Très récemment, notre équipe a mis en évidence une réaction dite de ligation et coupure entre une famille de composés mésoioniques, les sydnone-imines, et les cyclooctynes. Cette réaction bioorthogonale agit selon un processus en deux étapes, une cycloaddition [3+2] suivie d’une rétro Diels-Alder, qui génère deux nouveaux composés : un produit de ligation et un produit de coupure. L’objectif de cette thèse consiste à améliorer la cinétique de réaction entre ces deux partenaires afin de pouvoir l’utiliser en tant qu’outil pour la libération contrôlée de principes actifs in vivo.Trois stratégies ont été développées lors de cette thèse afin d’optimiser ce système réactionnel : l’étude d’une relation structure/réactivité du partenaire sydnone-imine vis-à-vis de la réaction bioorthogonale; l’utilisation de micelles constituées d’amphiphiles possédant un motif sydnone-imine en tant que lien clivable entre la partie hydrophobe et la partie hydrophile de la molécule; et enfin, l’étude de l’utilisation de la reconnaissance moléculaire entre deux brins d’acides nucléiques peptidiques (ANP) complémentaires. / Recently, our laboratory has discovered a click and release reaction involving iminosydnones, a family of mesoionic compounds, and cyclooctynes. This bioorthogonal reaction occurs via a two step process: a [3+2] cycloaddition followed by a retro Diels-Alder, to give two new compounds: a click product and a release product.The main goal of this work is to improve the kinetic of the reaction between these two partners in order to use it as a powerful tool for in vivo drug delivery. Three strategies were developed during this thesis to optimize this reaction system: the study of a structure/reactivity relationship of the iminosydnone partner regarding the bioorthogonal reaction; the development of micelles built by amphiphiles containing an iminosydnone moiety as a cleavable linker, strategically located between the hydrophobic and the hydrophilic part of the compound and finally, the use of molecular recognition between two peptide nucleic acids (PNA) complementary strands.

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Molecular electronics based on bottom-up electronic circuit design is a potential solution to meet the continuous need to miniaturize electronic devices. The development of highly conductive molecular wires, especially for long distance charge transfer, is a major milestone in the molecular electronics roadmap. A challenge presented by single molecule conductance is to define the relative influence of the molecular "core" and the molecular "interconnects" on the observed currents. Much focus has been placed on designing conductive, conjugated molecules. However, the electrode-molecule contacts can dominate the responses of metal-molecule-metal devices. We have experimentally and theoretically probed charge transfer through single phenyleneethynylene molecules terminated with thiol and carbodithioate linkers, using STM break-junction and non-equilibrium Green's function methods. The STM break-junction method utilizes repeatedly formed circuits where one or a few molecules are trapped between two electrodes, at least one of which has nanoscale dimensions. The statistical analysis of thousands of measurements yields the conductance of single molecules. Experimental data demonstrate that the carbodithioate linker not only augments electronic coupling to the metal electrode relative to thiol, but reduces the barrier to charge injection into the phenyleneethynylene bridge. The theoretical analysis shows that sulfur hybridization provides the genesis for the order-of-magnitude increased conductance in carbodithioate-terminated systems relative to those that feature the thiol linker. Collectively, these data emphasize the promising role for carbodithioate-based connectivity in molecular electronics applications involving metallic and semi-conducting electrodes. One of the strategies for building molecular wires that can transfer charge over long distance is to incorporate metal ions into the conductive molecular core. Peptide nucleic acid (PNA) is a great candidate for this purpose. Studying the conductivity of PNA can not only contribute to a better understanding of charge transfer through biomolecules, but can also help develop better molecular wires and other building blocks of molecular electronics. We study the charge transfer of PNA molecules using the STM break-junction technique and compare with traditional macroscopic voltammetric measurements. By measuring the resistance of different PNA molecules, we hope to develop a deep understanding of how charge transport though PNA is affected by factors such as the number and type of natural and artificial bases, embedded metal ions, pH, etc. Self-assembled monolayers (SAMs) of porphyrins are of great interest due to their diverse applications, including molecular devices, nano-templates, electrocatalysis, solar cells, and photosynthesis. We combined a molecular level study of the redox reactions using electrochemical scanning tunneling microscopy (EC-STM) with a macroscopic electrochemical technique, cyclic voltammetry (CV), to study two redox active porphyrin molecules, TPyP (5,10,15,20-Tetra(4-Pyridyl)-21H,23H-Porphine) and 5, 10, 15, 20-tetrakis (4-carboxylphenyl)-21H, 23H-porphine (TCPP). We showed that the adsorbed oxidized TPyP molecules slowly change to brighter contrast, consistent with the appearance of the reduced form of TPyP, under reduction condition (0.0VSCE). The time scale of the slow reduction is in the order of tens of minutes at 0.0VSCE, but accelerates at more negative potentials. We propose that protonation and deprotonation processes play an important role in the surface redox reaction due to geometric restriction of the molecules adsorbed on the surface. EC-STM and CV experiments were performed at various pH values to investigate the mechanism of this anomalously slow redox reaction. Our results show that the increased concentration of H+ hinders the reduction of porphyrins, a feature that has not been reported preciously. This provides insight into the details of the surface redox reaction. / Chemistry

Le but de cette thèse a concerné le développement de deux types de structures oligomériques contraintes, basées soit sur des dérivés non naturels d’acides aminés cycliques, soit sur des dimères cycliques de Peptide Nucleic Acids (PNA), en vue d’analyser leur tendance à adopter des conformations pré-organisées, imitant les conformations actives des protéines ou des acides nucléiques. La première partie de cette thèse a trait à l’élaboration de synthons clefs dérivant d’acides α-aminés cycliques non naturels (acides 4-oxopipécoliques 6-substitués), à leur utilisation potentielle dans la synthèse de peptidomimétiques contraints, homogènes et hétérogènes, ainsi qu’à leurs limites dans cette utilisation. Dans le cadre de ce travail, une nouvelle voie de synthèse permettant d’accéder à des résidus N-protégés d'acides 4-oxo-pipécoliques 6substitués a été mise au point. La deuxième partie de cette thèse concerne l’élaboration de dimères d’α-PNA (di-α-PNA) cycliques, dans lesquels les chaînes latérales de deux monomères d’α-PNA consécutifs sont «agrafées» via un pont lactame. Une stratégie de synthèse a tout d'abord été développée en phase liquide, puis appliquée à la synthèse en phase solide de di-α-PNA «agrafés» modèles, incorporant des bases nucléiques thymine. / The purpose of this thesis concerned the development of two kinds of constrained oligomeric structures, based either on unnatural cyclic α-amino acids derivatives or on cyclic Peptide Nucleic Acid (PNA) dimers, in view of analyzing their propensity to adopt pre-organized conformations mimicking the active conformations of proteins or nucleic acids. The first part of this thesis reports on the elaboration of new cyclic αamino-acids (6-substituted 4-oxopipecolic acids) building blocks, their potential use in the synthesis of constrained homogenous and heterogeneous peptidomimetics as well as their limitations in this use. As part of this work, a new methodology has been developed for the synthesis of N-protected 6-substituted 4-oxo-pipecolic acids residues. The second part of this thesis reports on the elaboration of constrained α-PNA dimers (di-α-PNA), in which the side-chains of two consecutive α-PNA monomers are “stapled” via a lactam bridge. A synthetic orthogonal strategy has been first developed in liquid-phase then applied to the solid-phase synthesis of models “stapled” di-α PNA incorporating thymine nucleobases.

Im ersten Teil der Arbeit wurde die Verwendung von Präkursor microRNA-21(pre-miR21)-spezifischen Peptidnukleinsäure(PNA)-Sonden zur Inhibierung der Dicer-vermittelnden miRNA-Reifung untersucht. Im Gegensatz zur Arbeitshypothese wurde bei der Behandlung von Zellen mit den pre-miR21-spezifischen PNA-Sonden jedoch keine Änderung des miR-21 Niveau beobachtet. Um die Hybridisierung der Sonde an die Zielsequenz nachzuweisen, wurden fluorogene Hybridisierungssonden zur erzwungenen Interkalation (FIT-Sonden), unter Verwendung des Interkalationsfarbstoffes Thiazolorange (TO), entwickelt. Wie vorläufige Ergebnisse zeigen, könnte die TO-PNA Sonde für die Unterscheidung von Zellen mit hohem miR-21-Gehalt nützlich sein, aber eine weitere Verbesserung der Sonde ist noch erforderlich. Im nächsten Teil der Arbeit wurden neuartige FIT-Sonden für die Analyse der Dicer-vermittelnden miR-21-Reifung entwickelt. Um die gleichzeitige Detektion der entstehenden pre-miR21 und der antisense miR-21 (as-miR21) in Echtzeit zu ermöglichen, wurden die Verwendung von spektral unterscheidbaren FIT-Sonden auf Quinolinblau(QB)-und TO-Basis getestet. Das entwickelte Sonden-Paar ermöglichte die Analyse der rhDicer-Reaktion. Dabei wurde entdeckt, dass die rhDicer-Reaktion an der in vitro transkribierten pre-miR21 unspezifisch spaltet. Zusätzlich wies die kürze as-miR21 spezifische TO-Sonde (7nt) eine Sensitivität gegenüber der Anwesenheit des Ago-2 Proteins auf. In der Zukunft könnten die entwickelten Sonden für schnelle in vitro Screenings neuer Dicer-und Ago-2-Inhibitoren angewendet werden. Im zweiten Teil der Dissertation wurde die Verwendung von niedermolekularen Inhibitoren (small molecular inhibitors, SMIs) getestet. Zusammenfassend könnten die zwei identifizierten SMIs für die Inhibierung der miR-122-Reifung genutzt werden, allerdings bleibt die Spezifität der SMIs fraglich und mögliche off-target-Effekte können nicht ausgeschlossen werden. / MicroRNAs (miRNAs) represent small non-coding RNA molecules that mostly negatively regulate gene expression. To yield mature miRNAs, primary miRNA precursors go through two consequent cleavages by Drosha and Dicer RNAse. This work describes the development of tools for inhibition und monitoring the dicer-mediated miRNA processing. Here, peptide nucleic acid (PNA) based probes, targeting the precursor miR-21 (pre-miR21), were designed for inhibition the dicer-mediated miR-21 maturation. In contrast, no change in miR-21 level was observed after cell treatment with the pre-miR21 specific PNA probes. To detect the probe/target hybridization state, the fluorogenic forced intercalation (FIT) PNA probes, bearing thiazole orange dye (TO), were developed. As preliminary results show, the FIT PNA probe might be useful for discrimination of high miR-21 abundant cells, but further probe improvement is still required. To monitor the pre-miR21 cleavage, the combination of the two spectrally distinguishable FIT PNA probes, bearing quinoline blue (QB) and TO fluorophore, was developed to allow the rapid and simultaneous detection of pre-miR21 and antisense mature miR-21 (as-miR21). The probe set was successfully used for detection of the modelled dicer reaction. However, the monitoring of rhDicer reaction have revealed that rhDicer cleaves the in vitro transcribed pre-miR21 nonspecifically. Additionally, the short as-miR21 specific TO PNA probe (7nt) was responsive to the presence of Ago-2 protein. In future, the developed probes can be applied for the fast in vitro screening of new Dicer and Ago-2 inhibitors. In the second part of this work, an alternative approach, small molecular inhibitors (SMIs), was tested. Two identified pre-miR122-targeting SMIs might be used for inhibition of the miR-122 maturation, although, a specificity of these SMIs remains questionable and possible off target effects cannot be excluded.

Model ceria catalysts were evaluated for NOx storage and desorption performance under lean conditions. Three different storage temperatures (80 °C, 120 °C, and 160 °C) were utilized to evaluate NOx storage. Higher temperatures resulted in higher NOx storage. It was observed that storage of platinum promoted ceria resulted in higher NOx storage compared to promotion with palladium. NOx desorption behavior of platinum promoted ceria indicated that the majority of NOx is released at high temperatures (> 350 °C), comparatively palladium promotion released more of the stored NOx at lower temperatures. Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) indicated that platinum promotion results in NOx storage as thermally stabile nitrates, while palladium promotion results in NOx storage as thermally labile nitrites. Doping ceria with trivalent rare earth oxides has been shown to improve NOx storage by generating lattice oxygen vacancies. Ceria doped with Pr, Y, La, Sm, and Nd at two different concentrations (5 and 20 mol%) and promoted with Pt were evaluated. Doping ceria with 5% Sm, Nd, and Pr improved the amount of NOx stored while the addition of Sm and La did not improve storage. Upon increasing dopant concentration, NOx storage decreased in all cases but Pr. However, increasing Pr concentration was found to increase NOx storage as well as low temperature NOx release. Ceria doped with Pr promoted with Pd increased the amount of NOx released at lower temperatures compared to Pt promotion, although palladium promotion resulted in lower storage. Similar DRIFTS spectra were obtained with Ce-Pr when promoted with Pt or Pd compared to model catalysts. Platinum promotion results in the storage of NOx at nitrates, which require high temperatures for removal. Comparatively, Pd promotion results in NOx stored at nitrites requiring lower temperatures for removal. Ceria doped with Pr proved to be promising, although not thermally stable when exposed to high temperatures as may be seen during a DPF clean up. Therefor, stabilizing Ce-Pr catalysts with Zr were evaluated. It was found that stabilizing Ce-Pr with Zr was not found to be beneficial to the catalyst performance.

Development of chiral ligands capable of achieving high selectivity for various asymmetric catalytic reactions has been an important aim of both academia and industry. Nature is capable to selectively catalyze chemical reactions by using enzymes. An ideal catalyst would combine the selectivity of nature and the reactivity of man-made catalysts based on transition metal complexes. The two biomolecules chosen to achieve this are DNA and PNA. DNA is a chiral molecule with high binding selectivity towards small molecules and has been used as ligand for asymmetric catalysis. PNA is an achiral structural analogue of DNA that can form duplexes with DNA. To produce DNA based catalysts it is necessary to introduce a ligand such as a phosphine that will strongly coordinate to transition metals. To achieve this, functionalized linkers need to be introduced into a DNA strand, to covalently couple the phosphine moiety at a specific location of the DNA strand. Amine linkers and several modified nucleosides have been prepared containing thiol and amine functionalities and some of them were successfully introduced into DNA strands to function as linkers for the introduction of phosphine functionalities. Those strands were purified and an adequate procedure was developed for their analysis by MALDI-TOF. Diphenylphosphino carboxylic acids have been coupled to amine modified deoxyuridines by amide bond formation. The same coupling method has been used for oligonucleotides. DNA strands containing phosphine moieties were characterized by MALDI-TOF and ³¹P NMR spectrometry. ³¹P NMR spectroscopy was also used to confirm coordination of a phosphine modified 15-mer to [PdCl(η³-allyl)]₂. The phosphine modified nucleobases were also tested as ligands for palladium catalyzed allylic alkylation and allylic amination with diphenylallyl acetate as substrate although no enantioselectivity was observed. A PNA monomer was also modified with a bidentate sulfur protected phosphine and successfully introduced into a short PNA strand using manual solid phase synthesis. This strand was analyzed by MALDI-TOF. Moreover, preliminary studies were performed to test the use of aptamers as scaffolds for targets containing a ligand functionality.

Développement et évaluation de nouvelles stratégies pour le traitement des hépatites B chroniques, dans le modèle du canard de Pékin infecté par le DHBVL’infection chronique par le HBV est la cause majeure de cirrhose hépatique et de carcinome hépatocellulaire, conduisant à plus d’un million de décès chaque année. Le faible taux de réussite des thérapies actuelles des hépatites B montre la nécessité du recours à des méthodes thérapeutiques alternatives. Ainsi, nous avons étudié une stratégie pertinente reposant sur l’utilisation de molécules antisens (PNAs) couplées à des peptides perméabilisants (CPPs). Nous avons démontré que les PNAs ciblant le signal d’encapsidation du DHBV couplés au CPP pénétraient dans les cellules et conduisait à une inhibition de la réplication virale. De plus, nous avons mis en évidence une activité antivirale du CPP (Arg)8 seul. Nous avons ensuite évaluer le mécanisme d’action antivirale du CPP in vitro et avons démontré qu’il inhibait les stades tardifs de la morphogénèse virale, conduisant à une inhibition forte de la sécrétion des particules virales. Par ailleurs, nous nous sommes intéressés à l’évaluation de stratégies immunothérapeutiques, reposant sur la vaccination génétique. Nous avons démontré les bénéfices de la co-administration de cytokines (IFNγ), avec un vaccin à ADN dirigé contre la grande protéine d’enveloppe du DHBV (preS/S), sur l’amplitude de la réponse humorale et sur le pouvoir neutralisant des anticorps induits. Enfin nous avons évalué les bénéfices d’une approche d’immunisation hétérologue « prime-boost » associant l’immunisation à ADN et un vecteur viral (AdénoCELO) recombinant, codant la protéine preS/S du DHBV et l’IFNγ. Nous avons montré que l’immunisation hétérologue induisait une réponse humorale plus forte que celle induite par l’immunisation homologue. / Development and evaluation of new strategies for treating chronic hepatitis B in the model of Peking duck infected with DHBVChronic infection with Hepatitis B virus (HBV) is the major cause of liver cirrhosis and hepatocellular carcinoma, leading to more than one million deaths each year. The low success rate of current therapies against HBV infection shows the need of alternative therapeutics. Thus, we studied a new strategy based on the use of antisense molecules (PNAs) coupled with cell penetrating peptides (CPPs). We have shown that PNAs targeting the DHBV encapsidation signal coupled to CPPs penetrated into the cells and led to an inhibition of viral replication. In addition, we have demonstrated an antiviral activity of the CCP (Arg)8 itself. We then evaluate the mechanism of antiviral action of this CPP in vitro and have shown that it inhibited the late stages of viral morphogenesis, leading to a strong inhibition of the release of viral particles. Furthermore, we were interested in evaluating immunotherapeutic strategies, based on DNA vaccination. We have demonstrated the benefits of co-administration of cytokines (IFNy), with a DNA vaccine directed against the DHBV large envelope protein (preS/S), enhancing the magnitude of humoral response and enhancing neutralizing anti-DHBV antibody response. Finally we evaluated the benefits of a heterologous immunization approach or prime-boost immunization involving DNA vaccination and a recombinant viral vector (AdenoCELO) encoding the DHBV preS/S and IFNy proteins. We have shown that heterologous immunization induced a humoral response stronger than that induced by homologous immunization. By contrast, the heterologous prime-boost strategy was less effective than homologous DNA immunization for therapy of chronic DHBV-carrier ducks.