Síntese de um novo polímero conjugado e reticulável e sua aplicação em células fotovoltaicas

Trabalho Final de Mestrado para obtenção do Grau de Mestre em Engenharia Química e Biológica

Expanding molecular modeling and design tools to non-natural sidechains.

Protein-protein interactions encode the wiring diagram of cellular signaling pathways and their deregulations underlie a variety of diseases, such as cancer. Inhibiting protein-protein interactions with peptide derivatives is a promising way to develop new biological and therapeutic tools. Here, we develop a general framework to computationally handle hundreds of non-natural amino acid sidechains and predict the effect of inserting them into peptides or proteins. We first generate all structural files (pdb and mol2), as well as parameters and topologies for standard molecular mechanics software (CHARMM and Gromacs). Accurate predictions of rotamer probabilities are provided using a novel combined knowledge and physics based strategy. Non-natural sidechains are useful to increase peptide ligand binding affinity. Our results obtained on non-natural mutants of a BCL9 peptide targeting beta-catenin show very good correlation between predicted and experimental binding free-energies, indicating that such predictions can be used to design new inhibitors. Data generated in this work, as well as PyMOL and UCSF Chimera plug-ins for user-friendly visualization of non-natural sidechains, are all available at http://www.swisssidechain.ch. Our results enable researchers to rapidly and efficiently work with hundreds of non-natural sidechains.

Molecular model of cyclin-dependent kinase 5 complexed with roscovitine

Here is described a structural model for the binary complex CDK5-roscovitine. Roscovitine has been shown to potently inhibit cyclin-dependent kinases 1, 2 and 5 (CDK1, 2, and 5), and the structure of CDK2 complexed with roscovitine has been reported; however, no structural data, are available for complexes of CDK5 with inhibitors. The structural model indicates that roscovitine strongly binds to the ATP-binding pocket of CDK5 and structural comparison of the CDK2-roscovitine complex correlates the structural differences with differences in inhibition of these CDKs by this inhibitor. This structure opens the possibility of testing new inhibitor families, in addition to new substituents for the already known lead structures of adenine derivatives. (C) 2002 Elsevier B.V. (USA). All rights reserved.

Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

Molecular organization and doping in poly(2-methoxyaniline)/Ni(dmit)(2) films obtained with the Langmuir-Blodgett technique

The control of the properties of materials at the molecular level is pursued for many applications, especially those associated with nanostructures. In this paper, we show that the coordination compound [Ni(dmit)(2)], where (dmit) is the 1,3-dithiole-2-thione-4,5-dithiolate ligand, can induce doping of poly(2-methoxyaniline) (POMA) in molecularly ordered Langmuir and Langmuir-Blodgett (LB) films. Doping was associated with interactions between the components and the compression of the Langmuir film at the air-water interface, according to polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS) data. Taking these results together with in situ UV-Vis absorption measurements, we could identify the molecular groups involved in the interaction, including the way they were reoriented upon film compression. The Langmuir films were sufficiently stable to be transferred as Y-type LB films, while the hybrid POMA/[Ni(dmit)(2)] films remain doped in the solid state. As expected, the molecular charges affected the film morphology, as observed from combined atomic and electric force microscopy measurements. In summary, with adequate spectroscopy and microscopy tools we characterized molecular-level interactions, which may allow one to design molecular electronic devices with controlled electrical properties.

Ligand- and Structure-Based Drug Design Strategies and PPAR delta/alpha Selectivity

Peroxisome-proliferator-activated receptors are a class of nuclear receptors with three subtypes: a, ? and d. Their main function is regulating gene transcription related to lipid and carbohydrate metabolism. Currently, there are no peroxisome-proliferator-activated receptors d drugs being marketed. In this work, we studied a data set of 70 compounds with a and d activity. Three partial least square models were created, and molecular docking studies were performed to understand the main reasons for peroxisome-proliferator-activated receptors d selectivity. The obtained results showed that some molecular descriptors (log P, hydration energy, steric and polar properties) are related to the main interactions that can direct ligands to a particular peroxisome-proliferator-activated receptors subtype.

A Combined Study Using Ligand-Based Design, Synthesis, and Pharmacological Evaluation of Analogues of the Acetaminophen Ortho-Regioisomer with Potent Analgesic Activity

A ligand-based drug design study was performed to acetaminophen regioisomers as analgesic candidates employing quantum chemical calculations at the DFT/B3LYP level of theory and the 6-31G* basis set. To do so, many molecular descriptors were used such as highest occupied molecular orbital, ionization potential, HO bond dissociation energies, and spin densities, which might be related to quench reactivity of the tyrosyl radical to give N-acetyl-p-benzosemiquinone-imine through an initial electron withdrawing or hydrogen atom abstraction. Based on this in silico work, the most promising molecule, orthobenzamol, was synthesized and tested. The results expected from the theoretical prediction were confirmed in vivo using mouse models of nociception such as writhing, paw licking, and hot plate tests. All biological results suggested an antinociceptive activity mediated by opioid receptors. Furthermore, at 90 and 120 min, this new compound had an effect that was comparable to morphine, the standard drug for this test. Finally, the pharmacophore model is discussed according to the electronic properties derived from quantum chemistry calculations.

Materials properties from electron density distributions: Molecular magnetism and linear optical properties

The general goal of this thesis is correlating observable properties of organic and metal-organic materials with their ground-state electron density distribution. In a long-term view, we expect to develop empirical or semi-empirical approaches to predict materials properties from the electron density of their building blocks, thus allowing to rationally engineering molecular materials from their constituent subunits, such as their functional groups. In particular, we have focused on linear optical properties of naturally occurring amino acids and their organic and metal-organic derivatives, and on magnetic properties of metal-organic frameworks. For analysing the optical properties and the magnetic behaviour of the molecular or sub-molecular building blocks in materials, we mostly used the more traditional QTAIM partitioning scheme of the molecular or crystalline electron densities, however, we have also investigated a new approach, namely, X-ray Constrained Extremely Localized Molecular Orbitals (XC-ELMO), that can be used in future to extracted the electron densities of crystal subunits. With the purpose of rationally engineering linear optical materials, we have calculated atomic and functional group polarizabilities of amino acid molecules, their hydrogen-bonded aggregates and their metal-organic frameworks. This has enabled the identification of the most efficient functional groups, able to build-up larger electric susceptibilities in crystals, as well as the quantification of the role played by intermolecular interactions and coordinative bonds on modifying the polarizability of the isolated building blocks. Furthermore, we analysed the dependence of the polarizabilities on the one-electron basis set and the many-electron Hamiltonian. This is useful for selecting the most efficient level of theory to estimate susceptibilities of molecular-based materials. With the purpose of rationally design molecular magnetic materials, we have investigated the electron density distributions and the magnetism of two copper(II) pyrazine nitrate metal-organic polymers. High-resolution X-ray diffraction and DFT calculations were used to characterize the magnetic exchange pathways and to establish relationships between the electron densities and the exchange-coupling constants. Moreover, molecular orbital and spin-density analyses were employed to understand the role of different magnetic exchange mechanisms in determining the bulk magnetic behaviour of these materials. As anticipated, we have finally investigated a modified version of the X-ray constrained wavefunction technique, XC-ELMOs, that is not only a useful tool for determination and analysis of experimental electron densities, but also enables one to derive transferable molecular orbitals strictly localized on atoms, bonds or functional groups. In future, we expect to use XC-ELMOs to predict materials properties of large systems, currently challenging to calculate from first-principles, such as macromolecules or polymers. Here, we point out advantages, needs and pitfalls of the technique. This work fulfils, at least partially, the prerequisites to understand materials properties of organic and metal-organic materials from the perspective of the electron density distribution of their building blocks. Empirical or semi-empirical evaluation of optical or magnetic properties from a preconceived assembling of building blocks could be extremely important for rationally design new materials, a field where accurate but expensive first-principles calculations are generally not used. This research could impact the community in the fields of crystal engineering, supramolecular chemistry and, of course, electron density analysis.

Estudo da microestrutura e dinâmica molecular do Poly(3-(2\'-ethylhexyl)thiophene)(P3EHT) via ressonância magnética nuclear

O estudo da microestrutura e dinâmica molecular de polímeros conjugados é de grande importância para o entendimento das propriedades físicas desta classe de materiais. No presente trabalho utilizou-se técnicas de ressonância magnética nuclear em baixo e alto campo para elucidar os processos de dinâmica molecular e cristalização do polímero Poly(3-(2’-ethylhexyl)thiophene) - P3EHT. O P3EHT é um polímero modelo para tal estudo, pois apresenta temperatura de fusão bem inferior a sua temperatura de degradação. Esta característica permite acompanhar os processos de cristalização in situ utilizando RMN. Além disso, sua similaridade ao já popular P3HT o torna um importante candidato a camada ativa em dispositivos eletrônicos orgânicos. O completo assinalamento do espectro de 13C para o P3EHT foi realizado utilizando as técnicas de defasamento dipolar e HETCOR. Os processos de dinâmica molecular, por sua vez, foram sondados utilizando DIPSHIFT. Observou-se um gradiente de mobilidade na cadeia lateral do polímero. Além disso, os baixos valores de parametros de ordem obtidos em comparação a experimentos similares realizados no P3HT na literatura indicam um aparente aumento no volume livre entre cadeias consecutivas na fase cristalina. Isso indica que a presença do grupo etil adicional no P3EHT causa um completo rearranjo das moléculas e dificulta seu empacotamento. Constatou-se ainda pouca variação das curvas de DIPSHIFT para os carbonos da cadeia lateral como função do método de excitação utilizado, o que aponta para um polímero que apresenta cadeia lateral móvel mesmo em sua fase cristalina. Os dados de dinâmica molecular foram corroborados por medidas de T1, T1ρ e TCH. Utilizando filtros dipolares em baixo campo observou-se três temperaturas de transição para o P3EHT: 250 K, 325 K e 350 K. A cristalização desse material é um processo lento. Verificou-se que o mesmo pode se estender por até até 24h a temperatura ambiente. Mudanças no espectro de 13C utilizando CPMAS em alto campo indicam um ordenamento dos anéis tiofeno (empacotamento π – π) como o principal processo de cristalização para o P3EHT.

Proteins accessible to immune surveillance show significant T-cell epitope depletion:implications for vaccine design

T cell activation is the final step in a complex pathway through which pathogen-derived peptide fragments can elicit an immune response. For it to occur, peptides must form stable complexes with Major Histocompatibility Complex (MHC) molecules and be presented on the cell surface. Computational predictors of MHC binding are often used within in silico vaccine design pathways. We have previously shown that, paradoxically, most bacterial proteins known experimentally to elicit an immune response in disease models are depleted in peptides predicted to bind to human MHC alleles. The results presented here, derived using software proven through benchmarking to be the most accurate currently available, show that vaccine antigens contain fewer predicted MHC-binding peptides than control bacterial proteins from almost all subcellular locations with the exception of cell wall and some cytoplasmic proteins. This effect is too large to be explained from the undoubted lack of precision of the software or from the amino acid composition of the antigens. Instead, we propose that pathogens have evolved under the influence of the host immune system so that surface proteins are depleted in potential MHC-binding peptides, and suggest that identification of a protein likely to contain a single immuno-dominant epitope is likely to be a productive strategy for vaccine design.

Novos compostos orgânicos reticuláveis para aplicações em células fotovoltaicas

Trabalho Final de Mestrado para obtenção do grau de mestre em Engenharia Química e Biológica

Augmented epithelial multidrug resistance-associated protein 4 expression in peritoneal endometriosis: regulation by lipoxin A(4).

OBJECTIVE: To compare the expression of the prostaglandin (PG) E(2) transporter multidrug resistance-associated protein 4 (MRP4) in eutopic and ectopic endometrial tissue from endometriosis patients with that of control subjects and to examine whether MRP4 is regulated by the antiinflammatory lipid lipoxin A(4) (LXA(4)) in endometriotic epithelial cells. DESIGN: Molecular analysis in human samples and a cell line. SETTING: Two university hospitals and a private clinic. PATIENT(S): A total of 59 endometriosis patients and 32 age- and body mass index-matched control subjects undergoing laparoscopy or hysterectomy. INTERVENTION(S): Normal, eutopic, and ectopic endometrial biopsies as well as peritoneal fluid were obtained during surgery performed during the proliferative phase of the menstrual cycle. 12Z endometriotic epithelial cells were used for in vitro mechanistic studies. MAIN OUTCOME MEASURE(S): Tissue MRP4 mRNA levels were quantified by quantitative reverse-transcription polymerase chain reaction (qRT-PCR), and localization was analyzed with the use of immunohistochemistry. Cellular MRP4 mRNA and protein were quantified by qRT-PCR and Western blot, respectively. PGE(2) was measured in peritoneal fluid and cell supernatants using an enzyme immunoassay (EIA). RESULT(S): MRP4 was expressed in eutopic and ectopic endometrium, where it was overexpressed in peritoneal lesions and localized in the cytoplasm of glandular epithelial cells. LXA(4) attenuated MRP4 mRNA and protein levels in endometriotic epithelial cells in a dose-dependent manner, while not affecting the expression of enzymes involved in PGE(2) metabolism. Investigations employing receptor antagonists and small interfering RNA revealed that this occurred through estrogen receptor α. Accordingly, LXA(4) treatment inhibited extracellular PGE(2) release. CONCLUSION(S): We report for the first time that MRP4 is expressed in human endometrium, elevated in peritoneal endometriosis, and modulated by LXA(4) in endometriotic epithelial cells.

COMPORTAMENTO DO ÓLEO DE GIRASSOL COM ALTO TEOR DE ÁCIDO OLÉICO EM TERMOXIDAÇÃO E FRITURA

Óleos de sementes de girassol com diferentes níveis de ácido oléico foram utilizados sob condições de termoxidação e fritura para avaliar o comportamento do óleo de girassol com alto teor de ácido oléico quanto ao seu grau de insaturação quando comparado com o óleo de girassol convencional. Os métodos analíticos aplicados incluíram a determinação de compostos polares totais, quantificação de compostos glicerídicos menores, quantificação da composição triglicerídica, período de indução a 100oC e níveis de a -tocoferol. Os resultados para compostos polares totais apresentaram menores valores em óleo de girassol com alto teor de ácido oléico quando comparados com óleo de girassol convencional. Quanto à distribuição dos compostos glicerídicos menores, verificou-se, de modo geral, que o aumento dos compostos polares totais estava relacionado essencialmente aos compostos de maior peso molecular, isto é, polímeros, dímeros e triglicerídios oxidados, os quais são representantes das alterações térmica e oxidativa. Já os diglicerídios e ácidos graxos, indicativos da alteração hidrolítica, permaneceram praticamente nos níveis originais; uma vez que a umidade não se encontrava presente no meio. A perda quantitativa da composição triglicerídica dependeu do grau de insaturação do triglicerídio, sendo mais elevada em triglicerídios que contêm duas ou três moléculas de ácido linoléico. Em todos os casos, o óleo de girassol convencional teve uma maior tendência à polimerização, um maior grau de alteração total e uma maior perda de triglicerídios majoritários que o óleo de girassol com alto teor de ácido oléico. Assim, dentre os óleos utilizados neste estudo, os resultados mostraram um excelente comportamento do óleo de girassol com alto teor de ácido oléico em relação à termoxidação, independente do tipo de aquecimento e à fritura descontínua. Tais resultados demonstraram que sua resistência à alteração termoxidativa estava relacionada com seu baixo teor em ácidos graxos polinsaturados e alto teor em ácido oléico e trioleína.

Polyoxométallates hybrides : vers des systèmes covalents photoactifs dans le visible

Réalisé en cotutelle, sous la direction du Pr. Bernold Hasenknopf, à l'Institut Parisien de Chimie Moléculaire, Université Pierre et Marie Curie (Paris VI, France) et dans le cadre de l'Ecole Doctorale "Physique et Chimie des Matériaux" - Spécialité Chimie Inorganique (ED397).

Mechanism of action of cyclic antimicrobial peptides

This PhD thesis is the result of the combination of experimental and computational techniques with the aim of understanding the mechanism of action of de novo cyclic decapeptides with high antimicrobial activity. By experimental techniques the influence of the replacement of the phenylalanine for tryptophan residue in their antimicrobial activity was tested and the stability in human serum was also analyzed, in order to evaluate their potential therapeutic application as antitumor agents. On the other hand, the interaction amongst the peptide BPC194 c(KKLKKFKKLQ), the best candidate from the whole library of cyclic peptides, and a model anionic membrane was simulated. The results showed a structure-function relationship derived from the stable conformation of the peptides involved in the membrane permeabilization. As a result, a rational design was performed being BPC490 the peptide with best antimicrobial activity compared with the best active peptide from the original library.