Hydrogels are promising materials for a number of biomedical applications, including tissue engineering, controlled drug delivery, and wound healing. Due to the semi-permeable nature of the water-swollen crosslinked polymer network, hydrogels have the unique ability to encapsulate materials, while allowing passage of any necessary resources, such as the import of oxygen or nutrients and the export of waste or therapeutic agents. Hydrogel properties vary greatly depending on the polymer material and crosslinking chemistry chosen, all of which can be tuned for a particular application. Current hydrogel systems typically involve either natural or synthetic polymers. Synthetic polymers afford more structural control to the resulting hydrogel, however the employed crosslinking chemistry is often non-ideal, due to the high temperatures required or the presence of cytotoxic catalysts. Click chemistry, particularly the strain-promoted alkyne-azide cycloaddition (SPAAC), is ideal for hydrogel crosslinking as it is fast at physiological temperatures, bio-orthogonal, doesn’t produce any byproducts, and doesn’t require a catalyst or external stimuli. For the hydrogel material, synthetic poly(ethylene glycol) (PEG) is most appealing since it is non-toxic, easy to functionalize, and physiologically stable. At the time of this thesis, there were few examples of PEG hydrogels prepared via SPAAC, with limited characterization of the physical properties of these gels and the parameters that dictate their gelation behavior. The work presented in this thesis involved the optimized synthesis of a cyclooctyne derivative, aza-dibenzocyclooctyne (DIBAC), which was subsequently used for the preparation and characterization of a series of PEG hydrogels crosslinked via SPAAC. We showed that the PEG chain length and number of crosslinking groups had a significant effect on the swelling, degradation time and stiffness of the resulting hydrogels. Additionally, there was very little protein adsorption on the surface of the hydrogels, and the polymer components proved non-cytotoxic. A second objective of this work was to investigate reproducible hydrogels. We created novel, SPAAC crosslinked PEG hydrogels that contained well-defined dendritic crosslinking groups, making them more reproducible than the previous linear analogs. These hydrogels have short gelation times at low polymer concentration, minimal swelling at physiological temperatures, and kept human mesenchymal stem cells (hMSCs) viable for over 15 days. / Thesis / Doctor of Philosophy (PhD)

The strain promoted azide alkyne cycloaddition (SPAAC) of azido nucleobase modified nucleosides and nucleotides with cyclooctynes to give fluorescent triazoles has been relatively unexplored. Thus, SPAAC between azido-nucleobases and various cyclooctynes in aqueous solution at ambient temperature resulted in the efficient formation (3 min - 2 h) of triazole products with inherent fluorescent properties. The 2- and 8-azidoadenine nucleosides reacted with fused cyclopropyl cyclooctyne, dibenzylcyclooctyne or monofluorocyclooctyne to produce click products functionalized with hydroxyl, amino, N-hydroxysuccinimide, or biotin moieties. The previously unexplored 5-azidouridine and labile 5-azido-2'-deoxyuridine were similarly converted to the analogous triazole products in quantitative yields in less than 5 minutes. The 8-azido-ATP quantitatively afforded the triazole product with fused cyclopropyl cyclooctyne (3 h). Addition of a triazole ring at the 2 or 8 position of adenine or 5-position of uracil induces fluorescent properties which were used for direct imaging with fluorescent microscopy in MCF-7 cancer cells without the need for traditional fluorogenic reporters. Fluorescent lifetime imaging microscopy of the click adducts in live cells were used to determine the lifetime of each fluorophore in the cellular nuclei demonstrating the potential utility of the synthesized triazole adducts for dynamic measuring and tracking of events inside single living cancer cells. The SPAAC methodology developed has also been applied to study the cellular targets in protozoal parasite, Trichomonas vaginalis and bacteria, Pseudomonas aeruginosa. The 9-(2-deoxy-2-fluoro-β,D-arabino-furanosyl)adenine (arabino-F-Ado) was modified with an azido moiety at the C8 position for use in click chemistry. Tagging and subcellular localization studies using azido modified arabino-F-Ado could provide insight into the mechanism of action of arabino-F-Ado. An activated analogue of S-adenosyl-L-methionine (SAM) with an EnYn group on the sulfur instead of a methyl group was prepared to study the transfer of the methyl group from SAM. I found that the EnYn group was transferred from SAM to a guanosine on tRNA by methytransferase Trm1. Thus, AdoEnYn is a competitive inhibitor of SAM and can be incorporated into tRNA in place of SAM.

La recherche de nouvelles molécules à activité antiparasitaire pour lutter contre les parasites responsables de maladies telles que le paludisme ou la trypanosomiase humaine africaine est un enjeu primordial car il n’existe pas de vaccin pour ces maladies qui peuvent être mortelles et qui touchent près de 1/6 de la population mondiale. Dans ce contexte, il a été observé au laboratoire que l’amélioration de l’activité des molécules sur une cible isolée ne se retrouvait pas toujours sur les parasites. Une faible entrée de la molécule dans la cellule pourrait être une des causes de ce manque de corrélation, comme cela est souvent le cas dans la recherche de molécules actives.Pour valider ou non cette cause, ces travaux de thèse ont eu pour but de concevoir, synthétiser et évaluer de nouvelles sondes fluorescentes qui permettraient de visualiser la pénétration de molécules actives dans des cellules, en nous intéressant en particulier aux parasites responsables de la maladie du sommeil et du paludisme.Notre concept se base sur le principe de la chimie « click », sans catalyseur, impliquant une fonction alcyne et un groupement azoture. Ceci est possible lorsque la fonctionalcyne est insérée dans un cycle tendu comme celui d’un cyclooctyne qui lui confère une plus grande réactivité (Strain-Promoted Alkyne-Azide Cycloaddition).Nous avons synthétisé des dérivés de la dibenzocyclooctynone, une molécule fluorescente décrite pour réagir sans catalyseur avec des azotures, de manière à obtenir des sondes à détection « on-on’ ». Ainsi, sept nouvelles sondes fluorescentes ont été obtenues, dont trois réagissent avec des azotures avec une cinétique adéquate. Les propriétés photophysiques de ces molécules ont été caractérisées et nous avons vérifié qu’elles traversent bien la membrane des protozoaires parasites que nous étudions. La fluorescence n’est observée qu’à l’intérieur du parasite.La détection d’un azoture in cellulo a été vérifiée par HPLC- MS/MS avec une des sondes.Parmi les sept cyclooctynones obtenues, une sonde forme un adduit triazole fluorescent avec une cinétique acceptable, ce qui constitue le premier exemple de sonde « on-on’ » de cette série et une véritable avancée dans la chimie bio-orthogonale. / The discovery of new molecules with antiparasitic activity is crucial today to fight against infectious diseases such as malaria and HAT since no vaccine is available to cure these diseases. In our search for new antiparasitic compounds, we observed that activity improvement on an isolated target was not seen on parasite. We suspected an ineffective entry of the molecule into the cell to be one of the reasons for these uncorrelated results.To explore this possibility, this PhD work aimed to design, synthetize and evaluate new fluorescent probes that would allow the visualization of drug entry into parasites responsible for HAT and malaria.Our concept is based on “click” chemistry that can be achieved without catalyst, between an azide and a strained alkyne like cyclooctyne (Strain-Promoted Alkyne-Azide Cycloaddition).We synthetized derivatives of dibenzocyclooctynone, a fluorescent molecule described to undergo SPAAC reaction with azides, in order to obtain “on-on’” detection probes. Seven new fluorescent probes were therefore synthetized, among which three of them displayed adequate SPAAC kinetics. Photophysical properties of these molecules were characterized and their penetration into protozoan cells was demonstrated. Fluorescence was only observed in the parasitic cytosol.In cellulo azide detection was achieved and verified by LC- MS/MS with one of our probes.One out of the seven probes formed a fluorescent triazole adduct, which constitutes the first example of an « on-on’ » probe for this series and a real progress in bioorthogonal chemistry.

Le principal objectif de cette thèse a consisté au développement d’une méthode de screenning pour la découverte de nouvelles réactions de ligations bioorthogonales ainsi que son application sur une bibliothèque développée pour cette étude. Par conséquent, un système de screening a été conçu en trois étapes consistant au départ en une analyse HPLC, puis une évaluation basée sur la fluorescence de haute résolution et finalement un test de microscopie confocal in cellulo. Puis, nous avons standardisé toutes les analyses avec les réactions CuAAC et SpAAC. En outre, nous avons synthétisés 18 réactifs d’intérêts et effectué un screening de 58 expériences de ligation avec une évaluation par méthode HPLC. Parmi les 9 réponses positives obtenues figure 6 réactions impliquant de nouveaux réactifs et les analyses LC‐MS ont pu tous les valider comme des réactions de cycloaddition directe à l’exception d’une réaction. Finalement, nous avons pu appliquer la méthode in cellulo développée, afin d’évaluer la pertinence des réactions de chélation CuAAC pour une application sur cellules. / The main goal of this thesis was the development of a screening method for the discovery of new bioorthogonal ligation reactions as well as its application on a self‐designed library. Therefore we designed a three step screening system consisting of a preliminary HPLC assay, a high resolution fluorescence based assay and a final in cellulo confocal microscopy assay.Subsequently we standardized all assays with the highly established CuAAC and SpAAC. Furthermore, we successfully synthesized 18 reagents of interest and screened 58 ligation experiments with the help of the HPLC setup. The 9 positive hits from this screening contained 6 reactions involving novel reagents and LCMS analysis was able to validate all but one as straight forward cycloaddition reaction. Finally we were able to apply the newly developed in cellulo assay to assess the suitability of chelating CuAAC for in cell application.

Ce travail a consisté en la synthèse d’outils chimiques et au développement de leurs applications biologiques. Dans un premier temps, des sondes pour l’étude de la Topoisomérase IIA humaine ont été synthétisées. Ces sondes ont alors été testées sur lysat cellulaire pour la capture des protéines présentant une affinité pour ces médicaments. Dans un second temps, un nouveau lien clivable en conditions non dénaturantes pour des applications en protéomique chimique a été developpé. Ainsi, après optimisation de la structure, il a été intégré au sein d’une sonde d’affinité pour évaluer sa capacité de capture et libération de la PARP 1. Enfin, la réaction de click entre un azoture et un cyclooctyne a été appliquée à l’élimination d’une drogue circulante dans le sang.Après l’étude cinétique de la réaction, l’activité biologique et la pharmacocinétique des différents composés ont été évaluées pour optimiser la réaction de click in vivo. / The main goal of this work was to synthesize chemical tools and to developp their biological applications. In the first part, probes for the study of Topoisomerase II via chemical proteomic were synthesized. They were then used for pulldown experiments on cell lysats. In a second part, a new cleavable linker in non denaturing conditions was developped for chemical proteomic applications. After optimisation of the structure, it was incorporated in an affinity probe and tested for the pulldown of PARP 1. Finally, a click chemistry reaction, the SPAAC, was used to provok the elimination of a circulating drug. After the study of the kinetic of the reaction, the biological activity and the pharmacokinetic of the different compounds were evaluated to optimise the click reaction in vivo.

The thesis work described herein explores two avenues of post-functionalization of conjugated polymers using ‘click’ chemistry. The first avenue utilizes the Strain-Promoted Alkyne-Azide Cycloaddition (SPAAC) and the second an Inverse Electron-Demand Diels-Alder (IEDDA). In the first part of this thesis, various azide moieties were SPAAC ‘clicked’ onto a dibenzocyclooctyne-containing polymer, such as small molecules like para-phenyl-nitroazide, as well as larger azide-terminated chains like polystyrene and polyethylene glycol. Host-guest chemistry and self-healing organogels were also explored. The synthesis of each component, including the cyclooctyne diamine monomer, dialdehyde comonomer, resulting polymer, various azide moieties, as well as the SPAAC click reactions, are all described in detail along with extensive characterization. Similarly, the second part of this thesis involved the synthesis and characterization of several components, including the tetrazine monomer, fluorene comonomer, resulting polymer, and various TCO derivatives for the post-polymerization IEDDA ‘click’ reactions onto the backbone. Some of the click reactions described include small molecule TCO derivatives, polymeric PEG TCO, and a difunctional linker to generate a crosslinked foam. / Conjugated polymers attract significant attention due to their interesting optoelectronic and physical properties. Over the past few decades, tremendous effort has been devoted to expanding the structural diversity and applications of this class of macromolecules. The pursuit of structural variability of conjugated polymers has resulted in a broad range of research to understand their structure-property relationships via functionalization. This functionalization is crucial for tailoring performance in any given application. Thus, the ability to synthesize a library of homologous polymers would prove very useful. Efficiency is of utmost importance when creating a library of homologous conjugated polymers, as the faster a library can by synthesized, the sooner said polymers can be screened for any desirable properties. Such an approach requires a post-polymerization functionalization strategy, whereby a progenitor polymer undergoes efficient reactions at each repeat unit of the backbone. The work presented in this thesis involves synthesizing a reactive conjugated polymer scaffold, followed by efficiently post-polymerization functionalization via “click” chemistry. Two elegant click reactions are described in this work; the Strain-Promoted Alkyne-Azide Cycloaddition (SPAAC) and Inverse Electron-Demand Diels-Alder (IEDDA). The SPAAC reaction allowed for rapid functionalization of triazole moieties on a dibenzocyclooctyne-containing polymer backbone, creating a small polymer library with a consistent degree of polymerization (DP). Grafting with polystyrene and polyethylene glycol azide-terminated polymers allowed the efficient syntheses of a series of graft-co-polymers with Mn values up to 800 kDa and varying solubilities. Secondly, The IEDDA reaction was applied to a poly(tetrazine-co-fluorene) conjugated polymer, which resulted in the rapid and quantitative functionalization of the polymer backbone with trans-cyclooctene derivatives. These reactive conjugated polymers were explored in a variety of applications, including supramolecular chemistry and gel formation. / Thesis / Doctor of Philosophy (PhD) / Conjugated polymers are a class of macromolecular materials that attract significant attention due to their interesting behaviors and properties. Under certain conditions, these polymers even display conductivities like that of metals. As such, they show promise in applications such as organic solar cells, chemical sensors, organic light-emitting diodes, and supercapacitors. Over the past few decades, tremendous effort has been devoted to expanding on the types of conjugated polymers as well as their structural diversity. This, of course, has resulted in polymers that exhibit vastly different behaviours depending on what they are made of. As certain applications (e.g.: solar cells) require polymers with very specific properties, being able to ‘tune’ a conjugated polymer to ‘match’ a required property would be extremely useful. This tuning of polymer properties can be successfully accomplished by attaching different structures onto the polymer chain by utilizing a reaction known as ‘post-polymerization functionalization’. In doing so, a starting reactive polymer can be transformed into an entirely different polymer with specific chemical properties and behaviors. The work presented in this thesis involves synthesizing two types of conjugated polymers and attaching various structures onto their backbones to yield different properties. The synthesis, characterization, and potential applications of said polymers are described herein.

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.