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The pi-electron oligomers: Their synthesis and properties This diploma thesis is focused on the synthesis of p-oligophenyleneethynylene rods (dimer and trimer) containing laterally attached naphtalenediimide units as electron acceptor groups. These functionalised short oligomers are intended to serve as model oligodentate acceptors in the study on multiple interactions with electron rich molecules. The oligomers were assembled from building blocks such as aryl iodides and aryl alkynes bearing a naphthalenediimide unit. The functionalised monomers were combined in a stepwise way by using Sonogashira reaction to form the target p-oligophenyleneethynylene oligomers. The introductory UV-VIS spectroscopic studies on charge transfer complexes between electron donor (pyrene) and electron acceptor (a naphthalenediimide derivative) were performed. In addition, multiple noncovalent interaction between the electron acceptor dimer containing two naphthalenedimide moieties and the electron donor dimer containing two pyrene moieties were investigated by using 1 H NMR titration. The resulting oligomers and their precursors were characterized by using 1 H NMR, 13 C NMR, MS and IR spectroscopy.

L’acide γ-aminobutyrique ou GABA est le principal neurotransmetteur inhibiteur présent dans le système nerveux central (CNS). Afin d’obtenir un nouveau dérivé cyclobutanique du GABA, le cis-3,4CB-GABA, sous forme énantiomériquement pure, deux stratégies de synthèses efficaces et reproductibles ont été mises au point. Ces deux voies de synthèse impliquent toutes les deux une étape-clé de photocycloaddition [2+2] qui permet de créer le cycle à 4 chaînons. La première consiste en une homologation de l’acide cis-2-aminocyclobutanique (cis-ACBC), et la deuxième est une synthèse multi-étape qui utilise le caprolactame comme composé de départ.D’autre part, grâce à une synthèse stéréosélective du (1R,2S)-cis-2,3CB-GABA, quelques oligomères C- et N-protégés – di, tri, et tétra-peptides – de cet aminoacide ont été préparés. Ceux-ci ont été caractérisés par les techniques de RMN 1D et 2D, IR, RX. Les analyses ont montré qu’il n’existe pas d’interactions non-covalentes (liaisons hydrogène) inter-résidu au sein de ces structures moléculaires. En revanche, la propriété de gélification de ces oligomères dans différents solvants organiques a été mise en évidence. Des solutions et des gels formés à partir de ces peptides ont été analysés par microscope électronique à balayage et des clichés ont été obtenus montrant une organisation du dipeptide et du tetrapeptide en fibrilles. Le tripeptide lui n’a présenté aucun assemblage intermoléculaire régulier. / The γ-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system (CNS). In order to obtain new enantiomerically pure cyclobutanic derivative of GABA, the cis-3,4CB-GABA, two efficient synthetic strategies have been established. Both synthetic routes employed a photocycloaddition [2 +2] protocol, which provided the cyclobutanic ring. The first route involved the homolgation of the cis-2-aminocyclobutanecarboxylic acid (cis-ACBC), whereas the second route is a multi-step synthesis using caprolactam as starting material.On the other hand, the (1R,2S)-cis-GABA-2,3CB was synthetized, and a series of N- and C-protected oligomers of di, tri, and tetrapeptides of this amino acid were prepared. These oligomers were characterized by NMR (1D and 2D) techniques, IR, and X-ray. The analyses have shown that there are no non-covalent interactions (hydrogen bonds) between the residues of each oligomers. However, the gelation property of these oligomers in various organic solvents was demonstrated. Solutions and gels formed from these peptides were analyzed by scanning electron microscopy, and the obtained images showed a fibrous organization of the di- and tetrapeptide, while the tripeptide showed no regular intermolecular assembly.

Malaria is caused by a protozoan parasite belonging to the genus Plasmodia. Plasmodium falciparum is responsible for the fatal form of human malaria. Spread of drug resistant parasites warrants for sound biological understanding of the parasite at both cellular and biochemical level. Heat shock proteins are highly conserved group of proteins required for correct folding, transport, and degradation of substrate proteins in vivo. Hsp60 is found in eubacteria, mitochondria, and chloroplasts, where in cooperation with Hsp10, it participates in protein folding. Keeping in mind the central importance of chaperones in biological processes, our lab has been interested in examining roles of heat shock proteins in malarial parasite during its asexual growth in human erythrocytes. During its life cycle, the parasite continually shuttles between a cold-blooded insect vector with the body temperature of 27°C and a warm-blooded human host with the body temperature of 37°C and parasite experiences episodes of heat shock periodically. Therefore malaria parasite serves as good model to study heat shock protein functions. Like all biological systems, the malaria parasite expresses several chaperones including proteins of the Hsp40, Hsp60, Hsp70, Hsp90 and Hsp100 families. Towards this we have systematically characterized different families of stress proteins Hsp40, Hsp60, Hsp70, Hsp90 as well as Hsp100. In addition to cloning their genes we have studied their expression, localization, abundance, complexes and their biological roles. Earlier studies from our lab showed PfHsp90 is essential for parasite growth and survival in human erythrocytes. Our present study attempts to study heat shock protein 60 of the malarial parasite (PfHsp60). In this connection we have been successful to clone and express PfHsp60 gene from Plasmodium falciparum in E. coli and to raise antibodies specific to PfHsp60. We have examined its expression and import in the mitochondrion of malarial parasite during its asexual growth in human erythrocytes. Analysis of the total parasite lysates resolved by two-dimensional gel electrophoresis followed by western blotting using specific antibodies showed PfHsp60 exhibits an isoelectric point corresponding to its signal uncleaved precursor (pI - 6.2). Mass spectrometric analysis of the spot corresponding to precursor PfHsp60 confirmed the presence of signal peptide region. Co-immunoprecipitation analysis of total parasite lysates with antibodies specific to PfHsp60 showed precursor PfHsp60 to be associated with PfHsp70 and PfHsp90. Co-immunoprecipitation from the mitochondrial and cytoplasmic fraction confirmed the position of mature PfHsp60. Indirect immunofluorescence analysis also showed presence of a pool of PfHsp60 in the cytoplasm of the parasite, in addition to its expected localization in the mitochondrion. Treatment of parasite infected erythrocytes with an inhibitor of Hsp90 disrupted its association with cytoplasmic chaperones and targeted precursor Pfhsp60 for intracellular degradation. On the other hand treatment with the mitochondrial import inhibitor further inhibited the import of precursor PfHsp60 into the mitochondrion and stabilized its interaction with cytosolic chaperones. Previous reports have shown that there are four fold accumulations of PfHsp60 transcripts in heat shocked parasites. However, the expression of PfHsp60 was not induced upon heat shock in the blood stages of P.falciparum. Biochemical data indicate that the mitochondrion is not the source of ATP in the parasite. Furthermore the genome does not seem to encode the critical subunits of Fo-F1 ATP synthase. Yet, the active mitochondrial electron transport chain serves for regeneration of ubiquinone required for pyrimidine biosynthesis. The active electron transport chain is critical for parasite survival. Recent study with the lab-grown 3D7 strain of malaria parasite concluded that mitochondria are not required for energy conversion. Transcriptome analysis of the parasite derived directly from blood samples of infected patients showed that genes encoding the proteins of mitochondrial biogenesis, oxidative phosphorylation, respiration and highlighted the mean expression level for PfHsp60 is dramatically up regulated in parasites. Gene up regulation doesn’t always translate to increase in protein function or metabolic up regulation. When we analyzed the total parasite lysates of field isolates resolved by two-dimensional gel electrophoresis also showed presence of the precursor form of Pfhsp60 in the cytoplasm of the parasite. Overall, our observations indicated accumulation of precursor PfHsp60 in the parasite cytoplasm suggesting an inefficient mitochondrial protein import in the malarial parasite. The defect in mitochondrial protein import is possibly reflective of the compromised energy state of the parasite mitochondrion. This fits with the model that has been reported in mutant strains of yeast, Saccharomyces cerevisiae lacking functional F o-F1-ATPase. These strains were found to grow very poorly under anaerobic conditions and are known to accumulate Hsp60 protein in the cytoplasm mainly its precursor form. Under optimal growth conditions most eukaryotes maintain close co-ordination between gene expression, translation and translocation efficiently. As a result, mitochondrial precursor proteins are usually not found to accumulate in the cytoplasm. To our knowledge this the first report suggesting an inefficient co-ordination in the synthesis and translocation of precursor PfHsp60 and possibly other proteins during asexual growth of malarial parasite in human erythrocytes under optimal growth conditions. Finally, expression of the PfHsp60 gene in E.coli resulted in its association with bacterial GroEL subunits co-fractionating with a size of 920 kDa, corresponding to the tetra decameric form. The observation indicated possible existence of a hybrid chaperonin complex consisting of subunits from ectopically expressed PfHsp60 and endogenous GroEL.

Alzheimer’s disease (AD) is the most common cause of senile dementia worldwide. AD is a neurodegenerative disorder characterized by the loss of memory and language skill, collapse of the cognitive function, and distortion of social behavior. As of today, the onset mechanisms of AD and cure are unknown; however, three hallmarks are commonly encountered: extra and intracellular accumulation of amyloid beta (A!) peptide plaques, formation of intracellular neurofibrillary tangles, and inevitable neuronal death. Hypothetically, a possible scenario provoking or involved in the onset of AD is a cascade effect that starts with an imbalance in the production and clearance of Aß peptide that consequently leads to its accumulation, formation of tau protein tangles and neuronal death. This work studied and characterized the mechanisms governing A! peptide aggregation and the effects of using anti-Aß monoclonal antibodies to modify this process. These mechanisms play an important role in the formation of AD plaques and are critical in the search for therapies involving Aß peptide plaque clearance. Yet, antibody-based therapies for plaque clearance are not well understood, adding to the existing concerns about side effects in humans, hence there is a necessity of knowledge in this matter. In this work different Nterminus, C-terminus, and Mid-domain antibodies were used against Aß peptide species (monomers, oligomers, and fibrils) to probe peptide aggregates modification and disruption. Additionally, construction of a soft supported lipid bilayer membrane was proposed to study the adhesion mechanisms of Aß peptide and interactions with antibodies, mimicking the neuronal cell surface. The main characterization techniques used in this work were: atomic force microscopy (AFM) and transmission electron microscopy that allowed the physical exploration and visualization of the different processes of aggregation in terms of adhesion, size evolution, and distribution of the peptide; and attenuated total reflectance Fourier spectroscopy (ATR/FTIR) which allowed monitoring the change of secondary structures for the peptide during the processes studied. It is endeavored that this work will help to elucidate the effects attributed to the molecular interactions between A! peptide species and antibodies to target Aß plaque’s clearance in the brain of AD patients. Ultimately, this study provides novel information critical for the formulation of effective therapies to prevent and treat AD with less collateral effects. It also represents a contribution to the basic scientific knowledge regarding peptide-antibody interactions with application to other diseases related to protein misfolding.

The use of injectable biomaterials is growing as the demands for minimally invasive procedures, and more easily applicable implants become higher, but their availability is still limited due to the difficulties associated to their design. Each year, more than 700,000 vertebral compression fractures (VCF’s) are reported in the US and 500,000 VCF’s in Europe due to primary osteoporosis only. VCF’s can compromise the delicacy of the spinal canal and also cause back pain, which affects the patient’s quality of life. Vertebroplasty was developed in the 80’s, and has proven to be a safe minimally invasive procedure that can, quickly and sustainably, relieve the pain in patients experiencing VCF’s. However, biomaterials for vertebroplasty still have limitations. For instance, ceramic bone cements are difficult to distinguish from the bone using X-ray techniques. On the other hand, acrylic bone cements may cause adjacent vertebral fractures (AVF’s). Large clinical studies have indicated that 12 to 20% vertebroplasty recipients developed subsequent vertebral fractures, and that 41 to 67% of these, were AVF’s. This may be attributed to the load shifting and increased pressure on the adjacent endplates reached after vertebroplasty with stiff cements. The primary aim of this thesis was to develop better injectable biomaterials for spinal applications, particularly, bone cements for vertebroplasty. Water-soluble radiopacifiers were first investigated to enhance the radiopacity of resorbable ceramic cements. Additionally, different strategies to produce materials that mechanically comply with the surrounding tissues (low-modulus bone cements) were investigated. When a suitable low-modulus cement was produced, its performance was evaluated in both bovine bone, and human vertebra ex vivo models. In summary, strontium halides showed potential as water-soluble radiocontrast agents and could be used in resorbable calcium phosphates and other types of resorbable biomaterials. Conversely, linoleic acid-modified (low-modulus) cements appeared to be a promising alternative to currently available high-modulus cements. It was also shown that the influence of the cement properties on the strength and stiffness of a single vertebra depend upon the initial bone volume fraction, and that at low bone volume fractions, the initial mechanical properties of the vertebroplasty cement become more relevant. Finally, it was shown that vertebroplasty with low-modulus cements is biomechanically safe, and could become a recommended minimally invasive therapy in selected cases, especially for patients suffering from vertebral compression fractures due to osteoporosis.

Scanning ion conductance microscopy (SICM) is a technique for non-contact topographic imaging. In this thesis, a biophysical investigation into Alzheimer's Disease (AD) was carried, with toxic oligomers dosed locally and quantitatively on to single astrocytes using SICM and simultaneously monitoring the response of the target cell. Examination of the effectiveness of antibodies that bind to Abeta or alpha-synuclein (Asyn)peptides depends on the measurement of oligomer-induced abnormal calcium homeostasis in single astrocytes. The method was shown to work at physiological concentrations of oligomers. A series of experiments measuring the reduction in calcium inux in mixtures of antibodies and cerebrospinal fluid (CSF) of AD patients suggested that the binding to co-oligomers composed of Abeta and Asyn may be crucial in the treatment of AD. Furthermore, it may be beneficial to test antibodies before the clinical trial using this assay. The mechanism of this entry of calcium is hypothesised to be the result of the formation of oligomer-induced transient pores in the cell membrane. To verify this hypothesis, a new SICM instrument was built with two nanopipettes; one for dosing and one for detection of the adenosine triphosphate (ATP) release from these pores. A variety of different ATP sensors were made. The best had a sensitivity of 10 micro molar and works as a hexokinase-cofunctioned electrolyte-gated organic field-effect-transistor. However no statistically significant results for ATP release have been obtained in the experiments performed to date. Overall this thesis describes new biophysical methods to study the effect of protein aggregates on live cells and the effectiveness of potential therapies, such as antibodies and nanobodies, to reduce these aggregate induced effects. It can be applied to synthetic aggregates of Abeta or the aggregates present in human CSF.

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Cette thèse décrit le développement d’une gamme d’inhibiteurs de la protéase du VIH-1 et d’un oligomère bio-mimétique comportant en leur sein une ou plusieurs interactions réversibles entre une amine tertiaire et un carbonyle, appelée interaction NCO. Cette interaction est favorisée en milieu fortement protique polaire comme les milieux aqueux.Ces travaux ont permis de mettre au point une synthèse modulaire qui a donné lieu à l’obtention de 7 nouveaux candidats à l’inhibition de la protéase du VIH-1. Les modifications de synthèse ont notamment permis de travailler à de plus grandes échelles et d’apporter une grande versatilité à cette synthèse. Les candidats obtenus ont alors été testés in vitro et in cellulo avec une nouvelle méthode en collaboration avec Lorena Martinez et Pierre Falson, de l’Institut de Biologie et Chimie des Protéines (IBCP). Dans un deuxième temps, nous avons élaboré une nouvelle stratégie de synthèse d’un oligomère bio-mimétique. Plusieurs monomères et voies de synthèse ont été explorés et un tétramère a pu être isolé. Malheureusement, certains obstacles, notamment issus de la purification, ont limités les quantités obtenues ce qui n’a pas permis de pousser l’étude comportementale de ces oligomères. Les travaux présentés ici sont ceux de l’optimisation de la synthèse et des perspectives concernant ce sujet. Enfin ce manuscrit détaille le développement d’un nouveau procédé de synthèse permettant l’obtention de dérivés du 1,4,7-triazacyclononane présentant un motif de N-substitutions 2Ra/Rb, travail ayant abouti au dépôt d’un brevet. / This thesis relates the research performed on the design and synthesis of a new type of HIV-1 protease inhibitors and a new archetype of a bio-mimetic foldamer based on an unusual interaction, the NCO interaction. This interaction occurs between a tertiary amine and a carbonyl group in highly polar and protic media, such as aqueous media. The first half of my work focused on the development of a modular synthesis towards candidates for the inhibition of HIV-1 protease. This research enabled us to work on large scale and to be able to modify at will most of the candidates’ functions. Seven new inhibitors were isolated and tested in vitro and in cellulo with an original method, in collaboration with Lorena Martinez and Pierre Falson, from the Institute of Biology and Chemistry of Proteins (IBCP). The second half of my work was dedicated to the design of a new backbone for a bio-mimetic oligomer. A few strategies were explored and a monomer was chosen to be oligomerized. The coupling enabled the isolation of a tetramer. Unfortunately, serious purification issues limited the quantity of the previous tetramer and no foldamer study could be performed. The work presented here are the synthesis’ optimization and the perspectives to overcome the purification issues. In addition, a new process for the synthesis 1,4,7-triazacyclononanes displaying a 2Ra/Rb N-substitution pattern was developed from diethylenetriamine in only four steps. This work was patented during this PhD.

Cette thèse décrit la fonctionnalisation de poly(triméthylène carbonate) (PTMC) par des motifs à liaisons hydrogène multiples (HBM) ou permettre la réaction de Diels-Alder (DA) dans le but d’obtenir des réseaux thermoréversibles et d’étudier leurs relations structure-propriétés. Des oligomères de PTMC linéaires ont d'abord été synthétisés. Puis des structures polymères supramoléculaires multi-bras à base de PTMC portant des HBM de triuret ou de tétrauret téléchéliques ont ensuite été élaborés à partir d’'urée et d’un diisocyanate. Les constantes d'association (Ka) ont été déterminées par RMN dans CDCl3. L’augmentation de la fonctionnalité HBM ou la réduction des longueurs de chaînes PTMC ont amélioré la résistance au fluage et le module d’Young. Les morphologies et la dynamique de ces structures supramoléculaires ont été étudiées à l’état fondu pour révéler deux modes de relaxation correspondant à deux microdomaines, induits par les interactions entre groupes uréthane et HBM. Par l’étude des dynamiques d’association de PTMC supramoléculaires linéaires bifonctionnels en masse a démontré que seuls des dimères se formaient entre HBM de triuret aux temps courts, conduisant à une extension de chaîne équivalente à une polycondensation. Les Ka de ces triurets ont ensuite été calculé à partir d'un modèle simple et original basé sur des mesures de viscosité à l'état fondu. Des réseaux équivalents de différentes densités ont également été obtenus par la réaction DA entre chaînes de PTMC fonctionnalisées par un furanne et un bismaléimide. Des réseaux ont été obtenus et les effets de la fonctionnalité du furanne sur la densité et les propriétés du réseau ont été mis en évidence. Ce ph-D décrit la fonctionnalisation du poly (triméthylène carbonate) (PTMC) par des motifs de liaison hydrogène (HBM) et des réactions de Diels-Alder (DA) afin d’obtenir des réseaux thermoréversibles et de révéler leurs relations structure-propriété. Les oligomères de PTMC linéaires ont d'abord été synthétisés par polymérisation par ouverture de cycle. Des polymères supramoléculaires multi-bras à base de PTMC portant des HBM de triuret et de tétrauret téléchéliques ont ensuite été synthétisés en utilisant de l'urée et un diisocyanate en tant que lieur. Les constantes d'association (Ka) des HBM triuret et tétrauret ont été déterminées par RMN dans CDCl3. L’augmentation de la fonctionnalité HBM ou la réduction de la longueur de la chaîne PTMC ont doté les réseaux d’une meilleure résistance au fluage et d’un module de Young plus élevé lors des essais de traction. Les morphologies et la dynamique de ces polymères supramoléculaires ont été étudiées à l’état fondu pour révéler deux modes de relaxation correspondant à deux microdomaines, induits par la liaison hydrogène entre les groupes uréthane et HBM .. Par l’étude de dynamique d’association de PTMC supramoléculaires linéaires bifonctionnels en masse, comme un modèle, il a été révélé que seuls des dimères se formaient entre des HBM triuret à des temps courts, conduisant à une extension de chaîne linéaire équivalente à une polycondensation. Les ka de HBM de triuret ont ensuite été calculés à partir d'un modèle simple et original basé sur des mesures de viscosité à l'état fondu. Des réseaux équivalents de différentes densités ont également été obtenus par réaction de Diels-Alder entre une PTMC fonctionnalisée par un furanne et un bismaléimide. Des structures de réseau parfaites ont été obtenues et les effets de la fonctionnalité du furanne sur la densité et les propriétés du réseau ont été mis en évidence. La thermoréversibilité s'est produite de 130 ° C à 160 ° C sur la base de leurs densités. / This ph-D describes the functionalization of poly(trimethylene carbonate) (PTMC) by hydrogen bonding motifs (HBMs) and Diels-Alder (DA) reactions to obtain thermoreversible networks and to reveal their structure-property relationships. Linear PTMC oligomers were first synthesized by ring-opening polymerization. PTMC-based multiarm supramolecular polymers bearing telechelic triuret and tetrauret HBMs were then synthesized using urea and a diisocyanate as a linker. Association constants (Ka) of triuret and tetrauret HBMs were determined by NMR in CDCl3. Increasing the HBM functionality or reducing PTMC chain length endowed networks with better creep resistance and higher Young’s modulus in tensile tests. The morphologies and dynamics of these supramolecular polymers were investigated in the melt state to reveal two relaxation modes corresponding to two microdomains, induced by hydrogen bonding between urethane groups and HBMs.. By the association dynamics study of bifunctional linear supramolecular PTMC in bulk, as a model, it was revealed, only dimers were formed between triuret HBMs at short times, leading to the linear chain extension equivalent to a polycondensation. Ka of triuret HBMs were then calculated from a simple and original model based on viscosity measurements in the molten state. Equivalent networks with different densities were also obtained by Diels-Alder reaction between furan-functionalized PTMC and a bismaleimide. Perfect network structures were obtained and the effects of furan functionality on network density and properties were evidenced. The thermoreversibility was found to occur from 130 °C to 160 °C based on their densities.