Los distintos procesos involucrados en la industria química deben ser estudiados cuidadosamente con el fin de obtener productos de calidad al menor costo y causando el mínimo daño al medio ambiente (ej. industria de polímeros sintéticos y diseño racional de fármacos). Hace ya varios años que distintos métodos computacionales son utilizados en la industria química con el fin de lograr esos objetivos. En particular, el modelado QSAR/QSPR es una técnica de gran interés dentro del área de la informática molecular, ya que permite correlacionar de manera cuantitativa características estructurales de una entidad química con una determinada propiedad físico-química o actividad biológica. El objetivo de esa tesis fue desarrollar distintas metodologías para asistir a expertos en informática molecular en el proceso de predicción de propiedades fisicoquímicas o de actividad biológica. Más específicamente, las técnicas desarrolladas se enfocan en incorporar al proceso de modelado predictivo QSAR/QSPR, el conocimiento del experto en el dominio. De esta manera se logran mejorar ciertas características de los modelos, tales como su interpretación en términos físicos-químicos, las cuales permite aumentar la generalidad del modelo. Al respecto, se ha implementado una herramienta de analítica visual, denominada VIDEAN, que combina métodos estadísticos con visualizaciones interactivas para elegir un conjunto de descriptores que predigan una determinada propiedad objetivo. Otro de los aportes de esta tesis está relacionado con el dominio de aplicación de un modelo QSAR/QSPR. En este sentido, se ha implementado una técnica para determinar el dominio de aplicación de modelos de clasificación. Esto representa una novedad dado que la mayoría de las técnicas desarrolladas para este fin apuntan exclusivamente a los modelos de regresión. Los métodos implementados han sido evaluados mediante el estudio de propiedades de relevancia para tres campos de aplicación: el diseño racional de fármacos, el diseño de materiales poliméricos (plásticos) y las ciencias ambientales. Con este fin, se han desarrollado numerosos modelos predictivos de regresión y clasificación. En el área de diseño racional de fármacos, las propiedades que se estudiaron están relacionadas con el comportamiento ADMET (absorción, distribución, metabolismo, excreción y toxicidad) de los mismos: absorción intestinal humana (Human Intestinal Absorption, HIA) y el pasaje de la barrera hemato-encefálica (Blood-Brain Barrier, BBB), ambas esenciales para el desarrollo de nuevos fármacos. En el campo de los materiales poliméricos, se exploraron varias propiedades mecánicas, que proporcionan información relacionada con la ductilidad, resistencia y rigidez del material polimérico; y que, junto con otras propiedades, definen su perfil de aplicación estructural. Estas propiedades son: elongación a la rotura (elongation at break), resistencia a tensión en la rotura (tensile strength at break) y módulo elástico (tensile modulus). En el área de medioambiente, la propiedad que se estudió fue el coeficiente de distribución sangre-hígado (log Pliver) en compuestos orgánicos volátiles (VOCs), que son gases que se emiten de ciertos sólidos o líquidos y que son ampliamente utilizados como ingredientes en productos para el hogar (pinturas, los barnices, productos de limpieza, desinfección, cosmética, entre otros). Los resultados de estudios de este tipo de propiedades brindan un panorama de cómo se distribuyen estos tipos de compuestos en el organismo y pueden emplearse para la evaluación de riesgos y toma de decisiones en materia de salud pública. / The various processes involved in the chemical industry must be carefully studied in order to obtain quality products at the lowest cost and causing the least damage to the environment (e.g. synthetic polymer industry and rational drug design). During the last two decades, different computational methods have been used in the chemical industry in order to achieve these objectives. In particular, QSAR/QSPR modeling is a technique of great interest in the area of molecular informatics, since it allows to quantitatively correlate structural characteristics of a chemical entity with a given physical-chemical or biological activity. The objective of this thesis was to develop different methodologies to assist molecular computing experts in the process of predicting physicochemical or biological activity properties. More specifically, the techniques developed focus on incorporating domain expert's knowledge into the traditional automated predictive modeling process. In this way, certain characteristics of the models can be improved, such as their interpretation in physical-chemical terms, which allow to increase the generality on the model. In this sense, a visual analytics tool, called VIDEAN, has been implemented to combine statistical methods with interactive visualizations to choose a set of molecular descriptors that predict a specific target property. Another contribution of this thesis focuses on the implementation of a technique to determine the applicability domain of QSAR/QSPR classification models. In this regard, a technique has been implemented to determine the applicability domain of classification models. This represents a novelty given that most of the techniques developed for this purpose are exclusively intended for regression models. Implemented methods have been evaluated using target properties of relevance in three application areas: rational drug design, design of polymeric materials (plastics) and environmental sciences. To this end, different predictive regression and classification models were proposed that overcome in performance and interpretability to other traditional models have been developed. To this end, numerous regression and classification models have been developed. In rational drug design, the properties that were studied are related to the ADMET behavior (absorption, distribution, metabolism, excretion and toxicity): Human Intestinal Absorption (HIA) and Blood-brain barrier (BBB), both essential for the development of new drugs. In the field of polymeric materials, various mechanical properties, which provide information related to the ductility, strength and rigidity of the polymeric material were explored, and which, along with other properties define its structural application profile. These properties are: elongation at break, tensile strength at break and tensile modulus. In environment area, the property studied was the blood - liver distribution coefficient (log Pliver) in volatile organic compounds (VOCs), which are gases that are emitted from certain solids or liquids and are widely used as ingredients in products for the home (paints, varnishes, cleaning products, disinfection, cosmetics, among others). The results obtained from this studies provide an overview of how these types of compounds are distributed in the body and can be used for risk assessment and public health decision making.

El desarrollo de nuevos fármacos constituye un área de investigación fundamental en la medicina moderna. Más allá de los vertiginosos avances científicos en informática molecular y bioquímica que abonan a su mejora continua, la inversión en tiempo y recursos es sumamente elevada, en contraste a su exigua tasa de éxito. Las estrategias computacionales juegan un rol clave en la optimización y eficiencia de las múltiples tareas involucradas en el desarrollo de medicamentos, que abarcan desde la representación molecular y el modelado predictivo de bioactividad hasta el cribado virtual de fármacos y el diseño de nuevas estructuras químicas. El objetivo de esta tesis se centró en el desarrollo y aplicación de estrategias computacionales novedosas basadas en aprendizaje profundo para contribuir a la optimización de las diversas etapas del descubrimiento de nuevos medicamentos. Las contribuciones de la presente tesis parten de un análisis crítico y permanente del estado del arte en informática molecular e involucran el diseño de nuevas estrategias aplicando conceptos y desarrollos de vanguardia en aprendizaje profundo. Como resultado de este trabajo, se lograron propuestas novedosas alineadas en tres ejes fundamentales del proceso de desarrollo de fármacos: representaciones moleculares, modelado predictivo de bioactividad, y analítica visual aplicada a cribado virtual de fármacos. En materia de modelado predictivo de bioactividad, desarrollamos enfoques de modelado QSAR capaces de alcanzar rendimientos predictivos superiores a los previamente reportados para un gran número de propiedades de relevancia en el área, sin necesidad de realizar selección de características. Propusimos un enfoque de definición del dominio de aplicabilidad químico para dichos modelos eficaz en la determinación del rango de confiabilidad de las predicciones, y desarrollamos una estrategia para brindar interpretabilidad a modelos QSAR basados en redes neuronales. Además, experimentamos con aprendizaje profundo multi-tarea, logrando un enfoque pionero para el modelado de mutagenicidad de Ames, que permite el aprendizaje conjunto de información de diferentes blancos farmacológicos, superando en rendimiento a los resultados previamente publicados. En el área de representación molecular, desarrollamos un riguroso trabajo de investigación y análisis comparativo de diversas estrategias de representación molecular tradicionales y basadas en aprendizaje profundo. Propusimos un diseño experimental para la comparación y evaluación del desempeño de dichas representaciones en modelado QSAR, cuyos resultados evidenciaron la importancia de la selección cuidadosa de la representación elegida y proporcionan un marco de referencia para posteriores estudios similares. Por último, presentamos una herramienta integral de analítica visual para cribado virtual que integra diferentes fuentes de información química y representaciones moleculares complementarias. Esta herramienta interactiva demostró ser eficaz en la asistencia a expertxs de química medicinal para la exploración visual de patrones de similitud estructural en grandes conjuntos de datos químicos y para el diseño de nuevos compuestos candidatos. / The development of new drugs constitutes a fundamental research area in modern medicine. Beyond the rapid scientific advances in molecular informatics and biochemistry, which contribute to its continuous improvement, the investment in time and resources is extremely high, in contrast to its limited success rate. Computational strategies play a key role in optimizing and streamlining the multiple tasks involved in drug development, ranging from molecular representation and predictive modeling of bioactivity profiles, to virtual drug screening and the design of novel chemical structures. The goal of this thesis focused on the development and application of novel computational strategies based on deep learning to contribute to the optimization of the many stages involved in the drug discovery process. The contributions of this thesis stem from a critical and ongoing analysis of the state of the art in molecular informatics and involve the design of new strategies by applying recent concepts and developments in deep learning. As a result of this work, we achieved a series of innovative proposals which align to three fundamental cornerstones of the drug development process: molecular representation, predictive modeling of bioactivity profiles, and visual analytics applied to virtual drug screening. In the field of predictive bioactivity modeling, we developed QSAR modeling approaches that achieved higher predictive performances than those previously reported for numerous relevant biochemical properties, while at the same time overcoming the need for a feature selection step. We proposed an approach to define the chemical applicability domain for these models, effectively determining the reliability range of predictions, and developed a strategy to provide interpretability to QSAR models based on neural networks. Additionally, we experimented with multi-task deep learning, achieving a pioneering approach for modeling Ames mutagenicity that allows the joint learning of information from different pharmacological targets, which outperformed previously published results. In the field of molecular representation, we conducted a rigorous research and comparative analysis of various traditional and deep learning-based molecular representation strategies. We proposed an experimental design for the comparison and evaluation of the performance of these representations in QSAR modeling, and the results highlighted the importance of carefully selecting the molecular representation for each task, while also providing a reference framework for subsequent similar studies. Finally, we introduced a comprehensive visual analytics tool for virtual screening that integrates different sources of chemical information and complementary molecular representations. This interactive tool proved to be effective in assisting medicinal chemistry experts in visually exploring structural similarity patterns in large chemical datasets and in the design of new candidate compounds.

No / Decaprenylphosphoryl-b-d-ribose 20-epimerase (DprE1) is a potential drug target for development of antitubercular agents. Structure based drug discovery approach yielded twenty novel derivatives of benzothiazolylpyrimidine-5-carboxamides (7a–t) which were synthesised by three component one pot reaction involving benzothiazolyl oxobutanamide, thiourea and substituted aromatic benzaldehydes. These derivatives were evaluated for antitubercular activity to determine MIC and compound 7a, 7e, 7f and 7o were found to be potentially active against Mycobacterium tuberculosis (H37Rv). Log P of these compounds was found to be between 2.0 and 3.0 making them suitable for oral dosing. DprE1 selectivity and pharmacokinetic studies were carried out for these compounds of which 7a and 7o were found to be highly selective and bioavailability was found to be above 52% by oral dose. Crystal structure of 7a was studied and molecular packing was determined, it exhibited a triclinic crystal lattice arrangement having hydrogen bonded dimeric arrangement. Drug receptor interactions were studied which exhibited docking in the active site of receptor with hydrogen bonding, hydrophobic interactions, vdW interactions with amino acid residues such as Cys387, Asn385, Lys418, Tyr314, Gln334 and Lys367 respectively. 3D QSAR analysis was carried out by kNN-MFA method to determine and develop theoretical model, best suitable model was found to be based on Simulated Annealing k-Neariest Neighbour Molecular Field Analysis (SA kNN-MFA). The model provided with hydrophobic descriptors in positive side indicating the need of bulky groups, steric and electronegative descriptors in negative coordinates hints with contribution by the electronegative substitutions as favourable and desirable moieties for enhancing the activity. The q2, q2_se and Pred_r2se were found to be 0.5000, 0.6404 and 1.0094 respectively. A pharmacophore model was generated which suggested for necessity of aromatic, aliphatic carbon centre and hydrogen bond donor for development of newer DprE1 selective inhibitors. / Council of Scientific and Industrial Research

Nesta pesquisa, calculou-se, por meio da modelagem molecular, parâmetros físico-químicos importantes à capacidade anti-radicalar de compostos fenólicos extraídos de plantas da flora nacional, Chimarrhis turbinata e Arrabidaea samydoides. As propriedades eletrônicas também podem ser analisadas por meio de superfícies representadas por legendas de cores no campo 3D. Mapa de potencial eletrostático, distribuição orbitalar de HOMO e de LUMO e densidade de spin foram superfícies avaliadas neste trabalho. Em adição, estudos de QSAR (Quantitative Structure-Activity Relationships), cálculos de descritores moleculares holísticos por meio dos programas DRAGON e VOLSURF, cálculos estatísticos incluindo algoritmo genético e PLS (Partial Least Squares), demonstraram a influência de determinadas características moleculares como fundamentais à atividade biológica. A pesquisa concluiu que o grupo farmacofórico favorável à atividade antioxidante é estrutura que apresenta predominantemente características hidrofílicas, grupos hidroxila como substituintes, características eletrônicas favoráveis à doação de elétron e à estabilização do radical fenóxi formado, além de reduzido comprometimento estérico. Consideramos que os métodos empregados no trabalho podem ser considerados como abordagem inovadora para a Ciência Cosmética, indicando potencial ação antioxidante, que poderá ser utilizada em formulações antienvelhecimento. / In this research, the calculated physico-chemical parameters, by molecular modelling, have been reported in the literature for supplying important information about the antiradicalar behavior of phenolic compounds, as the studied herein from Chimarrhis turbinata sp. and Arrabidaea samydoides sp. The electronic properties also can be analyzed by means of surfaces represented by legends of colors in the 3D field. Map of electrostatic potential, HOMO and LUMO distribution orbitalar and spin density have been used in this work. In addition, QSAR studies (Quantitative Structure-Activity Relationships), calculations of holistic molecular descriptors by softwares DRAGON and VOLSURF, statistical analysis including genetic algorithm and PLS (Partial Least Squares), demonstrate the influence of the molecular structure in the biological activity. Therefore, pharmacofor favorable to the antioxidant activity structure that presents predominantly characteristic hydrophilic, groups hydroxyl as substituintes, electronic characteristics favorable to the donation of electron and the stabilization of the radical formed, besides reduced inibition esteric. These recent methods can be considered as an innovative approach for Cosmetic Science toward antioxidant action that could be used in antiaging products.

Doenças como malária, esquistossomose, filaríase linfática, dengue, leishmaniose e mal de Chagas são endêmicas em países tropicais. Referente ao período entre 1975 e 2004, apenas 1% dos 1.556 novos fármacos registrados foi destinado ao tratamento destas doenças. Somente a doença de Chagas possui aproximadamente 18 milhões de casos em todo mundo. Até o momento, a quimioterapia para o tratamento dessa antropozoonose constitui-se basicamente de dois fármacos, o nifurtimox, proscrito no Brasil, e o benznidazol. Estes fármacos, além de apresentarem vários efeitos colaterais, são pouco eficazes, o que dificulta a adesão dos pacientes ao tratamento. Diante da necessidade imediata de novos fármacos para o combate de tripanossomíase americana, estratégias de modificação molecular têm se mostrado como ferramenta promissora para obtenção de novos fármacos, geralmente inspirados na estrutura molecular de fármacos já conhecidos. A estratégia de modificação molecular permite aumentar as chances de sucesso no processo de descoberta de novos fármacos, reduzindo tempo e custo da pesquisa. Este trabalho teve como objetivo o planejamento, a síntese e a avaliação da atividade anti-T. cruzi e a identificação das propriedades físico-químicas que são responsáveis por modular a atividade anti-T. cruzi da série dos 2-[5-nitrotiofeno- 2-il]-3-acetil-5-[4-fenil-substituído]-2,3-diidro-1,3,4-oxadiazolinas, compostos com estrutura análoga à nifuroxazida, fármaco antimicrobiano que também apresenta atividade antiparasitária. O planejamento da série de compostos estudados foi realizado com base no diagrama de Craig. A obtenção dos derivados 1,3,4-oxadiazolínicos foi realizada em quatro etapas sintéticas: esterificação, amonólise, obtenção da base de Schiff e ciclização oxidativa. As estruturas planejadas foram confirmadas por RMN 1H e RMN 13C, enquanto a pureza foi avaliada pela faixa de fusão e de análise elementar de CHN. A atividade antiparasitária dos compostos foi determinada frente à cepa Y da forma epimastigota do T. cruzi e a concentração de parasitas foi quantificada através da absorbância em espectrofotômetro UV/Vis (λ = 580 nm). Os quinze compostos da série foram avaliados em 6 diferentes concentrações (3,75; 5; 7,5 ; 10; 15; 20 µM), sendo que somente o etoxi-derivado não foi mais ativo que o fármaco padrão, o benznidazol. Entre os compostos analisados identificaram-se o mais e o menos ativo da série, respectivamente: o 2-[5-nitro-tiofeno-2-il]-3-acetil-5-[4 fenil-acetoxi]-2,3-diidro-1,3,4-oxadiazolinas (IC50=7,91 µM) e o 2-[5-nitrotiofeno-2-il]-3-acetil-5-[4 fenil-etoxi]-2,3-diidro-1,3,4-oxadiazolinas ((IC50=26,60 µM). Através de estudos de QSAR-2D, a atividade anti-T. cruzi foi correlacionada com descritores físico-químicos, como a hidrofobicidade, os efeitos eletrônicos e o volume molecular. Com a aplicação de modelos matemáticos, ficou evidenciado que a atividade anti-T. cruzi desta série de compostos sofre notável influência da hidrofobicidade e dos efeitos eletrônico de ressonância, o que permite a continuidade deste trabalho através da variação planejada destas propriedades, visando identificar o análogo mais potente da série de compostos estudados. / Diseases like malaria, schistosomiasis, lymphatic filariasis, dengue, leishmaniasis and Chagas\'disease are endemic in tropical countries. From 1975 to 2004, only 1% of 1.556 new drugs were registered for the treatment of these diseases. Chagas disease itself has approximately 18 million of cases worldwide, and the chemotherapy for the treatment of this anthropozoonosis consists basically of two drugs, nifurtimox, which is prohibited in Brazil, and benznidazole. These drugs have various side effects and can also be ineffective, making patients give up the treatment. Given the immediate need for new drugs to treat american trypanosomiasis, molecular modification strategies have been shown as a promising tool for obtaining new drugs, often inspired by the molecular structure of known drugs. The strategy of molecular modification will increase the chances of success in the discovery process of new drugs, reducing the time and the costs of research. Given the situation above described, this work aims to design synthesis and evaluate the anti-Trypanosoma cruzi activity of new drugs as well as identification physicochemical properties that are responsible for modulating the anti-T. cruzi activity. Series of 2-[5-nitro-thiofen-2-yl]-3-acetyl-5-[4-phenyl-substituted]-2,3-dihydro-1,3,4-oxadiazolines, compounds with similar structure to nifuroxazide, an antimicrobial drug that also has antiparasitic activity. The planning of the series of compounds was carried out based on the Craig diagram. The obtainment of the1,3,4-oxadiazolinics derivatives was performed with four synthetic steps, as follows: esterification, ammonolysis, obtention of the Schiff base and oxidative cyclization. The designed structures were confirmed by 1H and 13C NMR and purity was assessed by melting point and elemental analysis of CHN. The antiparasitic activity of compounds was determined against the Y strain of T. cruzi in the epimastigote form and the concentration of parasites was quantified by absorbance in a spectrophotometer UV / Vis (λ = 580 nm). The fifteen compounds obtained were evaluated in six different concentrations (3.75, 5, 7.5, 10, 15, 20 µM), and only the ethoxy-derivative was less active than the standard drug, benznidazole. The 2-[5-nitrothiofen- 2-yl]-3-acetyl-5-[4-acetoxyphenyl]-2,3-dihydro-1,3,4-oxadiazolines (IC50=7.91µM) and of 2-[5-nitro-thiofen-2-yl]-3-acetyl-5-[4-etoxyphenyl]-2,3-dihydro-1,3,4-oxadiazolines (IC50=26.60 µM) derivatives were identified as the most and the least active of the series, respectively. Through 2D-QSAR studies, the anti-T. cruzi activity was correlated with physicochemical descriptors such as hydrophobicity, molecular volume and electronic effects. Applying mathematical models, it became evident that the activity of anti-T. cruzi activity in this series of compounds undergoes remarkable influence of hydrophobicity and electronic effects of resonance, which allows the continuity of the work planned by varying these properties to identify the most potent analogue among the series of compounds studied.

Doenças como malária, esquistossomose, filaríase linfática, dengue, leishmaniose e mal de Chagas são endêmicas em países tropicais. Referente ao período entre 1975 e 2004, apenas 1% dos 1.556 novos fármacos registrados foi destinado ao tratamento destas doenças. Somente a doença de Chagas possui aproximadamente 18 milhões de casos em todo mundo. Até o momento, a quimioterapia para o tratamento dessa antropozoonose constitui-se basicamente de dois fármacos, o nifurtimox, proscrito no Brasil, e o benznidazol. Estes fármacos, além de apresentarem vários efeitos colaterais, são pouco eficazes, o que dificulta a adesão dos pacientes ao tratamento. Diante da necessidade imediata de novos fármacos para o combate de tripanossomíase americana, estratégias de modificação molecular têm se mostrado como ferramenta promissora para obtenção de novos fármacos, geralmente inspirados na estrutura molecular de fármacos já conhecidos. A estratégia de modificação molecular permite aumentar as chances de sucesso no processo de descoberta de novos fármacos, reduzindo tempo e custo da pesquisa. Este trabalho teve como objetivo o planejamento, a síntese e a avaliação da atividade anti-T. cruzi e a identificação das propriedades físico-químicas que são responsáveis por modular a atividade anti-T. cruzi da série dos 2-[5-nitrotiofeno- 2-il]-3-acetil-5-[4-fenil-substituído]-2,3-diidro-1,3,4-oxadiazolinas, compostos com estrutura análoga à nifuroxazida, fármaco antimicrobiano que também apresenta atividade antiparasitária. O planejamento da série de compostos estudados foi realizado com base no diagrama de Craig. A obtenção dos derivados 1,3,4-oxadiazolínicos foi realizada em quatro etapas sintéticas: esterificação, amonólise, obtenção da base de Schiff e ciclização oxidativa. As estruturas planejadas foram confirmadas por RMN 1H e RMN 13C, enquanto a pureza foi avaliada pela faixa de fusão e de análise elementar de CHN. A atividade antiparasitária dos compostos foi determinada frente à cepa Y da forma epimastigota do T. cruzi e a concentração de parasitas foi quantificada através da absorbância em espectrofotômetro UV/Vis (λ = 580 nm). Os quinze compostos da série foram avaliados em 6 diferentes concentrações (3,75; 5; 7,5 ; 10; 15; 20 µM), sendo que somente o etoxi-derivado não foi mais ativo que o fármaco padrão, o benznidazol. Entre os compostos analisados identificaram-se o mais e o menos ativo da série, respectivamente: o 2-[5-nitro-tiofeno-2-il]-3-acetil-5-[4 fenil-acetoxi]-2,3-diidro-1,3,4-oxadiazolinas (IC50=7,91 µM) e o 2-[5-nitrotiofeno-2-il]-3-acetil-5-[4 fenil-etoxi]-2,3-diidro-1,3,4-oxadiazolinas ((IC50=26,60 µM). Através de estudos de QSAR-2D, a atividade anti-T. cruzi foi correlacionada com descritores físico-químicos, como a hidrofobicidade, os efeitos eletrônicos e o volume molecular. Com a aplicação de modelos matemáticos, ficou evidenciado que a atividade anti-T. cruzi desta série de compostos sofre notável influência da hidrofobicidade e dos efeitos eletrônico de ressonância, o que permite a continuidade deste trabalho através da variação planejada destas propriedades, visando identificar o análogo mais potente da série de compostos estudados. / Diseases like malaria, schistosomiasis, lymphatic filariasis, dengue, leishmaniasis and Chagas\'disease are endemic in tropical countries. From 1975 to 2004, only 1% of 1.556 new drugs were registered for the treatment of these diseases. Chagas disease itself has approximately 18 million of cases worldwide, and the chemotherapy for the treatment of this anthropozoonosis consists basically of two drugs, nifurtimox, which is prohibited in Brazil, and benznidazole. These drugs have various side effects and can also be ineffective, making patients give up the treatment. Given the immediate need for new drugs to treat american trypanosomiasis, molecular modification strategies have been shown as a promising tool for obtaining new drugs, often inspired by the molecular structure of known drugs. The strategy of molecular modification will increase the chances of success in the discovery process of new drugs, reducing the time and the costs of research. Given the situation above described, this work aims to design synthesis and evaluate the anti-Trypanosoma cruzi activity of new drugs as well as identification physicochemical properties that are responsible for modulating the anti-T. cruzi activity. Series of 2-[5-nitro-thiofen-2-yl]-3-acetyl-5-[4-phenyl-substituted]-2,3-dihydro-1,3,4-oxadiazolines, compounds with similar structure to nifuroxazide, an antimicrobial drug that also has antiparasitic activity. The planning of the series of compounds was carried out based on the Craig diagram. The obtainment of the1,3,4-oxadiazolinics derivatives was performed with four synthetic steps, as follows: esterification, ammonolysis, obtention of the Schiff base and oxidative cyclization. The designed structures were confirmed by 1H and 13C NMR and purity was assessed by melting point and elemental analysis of CHN. The antiparasitic activity of compounds was determined against the Y strain of T. cruzi in the epimastigote form and the concentration of parasites was quantified by absorbance in a spectrophotometer UV / Vis (λ = 580 nm). The fifteen compounds obtained were evaluated in six different concentrations (3.75, 5, 7.5, 10, 15, 20 µM), and only the ethoxy-derivative was less active than the standard drug, benznidazole. The 2-[5-nitrothiofen- 2-yl]-3-acetyl-5-[4-acetoxyphenyl]-2,3-dihydro-1,3,4-oxadiazolines (IC50=7.91µM) and of 2-[5-nitro-thiofen-2-yl]-3-acetyl-5-[4-etoxyphenyl]-2,3-dihydro-1,3,4-oxadiazolines (IC50=26.60 µM) derivatives were identified as the most and the least active of the series, respectively. Through 2D-QSAR studies, the anti-T. cruzi activity was correlated with physicochemical descriptors such as hydrophobicity, molecular volume and electronic effects. Applying mathematical models, it became evident that the activity of anti-T. cruzi activity in this series of compounds undergoes remarkable influence of hydrophobicity and electronic effects of resonance, which allows the continuity of the work planned by varying these properties to identify the most potent analogue among the series of compounds studied.

Les antalgiques utilisés aujourd’hui sont des produits anciens et plusieurs d’entre eux datent du 19ème siècle. La morphine demeure l’antalgique de référence pour les douleurs dites par excès de nociception, mais elle est à l’origine d’effets indésirables gênants et graves. Il a été démontré que l’effet antalgique de la morphine passait par l’activation des canaux potassiques TREK-1. Les travaux de recherche ont donc comme objectif la recherche d’antalgiques originaux activateurs de TREK-1. Nous avons synthétisé des activateurs de TREK-1 décrits dans la littérature puis nous avons évalué leur activité antalgique in vivo (writhing test) ce qui nous a permis d’identifier le CDC comme molécule « lead ». Nous avons ensuite synthétisé 43 analogues du CDC que nous avons évalué pour leur effet antalgique ainsi que leur capacité à activer les canaux TREK-1 (électrophysiologie). Ces molécules ont été préparées en 3 à 12 étapes avec des rendements de 3 à 72 % en utilisant des réactions telles que : aldolisation, oléfination de Watsworth et Horner, Peterson, estérification …Des résultats très prometteurs ont émergé de cette étude de relation structure-activité avec 8 molécules qui se démarquent avec un très bon effet antalgique (>50% inhibition de la douleur) ainsi qu’une bonne activation des canaux TREK-1 (R>2). Enfin nous avons analysé les résultats de cette étude par modélisation moléculaire (QSAR) ce qui nous a permis d’identifier les caractéristiques structurales essentielles de ces molécules. / Analgesics used today are old products and several of them date from the 19th century. Morphine remains the analgesics of reference for pains called by excess of nociception, but it is at the origin of awkward and serious side effects. It was shown that the analgesic effect of morphine passed by the activation of potassium channels TREK-1. The objective of this work is thus to develop original analgesics, activators of TREK-1. We synthesized activators of TREK-1 described in the literature and we evaluated their analgesic activity in vivo (writhing test) which enabled us to identify CDC as a lead molecule. We then synthesized 43 analogues of CDC which we evaluated for their analgesic effect and their ability to activate TREK-1 channels (electrophysiology). These molecules were prepared in 3 to 12 steps with yields ranging from 3 to 72 % by using reactions such as : aldol reaction, Watsworth and Horner’s olefination, Peterson’s olefination, esterification … Very promising results emerged from this structure-activity relationship study with 8 molecules which display a very good analgesic effect (>50% inhibition of pain) as well as a good activation of TREK-1 channels (R> 2). Finally we analyzed the results of this study by molecular modeling (QSAR) which enabled us to identify the essential structural characteristics of these molecules.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-06-12T15:19:44Z No. of bitstreams: 2 Dissertação - Vinicius de Medeiros Alves - 2014.pdf: 3082084 bytes, checksum: da4838d5fe24841429f43de84204d98a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-06-12T15:21:40Z (GMT) No. of bitstreams: 2 Dissertação - Vinicius de Medeiros Alves - 2014.pdf: 3082084 bytes, checksum: da4838d5fe24841429f43de84204d98a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-06-12T15:21:40Z (GMT). No. of bitstreams: 2 Dissertação - Vinicius de Medeiros Alves - 2014.pdf: 3082084 bytes, checksum: da4838d5fe24841429f43de84204d98a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-05-12 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Introduction: Skin sensitization is a major environmental and human health hazard. Although many chemicals have been evaluated in humans, there have been no efforts to model these data to date. Skin sensitization is commonly evaluated using structural alerts. However, there has been a growing concern that alerts disproportionally flag too many chemicals as toxic, which questions their reliability as toxicity markers. The main goal of this thesis was to develop and apply new cheminformatics methods to predict skin sensitization of chemical compounds that lack experimental data. Methodology: It has been compiled, curated, analyzed, and compared the available human data and the murine (performed in mice) animal model data, named LLNA (local lymph node assay). Using these data, it was developed reliable computational models and applied them for virtual screening of chemical libraries to identify putative skin sensitizers. It was developed a freely accessible web-based application for the identification of potential skin sensitizers. In addition, it was demonstrated that contrary to the common perception of QSAR models as “black boxes” they can be used to identify statistically significant chemical substructures (QSAR-based alerts) that influence toxicity. Results and discussion: The overall concordance between murine LLNA and human skin sensitization responses for a set of 135 unique chemicals was low (R = 28-43%), although several chemical classes had high concordance. We have succeeded to develop predictive QSAR models of all available human data with the external correct classification rate of 71%. A consensus model integrating concordant QSAR predictions and LLNA results afforded a higher correct classification rate of 82% but at the expense of the reduced external dataset coverage (52 %). We used the developed QSAR models for virtual screening of CosIng database and identified 1,061 putative skin sensitizers; for seventeen of these compounds, we found published evidence of their skin sensitization effects. The developed Pred-Skin web app (http://www.labmol.com.br/predskin/) is based on binary QSAR models of human (109 compounds) and LLNA (515 compounds) data with good external correct classification rate (70-81% and 72-84%, respectively). It is also included a multiclass potency model based on LLNA data (accuracy ranging between 73-76%). Conclusions: Models reported herein provide more accurate alternative to LLNA testing for human skin sensitization assessment across diverse chemical data. In addition, they can also be used to guide the structural optimization of toxic compounds to reduce their skin sensitization potential. The Pred-Skin web app is a fast, reliable, and user-friendly tool for early assessment of chemically-induced skin sensitization. A new approach that synergistically integrates structural alerts and rigorously validated QSAR models for a more transparent and accurate safety assessment of new chemicals was also proposed. / Introdução: A sensibilização cutânea é um importante parâmetro de avaliação de toxicidade humana e ambiental. Embora muitos compostos tenham sido avaliados em seres humanos, não foi reportado até o momento modelos de QSAR (do inglês, quantitative structure-activity relationships) gerados com esses dados. Comumente, a sensibilização cutânea é avaliada computacionalmente usando-se alertas estruturais. No entanto, tem havido uma preocupação crescente de que alertas sinalizam a maioria dos compostos como tóxicos, o que questiona sua confiabilidade como marcadores de toxicidade. O objetivo geral do presente trabalho foi desenvolver e aplicar novos métodos de quimioinformática para predizer a sensibilização cutânea de compostos químicos que carecem de dados experimentais. Metodologia: Foram compilados, preparados, analisados e comparados os dados de sensibilização cutânea de pele humana e do modelo animal murino (realizado em camundongos), denominado LLNA (local lymph node assay). Modelos de QSAR foram desenvolvidos utilizando esses dados e aplicados para a triagem de quimiotecas virtuais para identificar potenciais sensibilizadores. Foi desenvolvido um aplicativo gratuito para a identificação de potenciais sensibilizadores cutâneos. Além disso, foi demonstrado que modelos de QSAR podem ser usados para identificar subestruturas químicas estatisticamente significativas (alertas estruturais baseados em QSAR) que influenciam a toxicidade. Resultados e discussão: A concordância global (R) entre respostas de sensibilização cutânea humana e murina para um conjunto de 135 substâncias químicas únicas foi baixa (R = 28-43%), embora várias classes químicas apresentassem alta concordância. Foi possível desenvolver modelos de QSAR preditivos com taxa de classificação correta externa de 71%. Um modelo de consenso que integrava predições concordantes de QSAR e dados de LLNA proporcionaram uma acurácia 82%. Utilizou-se os modelos de QSAR desenvolvidos para a triagem virtual da base de dados CosIng e foram identificados 1061 potenciais sensibilizadores cutâneos. Para dezessete desses compostos, encontrou-se evidências publicadas de seus efeitos de sensibilização cutânea em seres humanos. O aplicativo desenvolvido, Pred-Skin (http://www.labmol.com.br/predskin/), baseia-se em modelos de QSAR classificatórios de dados humanos (109 compostos) e murinos (515 compostos) com boa taxa de classificação correta externa (70-81% e 72-84%, respectivamente). Esse aplicativo também possui um modelo de multiclassificatório desenvolvido com dados de LLNA (precisão que varia entre 73-76%). Conclusões: Os modelos de QSAR desenvolvidos forneceram uma alternativa mais precisa do que o modelo animal para avaliação da sensibilização cutânea humana. Além disso, a interpretação dos modelos de QSAR permitem orientar a otimização estrutural de compostos tóxicos para reduzir o potencial de toxicidade. O aplicativo Pred-Skin é uma ferramenta rápida, confiável e de fácil utilização para a avaliação da sensibilização cutânea de compostos químicos. Foi também proposta uma nova abordagem que integra sinergicamente alertas estruturais e modelos de QSAR rigorosamente validados para uma avaliação de toxicidade mais transparente e precisa de novos produtos químicos.

Nesta pesquisa, calculou-se, por meio da modelagem molecular, parâmetros físico-químicos importantes à capacidade anti-radicalar de compostos fenólicos extraídos de plantas da flora nacional, Chimarrhis turbinata e Arrabidaea samydoides. As propriedades eletrônicas também podem ser analisadas por meio de superfícies representadas por legendas de cores no campo 3D. Mapa de potencial eletrostático, distribuição orbitalar de HOMO e de LUMO e densidade de spin foram superfícies avaliadas neste trabalho. Em adição, estudos de QSAR (Quantitative Structure-Activity Relationships), cálculos de descritores moleculares holísticos por meio dos programas DRAGON e VOLSURF, cálculos estatísticos incluindo algoritmo genético e PLS (Partial Least Squares), demonstraram a influência de determinadas características moleculares como fundamentais à atividade biológica. A pesquisa concluiu que o grupo farmacofórico favorável à atividade antioxidante é estrutura que apresenta predominantemente características hidrofílicas, grupos hidroxila como substituintes, características eletrônicas favoráveis à doação de elétron e à estabilização do radical fenóxi formado, além de reduzido comprometimento estérico. Consideramos que os métodos empregados no trabalho podem ser considerados como abordagem inovadora para a Ciência Cosmética, indicando potencial ação antioxidante, que poderá ser utilizada em formulações antienvelhecimento. / In this research, the calculated physico-chemical parameters, by molecular modelling, have been reported in the literature for supplying important information about the antiradicalar behavior of phenolic compounds, as the studied herein from Chimarrhis turbinata sp. and Arrabidaea samydoides sp. The electronic properties also can be analyzed by means of surfaces represented by legends of colors in the 3D field. Map of electrostatic potential, HOMO and LUMO distribution orbitalar and spin density have been used in this work. In addition, QSAR studies (Quantitative Structure-Activity Relationships), calculations of holistic molecular descriptors by softwares DRAGON and VOLSURF, statistical analysis including genetic algorithm and PLS (Partial Least Squares), demonstrate the influence of the molecular structure in the biological activity. Therefore, pharmacofor favorable to the antioxidant activity structure that presents predominantly characteristic hydrophilic, groups hydroxyl as substituintes, electronic characteristics favorable to the donation of electron and the stabilization of the radical formed, besides reduced inibition esteric. These recent methods can be considered as an innovative approach for Cosmetic Science toward antioxidant action that could be used in antiaging products.

Une approche intégrée physicochimie et relations structure-activité a été mise en œuvre afin d’étudier le phénomène rétention-libération des composés d’arôme dans un gel laitier allégé additionné de pectine. Notre objectif était d’identifier les propriétés moléculaires qui régissent ce phénomène en supposant que la modification de la structure entraîne forcement un changement dans la rétention-libération des composés d’arôme. Dans ce but, nous avons déterminé les coefficients de partage de 28 composés d’arôme dans l’eau, dans des gels de pectine et dans des gels laitiers avec ou sans de pectine, à l’équilibre en utilisant la méthode PRV (Phase Ratio Variation). Nous avons ensuite effectué une étude des relations structure-rétention en évaluant les corrélations entre les coefficients de partage et quatre descripteurs traduisant quatre propriétés moléculaires : l’hydrophobie globale, la surface moléculaire, la polarisabilité et la densité de charge négative. Notre démarche d’étude des relations structure-activité (Structure-Activity Relationships, SAR) consistait à étudier des composés d’arôme appartenant à une gamme de structures variée, dans un même ensemble, puis en sous-groupes en fonction d’une particularité structurale donnée afin de révéler les particularités de la structure qui influent sur le phénomène rétention-libération. La comparaison des rétentions entre les milieux n’a pas montré l’existence d’un effet pectine. Les études des relations structure-activité ont montré l’impact de certaines particularités structurales telles que la ramification et la double liaison sur la rétention. Elles ont également montré que l’hydrophobie globale des molécules n’était pas la propriété moléculaire la plus à même d’expliquer les phénomènes impliqués dans les interactions de molécules odorantes avec les constituants du milieu (eau ou gel laitier). La surface et la polarisabilité rendent mieux compte des rétentions des composés d’arôme. Les corrélations impliquant la surface, la polarisabilité et l’hydrophobie globale, confirment que les interactions de type van der Waals (essentiellement Keesom et London) sont favorables à la rétention dans les gels laitiers et défavorables à la rétention dans l’eau. De même, les corrélations impliquant la densité de charge montrent que les interactions polaires sont favorables à la rétention dans l’eau. Notre choix de départ, qui consistait à faire varier la structure des composés d’arôme afin d’apprécier son effet sur le phénomène rétention-libération des composés d’arôme, s’est avéré concluant, et le groupe de 28 composés permet effectivement de mener une étude quantitative des relations structure-propriété. Cette démarche QSAR pourra se transposer à des systèmes alimentaires simples ou complexes. / An integrated approach physicochemistry and structures activity relationships has been carried out to study the aroma compounds retention-release phenomenon in a fat free dairy gel added with pectin. This study aimed to identify the molecular properties that govern this phenomenon assuming that modifying the structure leads automatically to a change in the retention-release of aroma compounds. For this purpose, we have determined the partition coefficients of 28 aroma compounds in water, in pectin gels and in dairy gels supplemented or not supplemented with pectin, at equilibrium conditions using the PRV method (Phase Ratio Variation). Then, we have performed a structure-retention relationships study for the aroma compounds by estimating correlations between the partition coefficients and four descriptors representing four molecular properties: Global hydrophobicity, molecular area, polarizability and negative charge density. Our methodology concerning the structure-activity relationships study (SAR) consisted on studying a varied range of aroma compounds in terms of molecular structure, first taking into account all of them in the same set, then in separated subgroups according to a given structural particularity in order to reveal which structural particularities control the retention-release phenomenon. The comparison of retention between the several media has not shown any effect of pectin. Structure-activity relationships studies have shown the impact of some structural particularities like branching and double linking. They have also shown that the global hydrophobicity was not the best molecular property to explain the phenomena involved in the interactions between aroma compounds and matrix components (water and dairy gel). Molecular area and polarizability are more likely to report of aroma retention-release. Correlations implying molecular area, polarizability or global hydrophobicity confirm that van der Waals (especially Keesom and London) are involved in the retention in dairy gels and unfavourable in the retention in water. Correlations implying negative charge density show that polar interactions are favourable in the retention in water as well. Our strategy which consisted on varying the structure of aroma compounds to exanimate its effect on the retention-release phenomenon was found to be effective, and the set of 28 aroma compounds allowed as leading a quantitative structure-property relationships study. This QSAR approach can be transposed to simple or complex food systems.