluer le niveau d’oxygène contenu dans le myocarde ainsi que sa fonction microvasculaire. En combinant une séquence de résonance magnétique cardiovasculaire (RMC) pouvant détecter le niveau d’oxygène (OS), des manœuvres respiratoires ainsi que des analyses de gaz artériels peuvent être utilisés comme procédure non invasive destinée à induire une réponse vasoactive afin d’évaluer la réserve d'oxygénation, une mesure clé de la fonction vasculaire. Le nombre de tests diagnostiques cardiaques prescrits ainsi que les interventions, sont en pleine expansion. L'imagerie et tests non invasifs sont souvent effectués avant l’utilisation de procédures invasives. L'imagerie cardiaque permet d’évaluer la présence ou absence de sténoses coronaires, un important facteur économique dans notre système de soins de santé. Les techniques d'imagerie non invasives fournissent de l’information précise afin d’identifier la présence et l’emplacement du déficit de perfusion chez les patients présentant des symptômes d'ischémie myocardique. Néanmoins, plusieurs techniques actuelles requièrent la nécessité de radiation, d’agents de contraste ou traceurs, sans oublier des protocoles de stress pharmacologiques ou physiques. L’imagerie RMC peut identifier une sténose coronaire significative sans radiation. De nouvelles tendances d’utilisation de RMC visent à développer des techniques diagnostiques qui ne requièrent aucun facteur de stress pharmacologiques ou d’agents de contraste. L'objectif principal de ce projet était de développer et tester une nouvelle technique diagnostique afin d’évaluer la fonction vasculaire coronarienne en utilisant l' OS-RMC, en combinaison avec des manœuvres respiratoires comme stimulus vasoactif. Ensuite, les objectifs, secondaires étaient d’utilisés l’OS-RMC pour évaluer l'oxygénation du myocarde et la réponse coronaire en présence de gaz artériels altérés. Suite aux manœuvres respiratoires la réponse vasculaire a été validée chez un modèle animal pour ensuite être utilisé chez deux volontaires sains et finalement dans une population de patients atteints de maladies cardiovasculaires. Chez le modèle animal, les manœuvres respiratoires ont pu induire un changement significatif, mesuré intrusivement par débit sanguin coronaire. Il a été démontré qu’en présence d'une sténose coronarienne hémodynamiquement significative, l’OS-RMC pouvait détecter un déficit en oxygène du myocarde. Chez l’homme sain, l'application de cette technique en comparaison avec l'adénosine (l’agent standard) pour induire une vasodilatation coronarienne et les manœuvres respiratoires ont pu induire une réponse plus significative en oxygénation dans un myocarde sain. Finalement, nous avons utilisé les manœuvres respiratoires parmi un groupe de patients atteint de maladies coronariennes. Leurs myocardes étant altérées par une sténose coronaire, en conséquence modifiant ainsi leur réponse en oxygénation. Par la suite nous avons évalué les effets des gaz artériels sanguins sur l'oxygénation du myocarde. Ils démontrent que la réponse coronarienne est atténuée au cours de l’hyperoxie, suite à un stimuli d’apnée. Ce phénomène provoque une réduction globale du débit sanguin coronaire et un déficit d'oxygénation dans le modèle animal ayant une sténose lorsqu’un supplément en oxygène est donné. En conclusion, ce travail a permis d'améliorer notre compréhension des nouvelles techniques diagnostiques en imagerie cardiovasculaire. Par ailleurs, nous avons démontré que la combinaison de manœuvres respiratoires et l’imagerie OS-RMC peut fournir une méthode non-invasive et rentable pour évaluer la fonction vasculaire coronarienne régionale et globale. / This project encompasses five studies, which focus on developing a new cardiovascular diagnostic approach for assessing myocardial oxygenation and microvascular function. In combination with oxygenation-sensitive cardiovascular magnetic resonance (OS-CMR) imaging, breathing maneuvers and altered arterial blood gases can be used as a non-invasive method for inducing a vasoactive response to test the oxygenation reserve, a key measurement in vascular function. The number of prescribed cardiac diagnostic tests and interventions is rapidly growing. In particular, imaging and other non-invasive tests are frequently performed prior to invasive procedures. One of the most common uses of cardiac imaging is for the diagnosis of significant coronary artery stenosis, a critical cost factor in today’s health care system. Non-invasive imaging techniques provide the most reliable information for the presence and location of perfusion or oxygenation deficits in patients with symptoms suggestive of myocardial ischemia, yet many current techniques suffer from the need for radiation, contrast agents or tracers, and pharmacological or physical stress protocols. CMR imaging can identify significant coronary artery stenosis without radiation and new trends in CMR research aim to develop diagnostic techniques that do not require any pharmacological stressors or contrast agents. For this project, the primary aim was to develop and test a new diagnostic technique to assess coronary vascular function using OS-CMR in combination with breathing maneuvers as the vasoactive stimulus. Secondary aims then used OS-CMR to assess myocardial oxygenation and the coronary response in the presence of altered arterial blood gases. An animal model was used to validate the vascular response to breathing maneuvers before translating the technique to human subjects into both healthy volunteers, and a patient population with cardiac disease. In the animal models, breathing maneuvers could induce a significant change in invasively measured coronary blood flow and it was demonstrated that in the presence of a haemodynamically significant coronary stenosis, OS-CMR could detect a myocardial oxygen deficit. This technique was then applied in a human model, with healthy participants. In a direct comparison to the infusion of the coronary vasodilator adenosine, which is considered a standard agent for inducing vasodilation in cardiac imaging, breathing maneuvers induced a stronger response in oxygenation of healthy myocardium. The final study then implemented the breathing maneuvers in a patient population with coronary artery disease; in which myocardium compromised by a coronary stenosis had a compromised oxygenation response. Furthermore, the observed effects of arterial blood gases on myocardial oxygenation were assessed. This demonstrated that the coronary response to breath-hold stimuli is attenuated during hyperoxia, and this causes an overall reduction in coronary blood flow, and consequently an oxygenation deficit in a coronary stenosis animal model when supplemental oxygen is provided. In conclusion, this work has improved our understanding of potential new diagnostic techniques for cardiovascular imaging. In particular, it demonstrated that combining breathing maneuvers with oxygenation-sensitive CMR can provide a non-invasive and cost-effective method for assessing global and regional coronary vascular function.

Severe perinatal hypoxia represents a substantial brain injury in human newborns. This Diploma thesis is focused on long-term motor outcome of laboratory rat after moderate perinatal hypoxia. We described some behavioral test for detection motor development and presented the influence of perinatal hypoxia on central nervous system. We also discussed an effect of agonists and antagonists of adenosine A1 receptor in brain. The aim of an experimental part was an evaluation of long-term motor behavior in rats affected by perinatal hypoxia. To cause perinatal hypoxia we put pregnant female rats to a hypoxic (10% O2) normobaric room in 11th day of their gestation. The pregnant female rats stayed in hypoxic room until they gave a birth and 6 more days after birth with their litters. For classification of motor development we used battery of tests of motor coordination. These tests correspond to the level of development of the rat. Then a group of rats with perinatal hypoxia was treated by a single administration of an agonist of adenosine A1 receptor 2-chloro-N(6)- cyclopentyladenosin (CCPA) in postnatal day 14. The animals affected by perinatal hypoxia show motor deficits in 3 from 4 selected behavioral tests. Otherwise, this motor behavior was no longer detected in young adults. The rats affected by...

O diagnóstico da doença de Wilson (DW) é realizado por exames clínicos, laboratoriais, anatomopatológicos e de imagem. Mais de 500 mutações no gene ATP7B foram descritas como causadoras da DW. Para avaliar a importância da detecção de mutações no diagnóstico da DW em nosso meio, analisamos 35 pacientes com DW, 20 familiares de wilsonianos a partir de rastreamento familiar, 18 com hepatite crônica criptogênica e sete com insuficiência hepática aguda grave. Para o diagnóstico da DW foi utilizado o sistema de escore sugerido pela Sociedade Europeia para o Estudo do Fígado de 2012. Os dados demográficos, clínicos, laboratoriais e histológicos foram obtidos retrospectivamente. Obteve-se o DNA genômico de cada paciente a partir de sangue periférico e realizou-se o sequenciamento direto dos 21 éxons e suas bordas intrônicas do gene ATP7B. Todos os pacientes com DW apresentavam no mínimo quatro pontos. No grupo de rastreamento familiar o sequenciamento foi importante para o diagnóstico de DW em 14 familiares; no grupo de hepatite crônica criptogênica em oito pacientes e no grupo de insuficiência hepática aguda grave em três pacientes. Foi caracterizada uma família com cinco genótipos diferentes (dois homozigotos p.A1135Qfs/p.A1135Qfs e p.M645R/p.M645R), um heterozigoto composto (p.A1135Qfs/p.M645R) e dois heterozigotos simples (p.A1135Qfs/0 e p.M645R/0) com fenótipos variados. Foram detectadas duas mutações em heterozigose simples em pacientes com insuficiência hepática aguda grave. A mutação p.A1135Qfs e p.L708P foram as mais frequentes em todos os grupos. Foi identificada pela primeira vez a mutação p.M645R em homozigose. Concluímos que os resultados confirmaram que o sequenciamento do gene ATP7B foi útil: 1) para confirmar que as mutações p.A1135Qfs e p.L708P são as mais importantes na população brasileira; 2) para demonstrar que a mutação tida como a mais frequente na Europa, a p.H1069Q, tem bem menor importância em nosso meio, embora mais frequentemente do que o observado anteriormente; 3) para confirmar (ou excluir) precocemente o diagnóstico e evitar a realização de exames desnecessários e invasivos e iniciar (ou não realizar) o tratamento, com base mais sólida, em pacientes com hepatopatia crônica idiopática e em familiares de portadores de DW; 4) para definir o diagnóstico de DW em casos de insuficiência hepática aguda grave, diagnóstico ainda que tardio, mas de suma importância para realização de estudo familiar subsequente, 5) para identificação não esperada de heterozigotos simples e polimorfismos de significado ainda não esclarecido em pacientes com insuficiência hepática aguda grave; 6) para identificação de casos inusitados de três genótipos diferentes causadores da doença na mesma família (homozigose de duas mutações diferentes e heterozigose composta); 7) para melhor definir que a mutação p.M645R em homozigose tem potencial para desenvolver a DW, embora resultados de estudos em in vitro sugiram função normal da proteína defeituosa sintetizada; 8) para definir que há casos de doentes com a mutação p.M645R em heterozigose composta de evolução extremamente benigna, com diagnóstico após a quinta década de vida, com discretas alterações hepáticas. Porém há casos com evolução mais grave tanto do ponto de vista hepático quanto neurológico, possivelmente influenciados pelas mutações que a acompanham / Wilson\'s disease (WD) is an autosomal recessive disorder secondary to mutations in the ATP7B gene resulting in toxic accumulation of copper in various tissues. The diagnosis of WD is made by the analysis of clinical, laboratory, histological findings and imaging tests. More than 500 mutations have been described in the ATP7B gene as the cause of WD. In order to expand the knowledge of the importance of mutation detection in the diagnosis of WD, we analyzed 36 patients with WD, 20 individuals from family screening, 18 with cryptogenic chronic hepatitis and seven with severe acute liver failure. For the diagnosis of WD the International Scoring System suggested by the European Association for the Study of the Liver (EASL) in 2012 was used. Demographic, clinical, laboratory and histological data were obtained retrospectively. Direct sequencing of 21 exons and intron boundaries of ATP7B gene was performed in genomic DNA extracted from peripheral blood leucocytes of all subjects. All patients with WD have at least four points of the scoring system without considering the DPA challenge test. In the family screening group, sequencing was important for the diagnosis of DW in fourteen patients; eight patients in the group of cryptogenic chronic hepatitis, and three patients in the group of severe acute liver failure. Five different genotypes were identified in one family (two homozygous, p.A1135Qfs/p.A1135Qfs and p.M645R/p.M645R, one compound heterozygous p.A1135Qfs/p.M645R, and two simple heterozygous p.A1135Qfs/0 and p.M645R/0). Two patients with acute liver failure were detected as simple heterozygous. The p.A1135Qfs and p.L708P were the most frequent mutations in all groups. It is the first time p.M645R mutation was detected in homozygosity. The ATP7B gene sequencing was useful: 1) to confirm that p.A1135Qfs and p.L708P mutations are the most frequent in the Brazilian population; 2) to confirm that the most common mutation in Europe, p.H1069Q has lower frequency in our area; 3) to confirm (or exclude) an early diagnosis and to avoid unnecessary and invasive tests and to initiate (or not) the specific treatment with a stronger basis in patients with chronic liver disease and individuals from family screening of patients with Wilson disease; 4) to confirm the diagnosis, although late, of cases with severe acute liver failure, but very important to perform family screening; 5) to identify simple heterozygotes in patients with severe acute liver failure; 6) to describe unusual cases of three different genotypes of WD patients in a same family (two different homozygous mutations and one compound heterozygous); 7) to better define that p.M645R mutation in homozigosity develops WD, although the results from in vitro studies suggested a normal function for the defective synthesized protein; 8) to define that there are patients with p.M645R mutations in compound heretozigosity with a very benign clinical picture, with late diagnosis, after the fifth decade of life, with mild liver alterations. However, there are patients with a more severe clinical evaluation, hepatic or neurologic, probably secondary to the influence of the other mutation

Le remodelage ventriculaire est un processus réactionnel pouvant faire suite à un infarctus du myocarde (IDM), évènement ischémique aigu survenant lors de l'obstruction d'une artère coronaire. Le remodelage provoque alors des changements géométriques et fonctionnels du tissu myocardique qui permettent de maintenir et d'adapter la fonction cardiaque. Lorsque ce processus est délétère, la maladie évolue vers l'insuffisance cardiaque, ce qui altère le pronostic et la qualité de vie des patients. L'adénosine est un nucléoside ubiquitaire dont les effets sur le remodelage ventriculaire après IDM sont encore peu connus et dépendent du type de récepteur activé. Au sein de notre laboratoire, de précédentes études in vitro ont montré que l'adénosine régule de nombreux acteurs clés du remodelage. Dans ce travail de thèse, nous avons émis l'hypothèse que l'adénosine pouvait avoir un effet bénéfique sur le remodelage ventriculaire après la survenue d'un IDM. Dans un premier temps, nous avons montré que la tomographie par émission de positrons (TEP) permet de caractériser précisément les séquelles d'IDM et de prédire le remodelage ventriculaire chez le rat après occlusion coronaire. Cette technique nous a permis de mettre en évidence le cas d'un rat ayant survécu à un IDM touchant plus de 70% de son ventricule gauche. Dans un deuxième temps, nous avons montré que l'administration chronique d'adénosine, à long terme après IDM chez le rat, permet de maintenir la contractilité cardiaque dans la zone bordant l'IDM. Cet effet cardioprotecteur peut s'expliquer par une stimulation de l'angiogenèse elle-même due à un recrutement de cellules endothéliales progénitrices circulantes. Ensuite, nous avons montré que la chimiokine Monocyte Chemotactic Protein 3 est capable de stimuler la migration des cellules endothéliales progénitrices et est ainsi un agent thérapeutique potentiel après IDM. Enfin, nous avons commencé l'étude préclinique d'une molécule agoniste du récepteur A2A à l'adénosine et antagoniste du récepteur A3, un candidat particulièrement prometteur pour prévenir le remodelage ventriculaire après IDM / Left ventricular (LV) remodeling can follow myocardial infarction (MI), an acute ischemic event which occurs after occlusion of a coronary artery. Remodeling allows maintaining and adapting cardiac function by geometric and functional changes of the myocardium. If this process becomes maladaptive, the patients? prognostic and life quality are impaired by the development of heart failure. Adenosine is an ubiquitous nucleoside with partially characterized effects on LV remodeling. These effects depend on the type of receptor activated. Previous in vitro studies from our laboratory have shown that adenosine regulates several key processes involved in LV remodeling. Here, we hypothesized that adenosine may have beneficial effects on LV remodeling after MI. First, we showed that positon emission tomography (PET) can accurately characterize MI severity and predicts subsequent LV remodeling in the rat model of MI induced by coronary occlusion. Using this technique, we described the case of a rat that survived after a massive infarct covering 70% of the left ventricle. Second, we showed that a chronic administration of adenosine preserves cardiac contractility in the border zone, two months after MI. This cardioprotective effect can be explained, in part, by the stimulation of angiogenesis involving a stimulation of the recruitment of endothelial progenitor cells to the heart. Then, we showed that the Monocyte Chemotactic Protein 3 stimulates the migration of endothelial progenitor cells and is thereby a potential therapeutic target after MI. Finally, we started the preclinical study of an A2A agonist / A3 antagonist, a promising candidate to prevent LV remodeling after MI

A ecocardiografia com perfusão miocárdica em tempo real (EPMTR) permite a quantificação do fluxo sangüíneo miocárdico e, quando realizada durante o estresse, da reserva de fluxo miocárdico (reserva Axß). Essa técnica tem potencial para ser uma importante ferramenta para o diagnóstico não-invasivo da doença arterial coronariana (DAC). Apesar do conhecimento atual das alterações fisiológicas que ocorrem com o uso de agentes vasodilatadores ou catecolaminas na circulação coronariana, não há dados na literatura comparando diretamente o valor da EPMTR, sob estresse pela dobutamina e pela adenosina, para a detecção de DAC em humanos. Os objetivos deste estudo foram: avaliar, em um mesmo grupo de pacientes, a exeqüibilidade e a acurácia da EPMTR, sob estresse pela dobutamina e pela adenosina, para a detecção de estenose arterial coronariana angiograficamente significativa e determinar o valor adicional da análise quantitativa da perfusão miocárdica sobre o eletrocardiograma de 12 derivações, da motilidade segmentar e da análise qualitativa da perfusão miocárdica obtidas durante o estresse pela dobutamina e pela adenosina. Estudamos 54 pacientes (média etária de 60±9 anos, 33 homens) com suspeita clínica de DAC e indicação de angiografia coronariana. Todos os pacientes foram submetidos à EPMTR sob estresse pela adenosina na dose de 140 g/kg/min por seis minutos e, após um intervalo de três a cinco horas, à EPMTR sob estresse pela dobutamina-atropina. O contraste ecocardiográfico utilizado foi o PESDA (Perfluorocarbon-Exposed Sonicated Dextrose and Albumin), administrado por via intravenosa periférica de forma contínua. Para ambas as EPMTR sob estresse pela dobutamina e pela adenosina, foram feitas análises do eletrocardiograma em 12 derivações (ECG), da motilidade segmentar e análise qualitativa e quantitativa da perfusão miocárdica. A quantificação da velocidade do fluxo miocárdico (ß) e do fluxo sangüíneo miocárdico (Axß) foi realizada por meio da utilização do programa computacional QLab 3.0 (Philips Medical Systems, Bothell, WA, USA). Todos os pacientes foram submetidos à angiografia coronariana quantitativa (ACQ) em um intervalo de até 30 dias da EPMTR. Foi considerada DAC a presença de lesão coronariana > 50% do diâmetro luminal. Dos 54 pacientes estudados, 25 (46%) apresentaram lesão coronariana >50% e 29 (54%) não apresentaram lesão coronariana significativa. A exeqüibilidade da quantificação da reserva Axß foi semelhante para a EPMTR sob estresse pela adenosina e pela dobutamina (91% versus 90% dos territórios arteriais; p = ns). A variabilidade da quantificação interobservador para os parâmetros de reserva ß e Axß foi de 6,8% (r = 0,98) e 5,5% (r = 0,97), respectivamente. A variabilidade intra-observador para os mesmos parâmetros foi de 2,1 % (r = 0,99) e 7,4 % (r = 0,95), respectivamente. A análise quantitativa da perfusão miocárdica, obtida pela EPMTR sob estresse pela dobutamina, apresentou sensibilidade de 84%, especificidade de 76% e acurácia de 80% para a detecção de DAC, enquanto que a EPMTR sob estresse pela adenosina apresentou sensibilidade de 88%, especificidade de 72% e acurácia de 80%. O valor incremental das modalidades estudadas para o diagnóstico de DAC foi analisado em modelo que incluiu o ECG, ECG e motilidade segmentar, ECG e motilidade segmentar e perfusão qualitativa e, por último, ECG e motilidade segmentar e perfusão qualitativa e quantitava, tanto para a EPMTR sob estresse pela dobutamina como pela adenosina (2 de 4,9 versus 20,1 versus 23,7 versus 38,4) e (2 de 9,9 versus 20,1 versus 26,7 versus 59,4), respectivamente. Concluímos que a avaliação quantitativa da EPMTR apresenta boa exeqüibilidade. A EPMTR sob estresse pela dobutamina e a pela adenosina apresentam acurácias diagnósticas similares para a detecção de lesão angiograficamente significativa. A análise quantitativa da perfusão miocárdica apresenta valor diagnóstico adicional aos outros parâmetros obtidos durante o estresse pela dobutamina e adenosina. / Real time myocardial contrast echocardiography (RTMCE) has allowed for the quantification of myocardial blood flow reserve (MBFR). This technique is a valuable tool for the noninvasive detection of coronary artery disease (CAD). Both adenosine and dobutamine are currently used stressor agents during RTMCE. Although it has already been shown the effects of these drugs on the coronary physiology, no study has directly compared both agents during RTMCE. The aims of this study were to determine the feasibility and diagnostic accuracy of adenosine versus dobutamine stress RTMCE for the detection of angiographically significant CAD. In addition, we sought to determine the additional value of quantitative RTMCE over the electrocardiogram, wall motion, and qualitative analysis of myocardial perfusion. The study involved 54 patients (60±9 years, 33 men) with suspected CAD. Patients underwent RTMCE at rest and during continuous infusion of 140g/kg/min of adenosine for six minutes, and dobutamine stress. The contrast agent used in the study was PESDA (Perfluorocarbon-Exposed Sonicated Dextrose and Albumin) administered in continuous intravenous infusion. Quantification of plateau of acoustic intensity (A) and microbubble velocity () was performed off line using a specific software (QLab 3.0, Philips Medical Systems, Bothell, WA, USA). Myocardial blood flow was determined as Ax. Quantitative coronary angiography was performed in all patients within 30 days of RTMCE, and CAD was defined as >50% luminal diameter coronary stenosis. There were 25 (46%) patients with CAD and 29 (54%) patients without obstructive lesion. The feasibility of quantitative MBFR was the same for adenosine and dobutamine stress RTMCE (91% versus 90% in all arterial territories; p=ns). The intraobserver variabilities for the measurements of ß and Axß reserve were 2.1% (r = 0.99) and 7.4% (r = 0.95), respectively. The interobserver variabilities for the same parameters were 6.8% (r = 0.98) and 5.5% (r = 0.97), respectively. The sensitivity, specificity and diagnostic accuracy of ß reserve obtained during dobutamine stress RTMCE for detecting CAD were 84%, 76%, and 80%, respectively, and during adenosine stress RTMCE they were 88%, 72% and 80%. The incremental value for the diagnosis of CAD was analyzed in a model that included the EKG, EKG and wall motion, EKG and wall motion and qualitative perfusion analysis and finally, EKG and wall motion and qualitative and quantitative perfusion analysis, for dobutamine and adenosine RTMCE (2= 4,9 versus 20,1 versus 23,7 versus s 38,4) and (2= 9,9 versus 20,1 versus 26,7 versus 59,4), respectively. In conclusion, quantitative RTMCE is a feasible technique in patients with suspected CAD. Dobutamine and adenosine stress RTMCE had similar diagnostic accuracy for the detection of angiographically significant lesion. Quantitative analysis of myocardial perfusion had incremental diagnostic value over the other parameters obtained during both dobutamine and adenosine stress RTMCE.

Les Récepteurs Couplés aux Protéines G (RCPG) constituent la plus grande famille de protéines membranaires chez l’Homme, et leur implication dans un grand nombre de processus physiologiques justifie pleinement l’intérêt de leur étude. Les anticorps spécifiques de ces récepteurs sont des outils polyvalents à haute valeur ajoutée, qui restent toutefois encore trop rarement disponibles, notamment en raison des difficultés techniques posées par leur génération. Ce manuscrit présente la mise au point d’une méthode d’immunisation alternative et innovante, mettant en jeu des particules virales recombinantes dérivées du Virus de la Forêt de Semliki (SFV) codant pour le récepteur d’intérêt. Appliquée au récepteur de l’adénosine A2A humain, l’immunisation permet d’engendrer la surexpression de celui-ci à la surface des cellules de l’animal infecté, et de provoquer l’apparition d’une réponse immunitaire. Cette approche permet d’une part de générer un sérum polyclonal de souris spécifique au récepteur, et ouvre donc une nouvelle voie pour l’obtention d’anticorps monoclonaux murins. Elle semble d’autre part prometteuse pour la génération de nanobodies. / G Protein Coupled Receptors (GPCRs) constitute the largest membrane protein family represented in the human genome. Their involvement in a wide number of biological processes fully supports their study. GPCR-targeting antibodies are versatile and valuable tools, which remain scarcely available, chiefly because their generation is a challenging process. This thesis presents an alternative and innovative strategy in which recombinant Semliki Forest Virus (SFV) particles coding for the receptor of interest are used as immunogens. When applied to the human version of the Adenosine A2A receptor, this method enables to cause the receptor’s overexpression at the surface of the infected animal cells, which generates an immune response. This strategy enables to raise receptor-specific mouse polyclonal serum. It opens a new path towards the generation of monoclonal mouse antibodies. Additionally, it seems to also be a promising approach to develop nanobodies.

Biological processes are so complicated that to understand the mechanisms underlying the functioning of biomolecules it is inevitable to study them from various perspectives and with a wide range of tools. Understanding the function at the molecular level obviously requires the knowledge of the three dimensional structure of the biomolecules. Experimentally this can be obtained by techniques such as X‐ray crystallography and NMR studies. Computational biology has also played an important role in elucidating the structure function relationship in biomolecules. Computationally one can obtain the temporal as well as ensemble behavior of biomolecules at atomic level under conditions that are experimentally not accessible. Molecular dynamics(MD) study is a technique that can be used to obtain information of the dynamic behavior of the biomolecules. Dynamics of large systems like proteins can be investigated by classical force fields. However, the changes at the level of covalent bond involve the reorganization of electron density distribution which can be addressed only at Quantum mechanical level. In the present thesis, some of the biological systems have been characterized both at the classical and quantum mechanical level. The systems investigated by MD simulations and the insights brought from these studies are presented in Chapters 3 and 4. The unusual bonds such as pyrophosphate linkage in ATP and short strong hydrogen bonds in proteins, investigated through high level quantum chemical methods, are presented in Chapters 5, 6 and 7. Part of this thesis is aimed to address some important issues related to the dynamics of Tryptophanyl tRNA synthetase (TrpRS) which belongs to classic of aminoacyl‐tRNA synthetases (aaRS). aaRSs are extremely important class of enzymes involved in the translation of genetic code. These enzymes catalyze the aminoacylation of tRNAs to relate the cognate amino acids to the anticodon trinucleotide sequences. aaRSs are modular enzymes with distinct domains on which extensive kinetic and mutational experiments as well as structural analyses have been carried out, highlighting the role of inter‐domain communication (Alexander and Schimmel, 2001). The overall architecture of tRNA synthetases consists of primarily two domains. The active site domain is responsible for the activation of an amino acid with ATP in synthesizing an enzyme‐bound aminoacyl‐adenylate, and transfer of the aminoacyl‐adenylate intermediate to the 3’end of tRNA. The second domain is responsible for selection and binding of the cognate tRNA. aaRSs are allosteric proteins in which the binding of tRNA at the anticodon domain influences the activity at the catalytic region. These two binding sites are separated by a large distance. One of the aims of this thesis is to characterize such long distance communication (allosteric communication) at atomic level in Tryptophanyl tRNA synthetase. This is achieved by generating ensembles of conformations by MD simulations and analyzing the trajectories by novel graph theoretic approach. Graph and network based approaches are well established in the field of protein structure analysis for analyzing protein structure, stability and function (Kannan and Vishveshwara, 1999; Brinda and Vishveshwara, 2005). The parameters such as clusters, hubs and shortest paths provide valuable information on the structure and dynamics of the proteins. In this thesis, network parameters are used for the analysis of molecular dynamics MD) simulation data, to represent the global dynamic behavior of protein in a more elegant way. MD simulations are performed on some available (and modeled) structures of TrpRS bound to a variety of ligands, and the protein structure networks( PSN) of non‐covalent interactions are characterized in dynamical equilibrium. The ligand induced conformational changes are investigated through structure networks. These networks are used to understand the mode of communication between the anticodon domain and the active site. The interface dynamics is crucial for the function of TrpRS (since it is a functional dimer) and it is investigated through interface clusters. The matter embodied in the thesis is presented as 9 chapters. Chapter 1 lays the suitable background and foundation for the study, surveying relevant literature from different fields .Chapter 2 describes in detail the various materials, methods and techniques employed in the different analyses and studies presented in this thesis. A brief description of well‐known methods of molecular dynamics simulations, essential dynamics calculations, cross correlation maps, conformational clustering etc.is presented. The methods for constructing protein structure graphs and networks, developed in our lab, are described in detail. The use of network parameters for the analysis of MD simulation data to address the problem of communication between the two distal sites is also presented. Some descriptions of the ab initio quantum mechanical methods, which are used to investigate the unusual bonds in biomolecules, are also presented in this chapter. Chapter 3 is devoted in discussing the results from several normal as well as high temperature MD simulations of ligand‐free and ligand bound Bacillus stearothermophilus Tryptophanyl‐tRNA synthetase (bsTrpRS). The essential modes of the protein in the presence of different ligands are captured by essential dynamics calculations. Different conformations of the protein associated with the catalysis process of TrpRS, as captured through experiments, are discussed in the context of conformational sampling. High temperature simulations are carried out to explore the larger conformational space. Chapter 4 is focused on the results obtained from the MD simulation of human Tryptophanyl‐tRNA synthetase (hTrpRS). The structure of human TrpRS bound to the activated ligand (TrpAMP) and the cognate tRNA(tRNATRP) is modeled since no structure in the presence of both TrpAMP and tRNATRP is available. MD simulations on these modeled as well as other complexes of hTrpRS are performed to capture the dynamical process of ligand induced conformational changes (Hansiaetal., communicated). Both the local and the global changes in the protein conformation from the protein structure network (PSN) of MD snapshots are analyzed. Several important information such as the ligand induced correlation between different residues of the protein, asymmetric binding of the ligands to the two subunits of the protein, and the path of communication between the anticodon region and the aminoacylation site are obtained. Also, the role of the dimmer interface, from a dynamic perspective, is obtained for the first time. The interface dynamics which stabilize different quaternary structures of lectins (with high sequence and structure similarity) were investigated in a collaborative work (Hansiaetal.,2007). The lectin peanut agglutinin (PNA) is a tetramer with three different types of interfaces. The interface dynamics of this protein in the presence and in the absence of metal ions was investigated and the paper reporting the results from this study is included as appendix in this thesis. Chapter 5 deals with high level ab initio quantum chemical calculations on tri‐ and diphosphate fragments of adenosine triphosphate (ATP). Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of calculations (Hansiaetal., 2006a). The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the‘‘highenergy’’character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results aid in the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. Hydrogen bonding is fundamental in understanding the structure and properties of molecules of biological interest including proteins. A recent analysis carried out in our lab showed that a significant number of short hydrogen bonds (SHB) are present in proteins (Rajagopal and Vishveshwara, 2005). Chapters 6 and 7 elucidate the results obtained from ab initio quantum chemical calculations on some of these SHBs to get aquantitative estimation of their geometry and strength. In chapter 6, asystematic analysis of the geometries and the energetics of possible SHB systems, which are frequently encountered in proteins, are presented at different levels of theory (HF,DFTandMP2). It is found that the SHBs involving both charged residues in the proteins are intrinsic in nature. However, two neutral residues form a SHB in the protein crystal structures either due to geometric constraints or due to the environment of these residues. This analysis enables one to distinguish SHBs which are formed because of geometric constraints from those which are formed because of the inherent property of the chemical groups involved in the hydrogen bonding. These results are useful in refining protein structures determined by crystallographic or NMR methods. In addition, sulfur atom of methionine and cysteinein proteins also participate in SHBs, which are not so well characterized. Chapter 7 presents the similar analysis carried out on short hydrogen bonds in proteins involving sulfur atom. A detailed analysis of SHBs of sulfur containing groups in a data set of proteins has been carried out. Some of the residue pairs from this analysis were considered for ab initio calculations. However, the optimization of these examples resulted in breaking of the hydrogen bonds involving sulfur atoms and formation of new hydrogen bonds with oxygen and/or nitrogen atoms. Hence model systems, which mimic the real examples, were designed to carry out ab initio studies and to investigate the short hydrogen bonds involving sulfur atoms. Another study on the protein‐water interaction, which does not fall under the realm of the main objective of the thesis, is discussed in Chapter 8. Protein–water interaction is crucial for accomplishing many biological functions of proteins. In the recent past, natural probe tryptophan, located at the protein surfaces, has been extensively investigated using femtosecond spectroscopy experiments to understand salvation dynamics (Peonetal.,2002). In this chapter a method is described to follow up the molecular events of the protein–water interactions in detail. Tryptophan–water interaction in the protein Monellin is investigated in order to get the atomic level insights into the hydration dynamics, by carrying out MD simulations on Monellin (Hansiaetal.,2006b). The results are compared with those obtained from femtosecond resolved fluorescence spectroscopy. The time constants of the survival correlation function match well with the reported experimental values.This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general. The last chapter (Chapter9) summarizes the results obtained from various studies and discusses the future directions. First part of this thesis aims to present the analysis by carrying out MD simulations on monomeric and dimeric TrpRS protein in order to understand the two steps of the aminoacylation reaction: activation of the aminoacid Trp in the first step and the transfer of the activated amino acid in the next step. In the second part, quantitative estimation of the geometry and the strength of pyrophosphate bond and short hydrogen bonds in proteins are reported in detail by subjecting the systems to high levels of quantum mechanical calculations(QM). The use of ab initio QM/MM calculations by combining the quantum mechanics(QM) with the molecular mechanics(MM) in order to study the enzymatic reactions is discussed as the future

El objetivo de la presente tesis es el de aportar conocimiento sobre la bioquímica y la farmacología de los receptores de adenosina, así como entender las relaciones entre estructura química y actividad farmacológica de los ligandos existentes para estos receptores. Con este objetivo se han empleado distintas técnicas y metodologías del diseño de fármacos asistido por ordenador. Los resultados presentados en este trabajo incluyen:· El desarrollo de una estrategia original para la selección de una muestra que cubra adecuadamente la diversidad molecular existente en una base de datos de compuestos químicos· La construcción de un modelo de la región transmembrana del receptor A1 humano de adenosina, en el que se ha localizado y caracterizado un sitio de unión de agonistas compatible con los datos experimentales.· Predicciones teóricas de las energías de unión de ligandos, realizadas a partir de los complejos agonista-receptor predichos sobre el modelo mencionado, obteniendo un grado de acuerdo con los datos experimentales que resulta esperanzador / The goal of the present thesis is to gain knowledge about the biochemistry and pharmacology of adenosine receptors, as well as to understand structure-activity relationships for the existing ligands for this receptors. In order to achieve this goal, we have used several techniques and methodologies from the computer-aided drug design field. Results presented in this work include:· The development of an original strategy of selection of a maximum diversity sample that adequately covers the original molecular diversity contained in a compound database· The building of the transmembrane region of a human A1 adenosine receptor model. In such a model, an agonists binding site has been located and characterized, showing agreement with experimental data.· The resulting ligand-receptor complexes have been studied with computational approaches for the prediction of ligand-binding free energies. A nice correlation with experimental results was observed

La adicción es un trastorno crónico de la conducta caracterizado por la búsqueda y el consumo compulsivos de la droga, la pérdida de control para limitar dicho consumo, a aparición de un estado emocional negativo cuando el acceso a la droga está impedido y la recaída en el proceso incluso tras largos períodos de abstinencia. El sistema dopaminérgico mesolímbico cortical ha sido propuesto como la principal base neurobiológica de la adicción, sin embargo existen otros sistemas de neurotransmision que participan en la consolidación del proceso adictivo.El sistema endocannabinoide, a traves del receptor CB1, participa en las propiedades adictivas de diferentes drogas de abuso como el delta9-tetrahidrocannabinol, la nicotina y la morfina. Sin embargo, hasta el momento de iniciar este trabajo, pocos estudios han demostrado una clara implicación del sistema endocannabinoide en las propiedades reforzantes de los psicoestimulantes. Mediante el uso de ratones CB1 knockout, hemos demostrado que el receptor CB1 participa en la eficacia reforzante de la cocaína. Además, la presencia de dicho receptor es necesaria para los procesos de consolidación de una conducta operante mantenida por la autoadministración de cocaína. Este estudio demuestra la importancia de dicho receptor CB1 en las propiedades adictivas de la cocaína, confirmando que el sistema endocannabinoide es un sustrato común para la adicción de drogas de abuso. Por otra parte, el sistema purinérgico modula numerosos sistemas de neurotransmisión en el SNC. La estrecha relación a nivel celular y funcional entre los receptores de adenosina y los receptores dopaminérgicos proporciona evidencias de que el sistema purinérgico podría modular los sistemas de recompensa. Utilizando diferentes modelos animales, hemos demostrado que los receptores de adenosina A2A son necesarios para que las propiedades adictivas de las drogas de abuso como los cannabinoides, los opioides, la nicotina y los psicoestimulantes se produzcan de un modo completo.Nuestros estudios nos permiten afirmar que ambos sistemas, el cannabinoide y el purinérgico podría suponer la existencia de nuevos sistemas de modulación común de los procesos adictivos. Asi, sería de gran interés desarrollar nuevas estrategias de bloqueo de los receptores A2A y CB1 para atenuar e incluso prevenir el desarrollo de la adicción. / Drug addiction is a chronically relapsing disorder that is defined by a compulsion to take the drug intake, a loss of control in limiting intake and a withdrawal-negative affect state when the access to the drug is interrupted. Mesolimbic dopaminergic system has been proposed as a fundamental neurobiological substrate for drug addiction. However, there is evidence for other neurotransmitter systems involved in the consolidation of the addictive process. The endocannabinoid system, through the activation of CB1 receptor, participates in the addictive properties of different drugs of abuse such as delta9-tetrahydrocannabinol, morphine and nicotine. Nevertheless, few studies have revealed an important implication of CB1 receptor in the reinforcing properties of psychostimulants. By using CB1 knockout mice, we have demonstrated that CB1 receptor participates in the reinforcing efficacy of cocaine. Moreover, this receptor is necessary for the consolidation processes involved in cocaine maintained intravenous self-administration. Therefore, this study reveals an essential role of CB1 receptor in cocaine addictive properties, confirming that the endocannabinoid system is a common substrate of addiction to drugs of abuse.On the other hand, the purinergic system modulates different neurotransmitter systems in the CNS. Adenosine receptors are closely related to dopaminergic receptors at both cellular and functional levels, suggesting that purinergic system could modulate the reward systems. By using different animal models, we have demonstrated that A2A adenosine receptors are necessary for the development of the addictive properties of drugs of abuse such as opioids, cannabinoids, nicotine and cocaine. Our studies suggest that both cannabinoid and purinergic systems could represent new and common modulatory systems of addictive processes. Thus, it would be of interest to develop new therapeutic targets blocking CB1 and A2A receptors to attenuate the development of addiction.

Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutically relevant areas: a neglected tropical disease, an ion channel anti-drug-target, and GPCR drug-targets. We report three compounds inhibiting cruzain, the main cysteine protease of the protozoa causing Chagas’ disease. The compounds were found through an extensive virtual screening study and validated with experimental enzymatic assays. The compounds inhibit the enzyme in the μM-range and are therefore valuable in further lead optimization studies. A high-resolution crystal structure of the BRICHOS domain is reported, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry studies. This work revealed a plausible mechanism for how the chaperone activity of the domain may operate. Rationalization of structure-activity relationships for a set of analogous blockers of the hERG potassium channel is given. A homology model of the ion channel was used for docking compounds and molecular dynamics simulations together with the linear interaction energy method employed for calculating the binding free-energies. The three-dimensional coordinates of two GPCRs, 5HT1B and 5HT2B, were derived from homology modeling and evaluated in the GPCR Dock 2013 assessment. Our models were in good correlation with the experimental structures and all of them placed among the top quarter of all models assessed.  Finally, a computational method, based on molecular dynamics free-energy calculations, for performing alanine scanning was validated with the A2A adenosine receptor bound to either agonist or antagonist. The calculated binding free-energies were found to be in good agreement with experimental data and the method was subsequently extended to non-alanine mutations. With extensive experimental mutation data, this scheme is a valuable tool for quantitative understanding of ligand binding and can ultimately be used for structure-based drug design.