A hemoglobina (Hb) é uma fonte reconhecida de peptídeos com funções biológicas diversas. O fragmento 33-61 da cadeia α da Hb, isolado do trato gastrointestinal do carrapato Boophilus microplus, foi o primeiro a ser descrito com ação antimicrobiana. O seu análogo sintético amidado, Hb33-61a, mostrou-se ativo contra bactérias Gram-positivas e fungos [Fogaça et al. (1999) J. Biol. Chem. 274, 25330-4]. O estudo de análogos do Hb33-61 nas formas amidada e com carboxila livre revelou que a amidação provoca aumento significativo da atividade frente a Candida albicans. Por apresentar propriedades biológicas e estruturais idênticas às do Hb33-61a, o Hb40-61a pareceu ser a sua porção mÌnima ativa [Sforça et al. (2005) Biochemistry 44, 6440- 51; Machado et al. (2007) Biopolymers 88, 413-26]. Para comprovar tal sugestão, no presente trabalho, sintetizamos, purificamos e caracterizamos novos an·logos do Hb33-61a, bem como os avaliamos quanto às suas atividades frente a C. albicans e Micrococcus luteus. Os resultados confirmaram a sugestão apenas para a ação antifúngica. O análogo Hb40-61a também se mostrou ativo frente a C. albicans resistente a fluconazol. A sua atividade antifúngica se mostrou fortemente dependente da força iônica do meio. A sua baixa atividade hemolítica foi confirmada mesmo em meio de baixa força iônica. O peptídeo Hb40-61a não apresentou sinergismo com o fluconazol frente a C. albicans. A cinética de morte celular mostrou que ele mata a levedura de forma rápida. Portanto, esta hemocidina sintética pode apresentar valor comercial se a via de administração for tópica ou se o seu uso envolver meios de baixa força iônica. Além disso, ela é um modelo valioso para o estudo do mecanismo de ação de peptídeos antimicrobianos com características estruturais similares e pode servir de base para o desenho de novos agentes antibiôticos. / It is well known that hemoglobin (Hb) is a source of biologically active peptides. The fragment 33-61 of bovine hemoglobin α-chain, isolated from the gut contents of the tick Boophilus microplus, was the first identified with antimicrobial activity . Its amidated analogue, Hb33-61a, showed to be active against Gram-positive bacteria and fungi strains [FogaÁa et al. (1999) J. Biol. Chem. 274, 25330-4]. The study of a series of carboxyl-free and amidated synthetic analogues of Hb33-61 revealed that C-terminus amidation enhances the activity against Candida albicans. Since Hb33-61a and Hb40-61a presented identical biological and structural properties, it seemed that Hb40-61a was Hb33-61a minimal active motif [SforÁa et al. (2005) Biochemistry 44, 6440- To test this suggestion, in the present study 51; Machado et al. (2007) Biopolymers 88, 413-26]. we synthesized, purified and characterized Hb40-61a analogues and assayed them against C. albicans and Micrococcus luteus. The results confirmed the suggestion only for the antifungal activity. When tested against fluconazole-resistant C. albicans, Hb40-61a was also active. Its antifungal activity showed to be dependent on the ionic strength of the medium. Its low hemolytic activity was confirmed even under low ionic strength conditions. Hb40-61a had no synergic effect with fluconazole on C. albicans. In vitro time-kill assays demonstrated that Hb40-61a kills the yeast rapidly. Therefore, this synthetic hemocidin may be of commercial interest for topical application or other uses involving low ionic strength medium. Moreover, it can serve as a template for the study of the mechanism of action of structurally related antimicrobial peptides or for the design of novel antibiotic drugs.

N-methyl-D-aspartate (NMDA) receptors are glutamate-gated calcium permeable ion channels that play a key role in excitatory synaptic transmission and plasticity, and their dysfunction underlies several neuropsychiatric disorders. The overactivation of NMDA receptors by tonically increased ambient glutamate can lead to excitotoxicity, associated with various acute and chronic neurological disorders, such as ischemia, Alzheimer and Parkinson's disease, epilepsy or depression. On the opposite, NMDA receptor hypofunction is thought to be implicated in autism, schizophrenia, or intellectual disability. Recent DNA screening for neurological and psychiatric patients revealed numerous mutations in genes encoding for NMDA receptor subunits. The activity of NMDA receptors is influenced by a wide variety of allosteric modulators, including neurosteroids that could both inhibit and potentiate the activity of NMDA receptors, which makes them promising therapeutic targets. In this thesis, we describe new classes of neurosteroid analogues which possess structural modifications at carbons C3 and C17 of the steroidal core, and analogues without D-ring region (perhydrophenanthrenes). We evaluated the structure-activity relationship (SAR) for their modulatory effect on recombinant GluN1/GluN2B receptors. Our results...

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Higher alcohol synthesis (HAS) from syngas or biomass-derived syngas is an important process for the production of oxygenate fuels, fuel additives and other intermediates for valueded chemical feedstock to produce medicine, cosmetics, lubricants, detergents, and polyesters. Chapter I reviews biomass to liquid fuels technology, higher alcohols being used as alternative fuels and fuel additives, the historical perspective and commercial status of higher alcohols, the catalyst system and the reaction mechanism for HAS from syngas. Chapter II discusses the Zn-Mn promoted Cu-Fe based catalyst that was synthesized by the co-precipitation method. The reaction temperature has been tested to study the influence on the catalytic performance. The maximal CO conversion rate was 72%, and the yield of alcohol and hydrocarbon was also very high. Cu was the active site for alcohol synthesis, iron carbide was the active site for olefin and paraffin synthesis. The reaction mechanism of HAS from syngas over Zn-Mn promoted Cu-Fe based catalyst was proposed. Chapter III documents the three-dimensionally ordered macroporous (3DOM) Cu-Fe catalyst developed using a glyoxylate route colloidal crystal template method. The high intrinsic activity was ascribed to three factors. First, the unique ordered structure has a large pore size and interconnected macroporous tunnels of the catalyst with a large accessible surface area to improve the catalytic activity. Second, a high density of uniformly distributed defective Cu0 and Fe5C2 nanoparticles derived from the glyoxylate route helps to provide abundant, active, and stable dual sites. Third, atomic steps on the Cu surface, induced by planar defects and lattice strain, serve as high-activity oxygenation sites. Active Fe5C2 chain-growth sites intimately surround the defective and strained form of the Cu surface, which results in a synergetic effect between the active and stable Cu–FexCy dual site for HAS. In Chapter IV, in situ ambient pressure x-ray photoelectron spectroscopy and in situ synchrotron powder diffraction were applied to identify the active site of 3DOM Cu-Fe catalyst for HAS. The results show that after syngas pretreatment of the 3DOM Cu-Fe catalyst, Cu0 is the active oxygenation site for alcohol synthesis, and Fe5C2 is the active site for carbon chain growth.

Quantitative structure-activity relationship (QSAR) models based on machine learning algorithms are powerful tools to expedite drug discovery processes and therapeutics development. Given the cost in acquiring large-sized training datasets, it is useful to examine if QSAR analysis can reasonably predict drug activity with only a small-sized dataset (size < 100) and benchmark these small-dataset QSAR models in application-specific studies. To this end, here we present a systematic benchmarking study on small-dataset QSAR models built for prediction of effective Wnt signaling inhibitors, which are essential to therapeutics development in prevalent human diseases (e.g., cancer). Specifically, we examined a total of 72 two-dimensional (2D) QSAR models based on 4 best-performing algorithms, 6 commonly used molecular fingerprints, and 3 typical fingerprint lengths. We trained these models using a training dataset (56 compounds), benchmarked their performance on 4 figures-of-merit (FOMs), and examined their prediction accuracy using an external validation dataset (14 compounds). Our data show that the model performance is maximized when: 1) molecular fingerprints are selected to provide sufficient, unique, and not overly detailed representations of the chemical structures of drug compounds; 2) algorithms are selected to reduce the number of false predictions due to class imbalance in the dataset; and 3) models are selected to reach balanced performance on all 4 FOMs. These results may provide general guidelines in developing high-performance small-dataset QSAR models for drug activity prediction.

Over the course of more than ten years, there has been a significant increase in the approach employed to inhibit the function of soluble epoxide hydrolase (sEH). The phenomenon of upregulating soluble epoxide hydrolase (sEH) has been found to result in a decrease in the ratio of epoxyeicosatrienoic acids (EETs) to dihydroeicosatrienoic acids (DHETs) in the body. This has garnered significant attention due to the diverse biological functions attributed to EETs, including the regulation of vasodilation, neuroprotection, increased fibrinolysis, calcium ion influx, and anti-inflammatory effects. Consequently, there has been a growing interest in developing and discovering sEH inhibitors through chemical syntheses and natural extracts, with the aim of increasing the availability of these anti-inflammatory molecules by reducing their hydrolysis. A comprehensive examination of this project was conducted to explore the inhibitory effects of YMSV, a tetrapeptide derived from the castor bean (Ricinus communis), on sEH, as well as to elucidate its underlying mechanism of action. YMSV was determined to function as a mixed-competitive inhibitor of soluble epoxide hydrolase (sEH), and the interaction between the peptide and the protein resulted in the disruption of the secondary structural composition of sEH. Furthermore, the hydrogen bond interactions between YMSV and the Asp 333 residue in the active region of soluble epoxide hydrolase (sEH) were demonstrated using molecular docking investigations. However, quantitative structure-activity relationship (QSAR) research revealed that nonpolar, hydrophobic, and bulky amino acids are favored at the N- and C- terminals of peptides for sEH inhibition. The results of this study indicate that peptides obtained from dietary sources possess unique characteristics as inhibitors of soluble epoxide hydrolase (sEH), displaying significant potency. Consequently, these peptides have promise for further development as therapeutic medicines targeting inflammation and depression in the future.

Problématique : Le cancer du sein est un des types du cancer les plus diagnostiqués au Canada et il est une cause majeure de mortalité liée au cancer chez la femme. Le cancer du sein triple négatif (CSTN) a un mauvais pronostic dû à son agressivité clinique et à l’absence de réponse aux traitements habituels du cancer du sein tels que l’hormonothérapie et l’inhibition de HER2. En ce moment, les avancées pour le CSTN restent très négligeables. Il y a un besoin urgent d’identifier une nouvelle thérapie qui ciblerait les voies signalétiques pro-métastatiques du cancer du sein triple négatif et ainsi, bloquer idéalement la prolifération et la dissémination métastatique des cellules cancéreuses. Cadre conceptuel : Dernièrement le laboratoire de Sylvain Meloche à l’IRIC a montré qu’une déplétion génétique de ERK3 (Extracellular Regulated Kinase 3) inhibe la croissance des tumeurs mammaires dans un modèle de souris de CSTN et bloque la progression métastatique. Ainsi, suite à ces résultats, nous avons émis l’hypothèse que l’inhibition de ERK3 à l’aide de molécules engendrerait une diminution de la prolifération cellulaire au niveau du cancer du sein triple négatif. L’objectif principal du projet est de développer des molécules ayant des propriétés inhibitrices de ERK3 in vitro. Les deux objectifs secondaires sont d’évaluer leur potentiel d’inhibition vis-à-vis ERK3 dans des modèles in cellulo et de confirmer, parallèlement à la relation structure-activité (SAR), leur mode de liaison par des méthodes computationnelles. Méthodologie : Des composés tête de série ont été identifiés à la suite d’un criblage à haut débit d’une librairie d’inhibiteurs de kinases. Quelques composés intéressants démontrent une activité dont les IC50 (concentration inhibant 50% de l’activité de la kinase) sont inférieurs à 300 nM. Une molécule en particulier a été retenue compte tenu de son niveau d’activité et de sélectivité par rapport aux autres kinases. Une modification systématique des groupements fonctionnels lors de la synthèse d’analogues nous permet d’établir de façon claire le mode de liaison et ainsi, établir la SAR de notre composé tête de série et le site de liaison de ERK3. Les tests d’inhibition compétitifs in vitro seront effectués à l’IRIC à partir de la protéine ERK3 purifiée. Grâce à la SAR établie, on poursuit l’optimisation avec l’intégration de groupements moléculaires solubilisants qui vont permettre d’augmenter les propriétés pharmacocinétiques et ainsi, augmenter l’activité cellulaire de notre composé tête de série. En dernier lieu, à l’aide de la modélisation computationnelle, le mode de liaison de la molécule à ERK3 sera élucidé de façon à confirmer la SAR et aussi, permettre le développement de nouvelles structures (ex : bioisotères) pouvant avoir aussi une activité inhibitrice sur ERK3. Résultats : Une SAR étendue basée sur l’inhibiteur sélectionné a été obtenue. Un inhibiteur de ERK3 possédant une puissance cellulaire (IC50) de 2 μM a été synthétisé. Retombée scientifique : Les travaux effectués dans le cadre de ma maîtrise pourraient conduire au développement de nouveaux traitements pour le cancer du sein triple négatif en ciblant les voies de signalisation prométastatiques à l’aide de molécules inhibitrices. / Problem: Breast cancer is one of the most diagnosed type of cancer in Canada and it is a major cause of mortality linked to cancer for women. Triple-negative breast cancer (TNBC) is the form with the worse prognostic compared to the other forms of breast cancer due to clinical aggressiveness and the absence of response to conventional hormonal therapy and HER2 inhibition therapy. At this time, therapeutic advances for TNBC remain very negligible, which testifies to a need for a new therapy that would target the prometastatic signaling pathways of triple negative breast cancer and thus, ideally block the proliferation and the metastatic dissemination of cancer cells. Conceptual Basis: Recently, Sylvain Meloche's laboratory at IRIC showed that genetic depletion of ERK3 (Extracellular Regulated Kinase 3) inhibits the growth of mammary tumors in a TBNC mouse model and blocks metastatic progression. Thus, in view of these results, our hypothesis is that the inhibition of ERK3 using a specific inhibitor would cause a decrease in cell proliferation in triple negative breast cancer. The main objective of my project is to develop small molecules with inhibitory properties of ERK3 in vitro. The two secondary objectives are to evaluate their inhibitory potential toward ERK3 in cellulo models and to confirm, alongside the structure-activity relationship (SAR), the binding mode of inhibitors to ERK3 by computational methods. Methodology: Lead compounds have been identified following a high-throughput screening of a kinase inhibitor library. A few interesting compounds emerged with activities below 300 nM (IC50). One molecule in particular was chosen given its good selectivity as well as an acceptable inhibitory activity. Systematic modification of functional groups for analogs synthesis allows us to clearly establish the binding mode and thus, establish the SAR of our lead compound. The competitive inhibition tests in vitro have been carried out at IRIC using purified ERK3. With the established SAR, optimization is continued with the integration of solubilizing molecular groups which will increase the pharmacokinetic properties and thus increase the cellular activity of our lead compound.7 Finally, with the help of computational modeling, the binding mode of the molecule to ERK3 will be elucidated to confirm the SAR and also, allow the development of new structures (i.e. bioisosters) that can have an inhibitory activity on ERK3. Results: An extensive SAR of the inhibitor is obtained. A compound with 2 μM activity (IC50) on ERK3 in cell has been synthesized. Scientific outlook: The work done as part of my master's degree could lead to the development of a new treatment for triple-negative breast cancer by targeting prometastatic signaling pathways using small inhibitory molecules.

Cette thèse s’articule autour de deux grands axes indépendants. Le premier s’aligne sur les intérêts du groupe Collins pour la photocatalyse avec des complexes à base de cuivre. La photocatalyse apparait comme une branche de la chimie permettant de débloquer des réactivités difficilement accessibles par la chimie thermique. Si la majorité des réactions photocatalysées utilise des catalyseurs à base de ruthénium ou d’iridium, les complexes de cuivre(I) sont une alternative digne d’intérêt. Cependant, une connaissance plus profonde de la relation structure/activité de ces complexes est encore nécessaire. Cette thèse tentera donc d’apporter des éléments de réponse à cette problématique, en particulier pour les complexes de cuivre(I) hétéroleptiques, possédant un ligand diimine et un ligand diphosphine. Le premier chapitre présente le concept de la photocatalyse et les caractéristiques des photocatalyseurs de cuivre. Une sélection d’exemples de réactions photocatalysées par des complexes de cuivre permet d’établir l’état de l’art pour différents types de mécanismes. Le chapitre 2 présente l’étude de ligands diimine possédant un système π-étendu dans des complexes. Les complexes correspondants ont été étudiés dans trois réactions passant par des voies mécanistiques différentes. Si les complexes sont actifs pour les réactions de transfert d’électrons et d’énergie, ils ne possèdent pas une efficacité supérieure aux complexes précédemment reportés. Le chapitre 3 est une extension du chapitre 2. En effet, les ligands possédant un système π-étendu précédemment reportés ont été modifiés pour pouvoir former des complexes de cuivre avec la diphosphine BINAP. Les nouveaux complexes ont de nouveau été étudiés dans les trois réactions différentes, mais leur activité est semblable à celle des complexes reportés dans le chapitre 2. Les complexes ont aussi été étudiés pour leur activité anticancéreuse, et des résultats prometteurs ont été découverts. Le chapitre 4 résume l’étude d’une bibliothèque étendue de complexes de cuivre(I) pour l’isomérisation d’alcènes E→Z. L’efficacité des complexes dans la réaction est reliée à leurs propriétés photophysiques. Un complexe optimal a été trouvé, et utilisé pour isomériser une série de 25 alcènes différents. L’utilisation de la chimie en flux continu a aussi permis la mise en échelle de la réaction. Enfin un procédé séquentiel ATRA/PI a permis la formation d’alcènes tri- et tétra-substitués à partir d’alcynes et de chlorures de sulfonyles. Le deuxième axe de cette thèse se base sur le développement de diynes-1,3 pour leur utilisation dans les réactions de « click » promues par la tension. Le chapitre 6 introduit les concepts de chimie « click » et de cycloaddition alcyne-azoture promue par la tension (SPAAC), et l’état de l’art des diynes-1,3 et des alcynes tendus. Le chapitre 7 présente donc le développement d’une nouvelle classe de diynes-1,3 tendus pour la réaction de SPAAC. La vitesse de la réaction est étudiée et des calculs computationnels viennent corroborer la réactivité observée. Un diyne-1,3 , 3,5-TPDY, a été utilisé dans une application de bioligation, et son utilisation dans une réaction de « click » avec une hydrazine a été montrée. / The thesis is structured around two independent themes. The first concerns the Collins Group's interest in copper-based complexes for photocatalysis. Photocatalysis is a branch of chemistry that aims to unlock reactivities that are difficult to access through thermally-promoted chemistry. While the majority of photocatalytic reactions use ruthenium- or iridium-based catalysts, copper(I) complexes are a valuable alternative, but a deeper understanding of the structure/activity relationship of the complexes is still required. The thesis will describe work to gain a better understanding of the reactivities and behavior of heteroleptic copper(I) complexes possessing a diimine ligand and a diphosphine ligand. The first chapter introduces the concept of photocatalysis and the characteristics of copper-based photocatalysts. A selection of examples of reactions photocatalyzed by copper complexes establishes the state of the art for different types of mechanisms. Chapter 2 presents the study of diimine ligands possessing a π-extended system in copper-based complexes. The corresponding complexes have been studied in 3 different photochemical reactions proceeding through different mechanistic pathways. While the complexes are active in electron and energy transfer reactions, they are not more efficient than previously reported complexes. Chapter 3 is an extension of Chapter 2, in which the π-extended ligands previously reported are modified to form copper complexes with the diphosphine, BINAP. The new complexes are again studied in the 3 different reactions, but their activity is similar to that of the complexes reported in chapter 2. The complexes are also being studied for their anticancer activity, and promising results have been uncovered. Chapter 4 summarizes the study of an extensive library of copper(I)-based complexes for the E→Z isomerization of alkenes. The efficiency of the complexes in the reaction is compared with their photophysical data. An optimal complex is found and used to isomerize a series of 25 different alkenes. The use of continuous flow chemistry also enabled the reactions to be scaled up. Finally, a sequential ATRA/PI process enabled the formation of tri- and tetra-substituted alkenes from alkynes and sulfonyl chlorides. The second theme of the thesis is based on the development of 1,3-diynes for use in strain-promoted "click" reactions. Chapter 6 introduces the concepts of click chemistry and SPAAC, and the state of the art of 1,3-diynes and strained alkynes. Chapter 7 presents the development of a new class of strained 1,3-diynes for the SPAAC reaction called TPDYs. The reaction rates are studied and computational calculations corroborate the observed reactivity. A 1,3-diyne, 3,5-TPDY, is applied to a bioligation process, and its use in a potential new "click" reaction with a hydrazine is shown.

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