Le premier objectif de ce travail a consisté à développer la réaction CuSAC (découverte au laboratoire) pour la synthèse régiosélective de pyrazoles poly-substitués, dans un contexte de méthodologie de synthèse. Il existe de nombreux composés biologiquement actifs contenant le motif pyrazole et peu de méthodes régiosélectives décrites pour les synthétiser. Développer une nouvelle réaction pour obtenir des pyrazoles poly-substitués de façon contrôlée était donc très intéressant pour des applications synthétiques.Le deuxième objectif a été d’appliquer cette réaction à la bioconjugaison et notamment au développement de sondes profluorescentes Des coumarines-sydnones subissant un effet d’extinction de fluorescence par le phénomène PeT ont été développées. Suite au couplage avec un alcyne, le pyrazole formé n’éteint plus lafluorescence de la coumarine. Ce type de sondes est très intéressant pour le marquage de biomolécules, car il n’y a aucun parasitage de fluorescence et donc ne nécessite aucun lavage.Le troisième objectif de la thèse a été d’explorer la réactivité des composés mésoioniques pour un alcyne, sous une catalyse au cuivre, dans le but de découvrir de nouvelles réactions click. Un criblage de 24 composés dans 9 conditions de catalyses différentes, faisant plus de 200 réactions réalisées, a été effectué. Deux réactions ont été révélées, dont une très prometteuse. Celle-ci permet dans la même opération de lier deux partenaires tout en libérant un fragment d’un des deux partenaires. Cette réaction a été étudiée dans le but de développer un outil de théranostique où être utilisée pour la mise au point de nouveaux espaceurs clivables. / The first aim of this work was the development of a new regioselective synthetic access to poly-substituted pyrazoles via the CuSAC reaction, previously discovered in the laboratory. The development of new reactions leading to poly-substituted pyrazoles with a full control of regioselectivity is highly interesting for synthetic applications.The second aim of this work was the application of this reaction for the labeling of complex biomolecules. To broaden the scope of the CuSAC, fluorogenic coumarin-sydnones which undergo fluorescence extinction via PeT have been designed and synthetized. Following the coupling reaction, the newly formed pyrazole core allows huge enhancement of the fluorescence signal.This kind of probes is highly interesting in the specific labelling of biomolecules avoiding washing steps.The last project of this thesis have been focused on the discovery of new [3+2] cycloaddition reaction implying a mesoionic compound and a terminal alkyne under copper catalysis. 24 mesoionic dipoles were screened for their ability to react with a terminal alkyne in 9 different catalytic conditions, yielding to more than 200 reactions screened. Two hits were identified, one of them holding great promise. This hit allows an efficient “click and release” reaction which should find tremendous applications, especially in the fields of theranostic and cleavable linker development.

<div><p>The cellular protein pool exists in a state of dynamic equilibrium, such that a balance between protein synthesis and degradation is maintained to sustain protein homeostasis. This equilibrium is essential for normal cellular functions and hence alteration in protein dynamics has several pathological implications in developing and adult tissues. Recent progress in mass spectrometry (MS) and metabolic labeling techniques has advanced our understanding of the mechanisms of protein regulation in cultured cells and less complicated multicellular organisms. However, methods for the analysis of the dynamics of intra- and extra-cellular proteins in embryonic and adult tissues remain lacking.</p><p>To address this gap, we developed a metabolic labeling technique that enables labeling the nascent murine proteome via injection of non-canonical amino acids (ncAAs), which can be selectively enriched by “clickable” tags for identification and quantification. Using this technique, we developed a MS-based method for the selective identification and quantification of the intra- and extra-cellular newly synthesized proteins in developing murine tissues. We then applied this technique to study the dynamic regulation of extracellular matrix (ECM) proteins during embryonic and adolescent musculoskeletal development. We show that the applied technique enables resolving differences in the nascent proteome of different developmental time points with high temporal resolution. The technique can also reveal protein dynamic information that cannot be captured by the traditional proteomic techniques. Additionally, we identified key ECM components that play roles in musculoskeletal development to provide insights into the mechanisms of musculoskeletal tissue regeneration.</p><p>To fully characterize our labeling technique, we developed a mathematical model to describe the biodistribution kinetics of azidohomoalanine (Aha), the most widely used ncAA, in murine tissues. The model enabled measuring the relative rates of protein synthesis and turnover in different tissues and predicting the effect of different dosing regimens of Aha on the degree of protein labeling. Finally, we analyzed the plasma metabolome of Aha-injected mice to investigate the impact of Aha incorporation on normal physiology. The analysis revealed that Aha administration into mice does not significantly perturb metabolic functions. Taken together, the findings presented in this dissertation demonstrate the utility of the ncAA labeling technique in mapping protein dynamics in mammalian tissues. This will ultimately have a significant impact on our understanding of protein regulation in health and disease. </p></div><br>

Studies and development of artificial metalloenzymes have developed into vibrant areas of research. It is expected that artificial metalloenzymes will be able to combine the best of enzymatic and homogenous catalysis, that is, a broad catalytic scope, high selectivity and activity under mild, aqueous conditions. Artificial metalloenzyme consist of a host protein and a newly introduced artificial metal center. The host protein merely functions as ligand controlling selectivity and augmenting reactivity, while the metal center determines the reactivity. Potential applications range from catalytic production of fine chemicals and feedstock to electron transfer utilization (e.g. fuel cells, water splitting) and medical research (e.g. metabolic screening). Particularly modern asymmetric synthesis is expected to benefit from a successful combination of the power of biocatalysis (substrate conversion via multi-step or cascade reactions, potentially immortal catalyst, unparalleled selectivity and optimization by evolutionary methods) with the versatility and mechanism based optimization methods of homogeneous catalysis. However, so far systems are either limited in structural diversity (biotin-avidin technology) or fail to deliver the selectivities expected (covalent approaches). This thesis explores a novel strategy based on the site-selective incorporation of unnatural, metal binding amino acids into a host protein. The unnatural amino acids can either serve directly as metal binding centers can be used as anchoring points for artificial metallo-cofactors. The identification expression, purification and modification of a suitable protein scaffolds is fundamental to successfully develop this field. Chapter 2 and 3 detail a rational approach leading to a highly engineered host protein. Starting with fluorescent proteins, which combine high thermal and pH stability, high expression yields, and fluorescence for ease of quantification and monitoring an efficient and fast purification protocol was developed first. The purification protocol uses a combination of heat precipitation and three-phase-partitioning (TPP). It provides high yield and purity without requiring any tag. Building on the favourable properties of fluorescent proteins, the non-metal binding, highly stable host-scaffold mTFP* was generated through rational design. The incorporation of artificial metal binding sites, the allowed the selective formation of artificial metalloenzymes, which show catalytic activity and moderat to good chiral induction in the Diels-Alder Cyclization and Friedl-Crafts Acylation Chapter 4 of the thesis describes the use of UAA incorporation to generate artificial metal binding sites. Computational studies and homology modelling successfully highlighted several positions in mTFP*, which are particularly suitable for UAA incorporation without any disruption of the protein structure. Application of a functional orthogonal aaRS/tRNA pair developed by P.G. Schultz and co-workers allowed the site-specific incorporation of UAAs in the host protein framework. Changes in fluorescence intensity revealed preferences of varieous UAAs for specific incorporations sites. The three UAAs, pIF, pAzF, and pEynF were incorporated into mTFP* in good yields, while pBF does only deliver low protein yields. A successfully established on-protein MIYAURA borylation reaction allows convert well-incorporated pIF into pBF circumventing the problem of low expression yields. Chapter 5 details the use of the azide-functionality of pAzF for the bioconjugation of artificial metal-binding cofactors through CuAAC. The triazole ring formed during this reaction serves as an additional moderate σ -donor/π –acceptor ligand of the metal binding site. We demonstrated the potential of site-specific modifications within the protein host with a versatile subset of artificial cofactors. Following transition metal binding, the newly created metal sites show catalytic activities that nature does not provide. The proof of concept study highlights the potential of the present mTFP* based catalysts in asymmetric Tsuji Trost allylation reactions and Diels-Alder cycloadditions. Dual anchoring of the cofactor lead to increased enantioselectivities, which is a direct result of a better-defined orientation of the catalytic center on the protein surface. Following the utilization of the CuAAC click reaction for the generation of artificial metalloenzymes, the last chapter of this thesis reports the development of a heterogeneous catalyst system for this reaction, which overcomes limitations of homogenous protocols. The recyclable core-shell structured Cu2O/Cu-nanowire catalyst is highly active, does not lead to protein precipitation, can be filtered off after the reaction and provides copper free bioconjugation products.

Durant ma thèse, mes études ont été axées sur le développement de nouvelles sondes et des protocoles chimiques pour l'élucidation des mécanismes d'action et de résistance pour les trois médicaments anticancéreux (cisplatine, le vorinostat, topotécan). L'idée de sondes chimiques qui peuvent être étiquetés post-traitement in cellulo avec des fluorophores par exemple Alexa Fluor 488 ou affinité des fragments par exemple biotine, nous a fasciné pour effectuer petite visualisation de molécule par microscopie confocale, ou pour développer des protocoles tirer vers le bas pour les petites cibles moléculaires d'isolement. Beaucoup d'attention a été accordée à catalysée par du cuivre 1, 3 dipolaire cycloaddition Huisgen, connu sous le nom ''click'' la chimie au cours de la dernière décennie, car il est l'une des premières réactions qui peuvent être considérés comme des bio-orthogonale. Toutes les sondes portent soit un alcyne ou groupement azoture stratégiquement positionnés qui leur permet de participer à la réaction de clic avec des fluorophores ou biotine alcyne ou azoture fonctionnalisés que countrparts, et dans le même temps de conserver le profil pharmacologique du médicament parental. Un certain nombre de défis synthétiques ont été overcomed pour la préparation d'une sonde chimique de base de cisplatine. Les efforts visant à synthétiser des analogues alcynes fonctionnalisés de cisplatine ont été infructueuses, la sonde chimique à base de cisplatine était donc fonctionnalisés azoture. La mise au point d'un protocole d'imagerie pour la visualisation de lésions de l'ADN platiné nous a permis de cribler une banque limitée de petites molécules en même temps que la sonde de cisplatine, afin d'identifier des médicaments qui peuvent moduler le cisplatine ciblage ayant des lésions de l'ADN platiné comme une lecture. Il est frappant, nous avons constaté que le vorinostat a eu un effet dramatique sur motif de coloration de la sonde de cisplatine. D'autres études ont démontré que le prétraitement des cellules avec vorinostat augmente charge de platine sur certains loci génomiques. En outre, une évaluation biologique plus approfondie a montré que la combinaison de vorinostat avec des médicaments de platine atténue les dommages à l'ADN synthèse voie de tolérance de translésionnelles (TLS), ainsi, ce qui conduit à la mort cellulaire. Enfin, je l'ai mis au point un protocole tirer vers le bas pour l'isolement de l'ADN qui est lié à la cisplatine en étiquetant la sonde en platine avec un fragment de biotine. Cartographie des interactions ADN-platine en utilisant le séquençage à haut débit profonde est en cours d'exécution. Vorinostat sonde chimique à base a été préparé dans une voie de synthèse en quatre étapes. Bien que le vorinostat est un médicament connu pour inhiber des histone désacétylases (HDAC), petite visualisation de molécule a indiqué d'abord un profil de coloration cytoplasmique. Les futures études dans notre laboratoire se concentrera sur le développement d'un protocole déroulant, afin de caractériser complètement le vorinostat interactome. Quoique, trois sondes chimiques à base de topotécan différents ont été préparés de la personne a été visualisé les succès par microscopie confocale. L'échec a été attribué à l'échec de la réaction "click" pour marquer la sonde avec le fluorophore. Le topotécan est une petite molécule qui agit comme un inhibiteur d'interface, formant ainsi un complexe ternaire avec l'ADN et la topoisomérase 1. L'encombrement stérique généré par le complexe ternaire autour de la sonde, dicte l'inaccessibilité de l'alcyne de la sonde de "click" réactifs. / During my PhD, my studies have been focused on the development of novel chemical probes and protocols for the elucidation of the mechanisms of action and resistance for three anticancer drugs (cisplatin, vorinostat, topotecan). The idea of chemical probes that can be tagged post treatment in cellulo with fluorophores e.g. ALEXA FLUOR 488 or affinity moieties e.g. biotin, has fascinated us to perform small molecule visualization via confocal microscopy, or to develop pull down protocols for isolation small molecule targets. Much attention has been given to copper catalyzed 1, 3 dipolar Huisgen cycloaddition, known as ‘’click’’ chemistry over the past decade, since it is one of the first reactions that can be considered as bio-orthogonal. All the probes bear either an alkyne or azide moiety strategically positioned that allows them to participate in the click reaction with alkyne or azide functionalized fluorophores or biotin as countrparts, and at the same time to retain the pharmacological profile of the parental drug.A number of synthetic challenges have been overcomed for the preparation of a cisplatin based chemical probe. Efforts to synthesize alkyne functionalized analogues of cisplatin were unsuccessful, thus cisplatin based chemical probe was azide functionalized. The development of an imaging protocol for the visualization of platinated DNA lesions has enabled us to screen a limited library of small molecules along with the cisplatin probe, in order to identify drugs that can modulate cisplatin targeting having platinated DNA lesions as a readout. Strikingly, we found that vorinostat had a dramatic effect on cisplatin probe staining pattern. Further studies have demonstrated that pre-treatment of cells with vorinostat increases platinum loading on certain genomic loci. Furthermore, a more in depth biological evaluation has demonstrated that the combination of vorinostat with platinum drugs attenuates the DNA damage tolerance pathway translesion synthesis (TLS), thus, leading to cell death. Finally, I have developed a pull down protocol for the isolation of DNA that is bound to cisplatin by tagging the platinum probe with a biotin moiety. Mapping of DNA-platinum interactions using deep high throughput sequencing is currently running.Vorinostat based chemical probe has been prepared in a four step synthetic route. Although, vorinostat is a drug known to inhibit histone deacetylases (HDACs), small molecule visualization has indicated primarily a cytoplasmic staining pattern. Future studies in our laboratory will focus on the development of a pull down protocol, in order to fully characterize vorinostat interactome.Albeit, three different topotecan based chemical probes have been prepared none of the them has been successfully visualized by confocal microscopy. The failure has been attributed to the failure of the “click” reaction to tag the probe with the fluorophore. Topotecan is a small molecule that acts as an interfacial inhibitor, thus forming a ternary complex with DNA and topoisomerase 1. The steric hindrance generated by the ternary complex around the probe, dictates the inaccessibility of the alkyne moiety of the probe to “click” reagents.

Ce manuscrit débute par un panorama général de la chimie des carbènes vinyliques. Nous nous sommes ensuite intéressés à la génération de tels carbènes à partir de cyanoazétidines, qui conduisent à la formation d’amines homopropargyliques. L’extension de cette réactivité aux cyanoépoxydes nous a menés à la découverte d’une voie de synthèse d’ α-hydroxy-β-azidotétrazoles (AHBATs), qui ont fait l’objet d’une application originale en chimie de ligation. Ainsi, ces AHBATs permettent de réaliser des réactions click de CuAAC de façon orthogonale et itérative. Enfin, la dernière partie de ce manuscrit est consacré à l’étude mécanistique et à l’optimisation de la décomposition d’ α-hydroxytétrazoles en alcynes vrais. / This manuscript begins with a general description of the chemistry of alkylidene carbenes. We then studied the generation of such carbenes from 2-cyanoazetidines, leading to the formation of homopropargylamines. The extension of this reactivity to cyanoepoxides lead us to discover a way to synthesize α-hydroxy-β-azidotetrazoles (AHBATs), that appeared to have an interesting application in ligation chemistry. These AHBATs allow to realize sequential and iterative CuAAC reactions in an orthogonal manner. Finally, the last part of this manuscript describes the mechanistic and optimization studies of the decomposition of α-hydroxytetrazoles into alkynes.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20418号 / 農博第2203号 / 新制||農||1047(附属図書館) / 学位論文||H29||N5039(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 三芳 秀人, 教授 宮川 恒, 教授 森 直樹 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21161号 / 農博第2287号 / 新制||農||1060(附属図書館) / 学位論文||H30||N5135(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 小川 順, 教授 阪井 康能 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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<p>This project is undergoing the patent application, so it is confidential and should not be disclosed. Further questions can be asked by contacting Dr. Jeroen Goos, whose contact information was shown in the supervisor section.</p>