La première partie de ce projet à consisté à isoler la lignine à partir de liqueurs industrielles et à la purifier pour s’affranchir des sucres, des minéraux et autres constituants. Pour cela, un protocole efficace en trois étapes a été proposé pour obtenir des échantillons de lignine avec une pureté satisfaisante (95%) et pour récupérer 68% de la lignine initialement présente dans la liqueur alcaline de départ. La lignine alcaline purifiée a ensuite été caractérisée d’un point de vue moléculaire et par analyses thermiques. L’élucidation de la structure de la lignine alcaline a permis d’appréhender sa fonctionnalisation par oxydation. Les analyses par chromatographie d’exclusion stérique de la lignine après oxydation ont montré une diminution de la masse molaire confirmant ainsi le clivage. Trois fractions différentes ont été isolées après l’oxydation de la lignine selon le solvant d’extraction ; d’une part des oligomères (plus ou moins fonctionnalisés) et d’autre part des molécules aromatiques (dont15% de vanilline). Ce travail de thèse aura abouti à la synthèse de composés aromatiques à haute valeur ajoutée (vanilline) et d’oligomères de lignine fonctionnalisés par des fonctions acide carboxylique. Les applications envisageables de ces « polyacides » issus de lignine sont nombreuses pour la formation de nouveaux polymères bio-sourcés tels que des polyesters, polyamides ou encore polyuréthanes. / A valorization of alkaline lignin from an industrial pulping liquor has been proposed for this project. Before considering any chemical modification or potential applications, the lignin structure has been elucidated. An efficient three-steps protocol for extraction and purification of lignin from industrial liquor has been established. This protocol leads to high purity sample of lignin (95%) and allows the recovery (68%) of the lignin initially present in the alkaline liquor. Alkaline lignin has been characterized utilizing analytical methods and thermogravimetric analysis. This precise structure elucidation was critical for proceeding to chemical modification of alkaline lignin. Chemical modification of alkaline lignin has been done by oxidation in alkaline media. Three major oxidized products have been isolated depending on the extraction solvent: oligomers bearing carboxylic groups and aromatic molecules. This thesis work led to the synthesis of value-added bio-sourced chemicals and functionalized oligomers. The polyacids from lignin obtained should be studied to form new biobased polymers such as polyesters, polyamids or polyurethanes.

Les synucléionopathies représentent un groupe de maladies neuro-dégénératives incurables du système nerveux central. Elles regroupent entre autres la maladie de Parkinson, l’atrophie multi-systématisée et la maladie à corps de Lewy. Toutes ces maladies se caractérisent par un déclin progressif des fonctions motrices, cognitives, comportementales et autonomiques. La mal-conformation et l’agrégation de la protéine α-synuclein qui forme des inclusions intraneuronales sont des éléments communs à toutes les synucleinopathies. Ces inclusions portent le nom de corps de Lewy et se forment dans des neurones ou cellules gliales appartenant à des régions cérébrales spécifiques. Elles sont vraisemblablement à l’origine de la perte progressive de neurones dans certaines parties du cerveau. Dans le cas de la maladie de Parkinson et dans d’autres maladies neuro-dégénératives, il a été démontré que la pathologie se propage anatomiquement d’une manière spécifique et prévisible au niveau cérébrale. Ceci suggère donc que la progression de la maladie est étroitement liée au transfert des agrégats d’α-synucléine. Ce procédé est très similaire à celui impliqué dans la maladie du prion qui elle en revanche est infectieuse. Par ailleurs, des inclusions neuronales d’α-synucléine ont été identifiées dans des neurones dopaminergiques d’origine fœtaux qui avaient été transplanté dans des cerveaux de patients parkinsoniens. Cette étude a permis d’envisager pour la première fois la possibilité de la transmission d’inclusions d’α-synucléine entre les neurones. Bien que de nombreuses études aient démontré la propagation d’α-synucléine in vitro et in vivo, le mécanisme permettant ce transfert n’est pas clairement établi. Par conséquent, ma thèse s’attache à étudier le mécanisme de transfert d’assemblages d’α-synucléine (i.e., oligomères et fibrilles). Dans un premier temps, j’ai apporté la preuve que les assemblages d’α-synucléine transfèrent de manière efficace entre les cellules neuronales via les Tunneling nanotubes (TNT). Les TNT sont définis comme étant des ponts membranaires riches en F-actine et permettant de connecter physiquement le cytoplasme de cellules éloignées. Au niveau subcellulaire, j’ai démontré que les assemblages d’α-synucléine qui transfèrent se trouvent dans des lysosomes. En revanche, après le transfert, ces assemblages se retrouvent libres dans le cytoplasme. J’ai également mis en évidence qu’à la suite du transfert, permis par les TNT, les fibrilles d’α-synucléine sont capables de recruter et d’induire l’agrégation de l’α-synucléine soluble afin de perpétuer le processus d’agrégation à l’infinie. Ces résultats indiquent que les TNT peuvent représenter un moyen efficace permettant le transfert d’assemblages d’α-synucléine. Cette découverte offre de nouvelles opportunités pour le développement de nouveaux agents neuro-protectifs contre la propagation des synucléinopathies. / Synucleinopathies are a group of fatal neurodegenerative diseases including Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy, characterized by a chronic and progressive decline in motor, cognitive, behavioral, and autonomic functions. The hallmark of these diseases is the misfolding and aggregation of α-synuclein protein accumulating into intracellular inclusions Lewy bodies in neurons and glial cells which leads to the loss of neurons in specific brain regions. In the case of Parkinson’s disease and other neurodegenerative diseases, the pathology was shown to progress throughout the brain in a specific and predictable manner suggesting that the progression of the diseases is linked to the transfer of aggregated α-synuclein that is reminiscent of prion diseases that are infectious. Importantly, upon transplantation of fetal dopaminergic neurons in the brain of Parkinson’s patients, neuronal inclusions were found in the grafted neurons strongly suggesting that α-synuclein inclusions could transmit between neurons. While several studies showed α-synuclein propagation in vitro and in vivo the mechanism of intercellular transfer remains elusive. The aim of my thesis was to study the mechanism of transfer of α-synuclein assemblies (i.e., oligomers and fibrils) involved in Parkinson’s pathogenesis. I evidenced that α-synuclein assemblies transferred efficiently via tunneling nanotubes (TNT), F-actin based membranous bridges connecting the cytoplasm of remote cells. I demonstrated that, at the sub-cellular level, the transferred α-synuclein assemblies were specifically confined in lysosomes and that upon transfer a large amount of α-synuclein was found free in the cytosol of acceptor cells. Finally, I showed that after TNT-mediated transfer α-synuclein fibrils recruited and seeded the aggregation of the soluble α-synuclein protein in order to perpetuate aggregation. The identification of TNT as an efficient means of α-synuclein transfer opens new avenues to the development of novel therapies targeting the spreading into the brain of amyloidogenic proteins involved in neurodegenerative diseases.

La maladie d’Alzheimer est caractérisée par un déclin progressif des capacités cognitives. Les Aßo induisent des dysfonctionnements de la transmission via une altération des récepteurs au glutamate et une perte de synapses.Nos récents résultats démontrent que le VEGF facilite la plasticité synaptique et la mémoire chez des souris via son action sur son récepteur VEGFR2. Nous avons montré que le VEGF stimule l’insertion synaptique des récepteurs glutamatergiques et la formation de synapses, suggérant ainsi un rôle dans la modulation des altérations synaptiques observées dans la maladie d’Alzheimer.Notre objectif est d’étudier le rôle du VEGF, spécifiquement dans la maladie d’Alzheimer. Tout d’abord, nous avons examiné son expression en relation avec les plaques séniles chez des patients et dans un modèle de la maladie d’Alzheimer. Nos résultats ont démontré une colocalisation entre le VEGF et ces plaques.Afin d’examiner plus finement l’interaction Aß-VEGF, nous avons analysé la liaison entre les Aßo et le VEGF en test ELISA et puces à peptides. Nous avons ainsi démontré un potentiel blocage de l’interaction entre le VEGF et son récepteur, menant à des défauts de son activation.Enfin, nous avons examiné si le VEGF prévient les altérations synaptiques par des approches électrophysiologiques, biochimiques et immunocytochimiques. Nos résultats démontrent que lors d’un traitement aux Aßo, le VEGF restaure la LTP, l’expression des récepteurs au glutamate et limite la perte synaptique.Dans l’ensemble, nos résultats suggèrent que l’interaction Aß-VEGF altère la voie du VEGF chez les patients. De plus, le VEGF réduit la toxicité induite par les Aßo sur les synapses / Alzheimer disease (AD) is characterized by a progressive decline in cognitive abilities. Amyloid-ß oligomers (Aßo) trigger synapse dysfunction through defects in glutamate receptor function and subsequent dendritic spine loss. These synaptic impairments compromise memory and contribute to cognitive deficits.Our recent findings revealed that VEGF facilitates synaptic plasticity and memory in mice through its VEGFR2 receptor in neurons. We showed that VEGF promotes glutamate receptor synaptic insertion and stimulates dendritic spine formation, suggesting it may be a key candidate for alleviating synapse damage in AD.Our objective is to study the role of VEGF in synapse protection in AD models and unravel the underlying mechanisms.First, we examined the VEGF expression pattern in postmortem brain tissue from AD patients and APPPS1 model of AD. Our results showed a partial colocalization between VEGF and Aß plaques in AD patients and APPPS1 brains.To further investigate the Aß-VEGF interaction, we used Elisa assay and peptide arrays and demonstrated that Aßo binds several domains of VEGF, impedding VEGFR2 activation.Finally, we examined whether VEGF can prevent synapse damage induced by Aßo using electrophysiological, biochemical and 3D modelling approaches. Our results demonstrated that VEGF treatments can restore LTP in Aßo-treated hippocampal slices, glutamate receptor content at synapses and increase dendritic spine density.All together, our results suggest that Aß-VEGF interaction may alter VEGF pathway in AD and that VEGF reduces Aßo-induced toxicity at synapses by modulating glutamate receptor expression and promoting spine formation and/or stabilization

L’utilisation d’oligomères d’α-amino-γ-lactame (Agl-αAA) comme vecteurs de pénétration intracellulaire est décrite dans ce manuscrit. Nous avons montré que ces oligomères structurés en ruban sont capables de traverser la membrane plasmique pour atteindre le cytosol et y délivrer un cargo biologiquement actif. A la différence des séquences peptidiques, ces oligomères ont une très bonne résistance enzymatique. Une nouvelle famille de foldamères d’α-amino-γ-lactame (Agl-βAA) obtenus à partir de séquences /β peptidiques est également décrite. La structure secondaire de ces composés a été étudiée par RMN, IR-TF, CD et DRX. Nous avons montré que ces oligomères sont capables d’adopter une structure stable en hélice 12. De façon remarquable, ces oligomères sont solubles en milieux aqueux malgré une absence totale de chaînes latérales hydrophiles. / The use of α-amino-γ-lactam oligomers (Agl-αAA) as cell penetrating vectors are described in this work. These ribbon structured oligomers are able to cross the cell membrane to reach the cytosol and deliver a biologically active cargo. Unlike peptide sequences, these oligomers display a strong enzymatic resistance. A new family of α-amino-γ-lactam oligomers (Agl-βAA) obtained from conversion of /β peptide sequences are also described. Secondary structure of these molecules have been studied by NMR, FTIR, CD and XRD. These oligomers are able to adopt a stable 12-helix structure. Unexpectedly, these oligomers are soluble in aqueous mediums without any hydrophilic side chains

Structural studies of peptides are of great importance in developing novel and effective biomaterials ranging from drugs and vaccines to nano materials with industrial applications. In addition, they provide model systems to study and mimic the protein conformations. The ability to generate folded intramolecularly hydrogen bonded structures in short peptides is essential for peptide design strategies, which rely on the use of folding nuclei in the construction of secondary structure modules like helices and β-hairpins. In these approaches, conformational choices at selected positions are biased, using local stereochemical constraints, that limit the range of accessible backbone torsion angles. X-ray crystallographic studies of designed peptides provide definitive proof of the success of a design strategy, and provide essential structural information that can be utilized in the future design of biologically and structurally important polypeptides. Recent trends in peptide research focus on the incorporation of β-, γ- and higher homologs of the α-amino acid residues in designed peptides as they confer more proteolytic stability to the polypeptides. X-ray crystallographic studies of such modified peptides containing non-protein residues are essential, since information on the geometric and stereochemical properties of modified amino acids can only be gathered from the systematic structural studies of synthetic peptides incorporating them. This thesis reports a systematic study of the structures and conformations of amino acid derivatives and designed peptides containing stereochemically constrained α-, β- and γ-amino acid residues and the structural studies of polymorphic peptide helices. The structures described in thesis contain the Cα,α-dialkyalted α-residues α-aminoisobutyric acid (Aib) and 1-aminocyclohexane-1-carboxylic acid (Ac6c), the β-amino acid residue 1-aminocyclohexane acetic acid (β3,3Ac6c) and the γ-amino acid residue 1-aminomethylcyclohexaneacetic acid (gabapentin, Gpn). The crystal structure determination of peptides incorporating conformationally constrained α-, β- and γ- amino acid residues permitted the characterization of new types of hydrogen bonded turns and polymorphs. The studies enabled the precise determination of conformational and geometric parameters of two ω-amino acid residues, gabapentin and β 3,3Ac6c and provided detailed information about the conformational excursions possible for peptide molecules. This thesis is divided into 10 chapters. Chapter 1 gives a general introduction to the stereochemistry of the polypeptide chain, description of backbone torsion angles of α- and ω- amino acid residues and the major secondary structures of α-peptides, β-peptides, γ-peptides and hybrid peptides. A brief introduction to polymorphism and weak interactions, in particular aromatic interactions, is also provided, followed by a discussion on X-ray diffraction and solution to the phase problem. Chapter 2 describes the crystal structures of gabapentin zwitterion and its eight derivatives (Ananda, Aravinda, Vasudev et al., 2003). The crystal structure of the gabapentin zwitterions determined in this study is identical to that previously reported (Ibers, J. A. Acta Crystallogr. 2001, C57, 641-643). Eight of the nine achiral compounds crystallized in centrosymmetric space groups P21/c, C2/c or Pbca, while one derivative (Tos-Gpn-OH) crystallized in non-centrosymmetric space group Pna21 with four independent molecules in the asymmetric unit.The structural studies presented in this chapter reveal that the geminal substituents on the Cβ atom limits the values of dihedral angles θ1 and θ2 to ±60°, resulting in folded backbone conformations in all the examples. Intramolecular hydrogen bonds with 7-atoms in the hydrogen bond turn (C7) are observed in three derivatives, gabapentin hydrochloride (GPNCL), Boc-Gpn-OH (BGPNH) and Piv-Gpn-OH (PIVGPN), while a 9-atom hydrogen bonded turn (C9) is observed in Ac-Gpn-OH (ACGPH). Unique structural features, such as an unusual anti conformation of the COOH group (in ACGPH) and positional disorder of the cyclohexane ring (in BGPNN), indicating the co-existence of both the interconvertible chair conformations, are revealed by the crystal structure analyses. Chapter 3 describes the structural characterization of novel hydrogen bonded conformations of homo oligomers of Gpn. The crystal structures of three peptides, Boc-Gpn-Gpn-NHMe (GPN2), Boc-Gpn-Gpn-Leu-OMe (GPN2L) and Boc-Gpn-Gpn-Gpn-Gpn-NHMe (GPN4) provide the first crystallographic characterization of two new families of polypeptide structures, the C9 helices and C9 ribbons (Vasudev et al., 2005, 2007), in which the molecular conformations are stabilized by contiguous C9 turns formed by the hydrogen bonding between the CO group of residue (i) and the NH group of residue (i+2). The C9 hydrogen bond is characterized by a specific combination of the four torsion angles for the Gpn backbone, with the torsion angles θ1 and θ2 adopting g+/g+ or g /g- conformations. The structural analysis also permits precise determination of hydrogen bond geometry for the C9 structures, which is highly linear in contrast to the analogous γ-turn hydrogen bonds in α-peptides. A comparison of the backbone conformations in the three peptides reveals two classes of C9 hydrogen bonded secondary structures, namely C9 helices and C9 ribbons. The packing arrangement in these γ-peptides follows the same patterns as the helix packing in crystals of α-peptides. Chapter 4 describes ten crystal structures of short hybrid peptides containing the Gpn residue (Vasudev et al., 2007). In addition to the C7 and C9 hydrogen bonded turns which are defined by the backbone conformations at the Gpn residue, hybrid turns defined by a combination of backbone conformations at the α and γ-residues or at the β and γ-residues have been determined. Peptides Boc-Ac6c-Gpn-OH (ACGPH), Piv-Pro-Gpn-Val-OMe (PPGPV) and Boc-Val-Pro-Gpn-OH (VPGPH) reveal molecular conformation stabilized by intramolecular C9 hydrogen bonds, while Boc-Ac6c-Gpn-OMe (ACGPO) and Boc-Gpn-Aib-OH (GPUH) are stabilized by a C7 hydrogen bonded turn at the Gpn residue. An αγ hybrid turn with 12 atoms in the intramolecular hydrogen bonded rings (C12 turns) has been observed in the tripeptide Boc-Ac6c-Gpn-Ac6c-OMe (ACGP3), while βγ hybrid turns with 13 atoms in the hydrogen bonded ring (C13 turns) have been characterized in the tripeptides Boc-βLeu-Gpn-Val-OMe (BLGPV) and Boc- βPhe-Gpn-Phe-OMe (BFGPF). The two βγ C13 turns belong to two different categories and are characterized by different sets of backbone torsion angles for the β and γ residues. A γα C10 hydrogen bond, which is formed in the N→C direction (NHi ••• COi+2), as opposed to the regular hydrogen bonded helices of α-peptides, has also been observed in BFGPF. The Chapter provides a comparison of the backbone torsion angles of the Gpn residue in various hydrogen bonded turns and a brief comparison of the observed hydrogen bonded turns with those of the α-peptides. Chapter 5 describes the crystal structures of three αγ hybrid peptides which show C12/C10 mixed hydrogen bond patterns (Vasudev et al., 2007, 2008a; Chatterjee, Vasudev et al.,2008a). The insertion of gabapentin in the predominantly α-amino acid sequences in Boc-Ala-Aib-Gpn-Aib-Ala-OMe (AUGP5) and Boc-Leu-Gpn-Aib-Leu-Gpn-Aib-OMe results in the observation of helices stabilized by αα C10 (310-turn) and αγ C12 turns. The tetrapeptide Boc-Leu-Gpn-Leu-Aib-OMe reveals a novel conformation, stabilized by C12 (αγ) and C10 (γα) hydrogen bonds of opposite hydrogen bond directionalities. The conformations observed in crystals have been extended to generate C12 helix and C12/C10 helix with alternating hydrogen bond polarities in ( αγ)n sequences. The structure determination of three crystals, providing five molecular conformations, presented in this chapter provides the first crystallographic characterization of two types of helices predicted for the regular αγ hybrid peptides from theoretical calculations. The crystal structure of Boc-Ala-Aib-Gpn-Aib-Ala-OMe also provides an example for the co-existence of left-handed and right-handed helix in the asymmetric unit. Chapter 6 describes the structural studies of αγ hybrid peptides containing Aib and Gpn residues, and is divided into two parts. The first part presents the crystal structure analysis of peptides of sequence length 2 to 4, with alternating Aib and Gpn residues, and illustrates the conformational variability in αγ hybrid sequences as evidenced by the observation of conformational polymorphs (Chatterjee, Vasudev et al., 2008b; Vasudev et al., 2007; Ananda, Vasudev et al., 2005). The peptide Boc-Gpn-Aib-NHMe (GUN), Boc-Aib-Gpn-Aib-OMe (UGU), Boc-Gpn-Aib-Gpn-Aib-OMe (GU4O), Boc-Aib-Gpn-Aib-Gpn-OMe (UG4O) and Boc-Aib-Gpn-Aib-Gpn-NHMe (UG4N), all of which are potential candidates for exhibiting αγ C12 hydrogen bonds, reveal molecular conformations stabilized by diverse hydrogen bonded turns such as C7, C9, C12 and C17 in crystals. The conformational heterogeneity in this class of hybrid peptides is further evidenced by the observation of three polymorphs in the monoclinic space group P21/c for the tetrapeptide Boc-Aib-Gpn-Aib-Gpn-NHMe (UG4N), providing four independent peptide molecules adopting two distinct backbone conformations. In one polymorph, C12 helices terminated with an unusual three residue ( γαγ) C17 turn is observed, while the unfolding of helical conformation by solvent insertion into the backbone is observed in the other two polymorphs. The studies indicate the possible utility of Gpn residue in stabilizing locally folded conformations in the folding pathway, thus permitting their crystallographic characterization in multiple crystal forms. A discussion of the structural and conformational features of Gpn residues determined from all the crystal structures is presented in the Chapter, along with a φ-ψ plot for the Gpn residue. Part 2 of Chapter 6 describes the crystal structures of two octapeptides, Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (GU8) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (LFVUG8), featuring C12 turns at the Aib-Gpn segments (Chatterjee, Vasudev et al., 2009). GU8 folds into a C12 helix flanked by C9 hydrogen bonds at both the termini, while LFVUG8 adopts β-hairpin conformation with a chain-reversing C12 turn at the central Aib-Gpn segment. A remarkable feature of the Aib-Gpn turn in the β-hairpin structure is the anti conformation about the Cβ-Cα (θ2) bond, which is the only example of a Gpn residue not adopting gauche conformation for both θ1 and θ2. The crystal structures of the two peptides, mimicking the two major secondary structural elements of α-peptides in hybrid polypeptides, permits a comparative study of the mode of molecular packing in crystals of α-peptides and hybrid peptides. The chapter also discusses theoretical calculations on αγ hybrid sequences, which reveal new types of C12 hydrogen bonded turns. Chapter 7 describes the crystal structures of conformationally biased tert-butyl derivatives of Gpn. The crystallographic characterization of the E (trans) and Z (cis) isomers of the residue,three protected derivatives and a tripeptide provides examples of C7 and C9 hydrogen bonded conformations, suggesting that the C7 and C9 hydrogen bonds can be formed by Gpn residues with both the chair conformations of the cyclohexane ring. Chapter 8 describes the systematic structural studies of the derivatives and peptides of the stereochemically constrained β- amino acid residue, β3,3Ac6c (Vasudev et al., 2008c). The backbone torsion angles φ and θ adopt gauche conformation in majority of the examples, owing to the presence of a cyclohexane ring on the Cβ atom. In contrast to Gpn, β3,3Ac6c does not show strong preference for adopting intramolecularly hydrogen bonded conformations. Of the 16 crystal structures determined, intramolecular hydrogen bonds involving the β-residue are observed only in 4 cases. The amino acid zwitterion (BAC6C), the hydrochloride (BACHCL) and the dipeptide Boc-β3,3Ac6c-β3,3Ac6c-NHMe (BAC62N) form N-H•••O hydrogen bonds with 6-atoms in the hydrogen bond ring (C6 turns). An αβ hybrid C11 hydrogen bonded turn is characterized in the dipeptide Piv-Pro-β3,3Ac6c-NHMe, which is distinctly different from the C11 hydrogen bonds observed in αβ hybrid peptide helices. Several unique structural features such as a dynamic disorder of the hydrogen atom of the carboxylic acid group (in BBAC) and cis geometry of the urethane bond (in BBAC, BAC62N and BPBAC) have been observed in this study. A comparison of the backbone conformations of β3,3Ac6c with other β- amino acid residues is also provided. Chapter 9 describes the crystallographic characterization of a new polymorph of gabapentin monohydrate and crystal structures of the zwitterions of E and Z isomers of tert-butylgabapentin and its hydrochloride and hydrobromide (Vasudev et al., 2009). A comparison of the crystal structures of the monoclinic form (Ibers, J. A. Acta Crystallogr. 2001, C57, 641-643) of gabapentin monohydrate and the newly characterized orthorhombic form reveals identical molecular conformations and intermolecular hydrogen bond patterns in both the polymorphs. The two polymorphs show differences in the orientation of molecules constituting a layer of hydrophobic interactions between the cyclohexyl side chains. A comparison of the packing arrangements of the zwitterionic amino acid molecules in the crystal structures of gabapentin monohydrate, the tert-butyl derivatives and other co-crystals of gabapentin that had been characterized so far, is provided which would facilitate prediction of new polymorphs of the widely used drug molecule, Gpn. Chapter 10 describes the crystallization of α-peptide helices in multiple crystal forms (Vasudev et al., 2008b). Crystal structures of two peptides, Boc-Leu-Aib-Phe-Phe-Leu-Aib-Ala-Ala-Leu-Aib-OMe (LFF), Boc-Leu-Aib-Phe-Ala-Leu-Ala-Leu-Aib-OMe (D1) in two crystal forms and the crystal structure of a related sequence, Boc-Leu-Aib-Phe-Ala-Phe-Aib-Leu-Ala-Leu-Aib-OMe (D10) permit an analysis of the molecular conformation and packing patterns of peptide helices in crystals. The two polymorphs of LFF, crystallized in the space groups P21 and P22121, reveal very similar molecular conformation (α/310-helix) in both the polymorphic crystals; the two forms differ significantly in the pattern of solvation. The crystal structure determination of a monoclinic (P21) and an orthorhombic polymorph (P21212) of D1 provides five different peptide conformations, four of which are α-helical and one is a mixed 310/α-helix. The crystal structure determination of the three peptides provide an opportunity to compare the nature and role of aromatic interactions in stabilizing molecular conformation and packing and its significance in the observation of polymorphism. An analysis of the Cambridge Structural Database and a model for nucleation of crystals in hydrophobic peptide helices are also discussed.

Functional Dendritic Structures from Bile Acids: Supramolelcular Hosts, Light Harvesters and Drug Carriers Chapter 1. An Overview of Functional Dendrimers. Dendrimers are welldefined, hyperbranched macromolecules that are prepared by highly controlled iterative methodologies. The ability to modulate the size, molecular weight, chemical functionalities and the position and number of functional groups in dendrimers make them promising candidates for a wide variety of applications. In this chapter, three areas 1) hostguest chemistry 2) light harvesting and 3) drug delivery, where dendrimers are increasingly finding applications, are discussed with selected examples. Chapter 2. Hydroxyl Terminated Dendritic Oligomers from Bile Acids: Synthesis and Properties. Bile acids are excellent building blocks for dendritic construction because of their many interesting features. They are readily available, chiral, facial amphiphiles with complementary functionalities. Moreover, due to the large size of the bile acid units, a dendritic structure consisting of only a few such repeat units can have an extended structure with multiple functionalizable groups. (figure 1) The high reactivity of the chloroacetyl group has been exploited for the synthesis of bile acid based first and second-generation dendrons with glycolate linkers and multiple hydroxyl groups. The synthesis involves only a few steps and avoids the use of protecting groups for the terminal hydroxyl groups. The synthesis of a bile acid tetramer is shown here as an example (Figure 1). Carboxyl protected cholic acid was reacted with chloroacetylchloride to generate the trischloroacetylated derivative. This compound on reaction with excess of sodium cholate generated the tetramer with nine hydroxyl groups via displacement of the chlorides. In order to synthesize higher generation dendritic structures, perchloroacetylated firstgeneration dendrons were first synthesized. These were subsequently reacted with excess of sodium deoxcholate to generated secondgeneration dendrons with multiple hydroxyl groups (Figure 2). All the compounds were characterized by H NMR, C NMR, IR, ESIMS/MALDI-TOF, HPLC and elemental analysis(wherever possible) Figure 2. Structure of tridecamer. These dendritic structures with facially amphiphilic bile acid backbones on the periphery were able to solubilize cresol red, a hydrophilic dye, in a nonpolar solvent, thus exhibiting reverse micellar characteristics. Chapter 3. Multiple Naproxen Appended Bile Acid Dendrimers as Light Harvesters and Drug Carriers. Part I. Synthesis and Characterization. Using the same synthetic strategy as in Chapter 2, bile acid based dendritic structures appended with multiple bioactive (S)naproxens were generated as potential drug carriers. The construction of these dendrimers was accomplished using per(chloroacetylated) bile acid dendrons and conveniently displacing all the chlorides with naproxen units. Since naproxen is photoactive with a high fluorescence quantum Figure 3. Structures of secondgeneration dendrimers and a monomer with multiple naproxens. yield, the photophysical properties of these multichromophoric dendrimers could be further explored (Figure 3). By functionalizing the carboxyl group on the side chain with an anthracenyl moiety the energy transfer properties of these dendrimers could be studied. In this section the synthesis of first and secondgeneration dendritic structures with multiple naproxen units at the periphery and benzyl/anthracenyl moiety on the side chain are described (Figure 3). Model compounds using monomeric bile acid units were synthesized for comparison with the dendritic structures. All the compounds were characterized by H NMR, C NMR, IR, ESIMS/MALDITOF, HPLC and elemental analysis (wherever possible). Part II: Absorption, Fluorescence and Intramolelcular Energy Tranfer Studies. Absorption studies showed that the molar extinction coefficients increase linearly with increasing number of naproxen units and the absorption spectra of anthracenyl moiety remain unchanged in all the dendritic systems. These indicated the absence of ground state interaction between the chromophores. In the 275-290 nm absorption region, the molar extinction coefficient of naproxen is much greater than that of the 9-anthracenylmethyl chromophore. Hence excitation in this region would mainly excite the naphthalene chromophore. Upon excitation at 275 nm, there was predominant emission from the anthracenyl moiety in the dendritic structures (containing both chromophores) and the fluorescence intensity increased with increasing number of naproxens(Figure4). This indicated that the dendrimers act as efficient light harvesters with energy transfer from naproxen to anthracene (intramolecular nature of the energy transfer was confirmed through control experiments). (Figure 4: Refer PDF File) The fluorescence and energy-transfer properties were further investigated by time-resolved fluorescence spectroscopy. The presence of fast decay component(s) in the naproxen decay in dendritic structures (containing both chromophores) indicates that its fluorescence is quenched in the presence of anthracene due to energy transfer ((λex 275 nm, λem 350 nm (Figure 5). This was further confirmed by monitoring the fluorescence of the sensitized anthracenyl chromophore (λex 275 nm, λem 436 nm) which exhibited a fast rise comparable to he quenched naproxen lifetime(s). The efficiency of energy transfer was estimated by donor quenching by both steadystate and timeresolved techniques. The dendritic structures exhibited high energy transfer efficiencies (~ 70 – 90 %) with the net efficiency decreasing from the first to second-generation. Part III. In vitro Study of Hydrolysis of Naproxen Appended Bile Acid Prodrugs by Chemical and Enzymatic Methods. The naproxen appended bile acid dendrimers consist of hydrolyzable ester and glycolate linkers. Hence the chemical stability and enzymatic degradation with possible release of naproxen was studied. Two compounds, monomer appended with two naproxens and trimer with four naproxens have been used for the initial investigations (Figure 6). The compounds were found to be highly stable towards chemical hydrolysis and did not show any hydrolysis in phosphate buffer, pH = 7.4 even after 7 days. Since the compounds were not soluble in water, Arabic gum and TritonX were used for emulsification. Figure 6. Structures of monomer and trimer. (Refer PDF File) The enzymatic hydrolysis of the compounds was then studied using Candida Rugosa Lipase. In both cases, there was slow hydrolysis of the substrate and intermediates were formed (with release of free naproxen) which were detected by HPLC (reverse phase column with a UV detector). The trimer underwent much slower hydrolysis compared to the monomer. The intermediates were characterized by absorption and mass (ESIMSQTOF) spectrometry.

The work carried out in this thesis systematically investigates the correlation between microstructures and electronic properties of organic semiconductors. The major directions that were pursued in this thesis are: (i) studies on structure-property relationship by rational design and synthesis of monodisperse oligomers with varying chain-lengths (ii) role of electronic properties and aggregation (microstructures) in governing singlet fission (SF). In the first part of the thesis, the optical, structural and charge transport properties of Diketopyrrolopyrrole (DPP)-based oligomers, as a function of the chain length, has been discussed. The energy bands became wider with an increase in chain length and a gain in backbone electron affinity was observed, with an offset in microstructural order. With an increase in chain length, the tendency to form intramolecular aggregates increased as compared to intermolecular aggregates due to the onset of backbone conformational defects and chain folding. An insight into the solid-state packing and microstructural order has been obtained by steady-state and transient spectroscopy, grazing incidence small angle x-ray scattering (GISAXS), atomic force microscopy (AFM) and transmission electron microscopy (TEM) studies. The charge-carrier mobilities varied in accordance with the degree of microstructural order as: dimer > trimer > pentamer. A library of DPP-DPP based trimers was also generated by modifying the donor chromophore (phenyl, thiophene and selenophene) in the oligomer backbone. Highest n-channel mobility of ~0.2 cm2V-1s-1 was obtained which validated that: (a) the effect of solid-state packing predominates the effect of backbone electronic structure on charge carrier mobility. Although oligomers possess lesser backbone defects than polymers in general, their charge carrier mobilities were not comparable to that of 2DPP-OD-TEG polymer, which forms highly oriented and isotropic edge-on crystallites/microstructures in the thin film, shows high n-channel mobility of 3 cm2V-1s-1 and band-like transport ;(b) although delocalized electronic states are achieved at greater chain lengths, the degree of solid-state microstructural order drastically reduces which leads to lower charge carrier mobilities; (c) conformational collapse resulted in lower electron mobilities and an increase in ambipolarity. The later part of the thesis debates on the relative contribution of electronic structure and aggregation (microstructures) in governing singlet fission (SF). Motivated by the recent SF model in carotenoid aggregates, a DPP-DPP based oligomer was synthesized by incorporating a vinylene bridge to imbue “polyene” character in the chromophore. Transient Spectroscopy (TA) measurements were carried out to monitor the formation of triplet states in the oligomer and to probe the occurrence of singlet fission. Although the oligomer exhibits “polyene” character like a typical “carotenoid aggregate”, it did not show singlet fission because of the additional stabilization of the singlet (S1) state which reduces the ∆EST. This study rationalized the importance of judicious control of band structures as well as microstructures to observe the SF phenomenon in this category of chromophores. The novel synthetic protocol provides the scope to tailor DPP-DPP based materials with desired effective conjugation lengths and side chains and can foreshow great prospects for future generation of organic electronics.

Apresentamos os resultados do estudo das não-linearidades ópticas de origem eletrônica de duas moléculas da classe dos oligômeros de anilina: o dímero e o tetrâmero. Foram medidas quatro concentrações de tetrâmero, puras e também dopadas em 33 e 100%; uma de dímero pura e outra dopada em 100%. As soluções foram preparadas usando dimetil-sulfóxido (DMSO) como solvente e a dopagem foi realizada com ácido clorídrico. As amostras foram caracterizadas por medidas de absorção linear e fluorescência antes das medidas não-lineares. Obtivemos os valores da primeira hiperpolarizabilidade (?) para todas as amostras, o índice de refração não-linear (n2) do tetrâmero dopado e não dopado, e a absorção não-linear em função da intensidade e da concentração do tetrâmero. As medidas foram realizadas através das técnicas de Varredura-Z, absorção não-linear e espalhamento Hiper-Rayleigh. Os resultados foram interpretados em termos da comparação entre diferentes estados de dopagem e da variação da seção de choque do estado fundamental para o primeiro excitado. / We report on the study of electronic optical non linearities in two aniline oligomers: dimer and the tetramer. Four tetramer concentrations were measured, pure and also 33 and 100% doped; one of dimer non doped another 100% doped. The solutions were prepared using dimethyl sulfoxide (DMSO) as solvent and the doping was performed with hydrochloric acid. The samples were characterized by measurements of linear absorption and fluorescence. We obtained the values of the first hyperpolarizability (?) for all samples, the non linear index of refraction (n2) for non doped and doped tetramer, and the non linear absorption in function of intensity and concentration of the tetramer. The measurements were accomplished through the techniques of Z-Scan, non linear absorption and Hyper-Rayleigh Scattering. The results were interpreted in terms of the comparison among different doping states and of the variation of cross-section for the transition from ground to the first excited states.

Depuis quelques années, les oligomères du peptide Aβ sont identifiés comme étant responsables du déclenchement de la pathologie alors que les dépôts amyloïdes sont des conséquences aggravantes de la pathologie. Cependant, les formes oligomériques d’Aβ impliquées dans la pathologie ainsi que l’origine de ces peptides sont toujours débattues. Notre objectif principal était d’identifier des signatures Aβ oligomériques cérébrales et vasculaires et de déterminer si nous pouvions interférer avec ces signatures pour modifier le décours de la pathologie. Nous avons réalisé des analyses biochimiques qualitative des formes d’Aβ dans des échantillons de cerveau et de vaisseaux issus de patients atteints de la MA et de souris transgéniques modèle de la MA. Nous avons montré qu’une même forme Aβ oligomérique (17-18 kDa) est impliquée dans le développement de la pathologie cognitive chez l’homme et chez la souris APP/PS1. Une signature Aβ oligomérique vasculaire spécifique a été observée dans les vaisseaux périphériques et plus particulièrement la veine porte hépatique des souris APP/PS1. De plus, un traitement pharmacologique ciblant l’expression des protéines de transport de l’Aβ a permis de restaurer les profils Aβ oligomériques contrôles dans le cerveau des souris APP/PS1 tout en « chargeant » la veine porte des mêmes souris en Aβ oligomérique. Ces résultats montrent que les signatures Aβ vasculaires et cérébrales sont intimement liées. De plus, nos travaux mettent l’accent sur une possible intervention thérapeutique agissant sur les formes Aβ cérébrales et vasculaires. / Alzheimer's disease (AD) is a complex disorder of the central nervous system that affects an increasing number of people worldwide due to the overall aging of the human population. Vascular factors and mechanisms have emerged as an area of key importance. Accumulating evidence indicates that pre-fibrillar aggregates, specifically the low-molecular weight oligomers of Aβ peptide, are responsible for the synaptic dysfunction and neuronal loss that occur in AD pathology. But, these oligomeric forms implicated in the pathology are currently under debate. Our primary goal was to identify cerebral and vascular oligomeric signatures. Secondly, we try to interfere with these signatures in order to modify the evolution of AD. We realize qualitative analyses of cerebral and vascular oligomers Aβ by western-blot. Vascular and cerebral tissues were extracted from AD patients and from a transgenicmouse model of AD. We demonstrate that the same oligomer Aβ (17-18 kDa) is implicated in the cognitive impairment for patients and APP/PS1 mouse. A specific vascular signature of oligomer Aβ was detected in peripheral vessels and particularly in portal vein from liver of APP/PS1 mouse. Moreover, pharmacological treatment targeting clearance of soluble Aβ restored the control signature of oligomer Aβ in the brain of APP/PS1 mouse. This configurational change was associated with an increase of oligomer Aβ in portal vein from liver. These results show that cerebral and vascular oligomeric signatures were closely linked. Finally, our work emphasizes potential therapeutic strategies for AD by targeting cerebrals and vasculars oligomers Aβ.

Depuis une dizaine d'années, les polymères hyperbranchés sont apparus dans la littérature. Ils possèdent un grand nombre de branchements ainsi qu'un grand nombre de groupes terminaux. La structure globulaire des polymères hyperbranchés les empêche de former des enchevêtrements. Il en résulte un avantage décisif pour leur application sous forme de revêtement de surface: les polymères hyperbranchés ont une viscosité plus faible à l'état fondu que les polymères linéaires. Cela permet aisément de les étaler sous forme de films minces sans utiliser de solvant. De plus, les polymères hyperbranchés possèdent un grand nombre de groupes terminaux qui peuvent être fonctionnalisés avec des monomères photoréticulables.<p>Le but du travail de thèse est d'obtenir de nouveaux revêtements de surface, à partir de polymères hyperbranchés ou de polymères fortement branchés, qui trouveront leur application dans l'industrie chimique.<p><p>La thèse s'articule autour de trois chapitres de synthèse suivis d'un chapitre traitant de la photoréactivité des oligomères linéaires, fortement branchés, et hyperbranchés.<p><p>La première approche de synthèse envisagée est la copolymérisation alternante radicalaire. Divers maléimides ont été engagés dans des copolymérisations radicalaires avec des allyléthers sans succès. <p>Lorsque ces derniers sont remplacés par des vinyls éthers, une copolymérisation alternante est observée. Néanmoins, une importante irreproductibilité est constatée, certains batchs donnant lieu à une gélification.<p><p>La seconde voie de synthèse étudiée est l'approche classique de polycondensation de monomères de type AB2 .Le monomère AB2 est obtenu par addition de Michael de la diéthanolamine sur l'acrylate de méthyle. La polycondensation est concomitante avec l'acrylation des fonctions alcools. La compétition entre ces deux réactions limite les masses molaires accessibles bien que les réactions de transestérification soient catalysées par des dérivés du Zr et que la stoechiométrie ait été variée.<p><p>La troisième voie de synthèse se base aussi sur la réaction de Michael. Des oligomères fortement branchés sont obtenus à partir de 1,6-hexanedioldiacrylate et d'éthylènediamine. Leurs analogues linéaires sont synthétisés en remplaçant l'éthylènediamine par la propylamine. Lors de ces synthèses, il est apparu que les oligomères fortement branchés ont une viscosité supérieure à celle des oligomères linéaires!<p><p>Les oligomères hyperbranchés et acrylés, les oligomères linéaires et leurs analogues fortement branchés ont été étudiés du point de vue de leur photoréticulation sous rayonnement UV. Contrairement à ce qui était attendu, ils se sont montrés moins réactifs que les produits les plus performants de Cytec-Surface Specialties. Lors de cette étude, l'effet bénéfique des mines tertiaires sur l'inhibition par l'oxygène est apparu plus complexe que décrit dans la littérature. / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished