SIRT1 and SIRT2 are two NAD⁺-dependent deacetylases which negatively modulate the activity of p53, a protein which is involved in cell cycle arrest, senescence and apoptosis following genotoxic stress. Part I of the thesis describes the exploration of the chemical space around a reported unselective and modest inhibitor of SIRT1 and SIRT2 with the aim of improving the selectivity and potency of the inhibitor against the two isoforms. Particular emphasis is placed upon understanding the mode of binding of the novel analogues within the active site of the enzymes. Chapter 1 reviews the physiological roles of class III NAD⁺-dependent deacetylases, also known as sirtuins. In particular, the application of SIRT1 and SIRT2 inhibitors as potential anticancer agents is described. Amongst these, only cambinol and the tenovins showed in vivo activity in a mouse xenograft model. Previously only one analogue of cambinol had been reported in the literature. Chapter 2 describes the development of a small collection of novel cambinol analogues (First Generation Studies). The role played by different substituents at the phenyl group and at the N-1 of the thiouracil core is discussed. Along with the synthesis and structure activity relationship (SAR) associated with the core structure, in-cell experiments intended to confirm the activity of the most active compounds are reported. Chapter 3 provides a rationalisation for the SAR discussed in Chapter 2. Based on computational molecular modelling studies (GOLD), the activity of the most potent and selective SIRT2 inhibitors is explained. Two series of novel cambinol analogues were designed (Second and Third Generation Analogues) in order to assess further the proposed binding mode. Chapter 4 focuses on the development of the “Second Generation” analogues, characterised by the presence of lipophilic substituents at the sulfur atom and at the N-3 position of the thiouracil core. The synthesis, biological evaluation and SAR are discussed in detail. Chapter 5 reports the development of the “Third Generation” analogues, characterised by either a benzyl group or para-alkoxy-substituted benzyl group at the N-1 position of cambinol. Once again, the synthesis, biological evaluation and SAR data are presented. An improved understanding of the mode of binding of the novel compounds is proposed based on molecular dynamics (MD) studies. Indole-based alkaloids, such as Vincristine and Vinblastine, are well known for their anticancer activity. Recently, the anticancer activity of members of the calycanthaceous family of alkaloids has been discovered. Part II of the thesis focuses on model studies aimed at developing the total synthesis of one of these compounds, perophoramidine. Chapter 7 provides an overview of the calycanthaceous alkaloid family of natural products, including their biological properties. The structural features of perophoramidine, along with the previously reported synthetic studies are outlined. Chapter 8 describes the synthesis of an advanced intermediate in the total synthesis of dehaloperophoramidine, a structural analogue of perophoramidine Problems encountered, optimisation studies and the synthesis of a re-designed intermediate are also reported in this chapter.

Natural products provide some of the most potent anticancer agents and offer a template for new drug design or improvement with the advantage of an enormous chemical space. The overall goal of this thesis research is to enhance the chemical space of two natural products in order to generate novel drugs with better in vivo bioactivities than the original natural products. Polycarcin V (PV) is a gilvocarcin-type antitumor agent with similar structure and comparable bioactivity with the principle compound of this group, gilvocarcin V (GV). Modest modifications of the polyketide-derived tetracyclic core of GV had been accomplished, but the most challenging part was to modify the sugar moiety. In order to solve this problem, PV was used as an alternative lead-structure for modification because its sugar moiety offered the possibility of enzymatic O-methylation. We produced four PV derivatives with different methylation patterns for cytotoxicity assays and provided important structure-activity-relationship information. Mithramycin (MTM) is the most prominent member of the aureolic acid type anticancer agents. Previous work in our laboratory generated three MTM analogues, MTM SA, MTM SK, and MTM SDK by inactivating the mtmW gene. We developed new MTM analogues by coupling many natural and unnatural amino acids to the C-3 side chain of MTM SA via chemical semi-synthesis and successfully made some compounds with both improved bioactivity and in vivo tolerance than MTM. Some of them were consequently identified as promising lead-structures against Ewing’s sarcoma. The potential of selectively generating novel MTM analogues led us to focus on a key enzyme in the biosynthetic pathway of mithramycin, MtmC. This protein is a bifunctional enzyme involved in the biosynthesis of TDP-D-olivose and TDP-D-mycarose. We clarified its enzymatic mechanisms by X-ray diffraction of several crystal complexes of MtmC with its biologically relevant ligands. Two more important post-PKS tailoring enzymes involved in the biosynthesis of the MTM side chains, MtmW and MtmGIV, are currently under investigation. This would not only give us insight into this biosynthetic pathway but also pave the way to develop potentially useful MTM analogues by engineered enzymes.

Chapter 1 gives an overview of the fluorine chemistry field, from its early developments to recent applications in medicinal chemistry. The development of asymmetric electrophilic or nucleophilic installation of fluorine in organic molecules is highlighten. Chapter 2 of this thesis discusses the enantioselective synthesis of α-fluoroamides. The study is applied to the synthesis of fluoroenantiomers of the bioactive molecule capsaicin and short-chain analogues. The biological activity of these compounds is assayed with the TRPV1 receptor. Results show that enantioselective α-fluoroamides (R)-97, (R)-99 and (S)-99 can generate differentiated biological responses, from TRPV1 agonists to TRPV1 antagonists. Chapter 3 focuses on the optimisation and development of 2-(aminomethyl)piperidine (R)-251 dihydrochloride. The development of 2-(aminomethyl)piperidine (R)-251 as its ditetrafluoroborate salt proved to offer excellent reactivity and solubility for the preparation of derivatives. This tetrafluoroborate salt was used to improve the syntheses of organocatalysts 2,2,2-trifluoro-N-(piperidin-2-ylmethyl)acetamide 363 and 4-methyl-N-(piperidin-2-ylmethyl)benzenesulfonamide 364.The catalytic properties of these latter two molecules for asymmetric Mannich reaction is demonstrated. Both (R)-363 and (R)-364 show up to 86% ee, in a typical 20 mol% loading, but loading of (R)-363 as low as 5 mol% still induces the catalysis.

In the work presented this thesis, two different conditions that are classified as protein misfolding diseases: Alzheimer's disease and lysozyme amyloidosis and proteins that could have a beneficial effect in these diseases, have been studied using Drosophila melanogaster, commonly known as the fruit fly. The fruit fly has been used for over 100 years to study and better understand fundamental biological processes. Although the fruit fly, unlike humans, is an invertebrate, many of its central biological mechanisms are very similar to ours. The first transgenic flies were designed in the early 1980s, and since then, the fruit fly has been one of the most widely used model organisms in studies on the effects of over-expressed human proteins in a biological system; one can regard the fly as a living, biological test tube. For  most proteins, it is necessary that they fold into a three-dimensional structure to function properly. But sometimes the folding goes wrong; this may be due to mutations that make the protein unstable and subject to misfolding. A misfolded protein molecule can then aggregate with other misfolded proteins. In Alzheimer's disease, which is the most common form of dementia, protein aggregates are present in the brains of patients. These aggregates are composed of the amyloid-β (Aβ) peptide, a small peptide of around 42 amino acids which is cleaved from the larger, membrane-bound, protein AβPP by two different enzymes, BACE1 and γ-secretase. In the first part of this thesis, two different fly models for Alzheimer’s disease were used: the Aβ fly model, which directly expresses the Aβ peptide, and the AβPP-BACE1 fly model, in which all the components necessary to produce the Aβ peptide in the fly are expressed in the fly central nervous system (CNS). The two different fly models were compared and the results show that a significantly smaller amount of the Aβ peptide is needed to achieve the same, or an even greater, toxic effect in the AβPP-BACE1 model compared to the Aβ model. In the second part of the thesis, these two fly models for Alzheimer’s disease were again used, but now to investigate whether lysozyme, a protein involved in our innate immune system, can counteract the toxic effect of Aβ generated in the fly models. And indeed, lysozyme is able to save the flies from Aβ-induced toxicity. Aβ and lysozyme were found to interact with each other in vivo. The second misfolding disease studied in this thesis is lysozyme amyloidosis. It is a rare, dominantly inherited amyloid disease in which mutant variants of lysozyme give rise to aggregates, weighing up to several kilograms, that accumulate around the kidneys and liver, eventually leading to organ failure. In the third part of this thesis, a fly model for lysozyme amyloidosis was used to study the effect of co-expressing the serum amyloid P component (SAP), a protein that is part of all protein aggregates found within this disease class. SAP is able to rescue the toxicity induced by expressing the mutant variant of lysozyme, F57I, in the fly's CNS. To further investigate how SAP was able to do this, double-expressing lysozyme flies, which exhibit stronger disease phenotypes than those of the single-expressing lysozyme flies previously studied, were used in the fourth part of this thesis. SAP was observed to reduce F57I toxicity and promote F57I to form aggregates with more distinct amyloid characteristics. In conclusion, the work included in this thesis demonstrates that: i) Aβ generated from AβPP processing in the fly CNS results in higher proteotoxicity compared with direct expression of Aβ from the transgene, ii) lysozyme can prevent Aβ proteotoxicity in Drosophila and could thus be a potential therapeutic molecule to treat Alzheimer’s disease and iii) in a Drosophila model of lysozyme amyloidosis, SAP can prevent toxicity from the disease-associated lysozyme variant F57I and promote formation of aggregated lysozyme morphotypes with amyloid properties; this is important to take into account when a reduced level of SAP is considered as a treatment strategy for lysozyme amyloidosis.

Ebselen (Ebs) is considered as a glutathione peroxidase (GPx) mimetic and primarily thought to function by scavenging intracellular reactive oxygen species (ROS). Previous to our work, Deng et al. (2010a) demonstrated complete block of ICl,swell with 15 microM Ebs following endothelin-1 (ET-1) induced activation of the current in cardiomyocytes. This block was presumed to take effect mainly via the quenching of ROS. Nonetheless, our work with DI TNC1 astrocytes strongly emphasizes that Ebs might function by an alternative mechanism based on its kinetic profile in blocking ICl,swell. Our experiments showed that 45 nM Ebs can fully block ICl,swell thus suggesting an apparent IC50 result, we predicted Ebs to possess a high kon with a low koff close to zero. As predicted, Ebs failed to washout in the timescale covered by our patch-clamp experiments. The block was also distal to H2O2, previously considered as the most proximate regulator of ICl,swell. And based on further evidence demonstrating irreversible block of ICl,swell distal to H2O2 with Ebs congeners, complete suppression of native ICl,swell with MTS reagents, and failure of Ebs to block ICl,swell from the cytosol, we concluded that Ebs and its congeners can covalently modify important –SH groups required for current activation while functioning as sulfhydryl reagents. Complete irreversible block of ICl,swell with 110 mM cell impermeant MTSES in native DI TNC1 astrocytes contrasts sharply to SWELL1 (Qiu et al., 2014) or LRRC8A (Voss et al., 2014), the latest molecular entity presumably responsible for ICl,swell, where 3.33 mM MTSES failed to demonstrate block of ICl,swell in the wild-type stably expressing SWELL1 (Qiu et al., 2014). Our data with Ebs, its congeners, and MTS reagents indicate the existence of a common extracellular binding site which involves a selenenylsulfide (Se-S) bond that critically modulates ICl,swell. We, therefore, synthesized a derivative of Ebs called ebselen-para-yne (Ebs-p-yne), which provided an even higher affinity for blocking ICl,swell with a presumed IC50 ~picomolar range. Ebs-p-yne is a promising novel molecule that may serve as a tag in identifying the molecular fingerprint ultimately responsible for ICl,swell. Furthermore, we can take advantage of click chemistry to ultimately pull out the channel or channel component which has remained elusive for greater than two decades.

Dans le cadre d’un programme de recherche dédié à la découverte de petites molécules à visée anticancéreuse, nous avons envisagé de concevoir des composés originaux dérivés de quinones. Notre premier objectif a été d’élaborer des mimes non-peptidiques de la protéine Smac, susceptibles de participer à relancer le phénomène d’apoptose, dont la structure est rigidifiée par des contraintes conformationnelles. Par ailleurs, les kinases et les phosphatases, jouant des rôles complémentaires de phosphorylation / déphosphorylation dans le cadre du contrôle du cycle cellulaire notamment, apparaissent aussi comme des cibles intéressantes. Une étude attentive de leurs inhibiteurs connus nous a permis de mettre en avant des analogies structurales qui nous ont conduit à vouloir synthétiser des motifs fonctionnalisés de dérivés de naphtoquinones.L’introduction directe de chaînes latérales aliphatiques sur nos substrats, par création de liaisons de type C(sp2)–C(sp3), a été rendue possible grâce au développement d’une méthodologie de décarboxylation radicalaire. Dans les conditions réactionnelles mises au point, le couple Ag(I)/S2O82- est utilisé comme initiateur radicalaire et autorise la génération de radicaux alkyles par décarboxylation d’acides aminés. L’introduction directe de cycles aromatiques fonctionnalisés, via la création de liaisons de type C(sp2)–C(sp2), a été réalisée par l’intermédiaire de la génération de radicaux aryles issus de sels de diazonium stables ou d’anilines. Les procédés décrits dans ce manuscrit nous ont permis d’apporter certains éclaircissements sur la réactivité des substrats et sur les mécanismes réactionnels impliqués. / In our ongoing course dedicated to the discovery of small anticancer molecules, we designed novel quinone derivatives. Our first objective was to fashion non-peptidic Smac mimics, able to trigger apoptosis in tumor cells, displaying a structure rigidified by conformational restrictions. Otherwise, the kinases and the phosphatases, acting as phosphorylating / dephosphorylating agents mostly in the control of the cell cycle, were thought to be other relevant biological targets. An intent study of their known inhibitors allowed us to underline trends in their chemical structure and made us plan the synthesis of functionalized naphthoquinones.A dedicated approach involving radical decarboxylation of amino acids allowed the introduction of aliphatic side chains on our substrates though C(sp2)–C(sp3) bond formation. Ag(I)/S2O82- was used as alkyl radical initiator and the direct C-H alkylation of the quinonic positions could take place. C(sp2)–C(sp2) bonds were created through aryl radicals generation from stable diazonium salts or anilines which allowed the direct C-H arylation of quinones. The procedures described along this manuscript let us formulate several advances on the substrates reactivity and on the reaction mechanisms involved.

Dans la première partie nous décrivons la synthèse et l'évaluation biologique de nouveaux inhibiteurs de l'agrégation plaquettaire, composés dont la structure a été établie en partant du 12-HETE et du 13-HODE. Dans la seconde partie nous développons de nouvelles méthodologies pour la préparation de molécules contenant des motifs CF₂R. Tout d'abord une stratégie très flexible a été mise au point pour la préparation de composés gem-difluorobisaryliques et de leurs analogues hétéroaromatiques. Elle est basée sur l'emploi d'intermédiaires gem-difluoropropargyliques faciles d'accès. Par une séquence de Diels-alder-aromatisation on obtient les molécules cibles de la première série. Pour la seconde, des réactions de cycloaddition dipolaire 1,3 ont été utilisées. A partir de ces intermédiaires, des chimiothèques ciblées de molécules fluorées ont été préparées. Nous nous sommes intéressés ensuite à la synthèse de composés fluorés fonctionnalisés et chiraux à travers des réactions d'organocatalyse asymétrique. A partir d'énals gem-difluorés des réactions de Diels-Alder et des additions 1,4 asymétriques ont été réalisées avec succès. / The first part of the thesis deals with the synthesis and biological evaluation of new platelets aggregation inhibitors, based on 12-HETE, 13-HODE and their analogues. In the second part we are interested in novel methodologies for the preparation of CF₂-containing molecules : First, a flexible strategy for the synthesis of gem-difluoro-bisarylic derivatives and heteroaromatic analogues was designed based on the easy synthesis and the reactivity of gem-difluoro propargylic intermediates, which by Diels-Alder cycloaddition and 1,3-dipolar cycloadditions afforded respectively the bisarylic and mixed arylic heteroarylic scaffolds. In addition, two small libraries were constructed around a bisarylic scaffold as representative examples. Second, we were interested in the synthesis of optically active functionalized molecules containing a gem-difluoro group, using asymmetric organocatalysis protocols. After preparation of the gem-difluoro enals, from their difluoropropargylic precursors, asymmetric organocalytic Diels-Alder cycloaddition and 1,4-conjugated additions were successfully performed.

Les travaux présentés dans ce manuscrit ont pour objectifs la synthèse chimique de nouveaux ligands de la protéine de translocation 18 kDa (TSPO), leur évaluation in vitro et le radiomarquage isotopique des candidats les plus prometteurs par l’émetteur de positons à vie brève fluor-18 (t1/2 : 109,8 minutes). Ce travail a pour finalité le développement de nouvelles sondes moléculaires ou biomarqueurs pour l’imagerie non-invasive et atraumatique par Tomographie par Emission de Positons (TEP) de la neuroinflammation, processus reconnu dans les maladies neurodégénératives telles la maladie d’Alzheimer, de Parkinson, la sclérose en plaque et certaines maladies psychiatriques.Le radioligand de choix pour l’imagerie de la TSPO est actuellement le [18F]DPA-714, une pyrazolo[1,5-a]pyrimidine marquée au fluor-18 récemment développée au laboratoire. Cependant, cette molécule subit in vivo la perte rapide de l’atome de fluor radioactif par rupture du motif fluoroalkoxy comme démontrée lors de l’étude de son métabolisme. Mon projet de thèse a donc visé à concevoir et développer de nouveaux dérivés structurellement proches de DPA-714 (analogues) pour lesquelles la liaison entre le squelette principal et le fluor-18 serait renforcée. C’est dans ce cadre que dix-neuf composés ont été préparés et évalués pour leur affinité pour la TSPO, et que deux candidats prometteurs, DPA-C5yne et CfO-DPA-714, ont été radiomarqués au fluor-18 avec de bons rendements radiochimiques (20-30 %) et de hautes radioactivités spécifiques (50-90 GBq/µmol). Ces radioligands ont également été évalués in vivo par imagerie TEP et présentent, chez l’animal, des performances équivalentes voire légèrement supérieures à [18F]DPA-714. / The work presented in this manuscript aims to describe the synthesis of new ligands of the translocation protein 18 kDa (TSPO), their in vitro evaluation and, for the most promising candidates, their isotopic radiolabelling with the short-lived positron emitter fluorine-18 (t1/2 : 109.8 minutes). The ultimate goal of this work consists in developing new molecular probes, or biomarkers, for imaging neuroinflammation in a non-invasive and atraumatic manor using Positron Emission Tomography (PET). Neuroinflammatory processes have been identified in Alzheimer and Parkinson diseases, MS and various psychiatric pathologies.The radioligand of choice for imaging TSPO is currently [18F]DPA-714, a pyrazolo[1,5-a]pyrimidine radiolabelled with fluorine-18 which has been recently prepared in our laboratories. However, [18F]DPA-714 undergoes a rapid in vivo loss of the radioactive fluorine by cleavage of the fluoroalkoxy chain as demonstrated in metabolic studies. Therefore, my PhD project aimed to design and develop new structurally related analogues of DPA-714 where the linkage between the main backbone and the fluorine-18 would be reinforced. To this extent, nineteen compounds were prepared and their affinity towards the TSPO was evaluated. Two promising candidates, coded DPA-C5yne and CfO-DPA-714, were radiolabelled with fluorine-18 with good radiochemical yields (20-30 %) and high specific radioactivities (50-90 GBq/µmol). These radioligands were also evaluated by PET imaging at the preclinical stage and displayed equivalent or slightly improved results when compared to [18F]DPA-714.

A Doença de Chagas, causada pelo parasito tripanossomatídeo Trypanosoma cruzi, é endêmica e se distribuí por toda América Latina. É uma das parasitoses mais negligenciadas pela indústria farmacêutica e os únicos fármacos disponíveis para seu tratamento foram introduzidos há décadas. Infelizmente, eles são ineficientes e apresentam sérios efeitos colaterais. Esse panorama mostra a necessidade do desenvolvimento de novos fármacos para a quimioterapia contra a doença de Chagas. As enzimas pertencentes a vias metabólicas essenciais para a sobrevivência do parasito tais como a via glicolítica e a de síntese de novo de nucleotídeos de pirimidinas, têm sido propostas como alvos interessantes no planejamento novos fármacos para o tratamento da doença de Chagas. Neste trabalho, as enzimas Gliceraldeído 3-fosfato desidrogenase (TcGAPDH) e a Diidroorotato desidrogenase (TcDHODH) de Trypanosoma cruzi foram estudadas como alvos para o planejamento de inibidores enzimáticos com propriedades físico-químicas e características estruturais similares à de compostos-líderes. Para isso, foram utilizados métodos e ferramentas de Quiminformática tanto baseadas nas estruturas dos ligantes (LBVS) quanto dos receptores (SBVS). Para a identificação e seleção de potenciais inibidores da enzima GAPDH, uma coleção virtual obtida do banco de dados ZINC, contendo aproximadamente 2,5 milhões de compostos, foi avaliada através de vários filtros de seleção com o objetivo de priorizar aqueles compostos mais interessantes do ponto de vista estrutural, de propriedades físico-químicas e farmacocinéticas. A aplicação desses filtros originou uma subcoleção de aproximadamente 450 mil estruturas que foram avaliadas segundo a complementaridade de interações com a estrutura da enzima através de métodos de docagem molecular. Com base nestes resultados, doze compostos que se mostraram promissores foram selecionados e adquiridos comercialmente para serem testadas in vitro contra a enzima TcGAPDH. Dos doze compostos testados, três exibiram afinidade (Ki) pela enzima em concentrações inferiores a 80 μM, Além disso, esses compostos também são caracterizados pelo baixo peso molecular (274 a 330 g mol-1) e no máximo 24 átomos diferentes do hidrogênio e, como consequência, apresentam eficiências do ligante entre 0,24 e 0,34 Kcal mol-1 átomo-1, o que os tornam ótimos candidatos à otimização molecular visando aumento da afinidade pelo alvo. Para a busca de inibidores da enzima TcDHODH, primeiramente foi realizada uma busca por cavidades na estrutura 3D do alvo para a identificação de regiões distintas do sítio catalítico e passíveis de serem exploradas no planejamento de ligantes. Através desta análise foi possível o estabelecimento de quatro novas regiões com forma, volume e localizações adequadas para acomodar pequenas moléculas capazes de modular a atividade da TcDHODH. Uma destas regiões, chamada S2, localizada sob a alça β4-αA e no canal de acesso dos substratos ao sítio ativo, foi escolhida para o planejamento baseado na estrutura do alvo. As estruturas de aproximadamente cem compostos derivados de pirimidinas, substituídos em posições estrategicamente definidas e selecionados através de buscas por subestruturas, foram docadas no sítio de interesse e nove compostos adquiridos e testados in vitro contra a enzima com o objetivo de validar as hipóteses estabelecidas inicialmente. Destes, cinco compostos mostraram potências (IC50) superiores à do produto de reação (inferior a 150 μM), Os resultados encontrados validaram as hipóteses geradas na primeira etapa e foram usados para direcionar a seleção de outras quinze novas moléculas através de um protocolo de docagem molecular com ajuste induzido. A avaliação in vitro desses compostos contra a enzima TcDHODH resultou na identificação de outros 11 compostos ativos, dos quais o mais potente exibiu afinidade pela enzima em concentração igual a 124 nM. Este composto possui eficiência do ligante igual a 0,56 Kcal mol-1 átomo-1 e pode ser considerado um fragmento molecular com excelentes características do ponto de vista do potencial para futuro desenvolvimento como agente terapêutico. Os resultados encontrados também evidenciaram a importância de determinadas características estruturais impressas nos inibidores da TcDHODH para a complementaridade com o novo sítio de interação identificado. Assim, novos compostos foram propostos para otimização molecular com o objetivo de melhorar afinidade e aumentar a diversidade de classes e, deste modo, ampliar o espectro de perfis farmacocinéticos para posteriores ensaios celulares e in vivo, Através da realização deste trabalho foi possível validar as estratégias adotadas na utilização dos métodos computacionais e também as hipóteses construídas a partir da aplicação dos mesmos. A taxa de acerto (TA) alcançada foi superior a 30% no planejamento de inibidores para ambos os alvos, ou seja, muito superiores às encontradas em experimentos de ensaio em massa. Deste modo, este estudo contribuiu com a proposição de novos esqueletos moleculares que podem ser usados como compostos-líderes no desenvolvimento de novos agentes tripanocidas focando nas enzimas TcGAPDH e TcDHODH como alvos. / Chagas\' disease, an endemic illness widely distributed throughout Latin America, is caused by the protozoa parasite Trypanosoma cruzi. It is one of the tropical diseases that are among the most neglected by the pharmaceutical industry, for which available treatments were launched more than 30 years ago. In addition, these drugs are ineffective and cause severe side effects to patients. This panorama shows the need for the development of new and more effective chemotherapeutic agents for the treatment of the disease. Enzymes belonging to metabolic pathways that are essential for the parasite survival such as the glycolysis and pyrimidine nucleotide biosynthesis have been proposed as attractive targets for the design of new drugs for the treatment of Chagas disease. In this work, the enzymes Gyceraldehyde-3-phosphate dehydrogenase (TcGAPDH) and the Dihydroorotate dehydrogenase (TcDHODH) from Trypanosoma cruzi were studied as targets for the design of inhibitors with physicochemical properties and structural characteristics similar to lead-compounds. Methods in Cheminformatics within the Ligand- and Structure-based Virtual Screening (LBVS and SBVS, respectively) approaches were thoroughly employed as tools to identify new hits. For the selection and identification of potential inhibitors of the GAPDH enzyme, a compound database containing nearly 2.5 million of small molecules retrievable from ZINC was evaluated through several molecular filters aiming at prioritizing those compounds more interesting from the point of view of their structures, physicochemical and predicted ADME/Tox properties. The application of Filter originated a subcollection of approximately 450 thousand structures that were then scored according to their complementary interactions with the 3D structure of the enzyme through molecular docking. Based on docking results, twelve compounds that showed to be promising ligands were selected and commercially acquired for in vitro assays against the TcGAPDH. Of the twelve compounds evaluated in vitro, three exhibited affinity constants (Ki) at concentrations lower than 80 μM. Furthermore, the selected compounds are also characterized by the low molecular weight (274 to 330 g mol-1) and a maximum of non-hydrogen atom count of 24, as a result, they have Ligand Efficiencies between 0,24 and 0,34 Kcal mol-1 átomo-1, what grant them great potential as candidates for molecular optimization and potency improvement. For the search of TcDHODH inhibitors, cavities in the 3D structure of the target for the identification of areas apart from catalytic site but likely to be explored in the design of ligands were selected a priori. This resulted in four new regions with appropriate shape, volume and locations to accommodate small molecules capable of modulating the activity of TcDHODH. One of the areas, called S2 site, is located under the α4 - βA loop and in the access channel of the substrate to the active site and was chosen to be explored in the SBDD studies. Approximately one hundred of pyrimidine derivatives containing strategically defined posítions for molecular substitution were retrieved from commercially available compounds database through substructure searching and docked into the previously defined site. Based on the docking results nine compounds were selected, purchased and assayed in vitro against the enzyme with the objective of validating the hypothesis. Of these, five compounds showed potencies (IC50) better than that exhibited by the product of the reaction (values lower than 150 μM). Thus, the results found validated the hypotheses generated in the first stage of the designing and they were used to drive the selection of other fifteen new molecules through induced fit molecular docking protocol. The in vitro evaluation of those compounds against the TcDHODH enzyme resulted in the identification of other eleven ligands, of which the most potent exhibited affinity for enzyme at the concentration of 124 nM. This molecule has a Ligand Efficiency of 0.56 Kcal mol-1 atom-1 and can be considered a fragment-like compound with excellent characteristics from the point of view of its potential for future development as therapeutic agent. The results found also evidenced the importance of certain structural characteristics in the inhibitor of TcDHODH for the complementarily with the new identified site of interaction. Thus, new compounds were proposed for potency and class diversity improvement. By doing so we hope to enlarge ADME profile spectrum for further cellular and in vivo assays. Through the success of this work, it was possible to validate the strategies adopted in the use of computational methods and also the hypotheses built from the application of that. The success rate (TA) obtained was higher than 30% in the design of ligands for both studied targets, which is much better than that usually found along High Throughput Screening assays. Thus, this study contributed with the proposítion of new molecular scaffolds that can be used as lead compounds in the development of new tripanocidal agents having as targets the enzymes TcGAPDH or TcDHODH.

Os receptores dos hormônios da tireóide (TRs) são fatores de transcrição envolvidos na diferenciação celular, metabolismo e funções fisiológicas da maioria dos tecidos. Muitos estudos mostram que diversos efeitos farmacológicos mediados pelos TRs podem ser benéficos na farmacoterapia, especialmente aqueles mediados pelo TR que podem ser úteis em condições médicas importantes como obesidade, hipercolesterolemia e diabetes. Além disso, a descoberta que o TR é a isoforma predominante no coração, mediando a maioria dos efeitos cardiovasculares prejudiciais, estimulou a pesquisa por ligantes seletivos para o TR que poderiam ser utilizados em quadros clínicos importantes com perfil de segurança aceitável. Foi realizado um estudo das relações quantitativas entre a estrutura e atividade (QSAR) de um conjunto de compostos com atividade biológica descrita para TR e TR, que gerou modelos de Holograma QSAR com elevada consistência interna e externa, apresentando bom poder de correlação e predição das propriedades biológicas. Também foi realizado um minucioso estudo de triagem virtual, que propiciou a seleção de 7 compostos que foram adquiridos para terem suas atividades biológicas avaliadas. Ensaios de transfecção e gene repórter foram estabelecidos e utilizados na avaliação da atividade biológica dos compostos selecionados pelo ensaio virtual. Finalmente, um ensaio utilizando ressonância plasmônica de superfície (SPR) foi desenvolvido e utilizado para avaliar a atividade agonista desses compostos, e que pode ser útil para avaliar a atividade de novos ligantes. A técnica de SPR também foi empregada em um cuidadoso estudo da interação do TR com seus correguladores, que incluiu estudos cinéticos e termodinâmicos, propiciando a determinação das taxas cinéticas e parâmetros termodinâmicos para a interação do complexo TR-T3 com peptídeos derivados de dois de seus correguladores. Os resultados obtidos são relevantes e devem ser considerados no planejamento de futuros experimentos utilizando o LBD de TR e agonistas. / The thyroid hormone receptors (TRs) are transcriptional factors involved in cell differentiation, development, metabolism and physiological function of most tissues. Many lines of evidence show that several pharmacological actions of TRs might be beneficial in medical therapy, specially those mediated by TR that target important medical conditions like obesity, hypercholesterolemia and diabetes. Additionally, the findings that TR is the predominant isoform in the heart and mediates most of the TRs deleterious cardiovascular effects, stimulated the research for selective TR ligands which could address important medical needs with an acceptable safety profile. In this PhD thesis, studies of the quantitative structure-activity relationships (QSAR) of a dataset of compounds with reported biologic activity for both TR and TR were performed, and statistically significant Hologram QSAR models with good predictive ability for untested compounds were created. In parallel, a careful virtual screening procedure was executed, leading to the selection of 7 compounds which were purchased for the evaluation of their biological activities. Cell transfection and reporter gene assays were developed, validated and used to evaluate the biological activities of these compounds. Finally, a surface plasmon resonance (SPR) assay was developed and used to assess the agonistic activity of these compounds. The SPR technique was also employed in a careful study of the interaction between the ligand binding domain of TR and peptides derived from its coregulators, which included the determination of the kinetic and thermodynamic parameters for this interaction. The results suggest that flexibility plays an important role in the interaction between the receptor and its coregulators, and point out important aspects of experimental design that should be addressed when using TR LBD and its agonists. Furthermore, the methodology described here may be useful for the identification of new TR ligands.