Submitted by Rosivalda Pereira (mrs.pereira@ufma.br) on 2017-06-14T17:55:12Z No. of bitstreams: 1 RosaHelenaSilva.pdf: 2716670 bytes, checksum: 07dee1e77d704e91281c33c31e8c4938 (MD5) / Made available in DSpace on 2017-06-14T17:55:12Z (GMT). No. of bitstreams: 1 RosaHelenaSilva.pdf: 2716670 bytes, checksum: 07dee1e77d704e91281c33c31e8c4938 (MD5) Previous issue date: 2016-10-19 / 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.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2017-09-12T18:24:02Z No. of bitstreams: 1 2016 - Larissa Henriques Evangelista Castro.pdf: 3738174 bytes, checksum: 04e651a55fa9b4054c2810389592be67 (MD5) / Made available in DSpace on 2017-09-12T18:24:02Z (GMT). No. of bitstreams: 1 2016 - Larissa Henriques Evangelista Castro.pdf: 3738174 bytes, checksum: 04e651a55fa9b4054c2810389592be67 (MD5) Previous issue date: 2016-12-02 / CAPES / CNPq / FAPERJ / Trypanosoma cruzi is the parasite that causes american trypanosomiasis (or Chagas disease), a neglected tropical disease previously restricted to South and Central Americas and Mexico, but now with several cases around the world. Currently in Brazil, the treatment of Chagas disease is done, only using benznidazole, which is not effective for the disease?s chronic phase and causes aggressive side effects, which explains the necessity of researches to find novel anti-Chagas compounds. A strategy adopted for the development of bioactive compounds against T. cruzi consists on the inhibition of the sterol 14?-demethylase enzyme (CYP51), which is essential for the parasite?s cellular membrane integrity. The inhibition can be achieved by a complexation of heterocyclic ring-containing compounds with the iron atom of heme group, present on CYP51. Thus, molecular modeling techniques were used on this study to analyze the interaction of a heterocyclic compounds (with known activity) with T. cruzi CYP51 in order to obtain the necessary information to construct an effective model for the theoretical activity prediction of these and also novel compounds. The proposed model presented a good multiple correlation coefficient (r? = 0.84) with the terms used to its construction. The model was used to help the design of novel piperine derivatives with a triazole ring, that presented promising theorical activities against T. cruzi CYP51, calculated by the model. The most promising compounds were selected and synthesized with the purpose of being tested in vitro and in vivo against T. cruzi. / O Trypanosoma cruzi ? o parasito causador da tripanossom?ase americana (Doen?a de Chagas), uma doen?a tropical negligenciada antes restrita ? Am?rica do Sul, Am?rica Central e M?xico, mas que vem apresentando um n?mero cada vez maior de casos no mundo. Atualmente, o tratamento da Doen?a de Chagas no Brasil ? limitado ao uso do f?rmaco benzonidazol, que ? pouco eficaz para a fase cr?nica da doen?a e causa efeitos colaterais agressivos, o que torna a pesquisa por novos f?rmacos imprescind?vel. Uma estrat?gia adotada para o desenvolvimento de compostos bioativos contra T. cruzi consiste na inibi??o de uma enzima essencial para a integridade da membrana celular do parasito, a enzima esterol 14?-desmetilase (CYP51), causada pela coordena??o de compostos contendo an?is heteroc?clicos com o ?tomo de ferro do grupo heme presente na enzima, fundamental para a atividade. Dessa maneira, foram utilizadas nesse estudo t?cnicas de modelagem molecular, incluindo docagem molecular e c?lculos qu?nticos semi-emp?ricos, para analisar a intera??o de uma s?rie de compostos heteroc?clicos de atividade conhecida sobre a CYP51 do T. cruzi e com isso se obter informa??es necess?rias para a constru??o de um modelo efetivo para a previs?o te?rica da atividade destes compostos. O modelo proposto apresentou um bom coeficiente de correla??o m?ltipla com os termos utilizados para sua constru??o, com um r?=0,84. Esse modelo foi utilizado para o planejamento de novos triaz?is derivados da piperina, com atividade te?rica calculada promissora contra a CYP51 de T. cruzi. Alguns dos melhores compostos foram selecionados e sintetizados neste projeto, com a proposta de serem avaliados em testes in vitro e in vivo contra a doen?a de Chagas.

Les introns de groupe II forment une classe d’ARN connus avant tout pour leur activité ribozymique, qui leur permet de catalyser leur propre réaction d’épissage. Sous certaines conditions, ces introns peuvent s’exciser des ARN précurseurs dont ils font partie et assurer la ligation des exons qui les bordent sans l’aide d’aucune protéine. Les introns de groupe II sont généralement excisés sous forme d’un lariat, semblable à celui formé par les introns des prémessagers nucléaires, dont l’épissage est assurée par le spliceosome. De telles similarités dans le mécanisme d’épissage suggèrent que les introns de groupe II et les introns des prémessagers nucléaires pourraient avoir un ancêtre évolutif commun.Malgré leurs séquences très diverses, les introns de groupe II peuvent être définis par une structure secondaire commune, hautement conservée. Celle-ci est formée de six domaines (domaine I à domaine VI ; D1-D6), émergeant d’une roue centrale. L’épissage des introns de groupe II comprend deux étapes, et autant de réactions de transestérification, qui produisent les exons liés et l’intron excisé sous forme lariat. Il est généralement admis que la structure du ribozyme subit des changements conformationnels entre les deux étapes de l’épissage et que le domaine VI est un acteur clé dans ce phénomène. Cependant, malgré l’identification d’un certain nombre d’interactions tertiaires entre domaines, ni la RMN, ni les études faisant appel à des modifications chimiques ne sont parvenues à déterminer l’environnement immédiat, au niveau du site actif du ribozyme, de l’adénosine qui sert de point de branchement de la structure en lariat, ainsi que des nucléotides qui entourent cette adénosine au sein du domaine VI. A l’aide d’analyses phylogénétiques et d’une modélisation moléculaire tridimensionnelle, nous avons identifié plusieurs sections du ribozyme susceptibles de constituer le site de fixation du domaine VI au cours de l’étape de branchement. Des mutations ont été introduites dans ces sites de fixation potentiels et la cinétique de réaction des ARN mutants résultants a été déterminée. Afin de démontrer formellement l’interaction du domaine VI avec le site récepteur le plus probable, une molécule de ribozyme dont la réaction de branchement est assurée par l’addition d’oligonucléotides ADN ou ARN qui positionnent correctement le domaine VI vis-à-vis de son partenaire a été construite. En combinant l’information apportée par différentes expériences de ce type, nous avons pu générer un modèle à résolution atomique du complexe formé par le domaine VI, son site de branchement et le reste de l’intron au moment où l’épissage est initié. / Group II introns are a class of RNAs best known for their ribozyme-catalyzed, self-splicing reaction. Under certain conditions, the introns can excise themselves from precursor mRNAs and ligate together their flanking exons, without the aid of proteins. Group II introns generally excise from pre-mRNA as a lariat, like the one formed by spliceosomal introns, similarities in the splicing mechanism suggest that group II introns and nuclear spliceosomal introns may share a common evolutionary ancestor.Despite their very diverse primary sequences, group II introns are defined by a highly conserved secondary structure. This generally consists of six domains (Domain I-Domain VI; D1-D6) radiating from a central wheel. Each of the six intronic domains has a specific role in folding, conformational rearrangements or catalysis. The native conformation of a group II intron is sustained by intra- and interdomain long-range tertiary interactions, which are critical either for folding of the intron to the native state or for its catalytic activity. In brief, Domain V interacts with Domain I to form the minimal catalytic core; Domain VI contains a highly conserved bulged adenosine serving as the branch-point nucleotide. DII and Domain III contribute to RNA folding and catalytic efficiency. Domain IV, which encodes the intron ORF, is dispensable for ribozyme activity.Group II intron splicing proceeds through two step transesterification reactions which yield ligated exons and an excised intron lariat. It is initiated by the 2’-hydroxyl group of the bulged adenosine within Domain 6, which serves as a branch point and attacks the phosphate at the 5’-end of the intron, thus releasing the 5’-exon while forming a lariat structure in the first step. The released 5’-exon, which is bound to the intron through base pairing interactions, is then positioned correctly to attack the 3’-splice site with its free 3’-OH in the second step of splicing. It is generally believed that the structure of a group II ribozyme undergoes conformational rearrangements between first step and second step and domain VI must play a central role in the process. However, despite the identification of several interdomain tertiary interactions, neither NMR nor chemical probing studies have been successful in determining the local surroundings of the branch-point adenosine and neighboring domain VI nucleotides in the ribozyme active site. By using phylogenetic analysis and molecular modelling, we have identified several areas of the molecule which have the potential to constitute the docking site of domain VI. Mutations were introduced in putative binding sites and the resulting, mutant RNAs have been kinetically characterized. This has allowed us to identify a site within the ribozyme that appears to be specifically involved in the branching reaction. In order to further investigate the interaction between that site and domain VI, we set up a system in which the docking of domain VI into its presumed binding site is ensured by the addition of DNA/RNA oligos that position the two RNA elements in an appropriate orientation. By combining the information from such experiments, we have built an atomic-resolution model of the complex formed by domain VI, the branch site and the rest of the intron at the time at which splicing is initiated.

A flavonol specific glucosyltransferase cloned from Citrus paradisi has strict substrate and regio-specificity (Cp3OGT). The amino acid sequence of Cp3OGT was aligned with sequences of an anthocyanidin UDP- dependant glucosyltransferase (UGT) from Clitorea ternatea and a UGT from Vitis vinifera that can glucosylate both flavonols and anthocyanidins. Using homology modeling to identify candidate regions followed by site directed mutagenesis, three double mutations were constructed and biochemically characterized. S20G+T21S mutant protein retained activity with flavonols similar to the wildtype Cp3OGT but the mutant had optimum activity at 60°C and broadened substrate acceptance to include the flavanone naringenin. S290C+S319A mutant protein retained 40% activity with quercetin relative to WT, and had an optimum pH shift. H154Y+Q87I mutant protein was only 10% active with quercetin relative to WT. Docking analysis revealed that H154, Q87 and S20 could be involved in orienting the acceptor molecules within the acceptor binding site whereas S319 and S290 residues are involved in maintaining the active site conformation.

Hydropathic molecular modeling is a computer-aided molecular design technique for obtaining, representing, and understanding the properties and interactions of biomacromolecular complexes in the biological environment. Hydropathic INTeraction (HINT) is a novel empirical force field to calculate the free energy of intermolecular interaction based on experimentally determined partition coefficients (log Po/w). It includes all the expected interactions between molecules such as hydrogen bonding, hydrophobic, electrostatic, acid-base, and Coulombic interactions, entropy, solvation and others. HINT tools were used to determine, evaluate, and analyze protein-ligand interactions in different research projects: 1) We used these tools to discover small molecule inhibitors of PsaA, a potential target for Streptococcus pneumoniae. We screened and scored potential molecules to obtain hits. After the growth conditions for both the wild type and PsaA mutant of S. pneumoniae were optimized, we then tested our hits. A few compounds passed through the three-stage assay protocol and confirmed the inhibition of PsaA with MICs between 125-250 μM. 2) The SAR of C-3 and C-5 pyrrole-based antitubulin agents at the colchicine-binding site with explicitly solvated models was performed. After docking with GOLD at the colchicine site, post-docking scoring and evaluation were performed with HINT. The total HINT score correlates with binding and activity; similarly, the significance of individual functional groups, protein residues and interactions amongst a collection of compounds can be quantitated. The possibility of water-mediated interactions in a way solvent accessible part of the pocket was considered by subjecting molecular models to MD simulations. Several water molecules were identified to be contributing to the binding and were confirmed by HINT scoring. Finally, using hydropathic molecular modeling tools helped us to understand, evaluate, analyze, and improve protein-ligand interactions in different biological systems.

Les récepteurs muscariniques à l'acétylcholine sont des protéines transmembranaires jouant des rôles dans de nombreux processus physiologiques. La toxine MT7 est un puissant modulateur allostérique de ces récepteurs. De plus, cette toxine est le seul ligand connu spécifique du sous-type 1 des récepteur muscariniques (hM1). Nous avons étudié les bases moléculaires de l'interaction entre la toxine MT7 et le récepteur hM1 par modélisation. Tout d'abord un échantillonnage des structures des deux partenaires a été réalisé par dynamique moléculaire. Les mouvements de grande amplitude de la boucle e2 du récepteur ont été prédits par dynamique activée. Puis la toxine a été arrimée sur le récepteur par des calculs de dynamique moléculaire sous contraintes ambigües dérivées de données de mutagénèse. Ce modèle a ensuite été optimisé par une simulation de dynamique moléculaire libre, en environnement membranaire explicite. Enfin, des calculs en retour des valeurs d'énergie libre de liaison ont été effectués afin de valider le modèle. Nous prédisons que la toxine se lie sur un dimère de récepteurs hM1. Le cœur de l'interaction est localisé sur un des monomères en contact avec les boucles II et III de la toxine. Cette interaction est complétée par des interactions hydrophobes au niveau de la boucle I sur le second monomère. L'analyse de ce modèle apporte des éléments de compréhension à la fois sur bases structurale de la haute affinité de cette toxine ainsi que sur sa sélectivité pour ce sous-type de récepteur. Il apparaît que cette sélectivité est essentiellement portée par la boucle extracellulaire e2 du récepteur.

Les travaux présentés dans ce mémoire se situent dans le cadre général de la recherche de nouveaux médicaments par le biais de techniques informatiques. La première partie de ce document est centrée autour du développement de la plateforme logicielle VSM-G (Virtual Screening Manager for Grids). Le but poursuivi par ce projet est de fournir un outil convivial et simple d'utilisation afin de conduire des études de criblage virtuel à haut-débit. Le coeur de VSM-G repose sur une stratégie multi-étapes de filtres successifs permettant le traitement efficace de chimiothèques de grande taille. Deux filtres ont été utilisés pour ce travail et implémentés dans VSM-G : un programme innovant d'estimation rapide de complémentarité géométrique entre molécules-candidates et site actif (SHEF) précéde un algorithme de docking flexible plus conventionnel (GOLD). Les avantages de cette méthodologie, associée à la prise en charge de multiples conformations de la cible étudiée (le récepteur nucléaire LXRβ), sont présentés tout d'abord par une étude de preuve de concept, puis à travers une campagne de criblage virtuel à grande échelle. L'autre partie de ces travaux, exclusivement applicative, concerne l'étude du domaine FAT de la kinase d'adhérence focale FAK. FAK est une cible d'intérêt pharmaceutique particulièrement intéressante, car clairement impliquée dans divers processus de développement cancéreux. Le but de cette étude est double : il s'agit tout d'abord de mieux comprendre le mode de fonctionnement du domaine FAT de FAK à travers une étude biophysique pour en évaluer la flexibilité ; et ensuite concevoir in silico des petites molécules peptidomimétiques permettant de moduler son activité, ce qui pourrait limiter une progression tumorale.

En bloquant les deux voies majeures de métabolisation de l’acide arachidonique, les inhibiteurs mixtes 5-LOX/COX-2 sont de puissants agents anti-inflammatoires non stéroïdiens minimisant les effets secondaires gastro-intestinaux et allergiques (asthme). Par ailleurs, ils offrent de nouvelles perspectives dans le traitement préventif de certains cancers. Contrairement à la COX-2, déjà largement étudiée, le niveau de connaissances concernant la 5-LOX humaine est beaucoup plus restreint. Notre objectif a donc été de caractériser sa structure ainsi que son mode d’interaction avec des inhibiteurs de type non redox, dans le but d’aider à la conception rationnelle d’inhibiteurs mixtes 5-LOX/COX-2. Dans un premier temps, la comparaison d’inhibiteurs 5-LOX non redox de la littérature a permis de mettre en évidence un modèle de pharmacophore à 5 points. Par ailleurs, la structure 3D de la 5-LOX humaine n’étant pas encore déterminée, nous l’avons modélisée par homologie avec la 15-LOX de lapin cristallisée et nous avons étudié, par docking, le mode d’interaction d’inhibiteurs 5-LOX non redox au sein du site actif. La combinaison des approches centrées, respectivement, sur les ligands et sur la protéine, nous a permis d’affiner l’hypothèse de pharmacophore et de proposer un modèle général d’interaction au sein du site actif 5-LOX./Dual 5-LOX/COX-2 inhibitors, acting on both major arachidonic acid metabolic pathways, are potent non-steroidal anti-inflammatory agents, with a reduced gastro-intestinal toxicity and fewer allergic adverse reactions. Moreover, they are promising in the treatment of several cancers. Whereas COX-2 has already been extensively studied, little structural or mechanistic information is available regarding human 5-LOX. Therefore, we focussed on this enzyme and characterized its 3D structure as well as its interaction with non redox inhibitors in order to help the design of dual 5-LOX/COX-2 inhibitors. Firstly, comparison of non redox 5-LOX inhibitors from the literature led to the generation of a five-point pharmacophore model. The 3D structure of human 5-LOX was then modelled based on the crystal structure of rabbit 15-LOX and, the binding modes of representative ligands were investigated through docking studies. Combination of both ligand-based and target-based approaches allowed the refinement of the pharmacophore hypothesis and led to the proposal of an interaction model for non redox inhibitors inside the 5-LOX active site.

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.

In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The approach used in the population analysis included a least-square fit technique to match T1 elaxation parameters. The results showed good agreement with experimental T-ROE build-up curves, and three states were concluded to be involved. In Paper IV, carbohydrate moieties were used in the development of prodrug candidates, to “hide” peptide opioid receptor agonists. Langevin dynamics and quantum chemical methods were employed to elucidate the structural preference of the compound. The results showed a chemical shift difference between hydrogens across the ring for the two isomers as well as a difference in the coupling constant, when taking the dynamics into account. In Paper V, the interaction of the Salmonella enteritidis bacteriophage P22 with its host bacterium, involves an initial hydrolysis of the O-antigenic polysaccharide (O-PS). Docking calculations were used to examine the binding between the Phage P22 tail-spike protein and the O-PS repeating unit. Results indicated a possible active site in conjunction with NMR measurements.