Orientador: Prof. Dr. Rodrigo Maghdissian Cordeiro / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Ciência & Tecnologia - Química, 2015. / Os componentes lipídicos das membranas celulares são substratos comuns de ataque oxidativo. Durante uma oxidação não-enzimática, tanto os fosfolipídios quanto o colesterol podem reagir com moléculas de 1O2 geradas fotodinamicamente via adição ene, produzindo hidroperóxidos de fosfolipídios e colesterol, respectivamente. Os efeitos citotóxicos e apoptóticos desses hidroperóxidos estão relacionados com a sua influência sobre as propriedades biofísicas das membranas fosfolipídicas, assim como na sua habilidade em disseminar o stress oxidativo. Estas habilidades relacionam-se fortemente com a estrutura química destes hidroperóxidos. Contudo, os mecanismos moleculares subjacentes ainda não estão bem compreendidos. Aqui, foram realizadas simulações de dinâmica molecular de diferentes produtos da oxidação dos fosfolipídios e hidroperóxidos de colesterol em bicamadas de fosfatidilcolina monoinsaturadas. O efeito combinado da peroxidação do colesterol e fosfolipídio também foi investigado. Depois da oxidação, tanto o núcleo rígido de esterol quanto as cadeias acila sn-2 dos fosfolipídios reorientam-se e os grupos hidrofílicos inseridos formam ligações de hidrogênio com os grupos carboniléster dos fosfolipídios. Para o colesterol, esta reorientação provocou a perda das propriedades de condensação e ordenação, com possíveis implicações à formação de domínios laterais na membrana. No caso dos radicais peroxila de colesterol, pequenas mudanças na orientação foram observadas dependendo da posição dos grupos -OO no núcleo de esterol. As possíveis implicações para as habilidades do radical propagar a reação em cadeia foram discutidas. / Lipid components of cell membranes are common substrates for oxidative attack. During a non-enzymatic oxidation, both phospholipids as well as cholesterol molecules can react with photodynamically generated 1O2 via ene addition, producing phospholipids and cholesterol hydroperoxides, respectively. The cytotoxic and apoptotic effects of these hydroperoxides are related to their influence on the biophysical properties of phospholipid membranes, as well as their ability to disseminate oxidative stress. These abilities relate strongly to the chemical structure of these hydroperoxides. However, the underlying molecular mechanisms are not well understood. Here, molecular dynamics simulations of different oxidation products of phospholipids and cholesterol hydroperoxides in monounsaturated phosphatidylcholine bilayers have been performed. The combined effect of phospholipid and cholesterol peroxidation was also investigated. After oxidation, both the rigid ring sterol and the sn-2 acyl chains of the phospholipids tilt themselves and the inserted hydrophilic groups form h-bonds with carbonylester groups of phospholipids. For cholesterol, this tilting caused the loss of condensation and ordering properties, with possible implications for the formation of lateral domains in the membrane. In the case of cholesterol peroxyl radicals, small changes in orientation were observed depending on the position of -OO groups in the sterol ring. The possible implications for the radical skill to propagate the chain reaction were discussed.

La drépanocytose est une maladie génétique qui se caractérise par des globules rouges en forme de faucille. Chez les personnes atteintes de drépanocytose, ces globules rouges (GR) adhèrent à l’endothélium vasculaire et provoquent ainsi une vaso-occlusion. Ce phénomène s’explique par la surexpression de la protéine Lutheran (Lu) à la surface des globules rouges falciformes qui se lie fortement à la Laminine (Ln) 511/521 exprimée par l’endothélium vasculaire enflammé. Le but de cette étude est d’identifier un inhibiteur d’interaction protéine-protéine (PPI) qui possède une forte probabilité de liaison à Lu afin d’inhiber l’interaction Lu-Ln 511/521. Un criblage virtuel de 1 295 678 composés ciblant la protéine Lu a été réalisé. La validation préalable d’un protocole de scoring a été envisagée sur la protéine CD80 qui présente un site de liaison avec des caractéristiquestopologiques et physico-chimiques similaires au site de liaison prédit sur Lu ainsi que plusieurs ligands avec des constantes d’affinité connues. Ce protocole contient différentes étapes de sélection basées sur les affinités calculées (scores), des simulations de dynamique moléculaire et les propriétés moléculaires. Un protocole de scoring fiable a été validé sur CD80 avec le programme de docking DOCK6 et les fonctions de scoring XSCORE et MM-PBSA ainsi qu’avec la méthode decalcul FMO. L’application de ce protocole sur Lu a permis d’obtenir deux ligands validés par des tests in vitro qui font l’objet d’un dépôt de brevet. La fonction de scoring XSCORE a permis d’identifier neuf autres ligands qui semblent aussi être des candidats prometteurs pour inhiber l’interaction Lu-Ln 511/521. / Drepanocytosis is a genetic blood disorder characterized by red blood cells that assume an abnormal sickle shape. In the pathogenesis of vaso-occlusive crises of sickle cell disease, red blood cells bind to the vascular endothelium and promote vaso-occlusion. At the surface of these sickle red blood cells, the overexpressed protein Lutheran (Lu) strongly interacts with the Laminin (Ln) 511/521.The aim of this study was to identify a protein-protein interaction (PPI) inhibitor with a highprobability of binding to Lu for the inhibition of the Lu-Ln 511/521 interaction. A virtual screening was performed with 1 295 678 compounds that target Lu. Prior validation of a robust scoring protocol was considered on the protein CD80 because this protein has a binding site with similar topological and physico-chemical characteristics and it also has a series of ligands with known affinity constants. This protocol consisted of multiple filtering steps based on calculated affinities (scores), molecular dynamics simulations and molecular properties. A robust scoring protocol was validated on the protein CD80 with the docking program DOCK6 and the scoring functions XSCORE and MM-PBSA and also with the FMO method. This protocol was applied to the protein Lu and we found two compounds that were validated by in vitro studies. The protection of these ligands by a patent is under process. Nine other compounds were identified by the scoring functionXSCORE and seem to be promising candidates for inhibiting the Lu-Ln 511/521 interaction.

Submitted by ERNANE DE FREITAS MARTINS (ernanefmg@hotmail.com) on 2018-06-21T18:31:22Z No. of bitstreams: 1 Tese_Ernane_FINAL.pdf: 73762259 bytes, checksum: 783c569159077630257fc1df333452da (MD5) / Approved for entry into archive by Hellen Sayuri Sato null (hellen@ift.unesp.br) on 2018-06-22T17:57:30Z (GMT) No. of bitstreams: 1 martins_ef_dr_ift.pdf: 73762259 bytes, checksum: 783c569159077630257fc1df333452da (MD5) / Made available in DSpace on 2018-06-22T17:57:30Z (GMT). No. of bitstreams: 1 martins_ef_dr_ift.pdf: 73762259 bytes, checksum: 783c569159077630257fc1df333452da (MD5) Previous issue date: 2018-06-04 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Nanotechnology is an important and very active area of research contributing to many different fields. The development of new devices applied to personalized medicine is one of its applications. When we desire to develop new devices many effort are done, including experimental and theoretical investigations. The theoretical/computational physics can enormously contribute to this area, since the simulations can reveal the working mechanism in these systems being possible to understand and propose new devices with improved performance. We present an extensive theoretical investigation of the electronic transport properties of graphene-based devices for DNA sensing. We have used a hybrid methodology which combines quantum mechanics and molecular mechanics, the so called QM/MM method, coupled to electronic transport calculations using non-equilibrium Green’s functions. First, we studied graphene in solution in order to understand the effects of polarization on the electronic and transport properties under different salt concentrations. We also stud- ied graphene with Stone-Wales defect in pure water. For these systems we tested a simple polarization model based on rigid rods. Our analysis were also done over different QM/MM partitions including explicit water molecules in the quantum part. Our results showed that the inclusion of the solvent in the electronic transport calculations for graphene decreases the total transmission, showing the important role played by the water. Our results also showed that the electronic transport properties of graphene do not suffer significant changes as we increase the salt concentration in the solution. The inclusion of polarization effects in graphene, despite changing the structuring of water molecules that make up the first solvation shell of graphene, do not significantly affect the electronic transport through graphene. We then studied DNA sequencing devices. First we focused on sequencing using a nanopore between topological line defects in graphene. Our results showed that sequencing DNA with high selectivity and sensitivity using these devices appears possible. We also address nanogap in graphene. For this we looked at the effects of water on electronic transport by using different setups for the QM/MM partition. We showed that the inclusion of water molecules in the quantum part increases the electronic transmission in several orders of magnitude, also showing the fundamental role played by water in tunneling devices. The electronic transport simulations showed that the proposed device has the potential to be used in DNA sequencing, presenting high selectivity and sensitivity. We propose an graphene-based biochip for sequence-specific detection of DNA strands. The main idea of this sort of device is to detect hybridization of single-stranded DNA, forming double-stranded DNA. We showed that the vertical DNA adsorption, either through an anchor molecule (pyrene) or using the nucleotide itself as anchor, do not present good results for detection, since the signals for the single and double strands are quite similar. For the case of horizontal DNA adsorption on graphene our results indicated that the two signals can be distinguishable, showing promising potential for sensitivity and selectivity. / Nanotecnologia é uma importante e muito ativa área de pesquisa contribuindo para muitos campos diferentes. O desenvolvimento de novos dispositivos aplicados à medicina personalizada é uma de suas aplicações. Quando desejamos desenvolver novos dispositivos muitos esforços são feitos, incluindo investigações experimentais e teóricas. A Física teórica/computacional pode contribuir enormemente com esta área, já que simulações podem revelar o mecanismo de funcionamento nesses sistemas tornando possível entender e propor novos dispositivos com desempenho melhorado. Nós apresentamos uma extensa investigação teórica das propriedades de transporte eletrônico de dispositivos baseados em grafeno para sensoriamento de DNA. Utilizamos uma metodologia híbrida que combina mecânica quântica e mecânica molecular, o chamado método QM/MM, acoplado a cálculos de transporte eletrônico utilizando funções de Green fora do equilíbrio. Primeiramente nós estudamos grafeno em solução de modo a entender os efeitos de polarização nas propriedades eletrônica e de transporte em diferentes concentrações de sal. Também estudamos grafeno com defeito Stone-Wales em água pura. Para esses sistemas, testamos um modelo de polarização simples baseado em bastões rígidos. Nossas análises também foram feitas em diferentes partições QM/MM incluindo moléculas de água explícitas na parte quântica. Nossos resultados mostraram que a inclusão do solvente nos cálculos de transporte eletrônico para o grafeno diminui a transmissão total, mostrando o papel fundamento desempenhado pelo água. Nossos resultados também mostraram que as propriedades de transporte eletrônico do grafeno não sofrem mudanças significativas na medida em que aumentamos a concentração de sal na solução. A inclusão de efeitos de polarização em grafeno, apesar de mudar a estruturação das moléculas de água que compõem a primeira camada de solvatação do grafeno, não afeta significativamente o transporte eletrônico através do grafeno. Nós, então, estudamos dispositivos para sequenciamento de DNA. Focamos primeira- mente no sequenciamento usando nanoporo entre defeitos de linha topológicos no grafeno. Nossos resultados mostraram que o sequenciamento de DNA com alta seletividade e sensitividade usando esses dispositivos se mostra possível. Nós também abordamos nanogap em grafeno. Para tal, avaliamos os efeitos da água no transporte eletrônico utilizando diferentes configurações para a partição QM/MM. Mostramos que a inclusão de moléculas de água na parte quântica aumenta a transmissão eletrônica em várias ordens de grandeza, também mostrando o papel fundamental desempenhado pela água em dispositivos de tunelamento. As simulações de transporte eletrônico mostraram que o dispositivo proposto tem o potencial de ser usado em sequenciamento de DNA, apresentando alta seletividade e sensitividade. Propusemos um biochip baseado em grafeno para detecção de sequências específicas de fitas de DNA. A ideia principal desta classe de dispositivos é detectar a hibridização da fita simples de DNA, formando a fita dupla de DNA. Mostramos que a adsorção vertical de DNA, seja utilizando uma molécula âncora (pireno) ou utilizando o próprio nucleotídio como âncora, não apresenta bons resultados para detecção, já que os sinais para as fitas simples e dupla são bem próximos. Para o caso da adsorção horizontal de DNA em grafeno nossos resultados indicaram que os dois sinais podem ser distinguíveis, mostrando potencial promissor para sensitividade e seletividade.

La thèse est axée sur l'examen de l'effet de la contrainte sur la conductivité thermique des matériaux piézoélectriques. Les matériaux piézoélectriques sont des cristaux qui présentent une déformation mécanique lors de l'application d'un champ électrique. Des exemples de tels systèmes sont ZnO, AlN, et SiO2. En utilisant des simulations de dynamique moléculaire, nous avons calculé la conductivité thermique de cristaux de ZnO et AlN sous contrainte. Nous avons aussi calculé la résistance thermique des interfaces SiO/C et ZnO/C soumis à un champ électrique.Nous commençons par le calcul des propriétés piézoélectriques et élastiques de ZnO. Celles-ci serviront à valider les potentiels interatomiques utilisés, et à montrer l'ampleur de la contrainte qu’il est possible d'appliquer. En utilisant la dynamique moléculaire d'équilibre, nous avons estimé le coefficient élastique c33 de ZnO, qui se trouve être en accord avec les valeurs expérimentales. Il a aussi été déterminé que la limite élastique d'un cristal de ZnO est de 6 GPa, ce qui correspond à une déformation de 6%. Nous avons ensuite établi les coefficients piézoélectriques de ZnO en utilisant la dynamique moléculaire de non-équilibre, et il a été constaté que les coefficients piézoélectriques dij sont en accord avec les valeurs de la littérature.Deuxièmement, nous avons examiné l'effet de la pression sur la conductivité thermique intrinsèque de ZnO et d’AlN. La dynamique moléculaire de non-équilibre inverse a été mise en œuvre pour calculer la conductivité parce que les coûts de calcul sont nettement inférieurs à ceux de la méthode d'équilibre, d’autant plus pour ZnO dont le potentiel inter-atomique contient les interactions Coulombiennes. L'effet de taille sur la conductivité thermique de ZnO et AlN a ensuite été étudié. Nous avons montré que la formule de Schelling peut en effet être mise en œuvre pour les deux cristaux pour différentes valeurs de la contrainte. La conductivité thermique pour un cristal de ZnO de taille infinie est extraite de la formule de Schelling, et elle se révèle être de 410 W/mK. La conductivité thermique de cristaux de ZnO sous contrainte a ensuite été analysée. Nous avons montré que, après correction de l'effet de taille, la conductivité thermique suit une dépendance en loi de puissance à la contrainte uniaxiale. De plus, la conductivité thermique de ZnO est affectée par un champ statique externe en raison de la contrainte induite. La conductivité thermique d'AlN est estimée à 3000 W/mK, l'effet de la contrainte ne modifie pas cette valeur du fait du potentiel inter-atomique utlisé. Par conséquent, AlN n’est pas un matériau pertinent pour faire office de switch thermique.Troisièmement, nous avons exploré l'effet d’un déplacement piézoélectrique sur la conductance thermique d’interface de Si2O/graphène et ZnO/graphène. Utilisant la dynamique moléculaire d’équilibre, la conductivité thermique d'un super-réseau dont la période est composée de silice et de graphène polyfeuillet. Le super-réseau a été évalué pour différentes valeurs du champ électrique externe. Nous avons constaté que l'application d'un champ électrique de 20 MV/m positif parallèle à la direction hors-plan du super-réseau conduit à la réduction de la conductivité thermique d'un facteur deux. D'autre part, aucun changement dans la conductance thermique n’est noté pour le super-réseau ZnO/graphène. Cette différence est due aux différences de déformations induites au niveau des interfaces dans le super-réseau. L'effet est recréé dans un super-réseau Si/Ge en appliquant une déformation pour former les interfaces. Cette approche crée une déformation non uniforme qui est susceptible de diffuser les phonons. / The thesis is focused on investigating the effect of strain on the thermal conductivity of piezoelectric materials. Piezoelectric materials are crystals which display a mechanical deformation upon application of an electric field. Examples of such material are ZnO, AlN, and SiO2. Using Molecular Dynamics simulations, we calculate the thermal conductivity of unstrained and strained ZnO and AlN crystals. We also calculate the thermal resistance of SiO/graphene interfaces under strain.We calculate the piezoelectric and elastic properties of ZnO. These will serve as confirmation of the correctness of the inter-atomic potential used, and will serve to show the magnitude of strain that is possible to apply. Using non-equilibrium molecular dynamics, we determine the elastic coefficient of ZnO c33, and we see that it agrees with experimental values. We also determine that the elastic limit of a perfect ZnO crystal is 6 GPa which corresponds to a 6% strain. We also determine the piezoelectric coefficient of ZnO using NEMD, and we find that the piezoelectric coefficient d33 also agrees with literature values.Second, we look at the effect of strain on the intrinsic thermal conductivity of ZnO and AlN. We use reverse non-equilibrium molecular dynamics to calculate the conductivity because the computational costs are significantly lower than those for the equilibrium method; especially for ZnO whose inter-atomic potential contains Coulomb interaction. We also study the size-effect on the thermal conductivity of ZnO and AlN. We show that the Schelling formula can indeed be implemented to both crystals for different values of strain. The infinite length thermal conductivity for ZnO is extracted from the formula, and it is found to be 410 W/mK. We then calculate the thermal conductivity of strained ZnO crystals. We show that after correcting for the size effect the thermal conductivity follows power-law dependence to uniaxial strain. Also, we demonstrate that the thermal conductivity of ZnO can be affected by a static external field due to the induced strain. The infinite length thermal conductivity of AlN is found to be 3000 W/mK. We show that for the case of AlN the effect of strain does not affect the thermal conductivity due to the different inter-atomic bonding. Hence, AlN might not be a useful material for piezothermal application.Third, we explore the effect of piezoelectric strain on the thermal conductance of SiO2/graphene and ZnO/graphene superlattices. Using EMD we calculate the thermal conductivity of a superlattice composed of silica and graphene monolayers. The thermal conductance of the superlattice was evaluated under different values of external electric field. We find that applying a positive electric field parallel to the Z-direction leads to reduction of the thermal conductance by a factor of 2 for an electric field of 20 MV/m. On the other hand, no change in the thermal conductance is noted for ZnO/graphene superlattice. The effect is due to the non-uniform strain induced at the superlattice junctions. The effect is recreated in Si/Ge superlattice by mechanically applying a non-uniform strain at the interface. This approach might be responsible for the scattering of phonons.

As metaloproteinases de matriz (MMP) são enzimas superexpressas em quase todos os tumores humanos, sendo que os subtipos MMP-2 e MMP-9 têm sido associados ao potencial metastático e prognóstico desfavorável em neoplasias malignas como, por exemplo, melanoma metastático e glioma. Compostos capazes de inibir a atividade destas enzimas podem representar potenciais agentes terapêuticos. O composto 4-nerolidilcatecol (4-NC), isolado de plantas do gênero Pothomorphe, apresentou resultados promissores para o tratamento do melanoma e glioma e foi capaz de atuar em várias etapas bioquímicas importantes envolvidas na progressão dessas patologias, inclusive inibindo MMP-2 e MMP-9. No entanto, o mecanismo de ação do 4-NC não está completamente elucidado. O presente estudo envolveu a aplicação de métodos de modelagem molecular e de formalismos do planejamento de novas moléculas auxiliado por computador, CAMD (Computer-Aided Molecular Design) a fim de explorar a interação entre esta molécula e as enzimas MMP-2 e MMP-9, além de planejar novos inibidores para estes alvos. Análise exploratória de dados, que compreende a análise de agrupamentos hierárquicos e de componentes principais. foi desenvolvida para um conjunto de hidroxamatos (N=64) descritos como inibidores de MMP-2 e MMP-9, a fim de identificar as propriedades moleculares que mais influenciavam o processo de discriminação dos compostos. As propriedades termodinâmicas, eletrônicas e estéricas foram importantes para descrever os compostos mais ativos no conjunto de dados da MMP-2. Para a MMP-9, o coeficiente de distribuição (ClogD) em pH 1,5 foi relevante no processo de discriminação do conjunto. A presença de substituintes volumosos na porção R3 parece ser crucial para o conjunto de inibidores investigados. Esta região está envolvida em interações moleculares com a cavidade S1 de ambas as enzimas, mas há um limite de volume a ser considerado para estes substituintes. O formalismo QSAR-4D independente do receptor (IR) foi aplicado ao mesmo conjunto de dados e permitiu estabelecer o mapeamento do farmacóforo, além de explorar diferentes alinhamentos para a obtenção da hipótese de conformação bioativa prevista pelo melhor modelo de QSAR. OS modelos QSAR apresentaram boa capacidade de previsão, auxiliaram na proposição de novos inibidores e estimaram a atividade do 4-NC. Com o melhor modelo QSAR para MMP-9 (N=64), a atividade prevista para o 4-NC foi classificada na faixa dos inibidores com atividade moderada. Entretanto, o melhor modelo QSAR obtido para MMP-2 (N=38) não foi capaz de prever, de forma adequada, a atividade de compostos com arcabouço químico diferente daqueles utilizados na construção dos modelos. Estudos de ancoramento molecular foram desenvolvidos para investigar a orientação do 4-NC no sitio catalítico das duas enzimas e as interações que poderiam ser estabelecidas nestes complexos. Duas conformações favoráveis foram encontradas. Simulações computacionais de dinâmica molecular foram desenvolvidas com os complexos mais promissores selecionados nos estudos de ancoramento, a fim de obter informações mais detalhadas e de maior confiabilidade. sobre suas interações intermoleculares. O 4-NC tende a se orientar no sítio de forma a acomodar sua cadeia lateral no bolso S1 adjacente ao sítio catalítico em ambas as enzimas. Ensaios de zimografia também foram realizados com o objetivo de elucidar possíveis contribuições da cadeia lateral e do núcleo catecólico do 4-NC na atividade inibitória frente às enzimas em estudo. O núcleo catecólico parece ser o responsável por sua atividade, pois o composto 1,2dimetoxibenzeno, que possui as hidroxilas bloqueadas por grupos metil, não foi capaz de exercer atividade inibitória significante frente à MMP-2 e MMP-9. Estudos de voltametria reforçaram a hipótese de que o 4-NC tem a capacidade de quelar os íons zinco presentes no tampão de incubação. / Matrix metalloproteinases (MMP) enzymes are overexpressed in almost all human tumors, and MMP-2 and MMP-9 subtypes have been associated with metastatic potential and poor prognosis in malignant tumors, such as metastatic melanoma and glioma. Compounds capable of inhibiting the activity of theses enzymes would be considered as potential therapeutic agents. The 4-nerolidylcatechol compound (4-NC), isolated from plants of genus Pothomorphe, has showed promising results in the treatment of melanoma and glioma, and was able to act in several important biochemical steps involved in the progression of these diseases, as well as inhibiting MMP-2 and MMP-9. However, the 4-NC mechanism of action is not completely understood. This study has involved the application of molecular modeling methods and formalisms of computer-aided molecular design (CAMD) in order to explore the interaction between 4-NC and MMP-2/MMP-9, and to design new inhibitors for these targets. Exploratory data analysis, which comprises hierarchical cluster analysis and principal components analysis, was performed to a set of hydroxamates (N=64). previously reported as MMP-2 and MMP-9 inhibitors, in order lo identify the molecular properties that is most critical for the discrimination process regarding the investigated compounds. The thermodynamic, electronic, and steric properties were: quite important to describe the highly active compounds in the data set of MMP-2, whereas the apparent partition coefficient (ClogD) at pH 1.5 was the property more relevant for MMP-9 data set. The presence of bulky substituents on the R3 moiety seems to be crucial for this set of inhibitors due to the molecular interaction with the S1 subsite of both enzymes. However, there is a limit regarding the substituents volume in this region. Receptor independent (RI) 4D-QSAR analysis was applied lo the same data set and it was possible to establish the pharmacophore mapping, besides to explore different alignments in order to generate the hypothesized bioactive conformation through the best QSAR model. The QSAR models have presented good predictability, assisted in proposing new inhibitors, and estimated the activity of 4-NC. Regarding the best QSAR model for MMP-9 (N=64), the 4-NC predicted activity was classified in the range of the moderate active inhibitors. The best QSAR model obtained for MMP-2 (N=38), however was not able to properly predict the activity for compounds with different chemical scaffold from those used to build up the QSAR model. Molecular docking studies have been developed to investigate the 4-NC binding mode into the catalytic site of the two enzymes and the interactions that could be established in those complexes. The results have shown two favorable conformers regarding the MMP inhibition. Molecular dynamics computational simulation were combined to molecular docking studies in order to obtain more detailed and reliable information regarding the intermolecular interactions of each complex. The 4-NC molecule tends to accommodate the side chain in the S1 pocket adjacent to the catalytic site in both enzymes. Experimental zymography assays were also performed to elucidate the possible contribution of the side chain and the catechol core in the 4-NC inhibitory activity against the MMP-2 and MMP-9 enzymes. The catechol core seems to be responsible for its activity, since the 1,2 dimethoxybenzene compound, which has the hydroxyl blocked by a methyl group, was not able to exert any significant inhibition on enzymes. Voltametric assays confirmed the hypothesis that 4-NC chelates zinc ions present in the incubation buffer.

Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly used classes of drugs. They target the cyclooxygenases (COX) 1 and 2 to reduce the physiological responses of pain, fever, and inflammation. Due to their role in inducing angiogenesis, COX proteins have also been identified as targets in cancer therapies. In this thesis, I describe computational protocols of molecular docking, molecular dynamics simulations and free energy calculations. These methods were used in this thesis to determine structure-activity relationships of a diverse set of NSAIDs in binding to their target proteins COX-1 and 2. Binding affinities were calculated and used to predict the binding modes. Based on combinations of molecular dynamics simulations and free energy calculations, binding mechanisms of sub-classes of NSAIDs were also proposed. Two stable conformations of COX were probed to understand how they affect inhibitor affinities. Finally, a brief discussion on selectivity towards either COX isoform is discussed. These results will be useful in future de novo design and testing of third-generation NSAIDs.

Comprendre la dynamique locale des protéines dans leur état natif (structure repliée etfonctionnelle) est essentiel pour comprendre leur dynamique globale et leur fonction biologique. Aucours de cette thèse, nous avons étudié la dynamique locale de plusieurs petites protéines enmesurant les fluctuations de sondes locales le long de la séquence d’acide aminé de ces protéines.Nous avons essayé de comprendre la dynamique de ces sondes locales, comment celles-ci serelaxaient entre leurs différentes conformations, comment leurs fluctuations étaient corrélées lesunes aux autres et comment peuvent-elles être reliées à la fonction biologique des protéines.Dans les trois premiers chapitres, nous introduisons les concepts du mouvement Browniende rotation libre, de la spectroscopie par Résonance Magnétique Nucléaire (RMN) et de ladynamique moléculaire (DM). Dans les chapitres 4 et 5, nous avons étudié la dynamique desliaisons amides de la chaine principale (backbone) des protéines sur leurs paysages d’énergie libre.Dans le chapitre 4, nous avons démontré que les fluctuations des liaisons amide dubackbone de la protéine VA3 sont décrites par une diffusion rotationnelle anormale plutôt que parune diffusion rotationnelle libre généralement utilisée pour interpréter les données RMN enrelaxation de spins et en couplage résiduel dipolaire. [...] Dans le chapitre 5, nous avons démontré la diffusion rotationnelle anormale de ces liaisons jusqu’à une échelle de temps de 100 ns en utilisant dix simulations de DM de 1 μs de la protéineUbiquitine. Nous avons aussi étudié la convergence des paramètres RMN extraits des trajectoiresde DM en fonction de leur durée. [...] Dans le chapitre 6, nous avons réalisé une l’étude de la corrélation entre les mouvements du backbone et des chaines latérales des protéines. [...] Dans la première partie du dernier chapitre de cette thèse, nous avons étudié l’évolution de la corrélation dynamique entre les chaines latérales et la chaine principale d’une protéine durant des évènements de dépliement/repliement. Pour cette étude préliminaire, nous avons utilisé unesimulation de DM d’un « ultra-fast folder » nommé Trp-cage réalisée à 380K. Nous avons confirméles résultats précédemment trouvés pour les protéines dans leur état natif. Nous avons observél’augmentation de la corrélation entre les séries temporelles yn(t) and δn(t) pendant un évènementde dépliement caractérisé par la sortie du tryptophane de sa cage. Un paramètre stérique s aégalement été défini afin de quantifier les intéractions des chaines latérales avec leurenvironnement. Dans une seconde partie de ce dernier chapitre, nous présentons une étudepréliminaire du dépliement d’un « downhill folder » nommé gpW sous contrainte d’une force. Pourcaractériser le dépliement de la protéine gpW, nous avons calculé les chemical shifts des atomes Cª et Hⁿ du backbone le long de sa séquence en fonction d’une coordonnée réactionnelle choisie comme étant la distance entre les Cª de résidus C- et N- terminaux. Nous avons démontré qu’il était difficile de discerner un comportement particulier à partir des tous les chemical shifts en fonction de la distance. Cependant, en moyennant la valeur des chemical shifts en sur tous lesrésidus de la protéine nous trouvons que l’évolution de cette valeur moyenne en fonction de ladistance permettait de décrire les évènements du dépliement de la protéine en fonction de lacoordonnée de réaction durant la simulation de DM / Understand the local dynamics of proteins in their native state, i.e. in their folded functionalstructure, is a prerequisite to understand their global dynamics and their biological function. In thepresent thesis, we investigated the local dynamics of several small proteins by recording thefluctuations of local probes along the amino-acid sequence of those proteins. We tried tounderstand the dynamics of the local probe, i.e. how they relax between their differentconformations, how their fluctuations are correlated to each other, how their fluctuations arerelated to the function of the proteins. In the first three chapters, we introduced the concepts of the free rotational Brownian motion, of the Nuclear Magnetic Resonance spectroscopy and of the Molecular Dynamics (MD)simulations. In chapters 4 and 5, we studied the dynamics of the backbone amide bonds of theproteins on their free-energy landscape. In chapter 4, we demonstrated that the fluctuations of the backbone amide bonds of the protein VA3 are described by a rotational anomalous diffusion rather than by a free rotationaldiffusion, as often assumed in the interpretation of the raw NMR-measured data (Spin relaxation(SR) data and Residual Dipolar Coupling (RDC) data. [...] In chapter 5, we demonstrated the anomalous diffusion of backbone amide bonds up to 100 ns by using ten MD trajectories of 1 μs of duration for the protein ubiquitin. We also studied the convergence of the NMR-derived parameters extracted from the MD trajectories in function of their duration. [...] In chapter 6, we addressed the question of the correlation between the motions of the side chains and main chain of a protein. [...] In the first part of the final chapter of the present thesis, we investigated the evolution of the correlation between the side-chain and the main-chain motions of a protein during unfolding/folding events. In this preliminary work, we used a single MD simulation of the ultrafast folder Trp-cage performed at 380 K. We confirmed the results found for proteins in theirnative state. We observed an increase of the correlation between the two time series yn(t) and δn(t) during an unfolding event characterized, here, by the exit of the TRP residue of its “cage”.A steric parameter s was also defined in order to quantify interactions of the amino-acid side chainwith its environment. In a second part of the last chapter, we present a preliminary study of theunfolding of the downhill folder gpW under a mechanical force. To characterized the unfolding ofgpW, we computed the chemical shift of the Cª and of the Hⁿ atoms along the amino-acidsequence of the protein in function of a reaction coordinate: the distance, rCªCª , between the Cª atoms of the N and C terminal residues. We demonstrated that it is hard to distinguish a typical behavior of all the chemical shift of all the residues along the amino-acid sequence in function of the distance rCªCª . However, by averaging the chemical shift over all the residues of the protein we found that the evolution of the average value of the chemical shift described the unfolding eventsof the protein during the MD simulations

We have carried out structural studies on bovine pancreatic phospholipase A2 (BPLA2) and two proteins involved in molybdenum cofactor (Moco) biosynthesis pathway. In addition, molecular-dynamics simulations and other analyses have been performed to corroborate the findings obtained from the crystal structures. Crystal structures of the three active-site mutants (H48N, D49N and D49K) of BPLA2 were determined to understand the mechanism by which the mutant H48N is able to catalyze the reaction of phospholipid hydrolysis and to see the effect of the loss of Ca 2+ ion in the active site of D49N and D49K mutants. We found that Asp49 could possibly play the role of a general base instead of His48 in the case of the H48N mutant. In the case of D49N and D49K mutants, the active site of the enzyme is perturbed, whereas the overall tertiary structure of these mutants is intact. In addition, a total of 24 invariant water molecules were identified in all of the crystal structures of BPLA2 available in its archive, PDB. Out of these, four water molecules are essential for the catalytic activity, whereas, the remaining water molecules play a role in the stability of the enzyme. In addition, structural studies on two proteins MoaC and MogA involved in Moco biosynthesis pathway have been carried out. For the first time, crystal structure of MoaC bound with GTP molecule has been reported. The gene id TTHA0341, which is mentioned as MoaB in the CMR database, was annotated as MogA based the comparative analysis of sequences and structures (with the present work and the structures available in the literature). The role of N-and C-termini of MoaB and MogA proteins were proposed that these residues might stabilize the substrate and/or product molecule in the active site. In addition, the residues involved in the oligomerization are compared with MD simulations. The molecular docking studies show that MoaB proteins show more preference to GTP than ATP. The comparison of the two active (MPT and AMP-binding) sites revealed that MPT-binding site is preferred over AMP-binding site for nucleotide binding.

Dans la plupart des applications concernant un fluide s'écoulant sur une surface solide, la condition de non-glissement est largement utilisée car elle est simple et produit des résultats en accord avec les expériences. Toutefois, cette condition de limite n'est plus appropriée lorsque l'écoulement considéré est à l'échelle micro ou nano-métrique. Pour modéliser cet effet à l'échelle macroscopique, les conditions aux limites de Navier ont été introduites, avec la longueur de glissement comme paramètre. Lorsque le fluide est un gaz, cette longueur est liée au coefficient d'accommodation tangentiel (TMAC) et au libre parcours moyen, selon le modèle de Maxwell. Le but de ce travail est de traiter systématiquement ce modèle par une approche multi échelle et de l'étendre en incorporant la morphologie et l'anisotropie de la surface. La thèse est composée de cinq chapitres. Après l'Introduction, les notions de base de la théorie cinétique des gaz, l'équation de Boltzmann et les solutions associées (Navier-Stokes-Fourier, Burnett, Grad, Direct Simulation Monte Carlo…) sont rappelées dans le chapitre 1. Les modèles d'interaction gaz-paroi ainsi que les modèles de glissement introduits dans le cadre le la mécanique des fluides sont aussi rappelés. Le chapitre se termine par la description de la méthode de calcul par dynamique moléculaire (MD) utilisée dans ce travail. Le chapitre 2 est dédié au développement d'une technique simple afin de simuler les écoulements induits par la pression. Le principe est de se baser sur les formules atomistiques du tenseur des contraintes (Irving Kirkwood, Méthode de Plan, Contraintes Virielles) et de modifier les conditions périodiques, tout en maintenant la différence entre l'énergie cinétique des atomes à l'entrée et à sortie du domaine de calcul. Plusieurs types de conduite sont étudiés avec cette technique. Les résultats (température, vitesses, …) sont discutés et comparés. Le chapitre 3 concerne l'étude du potentiel d'interaction gaz-paroi par la méthode ab-initio. Le code CRYSTAL 09 est utilisé pour obtenir le potentiel entre un atome d'argon (Ar) et une surface de platine (Pt) <111> en fonction de la distance. Ensuite, le potentiel atome/surface est décomposé en potentiel binaire et approché par une fonction analytique. Cette fonction est ensuite implémentée dans un code MD pour simuler les collisions gaz-paroi et déterminer le coefficient TMAC.Dans le chapitre 4, l'effet de morphologie est étudié. Le potentiel multi-corps Quantum Sutton Chen(QSC) est utilisé pour le solide Pt <100> et un des potentiels binaires étudié dans le chapitre précédent pour le couple Ar-Pt. Le potentiel QSC est nécessaire pour reproduire l'effet de surface qui affecte le résultat final. Différentes surfaces sont traitées : surface lisse, surface nanostructurée, surface aléatoire obtenue par déposition de vapeur (CVD). Le coefficient TMAC est déterminé de façon généralisée, c.à.d en fonction de l'angle du flux d'atomes incidents sur la surface. Les anisotropies de surface et le noyau de collision sont également examinés. Dans le chapitre 5, on propose un modèle de glissement anisotrope pour les fluides en fonction du tenseur d'accommodation. Le modèle est obtenu par les calculs analytiques approchés développés dans le cadre de la théorie cinétique. On a ainsi généralisé l'équation de Maxwell en montrant que le tenseur de longueur de glissement est directement lié au tenseur d'accommodation. Le modèle est en bon accord avec les résultats de la méthode MD. Concernant la simulation MD, on a développé une technique pour reproduire l'anisotropie du tenseur d'accommodation. Le mémoire de thèse se termine par une synthèse des résultats obtenus. Des perspectives pour de futures études sont proposées / In most applications concerning a fluid flowing over a solid surface, the no-slip velocity condition was widely used because it is simple and produces the results in agreement with experiments. However, this dynamical boundary condition is not appropriate when the flow under consideration is at a micro or nano length scale.In order to model this effect at the macroscopic scale, the Navier boundary conditions have been introduced, with the slip length as a parameter. When the fluid is a gas, this length is related to the tangential momentum accommodation coefficient (TMAC) and the mean free path, according to the Maxwell model. The aim of this work is to systematically address this model using a multi-scale approach and to extend it by incorporating both the morphology and the anisotropy of a surface. The thesis consists of five chapters. In Chapter 1, the basics of the kinetic theory of gases, the Boltzmann equation and related solutions (Navier-Stokes-Fourier, Burnett, Grad, Direct Simulation Monte Carlo ...) are briefly presented. The models of gas-wall interaction and slip models introduced in the fluid mechanics are also recalled. The chapter ends with a description of the computational method used for the molecular dynamics simulations performed in this work. Chapter 2 is dedicated to the development of a simple technique to simulate the pressure driven flows. The principle is to rely on the atomistic formulas of the stress tensor (Irving Kirkwood, Method of Plane, Virial Stress) and to modify the periodic conditions by maintaining the difference between the kinetic energy of the ingoing and outgoing particles of the simulation domain. Several types of channels are studied with this technique. The results (temperature, velocity ...) are discussed and compared. Chapter 3 deals with the study of the gas-wall interaction potential by the ab-initio method. The code CRYSTAL 09 is used to obtain the potential between an atom of argon (Ar) and a surface of platinum (Pt) <111> as a function of distance. Then the gas-wall potential is decomposed into binary potential and approached by an analytic function. This function is then implemented in a MD code to simulate the gas-wall collisions and determine the TMAC coefficient. In Chapter 4, the effect of morphology is studied. The multi-body Quantum Sutton Chen (QSC) potential is used for Pt <100> solid and the binary potential proposed in the previous chapter for the Ar-Pt couple is employed. The QSC potential is needed to reproduce the surface effects that affect the final results. Different surfaces are treated : smooth, nanostructured surface and, random surface obtained by Chemical vapor deposition (CVD). The TMAC is determined using a generalized approach, i.e. depending on the angle of incident flux of gas atoms on the surface. The surface anisotropy and the scattering kernel are also examined. In Chapter 5, we propose a model of anisotropic slip for fluids based on accommodation tensor. The model is obtained by the analytical approximate calculations developed in the framework of the kinetic theory. We thus generalize Maxwell's equation by showing that the slip length tensor is directly related to the accommodation tensor. The model is in good agreement with the MD results. Thanks to our MD simulations, we develop a suitable technique for reproducing the anisotropy of the accommodation tensor. The thesis ends with a conclusion section in which we suggest some perspectives for a continuation of this work

Cette thèse présente une étude expérimentale et numérique des forces s'exerçant sur un objet en mouvement dans un milieu granulaire. La compréhension précise de ces forces présente en effet d'importants intérêts fondamentaux (rhéologie des milieux granulaires, phénomène de ségrégation) et appliqués (robotique, locomotion animale ...). Expérimentalement, un cylindre horizontal est mis en rotation à faible vitesse dans un bac de billes de verre. Les forces s'exerçant sur cet objet dans la direction du mouvement (forces de traînée) et dans la direction verticale (forces de portance) sont mesurées.Lors du premier demi-tour, avant que le cylindre ne repasse dans son propre sillage, nous mettons en évidence l'existence d'une force de portance élevée sur l'objet (bien qu'il soit symétrique), de l'ordre de 20 fois la poussée d'Archimède du milieu, et indépendante de la profondeur. Des études numériques de dynamique moléculaire (méthode éléments discrets) permettent de comprendre comment cette portance émerge de la modification de l'écoulement granulaire par la présence d'un gradient de pression dans le milieu. Aux temps longs, après plusieurs rotations du cylindre, on observe une chute de la force de traînée, qui devient indépendante de la profondeur. Le milieu se structure sous l'effet des passages répétés du cylindre dans son sillage, ce qui écrante le poids des grains situés au dessus. Enfin, une étude numérique des forces sur une grosse particule en écoulement avec le milieu granulaire est ébauchée, en lien avec le phénomène de ségrégation granulaire. / This thesis presents an experimental and numerical study of the forces experienced by an object moving in granular media. This problem, which is of practical importance in many applications (robots, animal locomotion), is also of fundamental interest (rheology of granular materials, granular segregation). The experiment consists in a horizontal cylinder rotating around the vertical axis in glass beads. Both drag forces and lift forces experienced by the cylinder are measured.During the first half rotation, before the cylinder crosses its own wake, we measure a strong lift force (despite the symmetry of the object), about 20 times the buoyancy of the cylinder, and independent of its depth. Molecular dynamic simulations (Discrete Element Method) shed lights on how this lift force arises from the modification of the grain flow due to the pressure gradient in the medium. After several rotations, when the cylinder goes through its own wake, the drag force drops and becomes independent of depth. The rotation of the cylinder induces a structure in the granular packing, which screens the weight of the grains above it. Finally, a numerical study of forces on a large particle flowing with the granular medium is sketched, in relation with the phenomenon of granular segregation.