Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2018-08-29T19:26:49Z No. of bitstreams: 1 2017 - Cristiane Frauches dos Santos.pdf: 7660831 bytes, checksum: d9f6418f111957d4be1789ee9411cc8f (MD5) / Made available in DSpace on 2018-08-29T19:26:49Z (GMT). No. of bitstreams: 1 2017 - Cristiane Frauches dos Santos.pdf: 7660831 bytes, checksum: d9f6418f111957d4be1789ee9411cc8f (MD5) Previous issue date: 2017-09-25 / CAPES / CNPq / FAPERJ / Petrobr?s / Corrosion is one of the serious problems faced in industrial processes, generating enormous financial losses. Several techniques are used to prevent or remedy corrosion in the different materials it affects. Among them, the use of organic or inorganic inhibitors has been widely used. Thus, in this thesis were synthesized 34 heterocyclic compounds, 18 chlorides of 1,3,4-thiadiazolium-2-phenylamines, (11 unpublished), and the other 16 compounds belonging to the class of mesoionic 1,3,4-triazolium -2-thiolate, (15 unpublished), with the objective of evaluating its efficiency as inhibitors of corrosion in acidic corrosion. Derivatives of the class 1,3,4-thiadiazolium-2-phenylamines were obtained with satisfactory purity and yields in the range of 42-96% and, in the class of 1,3,4-triazolium-2-thiolates in 20 -97%. All compounds were characterized by IR, 1H and 13C NMR spectroscopies. The theoretical study was conducted using the SPARTAN-PRO program in the semi-empirical method with the Hamiltonian AM1, to determine its structural and electronic properties of 1,3,4-thiadiazolium-2-phenylamines that could contribute to the efficiency of inhibition of corrosion. The compounds of 1,3,4-thiadiazolium-2-phenylamine class were tested against corrosion of AISI 1020 carbon steel in 0.5 mol L-1HCl and in 0.5 mol L-1 H2SO4. For this evaluation, the electrochemical techniques of Potenciodynamic Polarization (PP), Resistance to Linear Polarization (RPL) and Electrochemical Impedance Spectroscopy (EIS) were used. The results showed significant percentages of corrosion inhibition in both acidic solutions, reaching the rate of up to 95% efficiency for the compound 4-phenyl-5-(3'-methoxy-phenyl)-1,3,4-thiadiazolium-2-phenylamine chloride in the concentration of 3.5x10-4 mol L-1 for the HCl solution, and 99% efficiency for the 2'-chloro and 2'-fluorosubstituted compounds in the concentration of3.5x10-4 mol L-1 for the H2SO4 solution. In addition to the electrochemical techniques, the gravimetric technique was used, which presented 99% of anticorrosive efficiency for the 2'-trifluoromethyl-substituted 1,3,4-thiadiazolium-2-phenylamine derivative, showed the best inhibitory effect in HCl solution. However, the 2'-trifluoromethyl-substituted 1,3,4-triazolium-2-thiol derivative showed less corrosion efficiency than its corresponding isomer. The methodologies used to evaluate the corrosion activity (PP, RPL and EIE), including the theoretical evaluation by molecular modeling, indicated the mesoionic chloridrates as efficient mixed corrosion inhibitors. / S?ntese e avalia??o da atividade anticorrosiva de cloretos de 1,3,4-tiadiaz?lio-2-fenilaminas e 1,3,4-triaz?lio-2-tiolatos em meio ?cido. 2017. 251p Tese (Doutorado em Qu?mica, Ci?ncia exatas, s?ntese org?nica). Departamento de qu?mica, Universidade Federal Rural do Rio de Janeiro, Serop?dica, RJ, 2017. A corros?o ? um dos s?rios problemas enfrentados nos processos industriais, gerando enormes preju?zos financeiros. Diversas t?cnicas s?o utilizadas para evitar ou remediar a corros?o nos diferentes materiais que ela afeta. Dentre elas o uso de agentes inibidores org?nicos ou inorg?nicos tem sido muito utilizado. Assim, neste trabalho de tese foram sintetizados 34 compostos heteroc?clicos, sendo 18 cloretos de 1,3,4-tiadiaz?lio-2-fenilaminas (11 in?ditos) e os outros 16 compostos pertencentes ? classe dos mesoi?nicos 1,3,4-triaz?lio-2-tiolato (15 in?ditos), com o objetivo de avaliar sua efici?ncia como inibidores de corros?o em meio ?cido. Os derivados sintetizados da classe 1,3,4-tiadiaz?lio-2-fenilaminas foram obtidos com grau de pureza e rendimentos satisfat?rios na faixa de 42-96% e, da classe dos 1,3,4-triaz?lio-2-tiolatos em 20-97%. Todos os compostos foram caracterizados por espectroscopia de IV, RMN de 1H e13C. Foi realizado o estudo de modelagem molecular, utilizando o programa SPARTAN-PRO com o m?todo semi-emp?rico, hamiltoniano AM1, para determina??o das propriedades estruturais e eletr?nicas dos 1,3,4-tiadiaz?lio-2-fenilaminas que pudessem contribuir para a efici?ncia de inibi??o da corros?o. Os cloridratos mesoi?nicos da classe 1,3,4-tiadiaz?lio-2-fenilaminas foram testados frente ? corros?o de a?o carbono AISI 1020 em solu??o de HCl 0,5 mol L-1 e em H2SO4 0,5 mol L-1. Para tal avalia??o foram utilizadas as t?cnicas eletroqu?micas de Polariza??o potenciodin?mica (PP), Resist?ncia ? polariza??o linear (RPL) e Espectroscopia de imped?ncia eletroqu?mica (EIE). Os resultados mostraram percentuais significativos de inibi??o da corros?o em ambas solu??es ?cidas, alcan?ando o ?ndice de at? 95% de efici?ncia para o composto cloreto de 4-fenil-5-(3?-met?xi-fenil)-1,3,4-tiadiaz?lio-2-fenilamina na concentra??o de 3,5x10-4 mol L-1 para a solu??o de HCl e, 99% de efici?ncia para os compostos 2?-cloro e 2?-fluor-substitu?dos na concentra??o de 3,5x10-4 mol L-1 para a solu??o de H2SO4. Al?m das t?cnicas eletroqu?micas, foi utilizada a t?cnica gravim?trica que apresentou 99% de efici?ncia anticorrosiva para o derivado 2?-trifluormetil-substitu?do da classe 1,3,4-tiadiaz?lio-2-fenilamina que mostrou o melhor efeito inibidor em solu??o HCl. No entanto, o derivado 2?-trifluormetil-substitu?do da classe 1,3,4-triaz?lio-2-tiol apresentou menor efici?ncia anticorrosiva do que seu is?mero correspondente. As metodologias utilizadas para avalia??o da atividade anticorrosiva (PP, RPL e EIE), incluindo a avalia??o te?rica por modelagem molecular, indicaram os cloridratos mesoi?nicos como eficientes inibidores de corros?o mistos.

Os Fatores de Crescimento de Fibroblastos (\"Fibroblast Growth Factors\"; FGFs) participam de fenômenos biológicos de grande importância, tais como migração, divisão e diferenciação celulares. O presente trabalho teve como objetivo central a busca de compostos biologicamente ativos através de um desenho racional de peptídeos derivados do FGF-1 e do seu receptor (FGFR-1 ). A partir da análise dos dados disponíveis na literatura, aliada a técnicas de modelagem molecular, foram desenhados, sintetizados e testados dois grupos de peptídeos. O primeiro conjunto (R1 - R3) é constituído por peptídeos lineares derivados do FGFR-1. Os ensaios de atividade mitogênica dos FGFs 1 e 2 em presença dos peptídeos mostram que R1 e R2 foram capazes de inibir a ação mitogênica do FGF-1. Este efeito é seletivo, já que a atividade do FGF-2 não é afetada. A atividade inibitória é dose-dependente para ambos os peptídeos. Os resultados mostram ainda que o efeito é sequência-dependente, já que o peptídeo R3, correspondente à porção e-terminal de R2, é inativo. Por outro lado, o segmento N-terminal de R2 (representado por R1) é suficiente para desencadear o mesmo nível de inibição apresentado pelo peptídeo R2 inteiro. Os peptídeos sintéticos semi-cíclicos F1 - F3, correspondentes a um importante sítio de ligação no FGF-1, foram avaliados quanto à sua capacidade de estimular a síntese de DNA em fibroblastos em cultura. Os dados obtidos mostram que, na faixa de concentração testada (0,1 a 200 µM), o peptídeo F1 é inativo. O peptídeo F2 apresentou atividade mitogênica (ED50 = 60 -70 µM), estimulando a incorporação de timidina tritiada em até 66 % do valor máximo induzido por 10% de soro fetal bovino. Na mesma faixa de concentração, o peptídeo F3 apresentou atividade em níveis inferiores (ED50 > 100 µM) aos apresentados pelo peptídeo F2. Estes resultados indicam que os peptídeos F2 e F3 poderiam mimetizar a superfície correspondente a um sítio de ligação do FGF-1 ao receptor. Além disso, o fato de F2 ser mais ativo que F3 indica que, além dos resíduos hidrofóbicos Y e L (presentes em ambos), o resíduo R presente em F2 exerce um importante papel para a atividade mitogênica do peptídeo. Como já proposto por nós em trabalhos anteriores, os dados apresentados indicam que é possível obter compostos com atividade mitogênica através do desenho racional de estruturas peptídicas derivadas dos FGFs. A análise do conjunto de peptídeos estudados até o momento revela a existência de características químicas comuns a todos aqueles que se mostraram mitogênicos, ou seja, a presença de um núcleo hidrofóbico flanqueado por resíduos polares carregados. / The Fibroblast Growth Factors (FGFs) are involved in very important biological processes like cell migration, division and differentiation. The aim of this work was the search of biologically active compounds through a rational design of peptides derived from FGF-1 and its receptor (FGFR-1). On the basis on several data available in the literature and with the aid of molecular modeling techniques, we designed, synthesized and tested two sets of peptides. The first group (R1-R3) is composed by linear peptides derived from FGFR-1. The mitogenic activity assays of FGF-1 and FGF-2 in the presence of these peptides reveal that R1 and R2 were able to inhibit the mitogenic response elicited by FGF-1. This effect is dose-dependent and selective, since the FGF-2 activity was not affected. Also, the inhibitory activity is sequence-dependent since peptide R3, corresponding to the e-terminal stretch of R2, was inactive. On the other hand, the N-terminal segment of peptide R2, represented by R1, is sufficient to elicit about the same response observed for the longer peptide R2. The semi-cyclic synthetic peptides F1 - F3, corresponding to an important FGF-1 binding site, were tested for their ability to stimulate DNA synthesis on fibroblast cultures. The results show that F1 is inactive in the range tested (0.1 to 200 µM). Peptide F2 was able to elicit a mitogenic activity (ED50 = 60 - 70 µM), stimulating the incorporation of [methyl-3H] thymidine to a level corresponding to 66 % of the maximum response induced by 10 % fetal calf serum. In the same range, peptide F3 was less active (ED50 > 100 µM). These results suggest that peptides F2 and F3 could mimic a surface corresponding to a receptor binding site of FGF-1. Also, the better performance of F2 could be explained by the presence of the residue R (besides Y and L) that could be important to elicit a mitogenic response. These results, together with those presented in former papers, indicate that it is possible to obtain compounds with mitogenic activity through the rational design of peptides derived from the FGFs. The analysis of the assembly of peptides studied allow us to define a chemical pattern shared by all the mitogenic compounds obtained until now, namely the presence of a hydrophobic core flanked by polar charged residues.

Analytical Characterization of complex mixtures, such as crude oil, environmental samples, and biological mixtures, is challenging because of the large diversity of molecular components. Mass spectrometry based techniques are among the most powerful tools for the separation of molecules based on their molecular composition, and the coupling of ion mobility spectrometry has enabled the separation and structural elucidation using the tridimensional structure of the molecule. The present work expands the ability of analytical chemists by furthering the development of IMS-MS instrumentation by coupling Trapped Ion Mobility Spectrometry to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (TIMS-FT-ICR MS). The TIMS-FT-ICR MS platform combines the high-resolution separation of TIMS, which has mobility resolving powers up to 400, and ultra-high mass resolution of FT-ICR MS, with mass resolving power over 1,000,000. This instrumentation allows the assignment of exact chemical composition for compounds in a complex mixture, as well as measurement of the collision cross-section of the molecule. Herein, the principles of the TIMS separation and its coupling to FT-ICR MS are described, as well as how the platform can be applied to targeted analysis of molecules, and untargeted characterization of complex mixtures. Molecular standards were analyzed by TIMS-MS in order to develop a computational workflow that can be utilized to elucidate molecular structure, using the measured collision cross-section of the ion. This workflow enabled identification of structural, cis/trans isomers, and chelated molecules and provides the basis for unsupervised structural elucidation of a complex mixture, and in particular for the elucidation of hydrocarbons from fossil fuels. In summary, this work presents the coupling of TIMS-FT-ICR MS and provides examples of applications as a proof of concept of the potential of this platform for solving complex analytical challenges.

Des techniques combinées d'analyse/synthèse d'images et de simulation atomistique ont permis d’étudier la nanostructure/-texture de matériaux carbonés anisotropes et denses de type pyrocarbone (PyC) laminaire hautement texturé. Des représentations atomiques d’un PyC laminaire rugueux tel que préparé (AP) ainsi que d’un PyC laminaire régénéré AP et après plusieurs traitements thermiques (HT) ont été reconstruites pour mieux caractériser ces matériaux. Ces modèles comportent des domaines graphéniques de quelques nanomètres, joints entre eux par des lignes de défauts formées de paires de cycles à 5 et 7 carbones dans le plan et par des dislocations vis et des atomes tétravalents entre les plans. Les modèles les plus ordonnés ont des domaines plus étendus et un plus faible taux de connexions inter-plan. Les propriétés mécaniques et thermiques prédites à partir de ces modèles sont proches de celles du graphite et augmentent avec la cohérence intra-plan et la densité de connexions inter-plans. Des modèles de graphène polycristallins ont aussi été générés. Ils sont apparus, du point de vue structural et des propriétés mécaniques, très proches des feuillets de carbones des PyCs. Ils ont permis d'étudier la réorganisation structurale se produisant au cours du HT : formation de lignes de défauts, réparation de lacunes, … Il s'agit d'un premier pas vers l'étude de la graphitation des PyCs. La méthode de reconstruction a enfin été adaptée à l'étude de l'évolution structurale d'un graphite au cours de son irradiation par les électrons. Cela a permis d'observer à l'échelle atomique la création et la propagation des défauts au cours de l'irradiation. / Combined images analysis/synthesis techniques and atomistic simulation methods have allowed studying the nanostructure/-texture of anisotropic dense carbons of the highly textured laminar pyrocarbon (PyC) type.Atomic representations of an as-prepared (AP) rough laminar PyC as well as a regenerative laminar PyC AP and after several heat treatments (HT) were reconstructed to better characterize these materials.The models contain nanosized graphene domains connected between them by line defects formed by pairs of rings with 5 and 7 carbons inside layers and by screw dislocations and fourfold atoms between layers. The most ordered models have larger domains and a lower percentage of connections between the layers.Mechanical and thermal properties predicted from these models are close to those of graphite and increase with the coherence inside layers and the density of connections between layers.Models of polycrystalline graphene were also generated, showing structure and mechanical properties very close to those of the carbon layers extracted from PyCs. The structural reorganization occurring during the HT of such materials was studied: thinning of line defects and vacancy healing were observed. This represents a first step towards the study of the graphitization of PyCs.The reconstruction method was eventually adapted to study the structural evolution of a nuclear-grade graphite during its irradiation by electrons, allowing us to observe how defects are created and propagate during irradiation.

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

La medicina personalitzada i les teràpies dirigides són, avui dia, estratègies emergents en les companyies farmacèutiques. L’objectiu global, a llarg termini, és desenvolupar tractaments dirigits cap a mecanismes moleculars desregulats únicament en les cèl•lules afectades, reduint així els problemes de toxicitat d’aquests compostos. Aquest procés és llarg i costós però la introducció de les tècniques de disseny racional de fàrmacs ha permès reduir de manera considerable el temps d’identificació de molècules actives, agilitzant així les etapes inicials. Les teràpies antitumorals dirigides a promoure l’apoptosi i/o a controlar el procés de proliferació cel•lular es troben avui dia en ple desenvolupament. A més, les oportunitats d’intervenció terapèutiques en aquesta línia s’incrementen a mesura que augmenta el coneixement de les proteïnes involucrades en aquests processos. Avui dia els principals problemes dels compostos identificats radiquen però en la seva selectivitat i el gran nombre d’efectes secundaris que presenten, pel que el disseny del molècules selectives és un camp de recerca molt actiu. El present projecte es basa en la cerca de nous fàrmacs anticancerígens mitjançant la modelització molecular. D’una banda es tracta d’identificar inhibidors per a les proteïnes de la família Bcl-2 per a restablir els nivells normals d’apoptosi i, de l’altra, per a les proteïnes CDK4 i CDK6, importants reguladores del cicle cel•lular. L’objectiu plantejat a llarg termini en aquesta tesi és identificar compostos actius amb potència i selectivitat cap a aquestes proteïnes per tal de convertir-los en caps de sèrie que finalment puguin arribar a ser fàrmacs comercials. La utilització de compostos mimètics del domini BH3 per inhibir la funció dels membres antiapoptòtics de la família Bcl-2 és una de les estratègies més emprades per al control de l’apoptosi. En aquest marc, en funció de la selectivitat que presenten envers els pèptids BH3, podem trobar dues subfamílies de proteïnes antiapoptòtiques: Bcl-2, Bcl-xL i Bcl-w d’una banda i Mcl-1 i A-1 de l’altra. Diferents estudis suggereixen que per a produir la mort cel•lular és necessari intervenir al menys un membre de cadascuna de les subfamílies. Per tant, sota aquesta premissa, es van analitzar les interaccions establertes entre les proteïnes antiapoptòtiques i dominis BH3 tant pel cas de pèptids que s’uneixen amb igual afinitat a tota la família, com per a pèptids selectius de cadascun dels subgrups. Nombrosos estudis apunten a que la helicitat en els pèptids mimètics dels domini BH3 incrementa notablement l’afinitat d’enllaç. Sota aquesta premissa s’ha tractat de dissenyar pèptids derivats de la proteïna proapoptòtica Bak substituint alguns dels residus prescindibles per l’aminoàcid no natural Aib, inductor de conformacions helicoïdals. Actualment tots els inhibidors coneguts per a les CDKs, actuen sobre el lloc d’unió de l’ATP. Donat que existeix una gran quantitat de dades experimentals sobre aquests compostos es va decidir avaluar diferents algoritmes de docking i predicció d’afinitats experimentals amb cinc inhibidors coneguts de CDK6. Finalment, s’ha proposat també un desenvolupament metodològic que enfoca el problema del disseny de fàrmacs des d’una perspectiva més amplia: la quimiogenòmica. Amb la seqüenciació del genoma humà s’ha pres consciència de que resulta inviable avaluar el gran número de compostos químics coneguts actualment sobre totes les possibles dianes terapèutiques identificades en el genoma humà. Per aquest motiu és imprescindible desenvolupar mètodes teòrics més senzills per a la caracterització i comparació de molècules que permetin predir la seva activitat biològica. Així doncs, amb la realització d’aquesta tesi, queda patent que l’aplicació de mètodes teòrics pot contribuir de manera eficient al disseny de fàrmacs. D’aquesta manera es possible reduir el cost i temps necessari per al descobriment de compostos actius. / Nowadays, personalized medicine and directed therapies have emerged as appealing strategies for pharmaceutical companies. The long-term goal is developing new treatments to target molecular pathways altered only in affected cells, thus reducing undesired side effects and toxicity problems. This is a tedious and long process although the incorporation in its framework of rational drug design techniques has reduced the time needed to identify new active molecules. The knowledge of molecular mechanisms involved in a given pathology allows finding a point of the process that can be targeted, usually a protein, restoring the normal cell behavior. Once identified the therapeutic target it is possible to find compounds that reproduce interactions between this protein and the corresponding natural regulations by means of molecular modeling techniques. In principle, these compounds are expected to mimic the biological effect of the natural regulators. Antitumoral therapies oriented to promote apopotosis or control the cell proliferation process are gaining importance nowadays. In addition, opportunities for therapeutic intervention in this context are growing with the discovery of new proteins involved in these pathways. In fact, the drawback of compounds known at date relies on selectivity problems and, thus, the huge number of undesired side effects of these treatments. Hence, development of selective treatments is a very active research field. The goal of the present PhD project is to identify new anticancer agents using molecular modeling techniques. On the one hand, it has been tried to identify inhibitors of the Bcl-2 protein family in order to restore normal apoptosis levels in tumoral cells and, on the other hand, for the CDK4 and CDK6 proteins, key regulators of eukaryotic cell cycle. All these proteins are deregulated in many types of cancer and thus, are presented as interesting targets for the cancer treatment. The identification of compounds with potency and selectivity for these proteins that can be used as lead compounds that finally will become commercial drugs is seeked.

Chapter 1 gives background information on proteases and discusses the concept of protease inhibition as a therapeutic strategy for humans. It introduces the key concept that conformation defines biological activity. It also outlines how proteases almost universally bind their substrate/inhibitors in an extended β-strand conformation. The use of calpain as a prototype protease for the testing of β-strand mimics synthesised later in the thesis is also discussed. Chapter 2 describes how molecular modeling was used to rationalise the structure based activity relationships (SAR) of known calpain inhibitors. Molecular modeling was then used to successfully design a number of acyclic β-strand mimics. The synthesis and testing of eight such inhibitors is described. The most potent β-strand mimic prepared was 2.13. This was determined to have an IC₅₀ of 30 nM against calpain II. Chapter 3 outlines the history and application of ring closing metathesis (RCM) to the synthesis of cyclic compounds. The attempted synthesis of an eight membered cyclic nitrogen to nitrogen conformationally constrained dipeptide is described. The synthesis of a conformationally constrained β-amino acid calpain inhibitor (3.73) is also described. A novel calpain inhibitor motif was designed in Chapter 4. On the basis of this an in-silico combinatorial library of two hundred and eighty eight possible β-strand templates was prepared. Conformational analysis of this library was performed and from this a number of excellent β-strand templates were identified and selected for synthesis. The preparation of ten β-strand templates is described. New microwave irradiation methodology was developed to achieve this. vii The formation of a six-membered catalyst deactivating chelate is also proposed to explain why some dienes fail to undergo RCM. Two methods to circumvent the formation of such a chelate are outlined. The addition of Lewis acid chloro-dicyclohexyl borane to the RCM reaction mixture and chain length alteration are investigated. Chapter 5 describes the design of macrocyclic β-strand mimics using induced fit molecular modelling. The physicochemical properties of these were calculated in-silico. From this analysis a number of Tyr-XX-Gly based and Tyr-XX-Cys based macrocyclic calpain inhibitors were selected for synthesis. The preparation and testing of these are described. In the Tyr-XX-Gly macrocyclic system a number of variables were investigated and numerous SAR implications concluded. Aldehyde 5.14 was identified as the best electrophilic warhead macrocyclic calpain inhibitor with an IC₅₀ against calpain II of 27 nM. The best non-electrophilic warhead macrocycle (5.13) had an IC₅₀ against calpain II of 704 nM. Chapter 6 describes synthetic optimisation for the preparation of calpain inhibitors 2.13, 5.14 and 5.17. Multi-gram quantities of each were prepared. Aldehydes 2.13 and 5.14 were evaluated as anti-cataract agents using in-vivo cataract sheep model. Both of these β-strand mimics were demonstrated to retard cataract development. Macrocycle 5.14 was found to be the most effective, decreasing the rate of cataract development between forty four and forty nine per cent relative to control. Chapter 7 outlines the attempted development of RCM methodology for the chiral synthesis of α-α disubstituted amino acid lactams. In addition, methodology for the stereoselective incorporation of a C-N constrained β-amino acid carbocycle into a peptide or peptidomimetic is described.

Submitted by Maike Costa (maiksebas@gmail.com) on 2017-09-13T11:59:49Z No. of bitstreams: 1 arquivototal.pdf: 7758959 bytes, checksum: db745d41b196978192ebc789e25f442b (MD5) / Made available in DSpace on 2017-09-13T11:59:49Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 7758959 bytes, checksum: db745d41b196978192ebc789e25f442b (MD5) Previous issue date: 2016-02-26 / The use of plants for medicinal purposes is one of the oldest forms of medical practice of mankind, emphasizing the alkaloids because they present rich structural and pharmacological properties extensive variety. The drug design is aided by computer based strategies based on linkers or target. When developing new compounds, the structure-based techniques, such as docking, can be applied to study of certain receptor and its corresponding ligand, evaluating bindingprotein interactions. Whereas in the ligand-based methods, a database of known ligands is used, looking for ways to evaluate parameters (molecular descriptors) that can assist in the development of compounds with higher power. This study aimed to perform in silico studies to investigate drug-target interactions with alkaloids derived from natural products and their analogues with relevant pharmacological activity. Different molecular descriptors and methodologies were used in the studies developed. In chapter 2, the interaction of alkaloid bisindolic caulerpine (CLP) was evaluated with the enzyme involved in Alzheimer's disease (AD) monoamine oxidase B (MAO-B), and a database with 109 analogs. It was possible to observe a chemical parameter of inhibition of PLC analogues where the replacement of the radicals must be asymmetric with different polarity. The studies based on the linker and the structure associated with the classification drug-like chemical skeleton suggest that the PLC has potential use in the treatment of AD. In chapter 3, 8 alkaloids isolated Cissampelos sympodialis and 101 derivatives, had their inhibitory potential against enzyme (BACE, GSK-3β and MAO-A) involved in degenerative diseases assessed by in silico methods. consensual analysis showed affinity alkaloids bisbenzilisoquinolinics by BACE, incluindos the roraimine natural alkaloids and simpodialine-β-N-oxide, supporting interest in investigating this skeleton as an antagonist of this enzyme. In Chapter 4 we evaluated the multi-target potential of 148 aphorphinics alkaloids Annonaceae against Leishmania donovani. Six were selected enzymes of this neglected disease for theoretical study, which was associated with experimental four alkaloids available data and integrating the bank, which had pIC50 value inferior to 5.26. The xyloguyelline alkaloid was named as a potential multi-agent target, demonstrating activity against 5 of 6 enzymes evaluated, likely to activity of over 60%. fragment descriptors were used to create model-based binder in a parallel approach with molecular docking to predict the cytotoxic and against topoisomerase II activity azaphenantrene alkaloids in chapter 5. The cytotoxic activity of this skeleton alkaloids are well described in the literature, molecules having activity against several tumor cell lines. The IMB 6 analog and 23 IMB showed interesting activity and selectivity, with MolDock energy similar to liriodenine composed characterized by potent anti-tumor action, but with high toxicity. Important structural information is provided by spectroscopy nuclear magnetic resonance (NMR), and Chapter 6 aimed to discuss the importance of this technique for generating molecular descriptors. Studies that applied successfully in drug design NMR descriptors assisted by computer are described and several QSAR and QSPR having as support data chemical shifts. / A utilização de plantas com fins medicinais é uma das mais antigas formas de prática medicinal da humanidade, enfatizando os alcaloides, por apresentarem rica variedade estrutural e extensa propriedade farmacológica. O desenho de drogas auxiliado pelo computador é fundamentado em estratégias baseadas nos ligantes ou no alvo. No desenvolvimento de novos compostos, técnicas baseadas na estrutura, como o docking, podem ser aplicadas no estudo de um determinado receptor e seu respectivo ligante, avaliando as interações ligante-proteína. Ao passo que nos métodos baseados no ligante, um banco de ligantes conhecidos é utilizado, buscando modos de avaliar parâmetros (descritores moleculares) que possam auxiliar no desenvolvimento de compostos com maior potência. Este estudo teve como objetivo realizar estudos in silico para investigar interações fármaco-alvo com alcaloides oriundos de produtos naturais, e respectivos análogos, com relevante atividade farmacológica. Diferentes descritores moleculares e metodologias foram utilizadas nos estudos desenvolvidos. No capítulo 2, foi avaliado a interação do alcaloide bisindolico caulerpina (CLP) com a enzima envolvida na doença de Alzheimer (DA) monoamina oxidase B (MAO-B), além de um banco com 109 análogos. Foi possível observar um parâmetro químico de inibição dos análogos da CLP, onde a substituição dos radicais deve ser assimétrica com polaridade distinta. Os estudos dos baseados no ligante e na estrutura, associado à classificação drug-like, sugerem que o esqueleto químico da CLP tem potencial uso no tratamento da DA. No capítulo 3, 8 alcaloides isolados de Cissampelos sympodialis e 101 derivados, tiveram seu potencial inibitório contra enzimas (BACE, GSK-3β e MAO-A) envolvidas em doenças degenerativas avaliado por metodologias in silico. Análise consensual demonstrou afinidade de alcaloides bisbenzilisoquinolínicos pela BACE, incluindos os alcaloides naturais roraimina e simpodialina- β-N-oxide, suportando interesse em investigar este esqueleto como antagonista desta enzima. No capítulo 4 foi avaliado o potencial multi-target de 148 alcaloides aporfinicos de Annonaceae contra Leishmania donovani. Foram utilizadas seis enzimas desta doença negligenciada para o estudo teórico, que foi associado com dados experimentais de quatro alcaloides disponíveis e que integram o banco, que apresentaram valor pIC50 inferior a 5.26. O alcaloide xyloguyellina foi apontado como potencial agente multitarget, demonstrando atividade contra 5 das 6 enzimas avaliadas, com probabilidade de atividade superior a 60%. Descritores de fragmento foram utilizados para criar modelo baseado no ligante em uma abordagem paralela com docking molecular, para predizer a atividade citotóxica e contra topoisomerase II de azafenantreno alcaloides, no capítulo 5. A atividade citotóxica deste esqueleto de alcaloides está bem descrita na literatura, com diversas moléculas apresentando atividade contra linhagens de células tumorais. Os análogos IMB 6 e IMB 23 apresentaram interessante atividade e com seletividade, apresentando energia MolDock similar à liriodenina, composto caracterizado por potente ação antitumoral, porém com elevada toxicidade. Importantes informações estruturais são fornecidas pela espectroscopia de ressonância magnética nuclear (RMN), sendo o capítulo 6 destinado a discorrer sobre a importância desta técnica para geração de descritores moleculares. Estudos que aplicaram com sucesso descritores RMN em design de drogas assistida pelo computador encontram-se descritos, além de diversos estudos de QSAR e QSPR tendo como amparo dados de deslocamentos químicos.

Submitted by ÍCARO PUTINHON CARUSO null (ykrocaruso@hotmail.com) on 2016-09-19T16:20:38Z No. of bitstreams: 1 tese_doutorado_icaro_vf.pdf: 17027642 bytes, checksum: 71d2f869670d044aace5f2ab6326b657 (MD5) / Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-09-22T14:26:36Z (GMT) No. of bitstreams: 1 caruso_ip_dr_sjrp.pdf: 17027642 bytes, checksum: 71d2f869670d044aace5f2ab6326b657 (MD5) / Made available in DSpace on 2016-09-22T14:26:36Z (GMT). No. of bitstreams: 1 caruso_ip_dr_sjrp.pdf: 17027642 bytes, checksum: 71d2f869670d044aace5f2ab6326b657 (MD5) Previous issue date: 2016-08-26 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Os flavonóides fazem parte de uma ampla classe de compostos polifenólicos os quais ocorrem naturalmente nas plantas e podem ser encontrados nas sementes, caules, folhas, flores e/ou frutos. Estudos recentes indicam que esses compostos polifenólicos podem apresentar uma variedade significativa de atividades biológicas benéficas para a saúde humana, como por exemplo: antioxidante, anti-inflamatória, antibacteriana, antiviral e anticancerígena. A Albumina do Soro Humano (HSA) é a principal proteína extracelular presente no plasma sanguíneo. A função central dessa proteína é transportar e distribuir ligantes endógenos e exógenos para diferentes alvos moleculares no corpo humano. Por tais aspectos, torna-se importante o desenvolvimento de estudos que caracterizam a interação dos flavonóides com a proteína transportadora HSA. Este trabalho investiga a interação dos flavonóides Isovitexina (ISO) e 2-Fenilcromona (2PHE) com a HSA, utilizando técnicas experimentais de espectroscopia de fluorescência, absorbância UV-Vis, dicroísmo circular (CD) e infravermelho com transformada de Fourier (FT-IR); juntamente com ferramentas computacionais de cálculo {\it{ab initio}}, dinâmica molecular e modelagem molecular. A integração dessas abordagens experimentais e computacionais possibilita caracterizar a formação dos complexos HSA-flavonóides, determinando aspectos físico-químicos como: constantes de afinidade, parâmetros termodinâmicos, número de sítios de ligação, perfil de cooperatividade e resíduos de aminoácidos responsáveis pelas interações proteína-flavonóides (hidrofóbicas e eletrostáticas). / Flavonoids belong to a large class of polyphenolic compounds which occur naturally in plants and can be found seeds, stems, leaves, flowers and/or fruits. Recent studies indicate that these polyphenolic compounds can present a significant variety of beneficial biological activities on human health, such as: antioxidant, anti-inflammatory, antibacterial, antiviral, and anticancer. Human Serum Ambumin (HSA) is the main extracellular protein presents in blood plasma. The core function of this protein is to carry and distribute endogenous and exogenous ligands to different molecular targets in the human body. For these aspects, it is important to develop studies that characterize the interaction of the flavonoids with the carrier protein HSA. This work investigates the interaction of the flavonoids Isovitexin (ISO) and 2-Phenylchromone (2PHE) with the HSA, using experimental techniques of fluorescence, UV-Vis absorbance, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy; along with computational tools of ab initio calculation, molecular dynamics, and molecular modeling. The integration of these experimental and computational approaches allows to characterize the formation of the HSA-flavonoids complexes, determining physicochemical aspects, sucha as: affinity constants, thermodynamic parameters, number of binding sites, cooperativity profile and aminoacid residues responsable for the protein-flavonoids interactions (hydrophobic and electrostatic).

Made available in DSpace on 2014-12-17T14:10:24Z (GMT). No. of bitstreams: 1 JonasINO_DISSERT.pdf: 890224 bytes, checksum: a68b1b3f5f169bb87b98314d116a12b3 (MD5) Previous issue date: 2012-03-02 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicos?dico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced. / Nessa disserta??o, os princ?pios te?ricos que regem a Modelagem Molecular foram aplicados na caracteriza??o eletr?nica do oligopept?deo α3 e seus variantes (5Q,7Q)-α3, como tamb?m na descri??o qu?ntica da intera??o do aminoglicos?deo higromicina B e a subunidade 30S do ribossomo bacteriano. No primeiro estudo, os dipept?deos lineares e neutros constituintes das biomol?culas mencionados foram modelados e posteriormente otimizados at? uma estrutura de menor energia potencial e ?ngulos diedros adequados. No caso, tr?s processos de otimiza??o geom?trica, baseados subsequentemente na teoria cl?ssica newtoniana, na semi-emp?rica e na teoria do funcional da densidade (DFT), varreram a paisagem de energia de cada dipept?deos na busca de uma estrutura de energia m?nima ideal. Por fim, os conf?rmeros ?timos foram descritos quanto ao potencial eletrost?tico, energia de ioniza??o (amino?cidos), orbitais de fronteira HOMO/HOMO-1 e termo de hopping. A partir dos termos de hopping descritos nesse trabalho, foi poss?vel, em estudos subsequentes, caracterizar as propriedades de transporte de cargas destes modelos pept?dicos. Vislumbra-se uma nova tecnologia de biosensores capaz de diagnosticar doen?as amiloides, relacionadas ao ac?mulo de pept?deos disformes, a partir do perfil de condutividade el?trica apresentado pelas prote?nas do paciente. Em um segundo momento dessa disserta??o, realiza-se um estudo qu?ntico por modelagem molecular da energia de intera??o de um antibi?tico aminoglicos?dico em seu receptor riboss?mico. Sabe-se que a higromicina B (higB) ? um antibi?tico aminoglicos?deo que afeta a transloca??o ribossomal pela intera??o direta com a subunidade menor do ribossomo bacteriano (30S), especificamente com nucleot?deos da h?lice 44 do RNA riboss?mico 16S (rRNA 16S). Devido ao forte car?ter eletrost?tico desta conex?o, foi proposta a investiga??o energ?tica do mecanismo de liga??o da higB no 30S usando diferentes valores de constantes diel?tricas (ε=0, 4, 10, 20 e 40), as quais s?o amplamente utilizadas no estudo das propriedades eletrost?ticas de biomol?culas. Para isso, foram medidos raios crescentes centralizados no centr?ide da higB tendo por base a estrutura cristalina higB-30S (1HNZ.pdb), e apenas a energia de intera??o individual de cada nucleot?deo englobado foi calculada quanticamente utilizando a estrat?gia de fracionamento molecular com capuzes conjugados (MFCC). Percebeu-se que as constantes diel?tricas subestimam as energias de intera??o individuais, permitindo que o estado de converg?ncia energ?tica seja alcan?ado rapidamente. Por?m apenas para ε=40, a energia de intera??o total droga-receptor se estabilizou em r=18?, o que se constituiu como um adequado s?tio de liga??o, pois englobou os res?duos do 16S que interagem mais fortemente com a higB - C1403, C1404, G1405, A1493, G1494, U1495, C1496 e U1498. Assim, a constante diel?trica ≈40 ? ideal para o tratamento de sistemas com muitas cargas. Confrontando as energias de liga??o individuais dos nucleot?deos 16SrRNA com ensaios experimentais para determina??o da concentra??o inibit?ria m?nima (MIC) da higB, acredita-se que esses res?duos com elevados valores de intera??o gerariam resist?ncia bacteriana ? droga quando mutados. Com o mesmo racioc?nio, visto que aqueles com baixa energia n?o influenciariam de forma eficaz a afinidade da higB em seu s?tio de liga??o, n?o ocorreria perda de efic?cia caso fossem substitu?dos.