Dissertations / Theses: 'Molecuar dynamics and docking simulation'

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Trezza, Alfonso. "A novel computational way to unlock drug targets deep and transient secretes." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1072788.

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Ullmann, G. Matthias. "Simulation and analysis of docking and molecular dynamics of electron transfer protein complexes." [S.l. : s.n.], 1998. http://darwin.inf.fu-berlin.de/1998/23/index.html.

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Madhusudhan, M. S. "Computer Modeling and Molecular Dynamics Simulation Of Angiogenins And Its Ligand Bound Complexes." Thesis, Indian Institute of Science, 2000. http://hdl.handle.net/2005/211.

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Computational structural biology Even with rapid advances in structure determination methods, there is a long gap to be bridged between the number of proteins that have been sequenced and the number whose three-dimensional structures have been experimentally elucidated. Experimentally protein structures are determined by X-ray crystallography or by nuclear magnetic resonance spectroscopy (NMR). X-ray crystal structures give a time averaged picture but little information on conformational dynamics. Though NMR gives dynamical information, the technique cannot be applied to systems whose molecular weight is large. Only small proteins fall within the ken of NMR experiments. In most cases the three dimensional structure of the protein alone cannot give a complete picture of its mechanism. It is also essential to know the interactions of proteins with other proteins, with their ligands and substrates in order to have a better understanding of their functioning. Computer modeling and simulations are now indispensable supplements to experimental structural biology. The last word in protein structure prediction method is far from being said but the ever-improving homology and ab-initio modeling methods give rise to optimism that sometime in the near future these methods will become almost as reliable as experimental techniques. Ligand docking onto protein molecules is as challenging a problem as protein structure predicting itself. Computer modeling methods to dock ligands have to search a wide region of conformational space besides taking into consideration issues of charge and shape complementarities.

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Sousa, Rui. "Structural insights of Interleukin-15 through Molecular Dynamics simulations : Towards the rational design of specific inhibitors." Thesis, Nantes, 2019. http://www.theses.fr/2019NANT4081.

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L’Interleukine-15 (IL-15) est une cytokine impliquée dans un grand nombre de fonctions cellulaires. Elle participe ainsi notamment au développement et à l’activation de la réponse immunitaire. L’IL-15 est donc apparue comme une cible potentielle pour différentes applications thérapeutiques. La structure de cette cytokine est basée sur un complexe quaternaire entre IL-15 et ces récepteurs a (IL-15Ra), b (IL- 2Rb et y (yc). La modulation fonctionnelle d’IL-15 est liée à son interaction avec ces récepteurs, notamment avec IL-2Rβ L’interleukine-2 (IL-2) partageant deux de ses trois récepteurs ( IL-2Rβ et yc) avec l’IL-15, la recherche d’inhibiteurs spécifiques de l’IL-15 doit intégrer ces caractéristiques. Dans le cadre de ce travail, par des approches de Modélisation Moléculaire, en particulier de Dynamique Moléculaire (MD), nous avons: (i) déterminé l’influence de la forme complexée de l’IL-15 (dimère, trimère ou tétramère) sur les propriétés des interfaces (ii) mis en évidence les acides aminés « clés » des différentes interfaces (iii) étudié l’impact de mutations de certains de ces acides aminés (iv) utilisé ces informations pour mettre au point un pharmacophore ayant permis, dans un second temps, la découverte de nouveaux composés de faible poids moléculaire capables de cibler spécifiquement une des interfaces (IL-15/ IL-2Rβ). L’ensemble des données issues de ce travail a été confronté à des résultats biologiques obtenus dans le cadre du projet
Interleukin 15 (IL-15) is a cytokine involved in a plethora of different cellular functions. It participates, for instance, in the development and activation of immune responses. IL-15 has, therefore, clearly appeared as a potential target for several therapeutic applications. The structure of this cytokine is based on a quaternary complex between IL-15 and its a (IL-15Ra), b ( IL-2Rβ) and y (yc) receptors. The key to the functional modulation of IL-15 lies on its interaction with its receptors and, more particularly, with IL-2Rβ. Interleukin-2 sharing two out of the three receptors 2Rβ and yc), the search for specific IL-15 inhibitors has to take into account these features. In this work, through various Molecular Modeling approaches, specifically Molecular Dynamics (MD) simulations, we have (i) determined the influence of the complexed form of IL-15 (dimer, trimer or tetramer) on the interface properties (ii) highlighted the key amino acid (“hot spots”) of the various interfaces (iii) studied the impact of mutations of selected residues (iv) used this information to design a pharmacophore which has allowed, in a subsequent step, the discovery of new low-molecular weight compounds able to specifically target one of the IL-15 interfaces (IL- 15/ IL-2Rβ). The theoretical data have been compared to the results of biological experiments carried out in the framework of the project

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Madeleine, Noelly. "Recherche d'inhibiteurs de l'interaction Lutheran-Laminine par des techniques de modélisation et de simulation moléculaires." Thesis, La Réunion, 2017. http://www.theses.fr/2017LARE0054/document.

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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

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Haslak, Zeynep Pinar. "Approches numériques pour évaluer les propriétés de liaison de ligands : le cas du récepteur NMDA." Electronic Thesis or Diss., Université de Lorraine, 2019. http://www.theses.fr/2019LORR0240.

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L'un des problèmes importants dans la conception de médicaments est l'identification de l'activité biologique des ligands en regard de leurs récepteurs. Le développement, la synthèse et les mesures d'activité des ligands revêtent une importance majeure dans la conception de médicaments. Cependant, les études expérimentales ne peuvent qu'être limitées: la synthèse de toutes les molécules potentiellement actives est par exemple irréaliste. Les études numériques pourraient donc apporter une aide précieuse aux études expérimentales, notamment dans le cas de la conception de ligands pour les récepteurs au glutamate comme le récepteur NMDA. En combinant les points forts des approches par dynamique moléculaire et par chimie quantique, il est possible d’établir une inspection, une caractérisation et une rationalisation plus ciblées des études de conception de médicaments. Dans cette thèse, des méthodes numériques ont été utilisées pour étudier les propriétés intrinsèques des molécules biologiquement actives responsables de la sélectivité. Les résultats de cette étude sont présentés en 4 chapitres. Dans les deux premiers chapitres, nous avons cherché à différencier les agonistes, les antagonistes et les agonistes partiels au récepteur NMDA en fonction de descripteurs tirés de la chimie quantique et d'énergies libres de liaison de Gibbs. Plusieurs propriétés moléculaires qui pourraient jouer un rôle dans la liaison du ligand à la sous-unité glycine GluN1 du récepteur NMDA ainsi que les énergies libres de liaison ont été utilisées pour établir un lien entre les efficacités et les affinités de liaison des ligands. La prédiction des constantes de dissociation acide d'acides aminés dans les protéines et les ligands nous permet d'avoir des informations sur l'affinité de liaison et l'efficacité des ligands envers leurs protéines cibles. Considérant l'importance des \pka, nous avons exploré dans le chapitre suivant comment les charges atomiques des acides carboxyliques peuvent être liées à la prédiction de \pka de ligands. Afin de mettre en lumière les origines de la stéréosélectivité de ligands biologiquement actifs, plusieurs voies mécanistiques ont été évalués dans le dernier chapitre pour les 2-thiohydantoïnes, qui sont de puissants antagonistes des récepteurs aux androgènes
One of the important issues in drug design is the identification of the biological activity of receptor ligands. Development, synthesis and activity measurements of ligands have a major importance in drug design. However, there are certain limits in experimental studies; synthesis of a large number of compounds to cover all the potentially active molecules is unrealistic. Computational studies could therefore provide a valuable aid to experimental studies on ligand design for glutamate receptors. By combining the strengths of Molecular Dynamics and Quantum Chemical approaches, a more focused inspection, characterisation and rationalization of the drug design studies is allowed to be established. In this dissertation, computational methods have been used to investigate the intrinsic properties of the biologically active molecules that cause the selectivity. The results of this study will be introduced in 4 chapters. In Chapters 4 and 5, we aimed to differentiate between agonists, antagonists and partial agonists based on Quantum Chemical descriptors and binding Gibbs free energies. Several molecular properties that could play a role in ligand binding to the glycine GluN1 subunit of NMDA and calculated binding Gibbs free energies were further used to provide a link between the efficacies and binding affinities of the ligands. Prediction of the acid dissociation constants of amino acids in proteins and ligands allows us to have information about the binding affinity and efficacy of the ligand to its target protein. Considering the significance of p\textit{K_a}'s, how atomic charges of carboxylic acids can be related to the prediction of p\textit{K_a} of the ligands have been explored in Chapter 6. In order to shed light on the origins of the stereoselectivity of biologically active ligands, several mechanistic pathways have been evaluated for 2-thiohydantoins which are potent androgen receptor antagonists and the results are given in Chapter 7

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Touzeau, Jérémy. "Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales." Thesis, Sorbonne Paris Cité, 2018. https://theses.md.univ-paris-diderot.fr/Touzeau_jeremy_2_complete_20181203.pdf.

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La confection de dispositifs impliquant des biomolécules, notamment dans le cadre de la détection (biocapteurs) ou de la protection contre des pathogènes (revêtements antimicrobiens), compte toujours un grand nombre d’interrogations notamment à l’échelle atomique. Dans ce contexte, nous avons utilisé les outils de la modélisation moléculaire afin de réaliser des études multi-échelles (à la fois en quantique et en mécanique moléculaire) pour étudier des systèmes (expérimentaux) impliquant des biomolécules et solutionner des problématiques. L’étude a été menée au sein de deux projets. Dans le cadre du premier d’entre eux, nous nous sommes tout d’abord intéressé à l’optimisation d’un biocapteur impliquant un transistor à effet de champ de type EGOFET, en nous concentrant plus particulièrement sur le canal semi-conducteur du transistor. Dans un second temps, nous avons réalisé une étude autour de l’interaction biologique et spécifique du biocapteur. Dans le cadre du second projet, nous nous sommes intéressés à un revêtement antimicrobien. Celui-ci s’appuie sur le greffage d’un peptide comportant une séquence d’accroche, une séquence antimicrobienne ainsi qu’un site clivable par une enzyme spécifique au pathogène que l’on souhaite traiter. En présence de ce dernier uniquement, le peptide antimicrobien est ainsi libéré dans le milieu. Bien que ce système fonctionne parfaitement en solution, ses propriétés bactéricides sont perdues lorsqu’il est greffé sur une surface, une étape indispensable pour une utilisation dans le domaine biomédicale. Nous avons ainsi étudié ce système grâce à la modélisation moléculaire afin de comprendre la perte de ces propriétés
The tailoring of devices involving biomolecules, for applications such as the detection (biosensors) or protection against pathogens (antimicrobial coats), still introduce several interrogations at an atomic point of view. In this context, we used molecular modelling tools in order to realize multi-scale studies (quantic level and molecular mechanics level) about experimental systems and solve issues. We interested in two projects. In the first one, we firstly focused on biosensor involving filed effect transistor (EGOFET type), by studying the optimization of the semi-conductor channel. Then we interested in the specific biological interaction of the biosensor. In the second one, we interested in an antimicrobial coat. This device is composed by a peptide containing three parts: an anchoring one, a cleavable one which can be cut specifically by a surface protease of the target and so, release the last peptide in the area which involves antimicrobial properties. The system is very efficient in solution but when it’s grafted on a surface, antimicrobial properties disappear. Consequently, we used molecular modelling tools in order to prospect those antimicrobial properties loss

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Krebs, Fanny. "Etudes in silico et expérimentale de la DXR & synthèse de D- et L-GAP énantiomériquement purs." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAF059/document.

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La thèse porte sur l’étude des 2 premières enzymes de la voie du MEP: la DXS et DXR. La voie du MEP conduit à la biosynthèse des isoprénoïdes chez la plupart des bactéries, dont des pathogènes. Etant absente chez l’homme, les enzymes de cette voie cible idéale pour la recherche de nouveaux antimicrobiens. L’objectif principal était d’améliorer le développement de nouveaux antimicrobiens. Nous avons utilisé des outils computationnels : méthodes de docking et de mécanique moléculaire couplée à la méthode MM/PBSA. Nous avons identifié les résidus contribuant significativement à la fixation d’un ligand dans le site actif de la DXR. Ces résultats ont été utilisés lors de la conception de nouveaux candidats inhibiteurs de type bisubstrat, biligand et difluoro phosphonate, dont 2 ont pu être synthétisés. Nous avons également développé une méthode de synthèse donnant accès au L- et D-GAP énantiomeriquement purs, dans le but d’étudier l’énantiospécificité de la DXS face à son substrat D-GAP
This thesis concerns the study of the 2 first enzymes of the MEP pathway: DXS and DXR. The MEP pathway permits the biosynthesis of isoprénoïdes in most bacteria, including pathogenic one. As it is not present in human, enzymes of MEP pathway are effective targets in the research of new antimicrobial drugs. The objective was to advance the development of new antimicrobiotic compounds. We used computational tools: molecular docking and molecular dynamics simulations coupled with an MM/PBSA approach. We were able to identify residues that contribute significantly to the ligand binding in the DXR active site. These results were used to guide the conception of new inhibitor models, such as bisubstrates, biligands and α,α-difluoro phosphonates, two of which were synthetized. We also developed a synthesis method to obtain L- and D-GAP as enantiomerically pure molecules. The goal was to study the enantiospecificity of DXS to its substrate, D-GAP

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Abdulganiyyu, Ibrahim A. "A single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods." Doctoral thesis, Faculty of Science, 2021. http://hdl.handle.net/11427/33621.

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Flies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis all have the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be reasonably rigid, with an S 2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis were used to construct two models for each receptor: Drome-AKHR, Sarcr-AKHR, and Bacdo-AKHR. It is proposed that these two models represent the active and inactive state of the receptor. The models based on the crystal structure of the β-2 adrenergic receptor were found to bind Phote-HrTH with a predicted binding free energy of –107 kJ mol–1 for Drome-AKHR, –102 kJ mol–1 for Sarcr-AKHR and –102 kJ mol–1 for Bacdo-AKHR. Under molecular dynamics simulation, in a POPC membrane, the β-2AR receptor-like complexes transformed to rhodopsin-like. The identification and characterisation of the ligand-binding site of each receptor provide novel information on ligand-receptor interactions, which could lead to the development of species-specific control substances to use discriminately against these pest flies.

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Lundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.

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Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data. Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.

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Beck, Guillaume. "Recherche de nouveaux agents thérapeutiques dans le traitement des lymphomes à cellules B." Thesis, La Réunion, 2020. http://www.theses.fr/2020LARE0002.

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Le lymphome à cellule B est un type de cancer qui se développe dans le système lymphatique. Des études réalisées par Meadows et al ont indiqué que PI3Kδ pouvait constituer une cible thérapeutique dans ce cancer. Le but de cette étude est d’identifier des inhibiteurs du site de liaison à l’ATP de la protéine kinase PI3Kδ qui possède une forte affinité. Un criblage virtuel de 350 composés ciblant la protéine PI3Kδ a été réalisé. La validation préalable d’un protocole de scoring a été réalisée préalablement sur notre protéine d’intérêt PI3Kδ. Ce protocole contient différentes étapes de sélection basées sur les affinités calculées et les affinités expérimentales connues, telles qu’une étape de docking, une étape de relaxation des complexes et enfin une étape d’évaluation des affinités des ligands pour la protéine cible. Pour l’étape de scoring secondaire, nous avons testé différentes méthodes de calculs : des fonctions empiriques (X-Score, ID-Score, Cyscore) et knowledged-based (IT-Score) ainsi que des méthodes de calcul de chimie quantique (FMO dans GAMESS, PM6-D3H4X dans MOPAC, et DFT-D dans Terachem). Nous avons tout d’abord appliqué ce protocole sur la molécule MBL. Cette molécule de type chalconoïde s’avère posséder une affinité pour la protéine PI3Kδ. L’application de ce protocole sur la chimiothèque virtuelle nous a permis d’obtenir des prédictions de ligands avec une haute affinité pour PI3Kδ. À partir de ces résultats de criblage, nous allons pouvoir envoyer nos résultats à l’équipe MEDCHEM de l'Université Grenoble Alpes, pour une validation expérimentale
B cell lymphoma is a type of cancer that develops in the lymphatic system. Studies by Meadows et al have indicated that PI3Kδ may be a therapeutic target in this cancer. The aim of this study is to identify inhibitors of the ATP binding site of the protein kinase PI3Kδ. A virtual screening of 350 compounds targeting the PI3Kδ protein was carried out. The prior validation of a scoring protocol was carried out beforehand on our protein of interest PI3Kδ. This protocol contains different selection steps based on calculated affinities and known experimental affinities, such as a docking step, a complex relaxation step and a reevaluation of ligand affinities for the target protein. For the secondary scoring step, we tested different calculation methods: empirical (X-Score, ID-Score, Cyscore) and knowledged-based (IT-Score) functions as well as quantum chemistry calculation methods (FMO in GAMESS, PM6-D3H4X in MOPAC, and DFT-D in Terachem). We first applied this protocol to the MBL molecule. This chalconoid-like molecule appears to have an affinity for the PI3Kδ protein. The application of this protocol on the virtual chemistry library allowed us to obtain predictions of ligands with a high affinity for PI3Kδ. From these screening results, we will be able to send our results to the MEDCHEM team at Grenoble Alpes University, for experimental validation

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Chen, Sih-Yu. "Computational studies of biomolecules." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/11064.

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In modern drug discovery, lead discovery is a term used to describe the overall process from hit discovery to lead optimisation, with the goal being to identify drug candidates. This can be greatly facilitated by the use of computer-aided (or in silico) techniques, which can reduce experimentation costs along the drug discovery pipeline. The range of relevant techniques include: molecular modelling to obtain structural information, molecular dynamics (which will be covered in Chapter 2), activity or property prediction by means of quantitative structure activity/property models (QSAR/QSPR), where machine learning techniques are introduced (to be covered in Chapter 1) and quantum chemistry, used to explain chemical structure, properties and reactivity. This thesis is divided into five parts. Chapter 1 starts with an outline of the early stages of drug discovery; introducing the use of virtual screening for hit and lead identification. Such approaches may roughly be divided into structure-based (docking, by far the most often referred to) and ligand-based, leading to a set of promising compounds for further evaluation. Then, the use of machine learning techniques, the issue of which will be frequently encountered, followed by a brief review of the "no free lunch" theorem, that describes how no learning algorithm can perform optimally on all problems. This implies that validation of predictive accuracy in multiple models is required for optimal model selection. As the dimensionality of the feature space increases, the issue referred to as "the curse of dimensionality" becomes a challenge. In closing, the last sections focus on supervised classification Random Forests. Computer-based analyses are an integral part of drug discovery. Chapter 2 begins with discussions of molecular docking; including strategies incorporating protein flexibility at global and local levels, then a specific focus on an automated docking program – AutoDock, which uses a Lamarckian genetic algorithm and empirical binding free energy function. In the second part of the chapter, a brief introduction of molecular dynamics will be given. Chapter 3 describes how we constructed a dataset of known binding sites with co-crystallised ligands, used to extract features characterising the structural and chemical properties of the binding pocket. A machine learning algorithm was adopted to create a three-way predictive model, capable of assigning each case to one of the classes (regular, orthosteric and allosteric) for in silico selection of allosteric sites, and by a feature selection algorithm (Gini) to rationalize the selection of important descriptors, most influential in classifying the binding pockets. In Chapter 4, we made use of structure-based virtual screening, and we focused on docking a fluorescent sensor to a non-canonical DNA quadruplex structure. The preferred binding poses, binding site, and the interactions are scored, followed by application of an ONIOM model to re-score the binding poses of some DNA-ligand complexes, focusing on only the best pose (with the lowest binding energy) from AutoDock. The use of a pre-generated conformational ensemble using MD to account for the receptors' flexibility followed by docking methods are termed “relaxed complex” schemes. Chapter 5 concerns the BLUF domain photocycle. We will be focused on conformational preference of some critical residues in the flavin binding site after a charge redistribution has been introduced. This work provides another activation model to address controversial features of the BLUF domain.

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Andersson, Ida E. "Modified Glycopeptides Targeting Rheumatoid Arthritis : Exploring molecular interactions in class II MHC/glycopeptide/T-cell receptor complexes." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-42082.

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Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA. The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions. The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex. Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

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DI, MARINO DANIELE. "Molecular dynamics and docking simulations of the ADP/ATP mitochondrial carrier: structural-dynamical insights for the inactivation of pathological mutants and detection of potential ATP binding sites." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2010. http://hdl.handle.net/2108/1174.

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Il carrier mitocondriale ADP/ATP (AAC) è stato cristallizato in complesso con il suo inibitore carboxyatractyloside (CATR). La proteina è composta da un fascio di sei eliche trans membrana che forma un canale all'interno della membrane mitocondriale interna che si presenta chiuso verso il lato matriciale ed aperto verso lo spazio intermembrana, conformazione dovuta alla presenza di una prolina sulle eliche dispari che forma una piegatura dell' elica. Il ruolo di questa proteina è di importare ADP nella matrice mitocondriale ed esportare ATP nel citosol. L' insorgenza di alcune patologie è stata associata ad un malfunzionamento di questa proteina. Al fine di capire meglio le proprietà dinamico/strutturali del trasportatore sono stati eseguiti due diversi esperimenti computazionali, per analizzare sia il meccanismo di trasporto che il ruolo di determinate mutazioni patologiche. In un primo esperimento sono state condotte tre simulazioni di Dinamica Molecolare di 20 ns della protein wild type, del mutante patologico Ala113Pro e del doppio mutante Ala113Pro/Val180Met immerse in un doppio strato lipidico, al fine di capire il ruolo della seconda mutazione Val180Met capace di restaurare il corretto funzionamento del mutante Ala113Pro . L' analisi delle componenti principali ha evidenziato per i tre sistemi che il moto della proteina è caratterizzato dal movimento dei loops matriciali e delle eliche dispari che presentano una proline conservata nella regione centrale dell 'elica. L' analisi del moto mostra un comportamento diverso del singolo mutante rispetto a wild type e doppio mutante. La singola mutazione induce una regolarizzazione dellâ elica H3, che viene persa in seguito allâ introduzione della seconda mutazione. Questo è direttamente correlato alla distribuzione della rete di ponti salini che coinvolge i residui Arg79, Asp134, Arg234 coinvolti nellâ 'interazione con il substrato. Infatti, nella simulazione del wild type sono visibili due ponti salini stabili lungo tutta la dinamica e cruciali per il legame con il substrato, Arg79:Asp134 e Arg234:Asp134. Uno di questi ponti salini è perso nella dinamica del singolo mutante e viene ristabilito nella dinamica del doppio mutante, che si comporta come il wild type. Questo causa nel singolo mutante un errato assetto del sito di legame dellâ 'ADP, spiegando il malfunzionamento del carrier. Inoltre, abbiamo descritto le interazioni tra il lato matriciale del trasportatore e il substrato ATP attraverso l' utilizzo di simulazioni di dinamica molecolare classica e docking proteina-ligando. Dalla dinamica molecolare di 20 ns del wild type sono state estratte 15 strutture rappresentative della proteina attraverso il clustering, e per ognuna di queste strutture sono state effettuate 50 runs di docking, per un totale di 750 (MD-docking) i risultati sono stati analizzati in comparazione con quelli ottenuti dalle 750 runs di docking effettuate sulla struttura X-Ray (X-docking). L' analisi mostra la presenza di un unico sito di interazione sulla struttura X-Ray, mantenuto anche nelle strutture estratte dalla dinamica. L' MD-docking mostra la presenza di un secondo sito di legame, non presente nell' X-docking. Il meccanismo di interazione tra la proteina e il substrato ATP è stato studiato analizzando la composizione e l' arrangiamento 3D delle 2 tasche di interazione individuate, e l' orientazione del substrato allâ interno di esse. E' stata quindi proposta una relazione diretta tra la struttura tripartite del carrier e la presenza di più siti di legame per l' ATP.
The mitochondrial adenosine diphosphate/adenosine triphosphate, ADP/ATP carrier (AAC) has been crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). The protein is composed by a six trans-membrane helix bundle, defining the nucleotide translocation pathway, that is closed towards the matrix side due to sharp kinks in the odd-numbered helices. The role of the protein is to import ADP in the mitochondrial matrix and export ATP in the cytosol. Several disease have been associated to a malfunctioning of the protein. To better understand the structural/dynamical properties of the carrier, two different computational experiments have been performed, in order to understand both the translocation mechanism and the role of known pathological mutations. In a first experiment Molecular Dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 20 ns to shed a light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops and of the odd-numbered helices having a conserved proline in their central region. Analysis of the motions shows a different behaviour of single pathological mutant with respect of the other two systems. The single mutation induces a regularization and rigidity of the H3 helix, lost upon the introduction of the second mutation. This is directly correlated to the salt bridge distribution involving residues: Arg79, Asp134, Arg234; hypothesized to interact with the substrate. In fact, in the wild type simulation two stable inter-helices salt bridges, crucial for substrate binding, are present almost over all the simulation time. In line with the impaired ADP transport, one salt interaction is completely lost in the single mutant trajectory but reappears in the double mutant simulation, where a salt bridge network, as observed in the wild type, is restored. This causes a wrong assembly of the geometry of the binding site, explaining the impaired transport of the single mutant. Further, we describe the interaction between the matrix side of the AAC transporter and the ATP molecule using classical molecular dynamics simulation (MD) and protein-ligand docking procedure. From the 20 ns MD trajectory of the wild type protein, 15 structures have been extracted through clustering analysis and for each carrier conformation 50 docking runs have been carried out for a total of 750 (MD-docking). The results have been compared with 750 docking runs performed on the X-ray structure (X-docking). The docking procedure shows the presence of a single interaction site in the X-ray structure that is conserved in the structures extracted from the MD trajectory. MD-docking shows the presence of a second binding site, not found in the X-docking. The interaction strategy between the AAC transporter and the ATP molecule has been analyzed investigating the composition and 3D arrangement of the interaction pockets, together with the orientations of the substrate into them. A relationship between sequence repeats and the ATP binding sites in the AAC carrier structure is proposed.

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Flöck, Dagmar. "Protein-protein docking and Brownian dynamics simulation of electron transfer proteins." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969418736.

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PICCAGLI, Laura. "MOLECULAR MODELLING STUDIES OF THE NF-κB BIOLOGICAL SYSTEM AS RELEVANT DRUG TARGET." Doctoral thesis, Università degli studi di Ferrara, 2009. http://hdl.handle.net/11392/2389196.

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Background Virtual screening (VS) is now a well-established method for finding small molecular modulators of a biological relevant macromolecule function by using much older computational techniques, such as docking simulations. The NF-kB family consists of a group of eukaryotic inducible transcription factors that have evoked widespread interest until now. As a matter of fact, the dysfunction of NF-kB is associated with many serious disease states. In spite of the well-defined solved NF-kB 3D structures, to the best of our knowledge, nowadays VS applications against this interesting target for the discovery of new NF-kB/DNA inhibitors have not been published yet. Aims The project described in this thesis is aimed to the identification of low molecular weight compounds interacting with NF-kB and able to inhibit DNA/NF-kB complex formation and biological dependent functions. Methods As a first example towards the development of a docking protocol fit to the target under study (NF-kB p50 monomer and homodimer), a data set of 27 bioactive natural compounds were prepared. In the second example a chemical library was purpose-made for VS applying a filtering procedure on 3D ZINC commercial database containing more than 2 million compounds. Successively a focus furocoumarin library of 1700 molecules was prepared for subsequent docking runs. The three dimensional structure of the complex NF-kB-DNA was retrieved from the RCSB Protein Data Bank. The cocrystallized DNA macromolecule was removed from the structure. p50-p50 homodimer, p50-p65 heteodimer and p50 monomers were selected for the docking simulations and prepared using the graphical interface Maestro. All molecules under study were docked in to the binding site of the target using Glide software from Schrodinger. Grids were prepared for each proteins. The coordinates of the enclosing box were defined starting from the set of active site residues involved in hydrogen bonds with the NF-kB recognition site of DNA and optimised including the double strands DNA helices volume by visual inspection. Docking studies were based on rigid X-ray crystal transcription factor structures (1LE9, 1IKN) and no information is reported in literature on dynamic features of this protein. Thus, 14ns of canonical MD simulations were carried out in explicit solvent on structural models of NF-kB systems as free and bound both to DNA and IkB. CHARMM27 force field, TIP3P model for water and P.M.E. for electrostatic force calculation were used. Main Results We found that the adopted docking sampling method and the scoring function were successful in predict the ranking of active and inactive natural compounds into DNA binding site of the ensemble protein (NF-kB p50). Further EMSA assays and biological evaluation were in agreement with computational findings. A successful identification of a micromolar active compound from docking-based VS of the prepared compound library is described. Subsequent in silico screening of the developed focus furocoumarin library carried forward the identifications of five micromolar p50 binders. The binding modes of the best-scored compounds showed the involvement of an essential residue for p50 in vivo activity in DNA interaction. In depth investigations of these interesting hits are also reported, including docking analysis into p50-p65 heterodimer. The ligands showed a different occupation of the DNA binding region of the heterodimer. The structural and dynamics properties of NF-kB p50-p65 in free form and in complex with DNA and IkB have been analyzed showing quite pertinent differences. The most relevant configurations of the transcription factor have been clustered and selected for further docking studies and drug design. Conclusions Discovered micromolar bioactive compounds can be considered as “leads” for developing stronger NF-kB/DNA inhibitors. The encouraging computational and biological results here reported could open new perspectives in discovery of NF-kB/DNA interaction inhibitors by taking advantages from recent VS strategies.

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Sharp, Amanda Kristine. "Probing Orthologue and Isoform Specific Inhibition of Kinases using In Silico Strategies: Perspectives for Improved Drug Design." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/98471.

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Kinases are involved in a multitude of signaling pathways, such as cellular growth, proliferation, and apoptosis, and have been discovered to be important in numerous diseases including cancer, Alzheimer's disease, cardiovascular health, rheumatoid arthritis, and fibrosis. Due to the involvement in a wide variety of disease types, kinases have been studied for exploitation and use as targets for therapeutics. There are many limitations with developing kinase target therapeutics due to the high similarity of kinase active site composition, making the utilization of new techniques to determine kinase exploitability for therapeutic design with high specificity essential for the advancement of novel drug strategies. In silico approaches have become increasingly prevalent for providing useful insight into protein structure-function relationships, offering new information to researchers about drug discovery strategies. This work utilizes streamlined computational techniques on an atomistic level to aid in the identification of orthologue and isoform exploitability, identifying new features to be utilized for future inhibitor design. By exploring two separate kinases and kinase targeting domains, we found that orthologues and isoforms contain distinct features, likely responsible for their biological roles, which can be utilized and exploited for selective drug development. In this work, we identified new exploitable features between kinase orthologues for treatment in Human African Trypanosomiasis and structural morphology differences between two kinase isoforms that can potentially be exploited for cancer therapeutic design.
Master of Science in Life Sciences
Numerous diseases such as cancer, Alzheimer's disease, cardiovascular disease, rheumatoid arthritis, and fibrosis have been attributed to different cell growth and survival pathways. Many of these pathways are controlled by a class of enzymes called kinases. Kinases are involved in almost every metabolic pathway in human cells and can act as molecular switches to turn on and off disease progression. Due to the involvement of these kinases' in a wide variety of disease types, kinases have been continually studied for the development of new drugs. Developing effective drugs for kinases requires an extensive understanding of the structural characteristics due to the high structural similarity across all kinases. In silico, or computational, techniques are useful strategies for drug development practices, offering new information into protein structure-function relationships, which in turn can be utilized in drug discovery advancements. Utilizing computational methods to explore structural features can help identify specific protein structural features, thus providing new strategies for protein specific inhibitor design. In this work, we identified new exploitable features between kinase orthologues for treatment in Human African Trypanosomiasis and structural morphology differences between two kinase isoforms that can potentially be exploited for cancer therapeutic design.

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CHIAPPORI, FEDERICA. "Large scale docking screening and simulations of molecular dynamics for the study of ligand binding in different protein models." Doctoral thesis, Università degli Studi di Camerino, 2010. http://hdl.handle.net/11581/401914.

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Molecular recognition is central to biology, it is the starting point for almost all processes in biological systems; knowledge of the molecular association aids in understanding a variety of pathways taking place in the living cell. Molecular binding is an attractive interaction between two molecules which results in a stable molecular complex. Among computational applications, docking is the methodology for predicting the complex. There are many docking strategies, fast molecular docking and absolute binding free energies are applied in this work. These methodologies have been applied to three biological systems: neuraminidase of H5N1 influenza virus, human Endothelial Protein C receptor (EPCR) and Î²-tubulin of the psycrophilic organism, Euplotes focardii. In particular, the first study is a drug design application; two selective ligands for the open conformation of the H5N1 influenza virus neuraminidase has been obtained, performing a comparative binding study with fast molecular docking and specific interaction filters. In the second study structurally stable mutants of EPCR with impaired binding affinity for phosphatidylethanolamine (PTY), will be designed and selected for the analysis of the ligand role in EPCR function. In the third work the structural adaptation to low temperature of the three Î²-tubulin isotypes are analysed employing molecular dynamics simulations. The applied computational methods allow to obtain accurate predictions in the field of binding analysis. In particular, fast molecular docking allows to obtain the correct binding mode and provide a good approximation of the interaction energy; molecular dynamics supply accurate binding affinities and is a useful tool for the study of the effect of ligand binding on protein structures.

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De, Oliveira Eduardo Basilio. "Simulations moléculaires appliquées à l'acétylation de flavonoïdes catalysée par des lipases : influence des structures de la lipase et du flavonoïde et sur la régiosélectivité de la bioconversion." Thesis, Vandoeuvre-les-Nancy, INPL, 2009. http://www.theses.fr/2009INPL095N/document.

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Les flavonoïdes sont des composés poly-hydroxylés d’origine végétale, connus pour leurs vertus pour la santé. Afin d’obtenir des dérivés plus stables et solubles dans des formulations hydrophobes tout en conservant les activités biologiques des molécules d’origine, une solution consiste à acyler ces composés de manière régiosélective. Ceci peut être accompli en utilisant des lipases comme catalyseurs, en milieu organique. Grand nombre d’études expérimentales sur ces bioprocédés sont disponibles, mais aucune d’entre elles n’apporte d’explication, au niveau moléculaire, de la sélectivité de ces réactions d’acylation. Le but de cette étude est d’appliquer différents outils de simulation moléculaire pour mieux comprendre, au niveau moléculaire, les propriétés de sélectivité de l’acétylation de trois flavonoïdes (quercétine et ses dérivés glycosylés isoquercitrine et rutine), en utilisant les lipases CALB et PCL. D’abord, des simulations de docking ont été appliquées, afin d’obtenir les positions et les orientations les plus probables des flavonoïdes dans la cavité des lipases préalablement acétylées. Ensuite, des simulations de dynamique moléculaire ont été exécutées sur les complexes obtenus par docking, afin d’étudier stabilité structurale des complexes sur une période de temps et notamment la stabilité des interactions enzyme-substrats. Enfin, des simulations basées sur une approche de chimie quantique (DFT) ont été appliquées pour évaluer la réactivité chimique des flavonoïdes dockées dans les complexes. Les premières tendances observées aux cours des simulations ont présenté une bonne corrélation avec les résultats expérimentaux d’acétylation. Globalement, les résultats obtenus ont montré que la sélectivité de ces réactions dépend de l’orientation des substrats (flavonoïde et acétate) dans la cavité catalytique de la lipase, des interactions intermoléculaires stabilisant ces substrats et de la réactivité chimique intrinsèque des groupements OH des flavonoïdes se situant à proximité des résidus catalytiques
Flavonoids are plant-produced polyhydroxylated compounds, well-known for their beneficial health effects. In order to obtain more stable and soluble derivatives for incorporation in hydrophobic formulations without damaging the biological activities of the native molecules, a solution consists to perform a regioselective acylation of these molecules. This can be accomplished by using lipase biocatalysts, in organic media. Several experimental studies dealing with such processes are available, but none of them give any explanation, at the molecular level, for the regioselectivity of such reactions. This study aimed to apply different molecular modelling tools in order to better understand, at the molecular level, the selectivity properties of the acetylation of three flavonoids (quercetin and its glycosylated derivatives isoquercitrin and rutin), by using the lipases CALB and PCL. Firstly, docking simulations were applied, in order to obtain the most probable positions and orientations of the flavonoids in the cavities of acetylated lipases. Then, molecular dynamics simulations were performed, aiming to study the structural stability of the complexes upon a period of time and specially the stability of the enzyme-substrates interactions. Finally, quantum chemical simulations (DFT) were applied to evaluate the chemical reactivity of the flavonoids as docked in the complexes. The trends observed during the simulations were well correlated with previous experimental results on the acetylation reaction of these flavonoids. Overall, the results showed that the selectivity in such reactions depends upon the substrates (flavonoid and acetate) orientations in the enzyme catalytic cavity, the intermolecular interactions that stabilize these substrates and the intrinsic chemical reactivity of the flavonoids OH groups reaching the catalytic residues

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Haghighi, Fatemeh. "Prediction of ticagrelor's effect on the lipid composition and the P2Y12 receptor of platelet's membrane by molecular dynamic and docking." Thesis, Bourgogne Franche-Comté, 2019. http://www.theses.fr/2019UBFCE019.

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Les récepteurs P2Y12 constituent une cible majeure des médicaments antiplaquettaires dans le traitement préventif des évènements thromboemboliques chez les patients ayant un syndrome coronarien aigu. A ce titre, le ticagrelor, un antagoniste sélectif et réversible des récepteurs P2Y12, a une place de choix dans l’arsenal thérapeutique. L’objectif de ce travail est d’étudier les interactions entre le ticagrelor, l’ADP et les récepteurs P2Y12 et les lipides membranaires des plaquettes.Dans la première partie de ce travail, nos résultats ont montré que le ticagrelor et l’ADP modifient la composition, la distribution et la concentration des sphingomyélines contenues dans les microdomaines membranaires en lien avec l’activation ou l’inhibition des plaquettes.Dans la deuxième partie de ce travail, nous avons décrit, pour la première fois, l'interaction des récepteurs P2Y12 avec les deux métabolites du ticagrelor. En outre, nous avons montré des interactions similaires entre l’ADP et les antagonistes avec les récepteurs P2Y12 avec une différence au niveau de la poche de liaison indiquant le changement de la conformation des récepteurs.L’ensemble de nos données confortent le rôle du ticagrelor dans la réorganisation des lipides membranaires et suggèrent des interactions spécifiques et une modification de la conformation entre les récepteurs P2Y12, l’ADP, le ticagrelor et ses métabolites
P2Y12 receptors are a major target of antiplatelet drugs in preventing thromboembolic events in patients with acute coronary syndrome. As such, ticagrelor, a selective and reversible P2Y12 receptor antagonist, has a place of choice in the therapeutic management. The aim of this work is to study the interactions between ticagrelor, ADP and P2Y12 receptors and platelet membrane lipids.Our data support the role of ticagrelor in the reorganization of membrane lipids and suggest specific interactions and a modification of the conformation between P2Y12 receptors, ADP, ticagrelor and its metabolites.In the first part of this work, our results showed that ticagrelor and ADP modify the composition, distribution and concentration of sphingomyelins in membrane microdomains related to platelet activation or inhibition.In the second part of this work, we described, for the first time, the interaction of P2Y12 receptors with the two metabolites of ticagrelor. In addition, we showed similar interactions between ADP and P2Y12 receptor antagonists with a difference in the binding pocket indicating the change in receptor conformation

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Alonso, Hernan, and hernan alonso@anu edu au. "Computer Modelling and Simulations of Enzymes and their Mechanisms." The Australian National University. The John Curtin School of Medical Research, 2006. http://thesis.anu.edu.au./public/adt-ANU20061212.161155.

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Although the tremendous catalytic power of enzymes is widely recognized, their exact mechanisms of action are still a source of debate. In order to elucidate the origin of their power, it is necessary to look at individual residues and atoms, and establish their contribution to ligand binding, activation, and reaction. Given the present limitations of experimental techniques, only computational tools allow for such detailed analysis. During my PhD studies I have applied a variety of computational methods, reviewed in Chapter 2, to the study of two enzymes: DfrB dihydrofolate reductase (DHFR) and methyltetrahydrofolate: corrinoid/iron-sulfur protein methyltransferase (MeTr). ¶ The DfrB enzyme has intrigued microbiologists since it was discovered thirty years ago, because of its simple structure, enzymatic inefficiency, and its insensitivity to trimethoprim. This bacterial enzyme shows neither structural nor sequence similarity with its chromosomal counterpart, despite both catalysing the reduction of dihydrofolate (DHF) using NADPH as a cofactor. As numerous attempts to obtain experimental structures of an enzyme ternary complex have been unsuccessful, I combined docking studies and molecular dynamics simulations to produce a reliable model of the reactive DfrBDHFNADPH complex. These results, combined with published empirical data, showed that multiple binding modes of the ligands are possible within DfrB. ¶ Comprehensive sequence and structural analysis provided further insight into the DfrB family. The presence of the dfrB genes within integrons and their level of sequence conservation suggest that they are old structures that had been diverging well before the introduction of trimethoprim. Each monomer of the tetrameric active enzyme presents an SH3-fold domain; this is a eukaryotic auxiliary domain never found before as the sole domain of a protein, let alone as the catalytic one. Overall, DfrB DHFR seems to be a poorly adapted catalyst, a minimalistic enzyme that promotes the reaction by facilitating the approach of the ligands rather than by using specific catalytic residues. ¶ MeTr initiates the Wood-Ljungdahl pathway of anaerobic CO2 fixation. It catalyses the transfer of the N5-methyl group from N5-methyltetrahydrofolate (CH3THF) to the cobalt centre of a corrinoid/iron-sulfur protein. For the reaction to occur, the N5 position of CH3THF is expected to be activated by protonation. As experimental studies have led to conflicting suggestions, computational approaches were used to address the activation mechanism. ¶ Initially, I tested the accuracy of quantum mechanical (QM) methods to predict protonation positions and pKas of pterin, folate, and their analogues. Then, different protonation states of CH3THF and active-site aspartic residues were analysed. Fragment QM calculations suggested that the pKa of N5 in CH3THF is likely to increase upon protein binding. Further, ONIOM calculations which accounted for the complete protein structure indicated that active-site aspartic residues are likely to be protonated before the ligand. Finally, solvation and binding free energies of several protonated forms of CH3THF were compared using the thermodynamic integration approach. Taken together, these preliminary results suggest that further work with particular emphasis on the protonation state of active-site aspartic residues is needed in order to elucidate the protonation and activation mechanism of CH3THF within MeTr.

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Rieux, Charlotte. "Etude des ADN glycosylases de la superfamille structurale Fpg/Nei par modélisation moléculaire, de nouvelles cibles thérapeutiques potentielles dans les stratégies anti-cancer." Thesis, Orléans, 2017. http://www.theses.fr/2017ORLE2023/document.

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L’ADN, support de l’information génétique, est constamment altéré par des agents physiques ou chimiques d’origines endogènes (métabolisme) et exogènes (UV, radiations ionisantes, produits chimiques) dont les effets sont génotoxiques. Ces modifications structurales délétères de l’ADN sont éliminées par de nombreux mécanismes de réparation. Parmi eux, le système de réparation par excision de bases (BER) est initié par les ADN glycosylases qui reconnaissent et éliminent les bases endommagées. Dans certaines stratégies anti-cancéreuses, l’utilisation de la chimiothérapie et la radiothérapie ont pour but la destruction des cellules cancéreuses en altérant leur ADN. Dans ce contexte, les ADN glycosylases réparent l’ADN des cellules traitées et induisent une résistance non désirée au traitement, faisant de ces enzymes des cibles thérapeutiques intéressantes. Le but de ces travaux est d’approfondir la compréhension des mécanismes de réparation des ADN glycosylases de la superfamille structurale Fpg/Nei grâce à la modélisation moléculaire et de pouvoir identifier et concevoir des inhibiteurs de ces enzymes. Les simulations de dynamique moléculaire (DM) nous ont permis d’étudier la « Lesion Capping Loop » (LCL) et de l’associer à la stabilisation de la base endommagée positionnée dans le site actif. Nous avons également étudié les chemins de sortie possibles de la base après coupure par l’enzyme et l’implication de la boucle LCL dans ce phénomène grâce à des simulations de DM ciblée (TMD-1). De plus, les simulations de DM couplées à un protocole d’amarrage moléculaire « aveugle » nous ont permis d’identifier 2 sites de fixations possibles majoritaires pour des petites molécules potentiellement inhibitrices. Un de ces sites correspondant au site actif de hNEIL1 a fait l’objet d’un criblage virtuel d’une partie de la base de molécules Ambinter. Ceci nous a permis d’identifier des molécules potentiellement inhibitrices dont les effets seront prochainement testés in vitro dans l’équipe sur la protéine humaine hNeil1
The DNA, genetic information support, is frequently damaged by physical or chemical agents from endogenous (cell metabolism) and exogenous (UV, ionizing radiations, chemicals) factors whose effects are genotoxic. These deleterious DNA structural alterations are removed by many DNA repair mechanisms. Among them, the base excision repair (BER) is initiated by DNA glycosylases which recognize and remove damaged bases. In some anti-cancer strategies, the use of chemo- and radiotherapy is aimed to cancerous cells destruction by altering their DNA. In that specific context, DNA glycosylases repair the DNA of treated cells and induce unwanted resistance to treatments, making these enzymes interesting therapeutic targets. The purpose of this work is to deepen the repair mechanism knowledge of Fpg/Nei structural superfamily of DNA glycosylases using molecular modeling and designing inhibitors of these enzymes. Molecular dynamic simulations allowed us to study the « Lesion Capping Loop » (LCL) and to associate its role to substrate stabilization in the enzyme active site. We also studied some possible excision’s product release pathways and LCL implication in this phenomena by targeted molecular dynamic simulations (TMD-1). Furthermore, molecular dynamic simulations coupled to a blind molecular docking protocol allowed us to identify 2 possible main binding sites of potential inhibitiors. One of these binding sites corresponding to the hNEIL1 active site has been the object of a virtual screening of the Greenpharma database. This allowed us to identify potential inhibitors whom effects will be soon tested in vitro on the humain protein hNEIL1

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Silva, Rosa Helena Moraes. "Atividade antinociceptiva de Borreira verticillata (L.) G. Mey. e modo de interação com a cicloxigenase COX-2 e receptor N-metil-D-aspartato NMDA." Universidade Federal do Maranhão, 2016. http://tedebc.ufma.br:8080/jspui/handle/tede/1630.

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Borreria verticillata (L.) G. Mey species known as broom vassourinha has antibacterial, antimalarial, hepatoprotective, antioxidative, analgesic and antiinflammatory activities; however, its antinociceptive action still demands more thorough investigation. The present study was to assess the antinociceptive activity of B. verticillata crude hydroalcoholic extract (EHBv) and the ethyl acetate fraction (FAc) by means of in vivo and in silico studies. In vivo assessment included the paw edema test, the writhing test, the formalin test and the tail flick test. Wistar rats and Swiss mice were divided into 6 groups and given the following treatments oral: 0.9% NaCl control group (CTL), 10 mg/kg memantine (MEM), 10 mg/kg indomethacin (INDO), 500 mg/kg EHBv (EHBv 500), 25 mg/kg FAC (FAc 25), 50 mg/kg and FAc (FAC 50). EHBv, FAc 25 and 50 treatments exhibited anti-edematous and peripheral antinociceptive effects. For in silico assessment, compounds found in FAc were subjected to molecular docking, and the leading compound was selected for molecular dynamics (MD) simulations. Ursolic acid exhibited better affinity parameters with the enzyme COX-2 and the NMDA receptor subunits GluN1a and GluN2B on molecular docking. In MD simulations, AU exhibited highly frequent interactions with residues Arg120 and Glu524 in the COX-2 active site and NMDA, whereby it might prevent COX-2 and NMDA receptor activation. Treatment with ursolic acid 10mg / Kg (AU) showed peripheral and central antinoceceptivo effect. The antinociceptive effect of B. verticillata might be predominantly attributed to peripheral actions, including the participation of anti-inflammatory components. Ursolic acid is the main active component and seems to be a promising source of COX-2 inhibitors and NMDA receptor antagonists
Borreria verticillata (L.) G. Mey espécie conhecida como vassourinha apresenta atividade antibacteriana, antimalárica, hepatoprotetora, antioxidante, analgésica e anti-inflamatória, entretanto sua atividade antinociceptiva é pouco estudada. O objetivo deste trabalho foi avaliar atividade antinociceptiva do extrato hidroalcoólico bruto (EHBv) e fração acetato de etila (FAc) de B. verticillata realizando estudos in vivo e in silico. Para avaliação in vivo, foram utilizados os testes do edema de pata, contorções abdominais, formalina e tail flick. Ratos Wistar e camundongos Swiss foram tratados via oral e divididos em 6 grupos: controle-NaCl 0.9%(CTL), memantina 10 mg/Kg (MEM), indometacina 10 mg/Kg (INDO), EHBv 500 mg/kg (EHBv 500), FAc 25 mg/Kg (FAc 25), FAc 50 mg/Kg (FAc 50). O tratamento com EHBv 500, FAc 25 e 50 apresentou efeito antiedematogênico e antinociceptivo periférico. Para avaliação in silico os compostos identificados na FAc foram submetidos a docagem molecular, o melhor composto foi selecionado para simulações de dinâmica e testado in vivo molecular. O ácido ursólico apresentou melhores parâmetros de afinidade com COX-2, GluN1a e GluN2B durante a docagem molecular. Nas simulações por dinâmica molecular, o ácido ursólico apresentou alta frequência de contatos com Arg120 e Glu524 do local ativo da COX- 2 e com o domínio LBD da Glun1a e GluN2B podendo com isso, impedir a ativação da COX-2 e do receptor NMDA. O tratamento com ácido ursólico 10mg/Kg (AU) apresentou efeito antinoceceptivo periférico e central. Sugere-se que o efeito antinociceptivo periférico de B. verticillata pode ser atribuído predominantemente à ação de compostos com ação anti-inflamatória. O ácido ursólico é o principal composto ativo, sendo um composto promissor para o desenvolvimento de fármacos inibidores da COX-2 e antagonistas dos receptores NMDA.

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Asses, Yasmine. "Conception par modélisation et criblage in silico d'inhibiteurs du récepteur c-Met." Phd thesis, Université Henri Poincaré - Nancy I, 2011. http://tel.archives-ouvertes.fr/tel-00653609.

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L'enjeu des travaux effectués au cours de cette thèse est l'extraction in silico de molécules potentiellement intéressantes dans le processus d'inhibition du récepteur tyrosine kinase c-Met. La faculté de cette protéine à interagir dans les phénomènes d'embryogenèse et de réparation tissulaires rendent son inhibition cruciale dans les traitements contre les développements tumoraux où c-Met se trouve impliquée. Dans ce but, la stratégie que nous avons employée implique l'utilisation de plusieurs méthodes in silico de conception rationnelle de médicaments. Nous avons utilisé comme support les multiples structures cristallographiques publiées sur la ProteinData Base (PDB). Un travail de modélisation par homologie fut tout d'abord nécessaire pour combler les lacunes des structures cristallographiques collectées. Afin d'échantillonner au mieux l'espace conformationnel du récepteur kinase c-Met et de caractériser sa flexibilité, une longue campagne de simulation de Dynamique Moléculaire (DM) fut menée concernant les formes apo et holo des structures cristallographiques disponibles. Pour compléter ces simulations, une partie du travail consista à utiliser également la méthode des modes normaux de vibration (NM). De ces 2 approches (DM et NM), nous avons extrait un ensemble de 10 conformères considérés comme les plus représentatifs de l'espace conformationnel simulé pour la kinase c-Met et avons proposé un mode de fonctionnement de ce récepteur. Utilisant les conformations extraites de l'échantillonnage conformationnel, nous avons ensuite mené une importante campagne de criblage virtuel sur plusieurs chimiothèques constituant au total environ 70.000 composés. L'analyse des résultats de l'arrimage moléculaire nous a conduits à la sélection de plusieurs molécules intéressantes possédant théoriquement une bonne affinité pour la kinase c-Met. Ces molécules ont été soumises aux tests expérimentaux effectués par l'équipe de biologistes associée à nos travaux.

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Turra, Kely Medeiros. "Aplicação de modelagem molecular e de formalismo do CAMD (Computer-Aided Molecular Design) na elucidação do mecanismo de ação de inibidores de metalopropteinases de matriz." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/9/9138/tde-18022016-105120/.

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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.

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Shamsudin, Khan Yasmin. "Non-Steroidal Anti-Inflammatory Drugs in Cyclooxygenases 1 and 2 : Binding modes and mechanisms from computational methods and free energy calculations." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328478.

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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.

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Lopes, Alberto Jorge Oliveira. "Estudo computacional da interação de terpenos com acetilcolinesterase de Rhipicephalus microplus e potenciais novos candidatos a carrapaticidas." Universidade Federal do Maranhão, 2015. http://tedebc.ufma.br:8080/jspui/handle/tede/1625.

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Made available in DSpace on 2017-06-14T16:54:49Z (GMT). No. of bitstreams: 1 AlbertoLopes.pdf: 7651509 bytes, checksum: 542872f26d9cc8bf6b0b65d8a7151d16 (MD5) Previous issue date: 2015-07-07
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ)
Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão (FAPEMA)
The tick Rhipicephalus microplus is the major cattle ectoparasite of the world accounting for losses of billions of dollars that directly affect the return of such livestock. Its control is difficult due to the resistance of ticks to all chemical bases commercially available miticides. Acaricidal activity of terpenes has been evaluated in several studies that show satisfactory results, indicating these compounds are potential sources of new acaricidal products. The aim of this work was to select terpenes with potential activity against enzyme acetylcholinesterase (AChE) from R. microplus. Properties of the molecular volume, geometric parameters and vibrational terpenes were obtained from quantum chemical calculations the density functional theory level. Bioinformatic methodologies were applied to study the interaction of terpenes identified in essential oils of Citrus spp. and Lippia spp. with three AChE R. microplus. Since there are no available experimental structures, models of the three AChE were generated by homology modeling and then refined by molecular dynamics simulations. Soon after, were studies of molecular docking to detect best energy conformation of interaction and molecular dynamics simulations of this complex were carried out to study the behavior of this interaction. Our results suggest that the known acaricide activity of carvacrol is associated with its interaction with AChEs, while the acaricide activity of thymol is not associated with inhibition of that enzyme. Also, as expected, showed an excellent interaction coumafos acaricide and reports the first record of interaction of AChE from R. microplus with gammamuuruleno and elemol terpenes, molecules with few studies and that now configure themselves as candidates potential new acaricidal products.
O carrapato Rhipicephalus microplus é o principal ectoparasita da bovinocultura mundial sendo responsável por perdas de bilhões de dólares que afetam diretamente o retorno de tal produção animal. Seu controle é difícil devido à resistência dos carrapatos a todas as bases químicas de acaricidas comercialmente disponíveis. A atividade acaricida de terpenos tem sido avaliada em vários estudos que mostram resultados satisfatórios, indicando que estes compostos são fontes potenciais de novos produtos acaricidas. O objetivo desse trabalho foi selecionar terpenos com potencial atividade sobre a enzima acetilcolinesterase (AChE) de R. microplus. As propriedades do volume molecular, os parâmetros geométricos e vibracionais de terpenos foram obtidos a partir de cálculos de química quântica no nível da teoria do funcional de densidade. Metodologias de bioinformática foram aplicadas para estudar a interação de terpenos identificados em óleos essenciais de Citrus spp. e Lippia spp. com as três AChE de R. microplus. Como não existem estruturas experimentais disponíveis, modelos das três AChE foram gerados por modelagem por homologia e em seguida refinadas por simulações de dinâmica molecular. Logo após, foram realizados estudos de docagem molecular para detectar a melhor conformação energética de interação e simulações de dinâmica molecular desse complexo foram realizadas para estudarmos o comportamento dessa interação. Os resultados sugerem que a conhecida atividade carrapaticida do carvacrol está associada com a sua interação com a AChE, enquanto que a atividade carrapaticida do timol não está associado com a inibição dessa mesma enzima. Além disso, como esperado, mostrou uma excelente interação do carrapaticida cumafós e relata o primeiro registro da interação da AChE de R. microplus com os terpenos gama-muuruleno e elemol, moléculas com poucos estudos e que a partir de agora configuram-se como candidatos potenciais para novos produtos acaricidas.

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Tangella, Lokeswari Prathyusha. "An investigation on role of the ATP-binding cassette B5 (ABCB5) transporter as potential mediator of melanoma resistance to BRAF inhibition." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2020. https://ro.ecu.edu.au/theses/2369.

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Cutaneous melanoma is a highly metastatic and drug-resistant skin cancer type, responsible for a disproportionate number of skin cancer deaths. Targeted therapies, in the form of BRAF inhibitors (BRAFis), have been effective at treating BRAFV600 mutant melanomas. However, majority of the melanoma patients fail to respond to BRAFis due to intrinsic or acquired resistance within one year of treatment commencement. Multiple mechanisms that contribute to BRAFi resistance in melanoma cells have been identified, as discussed in the review in Chapter 1. Overexpression of ATP-binding cassette (ABC) transporters has been linked to multidrug resistance in numerous cancer types. These transporters expel the anti-cancer drugs out of the cell, thereby decreasing the intracellular concentration of the drug. In melanoma, the ATP-binding cassette B5 transporter (a member of ABC superfamily) has been linked to chemoresistance by drug extrusion. Moreover, overexpression of ABCB5 has been observed in BRAFV600 melanoma cells after short-term BRAFi treatment. In this study we investigated the role of the ABCB5 transporter as potential mediators of resistance to BRAFis by drug expulsion. In Chapter 2, we showed increased ABCB5 expression in melanoma cell lines after short-term treatment with the BRAFis accompanied by an increased expression of melanocytic signature. Gene expression of fluorescent activated cell sorted melanoma cells into ABCB5high and ABCB5low populations, revealed an increased melanocytic signature in the ABCB5high population. Moreover, analysis of single-cell RNA sequencing (scRNAseq) data of two BRAFV600 melanoma cell lines, A2058 and 451Lu, revealed a strong association between ABCB5 expression and melanocytic signature. Based on these initial observations, the capacity of the ABCB5 transporter to efflux BRAFis was evaluated indirectly through an in-silico approach using molecular docking simulations (Chapter 3 and 4), and directly through in vitro experiments using an ABCB5 overexpressing melanoma BRAFV600 cell line (Chapter 5). In Chapter 3, a full-length ABCB5 model was generated, based on mouse ATP-binding cassette B1 transporter (ABCB1; Pgp1), a close homologue of ABCB5. Molecular dynamics simulations were performed in 2 model cell membranes and the dominant conformation was identified. Docking simulations of known ABCB5 substrates such as taxanes, anthracyclines, camptothecin and etoposide enabled the identification of at least three putative substrate binding sites in ABCB5. The overlap of these three binding sites with validated binding sites for these chemotherapeutic drugs in Pgp1 corroborate our findings. In Chapter 4, docking simulations revealed at least one overlapping binding site for BRAFis and chemotherapeutic drugs on ABCB5, suggesting that BRAFis could potentially act as a substrate for ABCB5. In Chapter 5, we generated an ABCB5 overexpressing BRAFV600E melanoma cell line. However, no differences in sensitivity to BRAF inhibition was observed as a result of ABCB5 overexpression. Intracellular drug accumulation analyses revealed no reduction in vemurafenib or dabrafenib concentrations, indicating that BRAFis do not act as substrates for ABCB5. Altogether, our studies suggest that ABCB5 expression is linked to the melanocytic program. However, despite the molecular docking evidence that BRAFis may be substrates of ABCB5, in vitro studies failed to demonstrate direct efflux of BRAFis by ABCB5.

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Schmidt, Matthias Rene. "K+ channels : gating mechanisms and lipid interactions." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:51dc4149-d943-4dcd-bf5b-f04130456d84.

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Computational methods, including homology modelling, in-silico dockings, and molecular dynamics simulations have been used to study the functional dynamics and interactions of K⁺ channels. Molecular models were built of the inwardly rectifying K⁺ channel Kir2.2, the bacterial homolog K⁺ channel KirBac3.1, and the twin pore (K2P) K⁺ channels TREK-1 and TRESK. To investigate the electrostatic energy profile of K⁺ permeating through these homology models, continuum electrostatic calculations were performed. The primary mechanism of KirBac3.1 gating is believed to involve an opening at the helix bundle crossing (HBC). However, simulations of Kir channels have not yet revealed opening at the HBC. Here, in simulations of the new KirBac3.1-S129R X-ray crystal structure, in which the HBC was trapped open by the S129R mutation in the inner pore-lining helix (TM2), the HBC was found to exhibit considerable mobility. In a simulation of the new KirBac3.1-S129R-S205L double mutant structure, if the S129R and the S205L mutations were converted back to the wild-type serine, the HBC would close faster than in the simulations of the KirBac3.1-S129R single mutant structure. The double mutant structure KirBac3.1-S129R-S205L therefore likely represents a higher-energy state than the single mutant KirBac3.1-S129R structure, and these simulations indicate a staged pathway of gating in KirBac channels. Molecular modelling and MD simulations of the Kir2.2 channel structure demonstrated that the HBC would tend to open if the C-linker between the transmembrane and cytoplasmic domain was modelled helical. The electrostatic energy barrier for K⁺ permeation at the helix bundle crossing was found to be sensitive to subtle structural changes in the C-linker. Charge neutralization or charge reversal of the PIP2-binding residue R186 on the C-linker decreased the electrostatic barrier for K⁺ permeation through the HBC, suggesting an electrostatic contribution to the PIP2-dependent gating mechanism. Multi-scale simulations determined the PIP2 binding site in Kir2.2, in good agreement with crystallographic predictions. A TREK-1 homology model was built, based on the TRAAK structure. Two PIP2 binding sites were found in this TREK-1 model, at the C-terminal end, in line with existing functional data, and between transmembrane helices TM2 and TM3. The TM2-TM3 site is in reasonably good agreement with electron density attributed to an acyl tail in a recently deposited TREK-2 structure.

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Benabderrahmane, Mohammed. "Etude de la structure et la dynamique de Mcl-1 : application en cancérologie Binding mode of Pyridoclax to myeloid cell leukemia-1 (Mcl-1) revealed by nuclear magnetic resonance spectroscopy, docking and molecular dynamics approaches Insights into Mcl-1 Conformational States and Allosteric Inhibition Mechanism from Molecular Dynamics Simulations, Enhanced Sampling, and Pocket Crosstalk Analysis." Thesis, Normandie, 2020. http://www.theses.fr/2020NORMC426.

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Ce travail ayant pour objet l’étude de la structure et la dynamique de Mcl-1, une protéine anti-apoptotique d’intérêt en cancérologie, est scindé en trois parties.Une première étude concerne une caractérisation du mode d’interaction du Pyridoclax (un inhibiteur BH3-mimétique) avec Mcl-1 par des approches expérimentales (RMN) et théoriques (simulations de dynamique moléculaire). Une deuxième partie est consacrée à l’étude et à la caractérisation des espaces conformationnels de Mcl-1 et son mode d’inhibition allostérique. Le troisième volet de ce travail, traite d’une approche d’analyse, basée sur des simulations de métadynamique avec comme application la détection du répertoire des poches cryptiques de Mcl-1
This work, which aims to study the structure and dynamics of Mcl-1, an anti-apoptotic protein of interest in cancer, was carried out in three parts.A first study focused on a characterization of the interaction mode of Pyridoclax (a BH3-mimetic) with Mcl-1 by experimental (NMR) and theoretical approaches (molecular dynamics simulations). A second part is devoted to the study and characterization of the conformational space of Mcl-1 and its mode of allosteric inhibition. In the last part of this work, Metadynamics simulations on essential dynamics space as a general approach for Mcl-1’s cryptic pockets detection were evaluated

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Kumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.

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Bondoky, Karim [Verfasser], Klaus [Gutachter] Janschek, and Stefanos [Gutachter] Fasoulas. "A Contribution to Validation and Testing of Non-Compliant Docking Contact Dynamics of Small and Rigid Satellites Using Hardware-In-The-Loop Simulation / Karim Bondoky ; Gutachter: Klaus Janschek, Stefanos Fasoulas." Dresden : Technische Universität Dresden, 2020. http://d-nb.info/122783313X/34.

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Ullmann, G. Matthias [Verfasser]. "Simulation and analysis of docking and molecular dynamics of electron transfer protein complexes / vorgelegt von G. Matthias Ullmann." 1998. http://d-nb.info/962239143/34.

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吳冠緯. "Computational Study of Binding Energy of Protein-Ligand Complexes for Two Kinases: Thermodynamic Integration Molecular Dynamics and Docking Simulation." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/86923683324881538499.

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碩士
國立臺灣師範大學
化學系
100
Cancer has been one of the top ten leading causes of death for several decades. The target drugs research for cancer therapy is now a popular field among international medicinal chemists. Because of the significant amount of money and human resources spent in the drug development process, computer-aided drug design method is an attractive tool to reduce cost and assist drug discovery. Protein kinases are one of the protein families which are drug targets for cancer therapy. Here, we selected two kinases, which are ERK2 and FGFR1 kinases, and used computer modeling to investigate binding energy of inhibitor-protein complexes for these two kinases. In the part of ERK2, we used thermodynamic integration MD method to compute relative binding free energy of several ERK2-inhibitor complexes of interest. We carried out computations to predict G for new analogs, focusing on placing polar and nonpolar functional groups at the meta site of benzene ring, to see if these ligands have better binding affinity than the above ligands. The computations resulted that a ligand with polar –OH group has better binding affinity than the previous examined ligand by ~2.0 kcal/mol and two other ligands have better affinity by ~1.0 kcal/mol. The predicted better inhibitors of this kind should be of interest to experimentalists for future experimental enzyme and/or cell assays. In addition to TI-MD simulation, we also worked on interactions of FGFR1 kinase-inhibitor complexes using docking computation, focusing on how enrichment factor (EF) enhances in virtual screening by including side chain movement and applying hydrogen bond constraint for this kinase. To this end, active and decoy compounds from the Directory of Useful Decoys 1 database was obtained and benchmarked with GOLD program. Interestingly, among combinations of side chains which were allowed to move, EF is significantly higher with movement of Lys514 compared with others. In addition, the effect of adding hydrogen bond constraint at a residue located in the hinge segment, Ala564, was also examined. The results were analyzed and discussed. The present results should be useful for virtual screening of large databases against this kinase.

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Meduru, Harika, and Harika Meduru. "Dipeptidyl Peptidase-4 (DPP-4) Enzyme Inhibitor Study by In Silico Analysis: Molecular Docking, Pharmacophore Generation and Molecular Dynamics Simulation in Treatment of Type-2 Diabetes." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/55336938559078403490.

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博士
亞洲大學
生物資訊與醫學工程學系
104
Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme responsible for inactivating intestinal peptides Glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decrease in blood glucose levels. The aim of this study was to explore the inhibition activity of small-molecule inhibitors to DPP-4. AutoDock, CDOCKER and Standard dynamics cascade were used for molecular docking and molecular dynamics studies. Molecular docking was performed for structurally diverse compounds (Aminopiperdine-fused imidazoles, Thiazolopyrimidine derivatives, and quinolin-fused imidazoles) and the differences in their binding modes were investigated. Furthermore, good correlation (R2=0.72) was acquired for the DPP-4 inhibitors based on the predicted binding affinities (pKi) determined by using AutoDock, CDOCKER and experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out to determine the binding modes of structurally diverse compounds in the receptor active site. Study of the stability and flexibility of the DPP-4 inhibitor complexes by means of MD simulation specified that the inhibitors retained the binding mode observed in the docking study. The present studies provides some guiding information for further structural optimization and are helpful for future DPP-4 inhibitors discoveries in treatment of type-2 diabetes.

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KULIK, Natallia. "Modeling Substrate-Enzyme Interactions in Fungal Hydrolases." Doctoral thesis, 2011. http://www.nusl.cz/ntk/nusl-55347.

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Computational tools play an important role in the description of biological systems. Scientists describe and study structure, conformational changes and interactions between molecules in silico, often as a cheaper and faster alternative for biosynthesis. The simulated dynamic behavior in time of a molecular system is a straight forward source of information about substrate-enzyme interactions at the atomic level, and a powerful tool for the identification of molecular properties important in enzymatic reactions. Our study is focused on the computational investigation of structure and substrate specificity of hydrolases important in biotransformation. The computational work was performed in close collaboration with biochemists-experimentalists from Charles University and the Microbiological Institute of the Academy of Sciences of the Czech Republic. Hydrolases have great a potential in the chemoenzymatic synthesis of modified carbohydrates with regulated properties. Carbohydrates, as substrates of hydrolases, are important in normal functionality of many organisms. They have a dual role in immune response regulation: some carbohydrates (like GlcNAc and ManNAc) participate in activation and some (like GalNAc) in suppressing immunity; glycosidase deficiency is associated with a number of lysosomal disorders. We used homology modeling, computational docking and molecular dynamics simulation (MD) methods for the complex study of fungal hydrolases: alpha-galactosidase/alpha-N-acetylgalactosaminidase from Aspergillus niger; beta-N-acetylhexosaminidases (HEX) (from Aspergillus oryzae and Penicillium oxalicum); nitrilase from Aspergillus niger. Our structural study unambigously demonstrates that the enzyme encoded by genes variant A (aglA) from A. niger is able to accept alpha-N-acetylgalactosamine as its substrate and explains structural features responsible for its specificity. Homology models of HEXs from P. oxalicum and A. oryzae were built and compared. Homology models were used to study the role of protein glycosylation, disulfide bonds, dimer formation and interaction with natural and modified substrates. Model of nitrilase from Aspergillus niger helped to analyze multimer formation.

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DULEBO, Alexander. "Mechanizmy podílející se na aktivaci sodíkového transportu TIP peptidem odvozeným z faktoru nádorové nekrózy." Doctoral thesis, 2012. http://www.nusl.cz/ntk/nusl-85701.

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The Tumor Necrosis Factor derived-TIP peptide is a small 17 amino acids cyclic peptide with lectin-like activity, that possesses several therapeutically relevant biological activities, among which is activation of alveolar liquid clearance in both healthy and injured lungs in vivo. Accumulation of fluid in the lungs? alveoli and interstitial spaces is a life-threatening condition called pulmonary edema. The mortality rate due permeability pulmonary edema, accompanied by a dysfunction of the alveolar/capillary barrier, is high because no effective treatment lacking side effects exists nowadays. It is known that the TIP peptide is able to activate vectorial Na+ transport ? which mediates lung liquid clearance. However, the mechanism of action of remains elusive. The aim of this thesis was to investigate the initial steps of interaction between the TIP peptide and airway epithelial cells. Numerous novel methods and single-molecule techniques were used to unravel: (i) how the TIP peptide interacts with the molecules on the apical side of the lung epithelial cells; (ii) whether the TIP peptide need to be internalized inside of the cells to trigger its effects; (iii) the nature of the interaction between the TIP peptide and its putative receptor(s); (iv) the putative receptor(s) for the TIP peptide on the apical surface of the lung epithelial cells.

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Chen, Mu-Jia, and 陳沐家. "Discovery of novel anti-atherosclerotic compounds by pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulations." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/425azy.

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碩士
國立臺北科技大學
生物科技研究所
100
Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipids and fibrous elements in the large arteries; moreover, it is the primary cause of cardiovascular diseases. In previous studies, a great number of anti-atherosclerotic drugs have been developed but several side effects were found in animal and human studies. Until recently, an effective anti-atherosclerotic drug without side effects has not been discovered. Therefore, we applied many computational approaches including pharmacophore modeling, virtual screening, molecular docking and molecular dynamic for searching more effective and less side effects anti-atherosclerotic drugs. Furthermore, it was found that there are two predominant targets for anti-atherosclerotic: Acyl-coenzyme A: cholesterol acyltransferase (ACAT) and Cholesteryl ester transfer protein (CETP). For ACAT, there are two similar types ACAT-1 and ACAT-2, and then we constructed ligand-base pharmacophore models: HipHopRefine and HypoRefine for ACAT-1 and ACAT-2 respectively. After Güner–Henry (GH) scoring methods validation, both of HipHopRefine and HypoRefine show good predictive ability. Subsequently, we utilized two pharmacophore models to screen ZINC database for obtaining more potential dual ACAT inhibitors. After virtual screening, 10 hits with high pharmacophore fitvalue and diverse scaffolds were identified as potential lead compounds. As to CETP, we also constructed HipHop pharmacophore model by a series of CETP inhibitors to search another potential drugs of atherosclerosis. The best model HipHop-1 was further validated by GH scoring methods and applied to screen the NCI and Maybridge databases. Then, molecular docking and molecular dynamic were conducted to retrieve 4 potential compounds. In summary, the results of this study can be applied to the design of new and more potent anti-atherosclerotic drugs for clinical purposes.

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Wang, Chih-Lun, and 王志倫. "Discovery of novel 5α-reductase type II inhibitors by 3D-QSAR modeling, pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulations." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/42hwgv.

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碩士
國立臺北科技大學
化學工程研究所
101
Benign prostatic hyperplasia (BPH) is caused by the augmented levels of androgen dihydrotestosterone (DHT) that is involved in the growth of prostate in human. 5a-Reductase type II (5aR2) is an intracellular enzyme that catalyzes the formation of DHT from testosterone; hence the inhibition of 5aR2 has emerged as one of the most promising strategies for the treatment of BPH. However, the steroidal structure of 5aR2 inhibitors may incur hormonal adverse effects. Until recently, an effective anti-BPH drug without side effects has not been discovered. Therefore, we applied many computational approaches that integrate ligand-based pharmacophore, 3D-QSAR, virtual screening, molecular docking and molecular dynamic (MD) simulations for searching more effective and less side effects 5aR2 inhibitors. The best pharmacophore model (Hypo1) was validated by Guner-Henry (GH) scoring method. This well validated Hypo1 was then used as a 3D-query in virtual screening to identify potential hits from Maybridge and National Cancer Institute (NCI) databases. Then these hits were subsequently filtered by molecular docking and MD simulations. After screening, one hit was identified as a potential lead based on high predicted inhibitory activity and binding affinity to 5aR2 in comparison to the most active inhibitor (Finasteride). In appendixes, pharmacophore and CoMFA model was performed on a set of 25 human nonsteroidal 5?R2 inhibitors and successfully identified 7 hit compounds with novel scaffolds were retrieved as leads. In summary, the results of this study can be applied to the design of new and more potent anti-BPH drugs for clinical purposes.

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Lu, Shao-Chi, and 呂紹齊. "Proposing binding sites of small molecules with TRPV1 ion channel using a combination of molecular dynamics simulations and docking approach." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/7netnz.

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41

Flöck, Dagmar [Verfasser]. "Protein-protein docking and Brownian dynamics simulation of electron transfer proteins / vorgelegt von Dagmar Flöck." 2003. http://d-nb.info/969418736/34.

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Wacker, Sören. "Computer-Aided Drug Design for Membrane Channel Proteins." Doctoral thesis, 2012. http://hdl.handle.net/11858/00-1735-0000-000D-F08E-F.

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43

Seidel, Ute [Verfasser]. "Analysis of the mechanism of induction of selected tetracycline repressor variants using molecular dynamics simulations and protein-ligand docking / vorgelegt von Ute Seidel." 2008. http://d-nb.info/988606097/34.

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44

Alonso, Hernan. "Computer Modelling and Simulations of Enzymes and their Mechanisms." Phd thesis, 2006. http://hdl.handle.net/1885/49280.

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Although the tremendous catalytic power of enzymes is widely recognized, their exact mechanisms of action are still a source of debate. In order to elucidate the origin of their power, it is necessary to look at individual residues and atoms, and establish their contribution to ligand binding, activation, and reaction. Given the present limitations of experimental techniques, only computational tools allow for such detailed analysis. During my PhD studies I have applied a variety of computational methods, reviewed in Chapter 2, to the study of two enzymes: DfrB dihydrofolate reductase (DHFR) and methyltetrahydrofolate: corrinoid/iron-sulfur protein methyltransferase (MeTr).

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45

Wang, Shiao-Chun, and 王孝群. "Structural Biology Analysis System：Use BCL (Biosym Command Language) to Connect with the Command and to Execute Drug Docking and Molecule Dynamic Simulation." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/80809021186468370773.

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碩士
元智大學
資訊管理學系
94
The molecule simulation can be used to help to build the molecule mode, predict, and explain physical character or chemical character. Docking simulation, moreover, can be used to move or help medicine to develop fast, and to observe the interaction between the ligand and the biomacromolecuar. In this thesis, the molecule docking method will be stated, including Rigid-body docking、Flex-rigid docking and Full-flexible docking. We will also use Scripting Language BCL (Biosym Command Language) to create automatic processes and to predict the interaction of ligand with biomacromolecular targets on an infrastructure of Insight II. There will be two approaches mentioned in this thesis – ZDOCK and MolD (Molecule Dynamics). We will use ZDOCK first to search and to compare conformational space, and to find a probable position. Then, we will use MolD (Molecule Dynamics) to calculate the part energy and RMSD of this probable position.

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46

Δάλκας, Γεώργιος. "Διαμορφωτική μελέτη μέσω φασματοσκοπίας NMR του καταλυτικού τομέα του θανατηφόρου παράγοντα του άνθρακα και μελέτη των συμπλόκων του με πεπτιδικά υποστρώματα μέσω βιομοριακής προσομοίωσης." Thesis, 2010. http://hdl.handle.net/10889/4971.

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Η θανατηφόρος δράση του βακτηρίου του άνθρακα (Bacillus anthracis), στο οποίο οφείλεται η καλούμενη ως νόσος του άνθρακα, εντοπίζεται στη συνεργό δράση τριών εκλυόμενων τοξινών του και ειδικότερα στην πρωτεολυτική δράση του θανατηφόρου παράγοντα (anthrax Lethal Factor, LF). Ο LF είναι μία μεταλλοπρωτεάση ψευδαργύρου και ισχυρή τοξίνη, η οποία απελευθερώνεται στον οργανισμό στα πρώτα στάδια προσβολής του ατόμου από το βακτήριο. Το ενεργό/καταλυτικό κέντρο του αναγνωρίζει και υδρολύει με εξαιρετική εξειδίκευση πεπτιδικά υποστρώματα ΜΚΚ κινασών, αναστέλλοντας τις διαδικασίες μεταγωγής σήματος στα κύτταρα του μολυσμένου ξενιστή επιφέροντας το θάνατό του. Από την άλλη, η εξειδικευμένη πρωτεολυτική ικανότητα του LF έναντι αυτών των κινασών, οι οποίες πρόσφατα συσχετίστηκαν με ανάπτυξη καρκινικών όγκων, ενδέχεται να αποτελέσει μια καινοτόμο θεραπευτική οδό για την αντιμετώπιση καρκινικών όγκων εν τη γενέση τους. Ωστόσο, ο μηχανισμός της αλληλεπίδρασης σε μοριακό επίπεδο και της πρωτεολυτικής διάσπασης των υποστρωμάτων του LF παραμένει μέχρι και σήμερα αδιευκρίνιστος και συνεπώς χρήζει ιδιαίτερης μελέτης. Προς αυτή την κατεύθυνση εστιάστηκε το ενδιαφέρον της διατριβής έχοντας ως πρωτογενείς στόχους την in silico μελέτη της αλληλεπίδρασης, σε μοριακό επίπεδο, του καταλυτικού κέντρου του LF με τα υποστρώματα των ΜΚΚ κινασών που υδρολύει, και την μελέτη μέσω Φασματοσκοπίας NMR της δομής και δυναμικής του ενεργού κέντρου του LF σε ελεύθερη μορφή, το οποίο ευρίσκεται στο C-τελικό άκρο του. Με την εφαρμογή τεχνικών προσομοίωσης πρόσδεσης και μοριακής δυναμικής πραγματοποιήθηκε in silico μελέτη των συμπλόκων LF-υποστρώματα, και προσδιορίστηκε ένα ευρύ φάσμα αλληλεπιδράσεων, όχι μόνο γύρω από το μεταλλικό/καταλυτικό κέντρο αλλά και σε απόσταση 20 Å στην περιοχή δέσμευσης του Zn2+, υποδεικνύοντας έτσι τους δομικούς παράγοντες που πιθανόν καθορίζουν το είδος της αλληλεπίδρασής ενζύμου με τις κινάσες που υδρολύει, παρέχοντας έτσι σημαντικές πληροφορίες για τον σχεδιασμό και την αναζήτηση βιοδραστικών μορίων με φαρμακευτικό ενδιαφέρον έναντι στον LF. Τα δεδομένα αυτά μπορούν επίσης να αξιοποιηθούν σε μελέτες δομής-δράσης με σημειακές και/ή πολλαπλές μεταλλάξεις. Με την χρήση φασματοσκοπίας NMR, πραγματοποιήθηκε μελέτη της δομής και δυναμικής του ενεργού κέντρου του LF σε ελεύθερη μορφή (apoLF672-776). Η επίλυση των τρισδιάστατων NMR δομών του apoLF672-776 έδωσαν μια εξαιρετικά σαφή εικόνα για τη δομή του ενεργού κέντρου του LF, το οποίο βρίσκεται σε συμφωνία με τις υπάρχουσες κρυσταλλικές δομές. Τα συγκεκριμένα ΝΜR δεδομένα μπορούν να αξιοποιηθούν σε μελέτες με NMR υπό το καθεστώς αλληλεπίδρασης του LF με τα πεπτιδικά υποστρώματά του και χαρακτηρισμό της δυναμικής της αλληλεπίδρασης, όπως επίσης και τον υπολογισμό της συγγένειας δέσμευσής τους.
The anthrax toxin of the bacterium Bacillus anthracis consists of three distinct proteins, one of which is the anthrax lethal factor (LF). LF is a gluzincin Zn-dependent, highly specific metalloprotease with a molecular mass of ~90 kDa that cleaves most isoforms of the family of mitogen-activated protein kinase kinases (MEKs/MKKs) close to their amino termini, resulting in the inhibition of one or more signaling pathways. Previous studies on the crystal structures of uncomplexed LF and LF complexed with the substrate MEK2 or a MKK-based synthetic peptide provided structure-activity correlations and the basis for the rational design of efficient inhibitors. However, in the crystallographic structures, the substrate peptide was not properly oriented in the active site due to the absence of the catalytic zinc atom. The primary target of the thesis was to examine in silico the LF-MEK/MKK interaction along the catalytic channel up to a distance of 20 Å from the zinc atom, using docking and molecular dynamics protocols. This residue-specific view of the enzyme-substrate interaction provides valuable information about: (i) the substrate selectivity of LF and its inactivation of MEKs/MKKs, (an issue highly important not only to anthrax infection, but also to the pathogenesis of cancer), and (ii) the discovery of new, previously unexploited, hot-spots of the LF catalytic channel that are important in the enzyme/substrate binding and interaction. Given the importance of the interaction between LF and substrate for the development of anti-anthrax agents as well as the potential treatment of nascent tumours, the analysis of the structure and dynamic properties of the LF catalytic site are essential to elucidate its enzymatic properties. The thesis interest was oriented then to the solution structure of the catalytic domain of apo LF and present data on its dynamics. The solution nuclear magnetic resonance (NMR) structure and mobility studies of the catalytic domain of apoLF672-776 reveals that the conformation of the C-terminal construct of the LF catalytic domain and the orientation of the six helical motifs are remarkably similar to the native structure, indicating the LF polypeptides catalytic site as reliable models of the enzyme active centre.

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Bondoky, Karim. "A Contribution to Validation and Testing of Non-Compliant Docking Contact Dynamics of Small and Rigid Satellites Using Hardware-In-The-Loop Simulation." 2020. https://tud.qucosa.de/id/qucosa%3A73251.

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Spacecraft (S/C) docking is the last and most challenging phase in the contact closure of two separately flying S/C. The design and testing of S/C docking missions using software-multibody simulations need to be complemented by Hardware-In-The-Loop (HIL) simulation using the real docking hardware. The docking software multibody simulation is challenged by the proper modeling of contact forces, whereas the HIL docking simulation is challenged by proper inclusion of the real contact forces. Existing docking HIL simulators ignore back-reaction force modeling due to the large S/C sizes, or use compliance devices to reduce impact, which alters the actual contact force. This dissertation aims to design a docking HIL testbed to verify docking contact dynamics for small and rigid satellites by simulating the real contact forces without artificial compliance. HIL simulations of docking contact dynamics are challenged mainly by: I. HIL simulation quality: quality of realistic contact dynamics simulation relies fundamentally on the quality of HIL testbed actuation and sensing instrumentation (non-instantaneous, time delays, see Fig. 1) II. HIL testbed design: HIL design optimization requires a justified HIL performance prediction, based on a representative HIL testbed simulation (Fig. 2), where appropriate simulation of contact dynamics is the most difficult and sophisticated task. The goal of this dissertation is to carry out a systematic investigation of the technically possible HIL docking contact dynamics simulation performances, in order to define an appropriate approach for testing of docking contact dynamics of small and rigid satellites without compliance and using HIL simulation. In addition, based on the investigations, the software simulation results shall be validated using an experimental HIL setup. To achieve that, multibody dynamics models of docking S/C were built, after carrying out an extensive contact dynamics research to select the most representative contact model. Furthermore, performance analysis models of the HIL testbed were built. In the dissertation, a detailed parametric analysis was carried out on the available models’ design-spaces (e.g., spacecraft, HIL testbed building-blocks and contact dynamics), to study their impacts on the HIL fidelity and errors (see Fig. 1). This was done using a generic HIL design-tool, which was developed within this work. The results were then used to identify the technical requirements of an experimental 1-Degree-of-Freedom (DOF) HIL testbed, which was conceived, designed, implemented and finally utilized to test and validate the selected docking contact dynamics model. The results of this work showed that the generic multibody-dynamics spacecraft docking model is a practical tool to model, study and analyze docking missions, to identify the properties of successful and failed docking scenarios before it takes place in space. Likewise, the 'Generic HIL Testbed Framework Analysis Tool' is an effective tool for carrying out performance analysis of HIL testbed design, which allows to estimate the testbed’s fidelity and predict HIL errors. Moreover, the results showed that in order to build a 6DOF HIL docking testbed without compliance, it is important to study and analyze the errors’s sources in an impact and compensate for them. Otherwise, the required figure-of-merits of the instruments of the HIL testbed would be extremely challenging to be realized. In addition, the results of the experimental HIL simulation (i.e., real impacts between various specimen) serve as a useful contribution to the advancement of contact dynamics modeling.

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Δημητρόπουλος, Νικόλαος. "Υπολογιστική μελέτη δομής και δυναμικής βιομοριακών συμπλόκων της α1 υπομονάδας του νικοτινικού υποδοχέα της ακετυλοχολίνης (nAChR) με άλφα-νευροτοξίνες." Thesis, 2010. http://nemertes.lis.upatras.gr/jspui/handle/10889/4165.

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Οι νικοτινικοί υποδοχείς της ακετυλοχολίνης (nAChRs) ανήκουν στην υπερ-οικογένεια των ιοντικών καναλιών που ενεργοποιούνται από τη δέσμευση ενός προσδέτη (LGICs) και αποτελούνται από πέντε ομόλογες υπομονάδες. Κάθε μονομερής υπομονάδα αποτελείται από μία Ν-τελική εξωκυττάρια περιοχή (ΕΚΠ), από τέσσερεις διαμεμβρανικές α-έλικες και από μία κυτταροπλασματική περιοχή. Στην ΕΚΠ βρίσκεται η χαρακτηριστική Cys-θηλιά της υπερ-οικογένειας, καθώς και οι θέσεις πρόσδεσης αγωνιστών και ανταγωνιστών του υποδοχέα. Οι γνώσεις μας γύρω από τη δομή των nAChRs προέρχονται κυρίως από κρυσταλλογραφικές δομές ομολόγων πρωτεϊνών δέσμευσης της ACh (AChBP) μαλακίων, από μια δομή του nAChR από ιχθείς του γένους Torpedo που προέρχεται από ηλεκτρονική μικροσκοπία, από την κρυσταλλογραφική δομή της α1-ΕΚΠ ποντικού σε σύμπλοκο με α-μπουγκαροτοξίνη (α-Btx) και από κρυσταλλογραφικές δομές δύο προκαρυωτικών LGICs. Παρά τη μεγάλη πρόοδο που πραγματοποιήθηκε με τα παραπάνω επιτεύγματα, ακόμη δεν έχει επιλυθεί πειραματικά η δομή ανθρώπινου υποδοχέα. Επίσης λίγα είναι γνωστά για την επίδραση της γλυκοζυλίωσης των ΕΚΠ στη λειτουργία του nAChR. Χρησιμοποιώντας ως εκμαγείο την κρυσταλλογραφική δομή του συμπλόκου α1-ΕΚΠ ποντικού/α-Btx δημιουργήθηκαν υπολογιστικά μοντέλα της ανθρώπινης α1-ΕΚΠ προσδεμένης στις τοξίνες α-μπουγκαροτοξίνη (α-Btx), α-κομπρατοξίνη (α-Cbtx), α-κωνοτοξίνη (α-Ctx) ImI και α-κωνοτοξίνη GI. Στα σύμπλοκα με α-Btx και α-Cbtx προστέθηκε η υδατανθρακική αλυσίδα, συνδεδεμένη με το κατάλοιπο Asn141, που συγκρυσταλλώθηκε μαζί με την α1-ΕΚΠ ποντικού. Για να μελετηθεί η δυναμική συμπεριφορά της αλληλεπίδρασης υποδοχέα-τοξίνης καθώς και η συνεισφορά των σακχάρων σε αυτήν πραγματοποιήθηκαν προσομοιώσεις Μοριακής Δυναμικής σε υδατικό περιβάλλον. Με τη χρήση υπολογιστικών εργαλείων για τη μελέτη των συμπλόκων προσδιορίστηκαν σε ατομικό επίπεδο οι αλληλεπιδράσεις που καθοδηγούν την πρόσδεση τοξινών στην α1-ΕΚΠ. Βρέθηκε ότι η υδατανθρακική αλυσίδα συμμετέχει δυναμικά στη δέσμευση της τοξίνης στον υποδοχέα. Τα σάκχαρα συγκλίνουν προς την προσδεμένη τοξίνη στηριζόμενα στα κατάλοιπα Ser187 και Trp184 της α1 υπομονάδας. Η τοξίνη επίσης μετακινείται φέρνοντας τη θηλιά Ι σε επαφή με τα σάκχαρα. Αναγνωρίστηκαν σημαντικές αλληλεπιδράσεις των σακχάρων με τα τοξινικά κατάλοιπα Thr6, Ser9, και Th15 της α-Btx και Thr6 και Pro7 της α-Cbtx. Επίσης επιβεβαιώθηκε η ύπαρξη μιας υδρόφιλης κοιλότητας στο εσωτερικό του υδρόφοβου πυρήνα της α1-ΕΚΠ, η οποία πιθανόν εμπλέκεται στο άνοιγμα του ιοντικού καναλιού του nAChR. Τα αποτελέσματα αυτά παρέχουν σημαντικά δεδομένα για την κατανόηση της επίδρασης της υδατανθρακικής αλυσίδας στη λειτουργία του υποδοχέα, η οποία μπορεί να αξιοποιηθεί στην αντιμετώπιση των πολλών παθολογικών καταστάσεων στις οποίες εμπλέκονται οι nAChRs.
Nicotinic acetylcholine receptors (nAChRs) belong to the superfamily of ligand-gated ion channels (LGICs). LGICs form homo- or hetero-pentamers of related subunits, and each of them consists of a N-terminal extracellular ligand-binding domain (ECD), four transmembrane α-helixes and an intracellular region. The characteristic Cys-loop of the superfamily is found in the ECD of each subunit. The ECD also contains binding sites for agonists and competitive antagonists. Our knowledge regarding the nAChR structure mainly derives from the X-ray crystal structures of the molluscan ACh-binding proteins (AChBPs), the electron microscopy structure of the Torpedo nAChR, the X-ray crystal structure of the mouse nAChR α1-ECD bound to α-bungarotoxin (α-Btx), and the X-ray crystal structures of two prokaryotic LGICs. Despite the progress made by these achievements, the determination of any human nAChR structure has not yet been accomplished. Furthermore, the effect of glycosylation on nAChR function has not yet been explored. Based on the crystal structure of the extracellular domain of the mouse nAChR α1 subunit bound to α-Btx we have generated in silico models of the human nAChR α1-ECD bound to the toxins α-bungarotoxin (α-Btx), α-cobratoxin (α-Cbtx), α-conotoxin (α-Ctx) ImI and α-conotoxin GI. In the case of the α1-ECD/α-Btx and α-Cbtx complexes, a Asn141-linked carbohydrate chain was modeled, its coordinates taken from the crystal structure of the mouse α1-ECD. To gain further insight into the structural role of glycosylation molecular dynamics (MD) simulations were carried out in explicit solvent so as to compare the conformational dynamics of the binding interface between nAChR α1 and the two toxins. The use of computational methods allowed the monitoring of the interactions that govern toxin binding. The MD simulations revealed the strengthening of the receptor-toxin interaction in the presence of the carbohydrate chain. A shift in the position of the sugars towards the bound toxin was observed. Residues Ser187 and Trp184 of nAChR act as critical anchor points for the stabilization of the sugar chain in a close position to the toxin. Toxin Finger I shifts closer to the mannoses, forming important toxin-sugar interactions that implicate residues Thr6, Ser9, and Thr15 of α-Btx, as well as Thr6 and Pro7 of α-Cbtx. Additionally the MD simulations of the human α1 ECD–toxin complexes confirmed the possible accommodation of two water molecules into a hydration cavity inside the hydrophobic core of the subunit, which may contribute to the gating mechanism of the receptor. These findings provide additional structural data that are intended to inspire biophysical studies on the functional role of glycosylation in the gating mechanism of nAChR and also guide the development of novel therapeutic agents for the treatment of nAChR-associated diseases.

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