Dissertations / Theses on the topic 'Γ-peptides'

L’élaboration de nouveaux oligomères capables de mimer les propriétés des protéines naturelles est devenue un domaine de recherche très important, non seulement du point de vue structural mais aussi médicinal. Les peptides comportant des acides β-aminés ont été extensivement étudiés tandis que les recherches dans le domaine des γ-peptides sont plus récentes. Néanmoins, ces derniers montrent déjà des propriétés structurales uniques ainsi que des activités biologiques prometteuses.Dans notre laboratoire nous nous intéressons au développement d’une synthèse générale de nouveaux acides β,γ-diaminés à partir d’acides ∝-aminés naturels, notamment à la 3-déoxyaminostatine, et à leur utilisation dans la synthèse peptidique pour obtenir des peptides non-naturels afin d’étudier leurs propriétés conformationnelles. La stratégie de synthèse élaborée dans notre laboratoire et améliorée au cours de ces travaux a permis d’élargir la gamme des acides β,γ-diaminés. Deux diastéréomères cis et trans issus de la L-leucine, de la L- et D-phénylalanine ont été obtenus et engagés dans la synthèse de nouveaux peptides hybrides α/γ. Deux séries de peptides hybrides α/γ ont été étudiées. Les analyses structurales de la série comportant des acides ∝-aminés de configuration L montrent une capacité à adopter des structures secondaires bien définies, stabilisées par des liaisons hydrogènes intramoléculaires, impliquant notamment l’azote situé en β. De plus, une voie de synthèse vers un analogue d’un antibiotique naturel, le gramicidine S, a été proposée. Dans cet analogue, le motif D-Phe-L-Pro est remplacé par l’acide β,γ-diaminé issu de la D-phénylalanine
The design of a new oligopeptides, capable to mimic the properties of natural proteins, is an important field not only for structural studies but also in the developpement of new efficient drugs. The peptides featuring β-amino acids have been extensively explored, whereas the research in γ-peptides is more recent. The studies of γ-peptides show their ability to adopt stable secondary structures and also to have a promising biological activity. Our laboratory is interested in the synthesis of new β,γ-diaminoacids.The aim of this work is a developpement of new synthetic route starting from different natural α -amino acids and to use obtained β,γ-diaminoacids to access novel unnatural peptides having specific conformational properties.The synthetic strategy, developed and optimized in our laboratory during this work, gives access to diastereomers cis and trans from L-leucine, L- and D-phenylalanine which were used in the synthesis of a new hybrid α/γ-peptides. The structural studies were performed on two series of hybrid α/γ-peptides consisting of β,γ-aminoacid from L-leucine and L- or D-α-amino acids. In the first case, the peptides are able to adopt stable secondary structures stabilized by intramolecular hydrogen bonds involving the nitrogen on the β-position. In addition, we present the synthesis of an analogue of gramicidine S, a naturally occuring antibiotic cyclic peptide. The dipeptide pattern D-Phe-L-Pro has been replaced with the β,γ-diaminoacid synthesized from D-phenylalanine

L'étude d'oligomères non naturels qui adoptent des conformations similaires à celles des structures secondaires des protéines est un domaine en plein essor. Ces oligomères capables d'adopter une conformation spécifique, plus connus sous le nom de foldamères, sont des cibles intéressantes susceptibles de présenter des activités antibiotiques et peptidomimétiques. L'objectif de cette thèse est à la fois de permettre le développement d'une nouvelle voie de synthèse d'acides β,γ-diaminés énantiomériquement purs et de les utiliser pour accéder à de nouveaux peptides possédant des propriétés conformationnelles spécifiques
Interest in unnatural oligomers with strong conformational propensities (« foldamers ») akin to those of proteins has led to numerous recent explorations in this field. These oligomers are interesting targets as they can be valuable for specific applications such as protein-protein interactions or antibodies activity. The aim of this work is both to allow the development of a new synthetic route to enantiopure β,γ-diaminoacids and to use them to access to novel peptides having specific conformational properties

Ce travail de thèse a porté sur la recherche, par modélisation moléculaire, de signatures RMN et DC caractéristiques pour les coudes γ et β dans les peptides bioactifs. Les coudes γ et β, avec les hélices, constituent des motifs privilégiés de reconnaissance des peptides bioactifs par leurs cibles. Or, bien qu’il existe, au sein des structures de polypeptides, plusieurs catégories de coudes possédant des géométries différentes (2 types de coudes γ et 12 types de coudes β), peu d’outils expérimentaux sont disponibles pour aider à leur distinction. Ainsi, seuls 4 types de coudes β (I, I’, II et II’) ont, pour l’instant été caractérisés par RMN et il n’existe pas de spectre DC de référence fiable pour aucun motif de type coude. Dans un premier temps, afin d’élargir la base de données de RMN pour tous les types de coudes β (I, I’, II, II’, IV₁, IV₂, IV₃, IV₄, Via1, Via2, VIb et VIII) et γ (classique et inverse), nous avons analysé les paramètres structuraux caractéristiques de RMN (distances inter-hydrogènes et constantes de couplages ᶾJʜɴ-ʜꭤ) sur un ensemble de peptides modèles, extraits de la banque de protéines PDB et représentatifs de ces coudes. Les analyses des distances inter-hydrogènes ont permis d’identifier des signatures RMN caractéristiques pour différencier les deux types de coudes γ et certains types de coudes β (IV₁, IV₂,, VIb et VIII). La constante de couplage ᶾJʜɴ-ʜꭤ pourra servir à confirmer l’identification et à lever des ambiguïtés. Dans un second temps, en couplant dynamique moléculaire et TDDFT, nous avons simulé les spectres de DC de référence de peptides modèles adoptant des conformations de coudes β de type I, I’, II et II’. Les simulations ont permis de discerner deux familles de spectres DC caractéristiques : les types I/II’ d’un côté et les types I’/II de l’autre. L’ensemble de ces résultats indique que les coudes ne présentent pas nécessairement les mêmes signatures pour les deux techniques. La combinaison des signatures discriminantes de RMN et de DC pourrait donc permettre une meilleure identification des natures et des différents types de coudes
The aim of this work is to identify NMR and CD characteristic patterns for β- and γ-turns in bioactive peptides by molecular modelling. With helices, β- and γ-turns constitute favoured recognition motifs in bioactive peptides by their targets. Even though several classes of turns with different geometries exist in polypeptide structures (2 γ-turn types and 12 β-turn types), few experimental tools are available for their characterization. Thus, only 4 types of β-turns (I, I’, II et II’) have been, at present, described by NMR and there are no reliable reference CD spectra for turns. In order to extend the NMR data for all β- and γ-turn types, we analyzed NMR structural parameters (inter-hydrogen distances and ᶾJʜɴ-ʜꭤ coupling constants) in a representative peptide model dataset extracted from the PDB. The inter-hydrogen distance analysis allowed to identify specific NMR patterns for the two γ-turn types and for four β-turn types (IV₁, IV₂,, VIb and VIII). ᶾJʜɴ-ʜꭤ coupling constant may be used to confirm the identification and to remove ambiguities. Then, we simulated the reference CD spectra of model peptides adopting type I, I’, II and II’ β-turn conformations by combining molecular dynamic simulations and TDDFT computations. These computations allowed to determine two families of specific CD spectra : types I/II’, on one side and types I’/II, on the other. All these results indicate that the turns do not present the same patterns in both techniques. The combination of NMR and CD could therefore allow a better identification of the nature and the different types of turns

Une des caractéristiques histopathologiques de la maladie d'Alzheimer (AD) est la présence de plaques amyloïdes formées par les peptides amyloïdes β (Aβ) de 40 et 42 résidus, qui sont les produits de clivage par des protéases de l'APP. Afin de comprendre le rôle des variations structurelles du TM dans le traitement de l'APP, les peptides APP_TM4K ont été étudiés dans la bicouche lipidique en utilisant l’ATR-FTIR et ssNMR. Tandis que la structure secondaire globale du peptide APP_TM4K est hélicoidale, hétérogénéité de conformation et d'orientation a été observée pour le site de clivage γ et , que peuvent avoir des implications dans le mécanisme de clivage et donc dans la production d’Aβ. Les peptides Aβ s'agrègent pour produire des fibrilles et aussi de manière transitoire d'oligomères neurotoxiques. Nous avons constaté qu'en présence de Ca2+, l’Aβ (1-40) forme de préférence des oligomères, tandis qu'en absence de Ca2+ l'Aβ (1-40) s’agrège sous forme de fibrilles. Dans les échantillons sans Ca2+, l’ATR-FTIR révèle la conversion des oligomères en feuillets β antiparallèles en la conformation caractéristique des fibrilles en feuillets β parallèles. Ces résultats nous ont amené à conclure que les Ca2+ stimulent la formation d'oligomères d'Aβ (1-40), qui sont impliqués dans l’AD. Les positions et une orientation précise de deux nouveaux médicaments puissants modulateurs de la γ-sécrétase - le benzyl-carprofen et le sulfonyl-carprofen  dans la bicouche lipidique, ont été obtenus à partir des expériences des ssNMR. Ces résultats indiquent que le mécanisme probable de modulation du clivage par la y-sécrétase est une interaction directe avec le domaine TM de l’APP
A histopathological characteristic of Alzheimer’s disease (AD) is the presence of amyloid plaques formed by amyloid β(A) peptides of 40 and 42 residues-long, which are the cleavage products of APP by proteases. To understand the role of structural changes in the TM domain of APP, APP_TM4K peptides were studied in the lipid bilayer using ATR-FTIR and ssNMR. While the overall secondary structure of the APP_TM4K peptide is helical, conformational and orientational heterogeneity was observed for the y- and for the -cleavage sites, which may have implications for the cleavage mechanism and therefore the production of Aβ. Starting from its monomeric form, Aβ peptides aggregate into fibrils and / or oligomers, the latter being the most neurotoxic. We found that in the presence of Ca2 +, Aβ (1-40) preferably forms oligomers, whereas in the absence of a2 + Aβ (1-40) aggregates into fibrils. In samples without Ca2 +, ATR-FTIR shows conversion from antiparallel β sheet conformation of oligomers into parallel β sheets, characteristic of fibrils. These results led us to conclude that Ca2 +stimulates the formation of oligomers of Aβ (1-40), that have been implicated in the pathogenesis of AD. Position and precise orientation of two new drugs  powerful modulators of γ-secretase  benzyl-carprofen and carprofen sulfonyl  in the lipid bilayer were obtained from neutron scattering and ssNMR experiments. These results indicate that carprofen-derivatives can directly interact with APP. Such interaction would interfere with proper APP-dimer formation, which is necessary for the sequential cleavage by β -secretase, diminishing or greatly reducing Aβ42 production

This thesis is focused on the development of synthetic approaches to obtain new bioactive peptides. The first part deals with the design of new antimicrobial peptide/cell-penetrating peptide conjugates as anticancer agents. Their conjugation enhanced the activity of the antimicrobial peptides against cancer cells while maintained their low toxicity. These compounds are interesting for the design of new anticancer agents. On the second part, a new versatile methodology for the synthesis of natural fengycin derivatives is described. Our strategy represents the first synthetic approach for the total solid-phase synthesis of these cyclic lipodepsipeptides and can be easily adapted to obtain a wide range of analogues.
Aquesta tesi doctoral s’ha centrat en el desenvolupament d’estratègies sintètiques útils per a l’obtenció de nous pèptids bioactius. Primerament, s’han dissenyat nous pèptids conjugats antitumorals a través de la unió d’un pèptid antimicrobià i un cell-pentrating peptide. Aquesta conjugació augmenta l’activitat antitumoral del pèptid mantenint la toxicitat baixa. Aquests conjugats són interessants pel desenvolupament de nous agents antitumorals. A continuació, s’ha desenvolupat una metodologia per a la preparació de pèptids cíclics derivats de les fengicines. Aquesta metodologia representa la primera estratègia sintètica descrita per a l’obtenció en fase sòlida d’aquesta família de ciclolipodepsipèptids i pot ser fàcilment adaptada per a l’obtenció d’una àmplia varietat d’anàlegs.

Le travail présenté concerne la conception et la synthèse de peptides modifiés et se divise en deux parties. La première est l'introduction d'un résidu aminé vinylogue à stéréochimie cis et trans dans un undécapeptide, la substance P pour comprendre ses interactions avec le récepteur NK-1. Une seconde étude a été orientée vers l'obtention de g-aminopeptides par hydrogénation des acides aminés vinylogues précédents. Cette modification structurale a donné un nouvel analogue de la SP. La seconde partie est de la méthodologie de synthèse en utilisant les peptides vinylogues. Un premier chapitre, la dihydroxylation de ces motifs avec une induction asymétrique en utilisant des réactifs chiraux, permet l'obtention de g-aminoacides dihydroxylés. Un second chapitre, une application par la synthèse totale d'un produit naturel issu d'une plante nyctinastique. Et le dernier chapitre est une autre application, la synthèse de lactames dihydroxylés conduisant à la synthèse de nouveaux azasucres
This work concerns conception and synthesis of modified peptides and is divided in two parts. Firstly, it's the insertion of vinylogous amino acids with cis and trans conformation in neuropeptide of eleven amino acids which is substance P in order to understand its interaction with NK-1 receptor. A second study has been oriented on the preparation of g-amino peptides by hydrogenation of previous vinylogous amino acids. This structural modification has given a new SP's analog which has been tested. The second part is the methodology of synthesis using vinylogous peptides and is divided in three chapters. First one presents dihydroxylation's results of these residues with an asymmetric induction using chiral catalyst to obtain dihydroxylated g-amino acids. Second one is an application of these studies with a total synthesis of natural product extracted from nyctinastic plant. And the last one deals with preparation of dihydroxylated lactams leading to the synthesis of new azasugars

Short helical peptides Peptides with a well-defined helical conformation were examined with the aims of reinforcing their secondary structure or using their rigid conformation to control asymmetric induction over long distances. In the first example, two consecutive i, i+4 intramolecular side chain-to-side chain macrocyclization reactions of different type, carried out on a preformed, partially helical linear peptide resulted in a double stapled, overlapping, bicyclic oligopeptide system. A detailed CD and NMR conformational study revealed that the mixed 310/α-helical conformation exhibited by the original linear peptide is converted into a fully-developed α-helix in the bicyclic peptide. In parallel, both the helix overall content and stability are significantly increased. In the second part, an achiral Aib-based helical foldamer was appropriately functionalized with the photoswitchable fumaramide/maleamide linkage, thus obtaining a system in which a screw sense preference may be activated by the absorption of UV light. The trans configuration in the fumaramide linkage holds the chiral residue away from the achiral portion of the oligomer, preventing the induction of a conformational preference. However, after photoisomerization, the cis configuration of the maleamide brings the chiral and achiral portions into proximity, generating a pronounced preference for one of the two possible, helical screw senses. In conclusion, we showed that it is feasible to use light to switch on and off the ability of the molecules to react strereoselectively in a chain extension reaction, or to modulate helix-to-helix communication. Functionalized helical polypeptides The well-known, rod-like α-helical polypeptide poly(γ-benzyl-L-glutamate) (PBLG) was selected for this study. The possibility to create self-assembled microstructures with different characteristics, shapes and functions from different PBLG-conjugates was explored. Mono- and bis-fullerene (C60)-PBLG conjugates were obtained by one-pot thiol-ene chemistry. These systems showed the propensity to self-assemble in water creating precise bulky microstructures of toroidal or vesicular shape. In a second part, we reported the synthesis of star-shaped carbon quantum dots (CQDs)-PBLG conjugates that self-assemble into microstructures and retain the characteristic emission properties of the native dots. CQDs, prepared by microwave-assisted carbonization of Arg and 1,2-ethylendiamine in water, were used either as initiators to afford a daisy-like peptide-polymer structure, or as capping agents towards more elaborated hybrid nanostructures that self-assemble into supramolecular aggregates of spherical shape. Finally, smart microstructures with photoresponsive behavior was obtained by the insertion of azobenzene-containing α-amino acids in PBLG systems. We created two systems, with either C2- or C3-symmetry, that self-assemble in spherical structures. The change in their 3D-structure after light irradiation is followed by a variation in the morphology of the aggregates. Self-assembling short peptides The synthesis and self-assembly properties of two different peptide systems were studied. The first series of compounds contain the photoswitchable α-amino acid bis[p-(phenylazo)benzyl]glycine, which undergoes a reversible cis-trans isomerization upon exposure to light at the appropriate wavelengths. Derivatives and short peptides containing this α-amino acid are able to promote the formation of well-ordered supramolecular structures. Interestingly, the morphological transition observed after UV-light irradiation proved to be reversible due to the presence of the two side-chain azobenzene groups. In the second part, we investigated the hydrophobic, terminally-protected dipeptide Boc-L-Cys(Me)-L-Leu-OMe that it is able to hierarchically self-assemble producing nano-, micro- and macroscale complex architectures, including hollow rods, under appropriate conditions. Our results suggested that its self-assembly properties might be related to the occurrence in its single crystal structure of a supramolecular sixfold helix motif. Subsequently, we decided to chemically modify the molecule to obtain a diacetylene derivative. This final compound is able to form an organogel or spherical aggregates, which undergo a topochemical polymerization under UV-light irradiation.
Peptidi elicoidali corti In questo lavoro di tesi sono stati studiati diversi peptidi caratterizzati da una ben definita conformazione elicoidale con lo scopo di stabilizzarne la struttura secondaria oppure di sfruttare la loro conformazione rigida come mezzo per controllare l’induzione asimmetrica su lunghe distanze. Il primo esempio, un sistema oligopeptidico biciclico doppiamente stabilizzato, è stato ottenuto tramite due reazioni di macrociclizzazione che hanno coinvolto le catene laterali dei residui in posizione i e i+4 di un peptide lineare. Un’indagine conformazionale dettagliata, condotta utilizzando le spettroscopie CD ed NMR, ha rivelato che la conformazione mista 310/α-elica, osservata per il peptide lineare, risulta completamente convertita in una struttura ad elevato contributo α-elicoidale nel peptide biciclico. In parallelo, sia il contenuto totale di elica sia la stabilità risultano significativamente aumentati. Nel secondo caso, un foldamero achirale elicoidale a base di Aib è stato opportunamente funzionalizzato con il gruppo fotoisomerizzabile fumarammide/maleammide contenente un residuo chirale. In questo modo è stato ottenuto un sistema in cui è stato possibile influenzare il senso di spiralizzazione dell’elica grazie all’uso di luce ultravioletta. La configurazione trans nella fumarammide, infatti mantiene il residuo chirale lontano dal segmento achirale dell’oligomero, rendendo impossibile l’induzione di una conformazione preferenziale. Tuttavia dopo l’isomerizzazione, la configurazione cis della maleammide consente alla parte chirale e a quella achirale di essere spazialmente vicine, con conseguente induzione di chiralità e adozione di un senso preferenziale di spiralizzazione. Sfruttando questo principio è stato quindi possibile utilizzare la luce per accendere o spegnere la capacità del sistema di reagire stereoselettivamente, oppure di modulare la comunicazione di chiralità tra due segmenti elicoidali. Polipeptidi elicoidali funzionalizzati Con lo scopo di ottenere tramite self-assembly microstrutture con differenti caratteristiche, forme e funzioni sono stati sintetizzati diversi sistemi coniugati a base di poli(γ-benzil-L-glutammato) (PBLG). Sistemi polipeptidici contenenti una o due unità di fullerene sono stati ottenuti tramite reazione tiol-ene one-pot. Questi due polimeri hanno mostrato una diversa propensione ad auto-assemblarsi in ambiente acquoso, formando microstrutture di forma toroidale oppure di tipo vescicolare. Come ulteriore esempio è stata riportata la sintesi di sistemi coniugati a base di PBLG e carbon quantum dots. I CQDs, preparati per trattamento in microonde a partire da una soluzione acquosa di arginina e 1,2-etilendiammina, sono stati usati come iniziatore, ottenendo una struttura polimerica a forma di stella, oppure come agente cappante, portando alla formazione di microstrutture più complesse. I sistemi ottenuti sono in grado di autoassemblarsi formando aggregati supramolecolari di forma sferica che mantengono le caratteristiche proprietà di emissione dei dots originali. Infine, microstrutture “smart” con comportamento fotoresponsivo sono state ottenute inserendo amminoacidi a base di azobenzene all’interno del sistema polipeptidico. Sono state quindi sintetizzate due strutture polipeptidiche con simmetria C2 e C3 che hanno evidenziato la formazione di strutture sferiche tramite self-assembly. Il cambiamento della loro struttura tridimensionale in seguito ad irraggiamento è accompagnato da una variazione nella morfologia degli aggregati. Peptidi corti auto-assemblanti In questo ultimo capitolo sono discusse la sintesi e le peculiari proprietà di self-assembly mostrate da due diversi sistemi peptidici. La prima serie di composti contiene l’amminoacido fotoisomerizzabile bis[p-(fenilazo)benzil]glicina, che è in grado di isomerizzare reversibilmente tra le due forme cis/trans in seguito ad irraggiamento con luce di adeguata lunghezza d’onda. Derivati e peptidi corti contenenti questo amminoacido sono in grado di promuovere la formazione di strutture supramolecolari ordinate. Inoltre, grazie alla presenza delle due unità di azobenzene sulle catene lineari, la transizione morfologica osservata in seguito ad irraggiamento si è dimostrata essere reversibile. Nella seconda parte di questo studio è stato esaminato il comportamento del dipeptide idrofobico protetto Boc-L-Cys(Me)-L-Leu-OMe. La formazione di nano-, micro- e macro- architetture complesse, tra cui bacchette caratterizzate da una cavità interna, è stata osservata in diverse condizioni sperimentali. I risultati ottenuti suggeriscono che le proprietà di self-assembly sono correlate all’organizzazione delle molecole nel cristallo singolo in cui è stata osservata la presenza di una particolare struttura supramolecolare elicoidale formata da sei molecole. Successivamente è stato deciso di modificare il dipeptide in modo da ottenere un derivato diacetilenico. Questo derivato è in grado di formare un organogel o delle strutture sferiche che possono subire polimerizzazione topochimica per irraggiamento UV.

La formation de nanostructures bien définies par autoassemblage de briques organiques a reçu de nombreuses attentions dues à leurs potentielles applications en chimie comme en biologie. Parmi toutes ces éléments organiques, les peptides et pseudopeptides font partie des plus prometteurs de par leur ressemblance aux protéines. Nous pouvons dénombrer de nombreux autoassemblages peptidiques, comme les nanotubes, les nanofibres, les vésicules, les nanosphères etc… Dans ce contexte, nous nous sommes intéressés à la synthèse et à l’étude structurale globale des hydrazinopeptides. Grâce à leur azote supplémentaire, ces pseudopeptides bis-azotés sont capables de s’auto-assembler en de nouvelles structurations. Les 1:1[α/α-Nα-Bn-hydrazino]peptides linéaires ont démontré se structurer en hydrazinoturn et γ-turn en solution. Nous mettrons en évidence la capacité des analogues 1:1[ß/α-Nα-Bn-hydrazino]peptides linéaires à s’autostructurer en hydrazinoturn en solution, n’impliquant pas le squelette du motif ß-aminoacide. De la même manière, nous démontrerons la capacité des pseudopeptides purs hydrazino à se structurer en solution en une structure très solide formées de successions d’hydrazinoturn, observable à l’état cristallin également. Dans un deuxième temps, et dans le cadre de l’élaboration de structures nanotubulaires, nous avons étudié une série de 1:1[α/α-Nα-Bn-hydrazino]peptides cycliques, et tout particulièrement les cyclotétramères. Dans ce contexte, nous avons cherché à mettre en lumière les différents paramètres pouvant influencer l’organisation nanotubulaires dans nos macrocycles, dans le but d’élaborer la meilleure stratégie afin d’obtenir cette nanostructuration en vues d’éventuelles applications. Les différents paramètres étudiés sont les suivants : la stratégie de synthèse, la chiralité, l’orientation des chaînes latérales, et enfin l’aptitude à former des gels
The formation of nanostructures with well-defined organic brick self-assembly has received much attention due to their potential applications in chemistry and biology. Among all these organic elements, peptides and pseudopeptides are among the most promising because of their similarity to proteins. We can enumerate many peptides self-assembly, such as nanotubes, nonafibres, vesicles, nanospheres etc … In this context, we are interested by the synthesis and overall structural study of hydrazinopeptides. Thanks to the additional nitrogen, these bis-nitrogen pseudopeptides are able to self-assemble into new structuring. The 1:1[α/α-Nα-Bn-hydrazino] linear peptides showed coalesce into hydrazinoturn and γ-turn in solution. We have highlighted the ability of analogues of 1:1[ß/α-Nα-Bn-hydrazino] linear peptides to be structured in hydrazinoturn only, in solution. Similarly, we have demonstrated the ability of pure α-Nα-Bn-hydrazino pseudopeptides to be structured in a very solid solution structure formed of hydrazinoturn observable also in crystal state. Secondly, and as part of the development of nanotube structures, we have studied a serie of 1:1[α/α-Nα-hydrazino] cyclic peptides, and especially cyclotetrameres. In this context, we have sought to highlight the various parameters that may affect the organization in nanotubes, in order to develop the best strategy to achieve this potential application in nanostructuring views. The various parameters studied are: the synthetic strategy, the chirality, the orientation of side chains, and finally the ability to form gels

Dans notre groupe, nous nous intéressons au développement de peptides contenant des acides γ-aminés. Comme d’autres peptides contenant des acides aminés non naturels, ils ont montré leur capacité à posséder des conformations stables et/ou des propriétés biologiques intéressantes. De plus, ces peptides sont généralement résistant à la protéolyse. Dans l’objectif de synthétiser des acides -diaminés sous la forme d’un seul stéréoisomère, nous avons développé une voie de synthèse reposant sur une réaction de Blaise suivie d’une réduction diastéréosélective. En appliquant cette méthode, nous avons synthétisé des acides β,γ-diaminés dérivés de la D-phénylalanine et de l’acide L-glutamique. Le premier a été utilisé pour concevoir des analogues d’un peptide antimicrobien, la gramicidine S. Comparé à la molécule parent, les analogues ont montré une cytotoxicité beaucoup moins importante pour les cellules hôtes tout en conservant une activité antibactérienne intéressante. Cette étude nous a donné de meilleures connaissances pour développer d’autres analogues de la gramicidine S ainsi que d’autres peptides antimicrobiens. Nous avons également effectué de nombreuses optimisations pour synthétiser de façon efficace des acides β,γ-diaminés cycliques à partir de l’acide L-glutamique. Les oligomères incorporant ces acides β,γ-diaminés et des acides α-aminés ont montré un fort potentiel pour l’adoption de conformations stables. Ces études vont être poursuivies
In our group, we are interested in developing peptides containing β,γ-diamino acids . Along with many other peptides containing unnatural amino acids, they have shown the ability to possess stable conformations and/or interesting biological activities. Moreover, those peptides are usually more resistant to proteolysis. In order to synthesize stereopure γ-amino acids, we have developed a synthetic route using Blaise reaction and subsequent diastereoselective reduction as key reactions. Through applying this method, we have synthesized β,γ-diamino acids derived from D-phenylalanine and L-glutamic acid. The former β,γ-diamino acid was used for designing antimicrobial peptide gramicidin S analogues. Compared with mother molecule, the analogues exerted much less host cell cytotoxicity while remaining interesting antibacterial activity. Meanwhile, it gave us more knowledge for further developing analogues of gramicidin S as well as other antimicrobial peptides. We also paid lots of effort to efficiently synthesize cyclic β,γ-diamino acids starting from L-glutamic acid. Interestingly, when oligomers incorporating this β,γ-diamino acids and α-amino acids, they have shown the potential to adopt stable conformations. The following studies will be continuously investigated

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

Seven novel, amphiphilic AApeptides were prepared. Two cationic, lipo-α-AApeptides, NA-75 and NA-77 were found to possess potent antimicrobial activity against Gram-positive bacteria, with almost no hemolytic activity. In addition to NA-75 and 77, four amphiphilic, γ-AApeptides, NA-133, 135, 137, and 139, and one anionic lipo-α-AApeptide, NA-81, were prepared for molecular self-assembly studies, with several interesting nanostructures observed by TEM. Mineralization of calcium carbonate from gaseous CO2 and Ca2+ in the presence of the 7 AApeptide amphiphiles was also observed by optical microscopy. Several AApeptides were found to be able to influence CaCO3 crystal morphology. Another α-AApeptide, NA-63, was synthesized by a novel, alternative method, which has several potential advantages over the previous synthesis methods.

Le travail décrit dans ce manuscrit est consacré à la synthèse et à la caractérisation structurale d'une nouvelle famille de γ-amino acides hétérocycliques contraints, les ATCs (acides 4-Amino-(méthyl)-1,3-Thiazole-5-Carboxyliques). Ces monomères sont construits autour d'un noyau thiazole inséré entre les carbones Cα-Cβ permettant de limiter la valeur de l'angle dièdre ζ à 0°. La présence de deux points de substitution, sur le carbone γ asymétrique et en position 2 du noyau aromatique, autorise une large diversification structurale des ATCs. Des séries d'oligomères, i.e. dimères, tétramères et hexamères solubles dans les solvants organiques halogénés, dans les alcools et dans l'eau ont été synthétisées par couplages peptidiques. La conformation adoptée par ces séquences a été déterminée en solution par RMN 1D et 2D associées à des techniques de modélisation sous contraintes RMN. Nous avons montré que les oligomères d'ATCs s'arrangeaient en hélices 39 droites, présentant un pas de 11,8 Å. La conformation hélicoïdale est stabilisée par un réseau de liaisons hydrogène de type CO(i)…NH(i+2) s'établissant tout au long de la séquence, faisant entrer les oligomères d'ATCs dans le monde des foldamères. Des mesures de dichroïsme circulaire ont permis d'apprécier la stabilité conformationnelle des édifices et l'analyse à l'état solide par diffraction des rayons X a confirmé l'arrangement observé par RMN. Dans une seconde partie nous avons étudié le rôle structurant d'un motif ATC placé au sein d'une petite séquence peptidique. Nous montrons au travers d'expériences RMN et de calculs théoriques que la configuration du monomère d'ATC conditionne la conformation de peptides hybrides αγαα en solution. En termes d'application nous décrivons l'utilisation du motif ATC comme mime de coude pour concevoir un analogue fonctionnel de la gramicidine S, un cyclodécapeptide symétrique antibactérien. La dernière partie de ce travail concerne nos efforts pour développer, à partir des connaissances acquises quant à la structure tridimensionnelle des oligomères d'ATCs, des inhibiteurs de l'interaction protéine-protéine STAT6-NCoA-1
The work described herein is devoted to the synthesis and the structural characterization of a new family of heterocyclic constrained γ-amino acids, named ATCs (4-Amino-(methyl)-1,3-Thiazole-5-Carboxylic acids). These building-blocks are built around a thiazole ring inserted between the Cα-Cβ carbons allowing the limitation of the ζ dihedral angle value to 0°. The presence of two diversification points both on the γ asymmetric carbon and on the position 2 of the aromatic ring, allows a large structural diversification of the ATCs. Series of oligomers consisting in dimers, tetramers and hexamers soluble in halogenated solvents, alcools and water have been synthesized according to peptide chemistry. The conformations of the sequences have been studied by various NMR experiments associated to modelling studies led under NMR constraints. The ATC oligomers adopt a right 39 helical shape, owning a pitch of 11.8 Å which has been confirmed by crystallography. The helix is stabilized by a conserved hydrogen bond pattern between CO(i)…NH(i+2) occurring all along the sequence axis. Circular dichroism measures have been done to check the conformational stability of the architectures. In the second part of the manuscript, we demonstrate by NMR and theoretical computing that when included in a short peptide sequence, ATCs could act as turns. The derived application consists in optimizing the biological behaviour of the ATC moiety as a turn mimetic thanks to the design and the antibacterial evaluation of a gramicidin S analogue. Based on our knowledge about the three-dimensional structure of ATC oligomers, the last part of this work deals with our efforts to develop inhibitors of protein-protein interaction STAT6-NCoA-1

WHO has reported that antibiotic resistance is the third major cause of human death all over the globe. Recent study, has focused on the development of new antibacterial resistance drugs. Herein, we tried to synthesis a series of polymers that can mimic the HDPs. HDPs can target the bacterial cell membrane and they have less chances to develop bacterial resistance. We synthesized the amphiphilic polycarbonates that are highly selective to Gram-positive bacteria, including multidrug resistant pathogens. The membrane disruption activity of these polymers was proved by fluorescence and TEM studies and the drug resistance study showed that the polymers don’t develop bacterial resistance. In order to further design the molecules that can target a broad spectrum of bacteria, we have designed a series of lipidated dendrimers that can target the Gram-positive and Gram-negative bacteria. These dendrimers mimic the HDPs and target the bacterial cell membrane. Dendrimers are reported to inhibit the formation of bacterial biofilm which makes them promising for their future development of antibiotic agents. Apart from the synthesis of polymers and dendrimers as antibacterial agents, we have designed a series of small molecular antibacterial agents that are based on the acylated reduced amide scaffold and small dimeric cyclic guanidine derivatives. These molecules display good potency against a panel of multidrug-resistant Gram-positive and Gram-negative bacterial strains. Meanwhile, they also effectively inhibit the biofilm formation. Mechanistic studies suggest that these compounds kill bacteria by compromising bacterial membranes, a mechanism analogous to that of host-defense peptides (HDPs). Lastly, we also demonstrate that these molecules have excellent in vivo activity against MRSA in a rat model. This class of compounds could lead to an appealing class of antibiotic agents combating drug-resistant bacterial strains.

Pericentrin is a molecular scaffold protein. It anchors protein kinases, (PKB, (Purohit, personal communication), PKC, (Chen et al., 2004), PKA Diviani et al., 2000), the γ tubulin ring complex, (γ TuRC) (Zimmerman et al., 2004), and possibly dynein (Purohit et al., 1999) to the spindle pole. The γ TuRC is a ~ 2 MDa complex which binds the minus ends of microtubules and nucleates microtubules in vitro, (Zheng et al., 1995). Prior to this work, nothing was known about the association of the γTuRC with pericentrin. Herein I report the biochemical identification of a large protein complex in Xenopus extracts containing pericentrin, the γ TuRC, and other as yet unidentified proteins. Immunodepletion of γ tubulin results in co-depletion of pericentrin, indicating that virtually all the pericentrin in a Xenopus extract is associated with γ tubulin. However, pericentrin is not a member of the, γ TuRC, since isolated γ TuRCs do not contain pericentrin. The association of pericentrin with the γ TuRC is readily disrupted, resulting in two separable complexes, a small pericentrin containing complex of approximately 740 KDa and the the γ TuRC, 1.9 MDa in Xenopus. Co overexpression/ coimmunoprecipitation and yeast two hybrid studies demonstrate that pericentrin binds the γTuRC through interactions with both GCP2 and GCP3. When added to Xenopus mitotic extracts, the GCP2/3 binding domain uncoupled γ TuRCs from centrosomes, inhibited microtubule aster assembly and induced rapid disassembly of pre-assembled asters. All phenotypes were significantly reduced in a pericentrin mutant with diminished GCP2/3 binding, and were specific for mitotic centro somal asters as I observed little effect on interphase asters or on asters assembled by the Ran-mediated centrosome-independent pathway. Overexpression of the GCP2/3 binding domain of pericentrin in somatic cells perturbed mitotic astral microtubules and spindle bipolarity. Likewise pericentrin silencing by small interfering RNAs in somatic cells disrupted γ tubulin localization and spindle organization in mitosis but had no effect on γ tubulin localization or microtubule organization in interphase cells. Pericentrin silencing or overexpression induced G2/antephase arrest followed by apoptosis in many but not all cell types. I conclude that pericentrin anchoring of γ tubulin complexes at centrosomes in mitotic cells is required for proper spindle organization and that loss of this anchoring mechanism elicits a checkpoint response that prevents mitotic entry and triggers apoptotic cell death. Additionally, I provide functional and in vitro evidence to suggest that the larger pericentrin isoform (pericentrin B/ Kendrin) is not functionally homologous to pericentrin/pericentrin A in regard to it's interaction with the γ TuRC.

L'activité g-secretase dépendante des présénilines est impliquée dans la production du peptide A-beta et nécessite la formation d'un complexe de haut poids moléculaire contenant au moins 4 protéines partenaires : la préséniline 1 ou 2, la nicastrine, Aph1 et Pen2. Au cours de ma thèse j'ai pu montré une implication de ce complexe gamma-sécrétase dépendant des présénilines dans la régulation de l'apoptose et la dégradation du peptide A-beta. L'implication des présénilines dans les processus de mort cellulaire a déjà été décrite dans la littérature, la présénilines 2 joue un rôle pro-apoptotique alors que la préséniline 1 semble protéger les cellules de l'apoptose. Nos expériences montrent pour la première fois, un phénotype anti-apoptotique de la nicastrine qui est associé à une baisse de l'expression et de l'activité transcriptionnelle de p53. Nous avons également mis en évidence une composante de cette réponse indépendante de p53 puisqu'en absence de p53, la nicastrine présente toujours un phénotype antiapoptotique. Par ailleurs, nous avons établi une fonction du complexe gamma-sécrétase dépendant des présénilines dans la régulation de la dégradation du peptide A-beta. En effet, l'activité gamma -secretase dépendante des présénilines libère en plus du peptide A-beta, sa contrepartie cytosolique, le fragment AICD qui est transloqué au noyau. Nous avons montré pour la première fois, que ce fragment AICD pouvait réguler la transcription de la néprilysine, un enzyme de dégradation du peptide A-beta.

Peptidomimetics can mimic hierarchical structures of peptides and proteins. Thus, they are extensively studied for therapeutic applications. To break the limitation of backbones and frameworks and expand the peptidomimetics family, a new class of peptidomimetics - “γ-AApeptides” was developed. Design of γ-AApeptides is based on the chiral peptide nucleic acids (PNAs) backbone. The World Health Organization estimates that one -third of all deaths in the world are on account of infectious diseases. AMPs are important because of their high activity against broad spectrum microbes, less susceptible to grow resistance and selectivity in binding to bacterial cells over human cells. γ-AApeptides as a new class of peptidomimetics have increased stability and enhanced chemical diversity. We have developed polymyxin mimic cyclic peptides, small linear molecules and hydantoin derivatives as potent antibiotic agents with γ-AApeptides. They have good bioactivity and selectivity. Combinatorial library is key technology for accelerating the discovery of novel therapeutic agents. One-bead-two-compound γ-AApeptides-based library was developed and screened against SMYD2 protein which is essential for tumor growing.

There has been increasing concern regarding the emergence of multi-drug resistant pathogens. The resistance develops when pathogens, especially bacteria, are frequently exposed to conventional antibiotics, as they are heavily used in both human and livestock. This is due to the high target specificity of conventional antibiotics, which places pathogens in high selective pressures and eventually results in drug resistant by mutations. To address this issue, global actions and cooperation are needed. At the same time, new technologies and strategies need to be developed. Host defense peptides (HDPs) are widely found in the innate immune system. They show both direct antimicrobial properties and immunomodulatory activities. The multifaceted functions of HPDs make them less likely to promote antimicrobial resistance. Thus, they are promising as new therapeutics to treat multi-drug resistant infections. In fact, several drug candidates derived from HDPs have entered the clinical trial, but none of them got into the clinic. This is due to several challenges associated with HDPs, such as low in vivo stability, high cost of manufacturing, and toxicity to mammalian cells. In this dissertation, we explored the ability of a new type of unnatural scaffolds (γ-AApeptides) to mimic the functions of HDPs, including both broad spectrum antimicrobial properties and immunomodulatory activities. Furthermore, the efforts to identify simpler and more drug like γ-AApeptide based antimicrobial agents were also discussed. The findings in this dissertation may lead to the development of potential drug candidates to treat multi-drug resistant infections.

La maladie d’Alzheimer se caractérise par des pertes de mémoire, des troubles cognitifs et une perte d’autonomie des patients. Les cerveaux des patients présentent des plaques séniles constituées principalement du peptide amyloïde (Aβ). Ce peptide contribue vraisemblablement à la dégénérescence des neurones observée dans la pathologie. Il est produit à partir de son précurseur la βAPP par deux activités enzymatiques, la β- puis la γ-sécrétase. L’activité β-sécrétase est portée par la protéine BACE1 tandis que la γ-sécrétase est un complexe protéique. Nous avons étudié la régulation transcriptionnelle des protéines impliquées dans la production d’Aβ car il constitue une cible thérapeutique importante. Le facteur de transcription NF-κB est activé dans la maladie d’Alzheimer. Nous avons montré que NF-κB affecte la production d’Aβ en réduisant la transcription de la βAPP et des β- et γ-sécrétases. Cette régulation est complexe car à des concentrations supraphysiologiques d’Aβ mimant les conditions pathologiques, NF-κB est activateur de la production du peptide amyloïde. Ces travaux suggèrent l’instauration d’un rétrocontrôle positif favorisant la production d’Aβ en conditions mimant la pathologie. La mort neuronale étant une caractéristique de la maladie d’Alzheimer, nous avons également étudié la régulation de la production d’Aβ par le facteur de transcription pro-apoptotique p53. Nos résultats préliminaires montrent que p53 inhibe la sécrétion d’Aβ. Enfin, dans le cadre de l’exploration du dialogue fonctionnel entre les deux sécrétases, nous montrons que le clivage γ-sécrétase des cadhérines épithéliale et neurale, ainsi que de Notch-1 régule la transcription de BACE1
Alzheimer’s disease (AD) is characterized by memory loss, cognitive deficits and a loss of the patient’s autonomy. AD brains harbor senile plaques mainly composed of amyloid peptide (Aβ). This peptide likely contributes to the neurodegeneration. Aβ is produced by cleavage of its precursor βAPP by two enzymatic activities, the β- and the γ-secretase. Aβ is an important therapeutic target; we thus studied the transcriptionnal regulation of the proteins involved in its production. The transcription factor NF-κB is activated in Alzheimer’s disease. We show that NF-κB reduces Aβ production by inhibiting the transcription of βAPP and of the β- and γ-secretases. This regulation is complex, as in supraphysiological Aβ concentration, a condition close to the pathology, NF-κB is an activator of Aβ production. This suggests a positive feedback loop favoring Aβ production in pathological conditions. Neuronal death is characteristic of Alzheimer’s disease. We thus studied the regulation of Aβ production by the pro-apoptotic transcription factor p53. Our preliminary results indicate that p53 inhibits Aβ secretion. Finally we show a functional dialogue between the two secretases. Thus the γ-secretase cleavage of Notch-1 and of the epithelial and the neural cadherins regulates BACE1 transcription

Alzheimer Disease (AD) is the most common neurodegenerative disorder in the world. One of the neuropathological hallmarks of AD is the senile plaques in the brain. The plaques are mainly composed of the amyloid β (Aβ) peptide. Aβ is generated from the amyloid precursor protein, APP, when it is first cleaved by the β-secretase and subsequently the γ-secretase complex. The γ-secretase complex cleaves at different sites, called γ and ε, where the γ-cleavage site generates Aβ peptides of different lengths and ε-cleavage generates the APP intracellular domain (AICD). The two major forms of Aβ is 40 and 42 amino acids long peptides, where the latter is more prone to aggregate and is the main component in senile plaques. The γ-secretase complex is composed of four proteins; Pen-2, Aph-1, nicastrin and presenilin (PS). The PS protein harbours the catalytic site of the complex, where two aspartate residues in position 257 and 385 (Presenilin 1 numbering) are situated. Most Familial AD (FAD) mutations in the PS gene cause a change in the γ-cleavage site, leading to a shift from producing Aβ40 to the longer more toxic variant Aβ42. Frequently, this often leads to impairments of the AICD production. Another substrate for the γ-secretase complex is Notch. It is important to maintain the Notch signaling since an intracellular domain (NICD) is formed after cleavage by the γ-secretase complex in the membrane (S3-site) and this domain is involved in transcription of genes important for cell fate decisions.

It has been reported that certain APP luminal juxtamembrane mutations could drastically alter Aβ secretion, however their effect on AICD production remains unknown. In this study we want to analyse wether the juxtamembrane region is important for the AICD production. To gain more insight into the luminal juxtamembrane function for γ-secretase-dependent proteolysis, we have made a juxtamembrane chimeric construct. A four-residue sequence preceding the transmembrane domain (TMD) of APP (GSNK), was replaced by its topological counterpart from the human Notch1 receptor (PPAQ). The resulting chimeric vector C99GVP-PPAQ and the wildtype counterpart were expressed in cells lacking PS1 and PS2 (BD8) together with PS1wt. We observed that the chimeric construct did not alter production of AICD when using a cell based luciferase reporter gene assay monitoring AICD production. We also introduced a PS1 variant lacking a big portion of the large hydrophilic loop, PS1∆exon10, since our group has previously observed that this region affect Aβ production¹⁴³. We found that the absence of the large hydrophilic loop in PS1 gave a 2-fold decrease in AICD-GVP formation from C99GVPwt compared to PS1wt.  The activity of PS1wt and PS1Δexon10 using C99GVP-PPAQ as a substrate gave similar result as the C99GVPwt substrate, i.e. a 2-fold decrease in AICD-GVP formation when comparing PS1Δexon10 with PS1wt. From this data we therefore suggest that the four residues in the juxtramembrane domain (JMD) (GSNK) is not altering ε-cleavage of APP when changed to Notch1 counterpart, PPAQ. Furthermore, we also show that the 2-fold decrease in AICD-production by the PS1Δexon10 molecule is not changed between the two substrates C99GVPwt and C99GVP-PPAQ. This indicates that the luminal region of APP is not directly involved in the ε-site processing. If the luminal region is affecting processing in the γ-cleavage sites, remains however to be investigated.

T lymphocytes are essential components of the immune system and as such are continually regulated by a variety of factors. Every step of their development, survival and function is tightly monitored to ensure their ability to recognize most foreign agents and mount adaptive immune responses during pathogenic infections, while remaining tolerant to self-antigens. Among the many factors that participate in the regulation of T cell development and function are the cytokines. Cytokines that signal through the common gamma (γс) chain and the Janus kinase 3 (Jak3) include IL-2, -4, -7, -9, -15, and -21 and have been implicated in the regulation of every stage in the life of a T cell. Therefore, it is not surprising that mutations in the γс chain or Jak3 lead to a SCID condition in humans and mice. Specifically, Jak3-deficient mice are characterized by a reduction in thymic cellularity and dysregulated T cell homeostasis. They have an expansion of memory-like CD4+ mature T cells and an almost complete absence of mature CD8+ T cells. By investigating the TCR repertoire of CD4+ T cells in the thymus and spleen of Jak3-/- mice, I deduced that the CD4+ T cell activation and expansion is TCR-specific and takes place in the periphery of the mice. After crossing Jak3-deficient mice to Bcl-2 transgenic mice I showed that the developmental block observed in Jak3-/- mice could not be rescued by the anti-apoptotic factor, despite the fact that its expression did increase, slightly, the total numbers of developing thymocytes. The enforced expression of Bcl-2 was also not sufficient to revert the dysregulation of T cell homeostasis in Jak3-/- mice. Finally, in order to further understand the role played by γс cytokines during T cell function, I investigated the ability of mature Jak3-/- CD8+ T cells to become activated and differentiate into effector cells in response to a viral infection. My results indicate that CD8+ T cells are activated and proliferate in response to a viral infection, but their survival, as well as their ability to proliferate and differentiate into effector cells are greatly impaired, resulting in the inability of Jak3-deficient mice to mount a protective response.

La présence de plaques séniles au niveau cérébral constitue l'une des marques histopathologiques caractéristiques de la maladie d'Alzheimer. Elles sont constituées du peptide amyloïde Aβ, issu du clivage séquentiel d'une protéine transmembranaire, la βAPP par deux enzymes, la β- et la γ-sécrétase. En conditions pathologiques, le peptide Aβ neurotoxique de 42 acides aminés (Aβ42), plus long et plus hydrophobe que celui de 40 acides animés (Aβ40), augmente, conduisant ainsi à la formation des plaques séniles et à une dégénérescence neuronale. Plusieurs stratégies thérapeutiques s'intéressent donc aux enzymes impliquées dans la production de ce peptide. Lors de ma thèse, je me suis intéressée plus particulièrement à la régulation transcriptionnelle de la β-sécrétase BACE1 par deux acteurs de la maladie : le peptide amyloïde et le facteur de transcription NFkB. En effet, la voie NFkB est activée dans l'inflammation cérébrale autour des plaques séniles par le peptide amyloïde et plusieurs gènes impliqués dans la maladie d'Alzheimer dont BACE1 présentent des sites consensus pour NFkB. J'ai pu démontrer qu'à des concentrations supra-physiologiques du peptide Aβ42 mais pas le Aβ40, augmentait l'activité transcriptionnelle de BACE1 et que ce processus était bloqué par un inhibiteur pharmacologique de la voie NFkB. La régulation de la y-sécrétase, un complexe multiprotéique composé des protéines Aph1, Pen2, des présénilines et de la nicastrine, par Aβ et NFkB, a aussi été examinée. L'effet de la suppression d'Aβ et de la modulation de la voie NFkB a été évalué sur l'expression de ces protéines ainsi que la transactivation de leur promoteur. Une régulation de l'activité transcriptionnelle et de l'expression de BACES1 dépendante de la y-sécrétase a été observée dans les cellules invalidées pour les présénilines. L'hypothèse que d'autres substrats de la y-sécrétase dont le clivage produit un fragment intracellulaire ayant la propriété de moduler la transcription, pouvaient être impliqué dans la régulation de l'activité transcriptionnelle de BACES1 a donc été examinée. Les résultats présentés dans ce manuscrit montrent que les fragments ECTF2, NCTF2 et NICD issus respectivement de l'E-Cadhérine, la N-Cadhérine et Noch semblent être de nouveaux modulateurs de l'activité transcriptionnelle de BCES1. Ces résultats impliquent que la y-sécrétase module la transactivation du promoteur de BACE1 via la coupure de divers substrats. Ce dialogue fonctionnel entre les deux sécrétases pourrait expliquer l'emballement moléculaire conduisant à la dégénérescence observée aux stades tardifs de la maladie.

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.

Les pyrrolodiazépinones ont des activités biologiques intéressantes sur différents récepteurs biologiques, ce qui en font une cible de choix pour développer de nouvelles petites molécules biologiquement actives. Une méthodologie en solution a été développée pour synthétiser des pyrrolo[3,2-e][1,4]diazépin-2-ones, qui utilise la réaction de Pictet-Spengler pour former le cycle diazépinone, comme réaction clé. Il a été démontré que le pyrrolo[3,2-e][1,4]diazépin-2-one mime un tour-γ inverse par l’analyse de cristaux par rayon X. Cette méthodologie a été transposée sur trois types de support, soit la résine de Merrifield, de Wang et un support soluble (TAP). Le système urotensinergétique joue un rôle dans certaines pathologies du système cardiovasculaire, comme l’hypertension artérielle, l’insuffisance cardiaque et l’athérosclérose. Le système urotensinergétique est exprimé dans le système circulatoire, extractoire et le système nerveux central et comprend l’UII, l’URP et le récepteur UT. L’UII et l’URP humains sont composés respectivement des séquences d’acides aminés : H-Glu-Thr-Pro-Asp-c[Cys-Phe-Trp-Lys-Tyr-Cys]-Val-OH et H-Ala-c[Cys-Phe-Trp-LysTyr-Cys]-Val-OH. L’UII est le peptide vasoconstricteur le plus puissant connu à ce jour, dont l’URP est son isoforme. Les deux peptides ont des effets biologiques différents et on peut supposer qu’ils jouent un rôle distinct dans certaines pathologies. Il a été démontré que la partie active de l’UII est composée du tripeptide : Trp-Lys-Tyr. Dans l’URP, il a été démontré que ce tripeptide forme un tour-γ inverse, ce qui fait du récepteur UT une bonne cible biologique pour tester une librairie de pyrrolo[3,2-e][1,4]diazépin-2-ones, reprenant le tripeptide Trp-Lys-Tyr. Dernièrement, l’équipe du professeur David Chatenet a mis au point un peptide, l’urocontrin en remplaçant le segment Trp par un groupement biphénylalanine, qui a démontré un comportement spécifique comme antagoniste du récepteur UT. La Librairie de pyrrolo[3,2-e][1,4]diazépin-2-ones est basée sur la séquence TrpLys-Tyr de l’UII et de l’URP et de la séquence Trp-Lys-Bip de l’urocontrin. La synthèse de la librairie est faite sur la résine de Wang. La chaîne latérale de Tyr est mimée en utilisant la tyramine, Lys et Orn sont utilisés et la chaîne latérale de Trp a été reproduite II en utilisant le biphényle (comme dans l’urocontrin), le 1-naphthyle et le 2-naphthyle, sont introduits en employant les aldéhydes respectifs dans la réaction de Pictet-Spengler, ce qui donne les pyrrolo[3,2-e][1,4]diazépin-2-ones insaturés et les saturés S- et R-. L’évaluation de l’activité biologique des pyrrolo[3,2-e][1,4]diazépin-2-ones obtenues sur le récepteur UT se fait par des tests in vitro et ex vivo. Les tests in vitro consistent en un essai de liaisons sur des cellules CHO exprimant le récepteur UT en employant hUII-125I, comme contrôle radiomarqé. Les tests ex vivo sont effectués sur des aortes de rats pour mesurer la capacité à induire des contractions ou de moduler les contractions induites par hUII et URP. Certains R-pyrrolo[3,2-e][1,4]diazépin-2-ones causent une réduction de 50% du signal radioactivité du hUII-125I. Les pyrrolo[3,2-e][1,4]diazépin-2-ones ne montrent guère d’activité ex vivo, mais ils ont la capacité de moduler les contractions induites par l’hUII et l’URP. Par exemple, l’analogue Lys R-saturé avec le biphényle inhibe toutes les contractions de l’aorte à 14 µM avec un pKb de 5,54 à 4 µM, sans influencer les contractions de l’aorte induites par l’URP. Les pyrrolo[3,2-e][1,4]diazépin-2-ones ont une sélectivité pour le système urotensinergétique et sont inactifs sur le récepteur de l’endotheline-1. Les pyrrolo[3,2-e][1,4]diazépin-2-ones sont les premières petites molécules qui peuvent moduler l’activité biologique de l’UII et URP et offrir un potentiel intéressant comme outil pour étudier le système urotensinergétique.
The pyrrolodiazepinones have interesting biological activities on various biological receptors, which makes them a prime target for developing new biologically active small molecules. A methodology in solution had been developed for synthesizing pyrrolo[3,2-e][1,4]diazepin-2-ones, which utilized the Pictet-Spengler condensation as the key reaction to form the diazepinone ring. Pyrrolo[3,2-e][1,4]diazepin-2-ones were found to mimic an inverse γ-turn conformation by X-ray crystallographic analysis. The methodology was subsequently implemented on three types of support: Merrifield resin, Wang resin and the soluble TAP support. The urotensinergic system plays a role in certain diseases of the cardiovascular system, such as hypertension, heart failure and atherosclerosis. The urotensinergic system is expressed in the circulatory system, excretory and central nervous systems and includes the endogenous ligands urotensin II (UII) and urotensin II-related peptide (URP), and the urotensin receptor UT. The ligands UII and human URP are composed of the respective amino acid sequences: H-Glu-Thr-Pro-Asp-c[Cys-Phe-Trp-Lys-Tyr-Cys]-Val-OH and H-Ala-c[Cys-Phe-Lys-Tyr-Trp-Cys]-Val-OH. The peptide UII is the most potent vasoconstrictor known to date. The two peptides have different biological effects and may exhibit distinct roles in certain diseases. Their common Trp-Lys-Tyr sequence is believed to play an important role in the activity of UII and URP, and has been suggested to adopt an inverse γ-turn conformation. Notably, the laboratory of Professor David Chatenet developed the UT receptor antagonist peptide urocontrin by replacing the Trp residue by biphenylalanine (Bip) in URP. A library of pyrrolo[3,2-e][1,4]diazepin-2-one analogs was thus designed to mimic the inverse γ-turn sequence and targeted against UT. The pyrrolo[3,2-e][1,4]diazepin-2-one library was designed based on the Trp-Lys-Tyr sequence of UII and URP, and Trp-Lys-Bip sequence of urocontrin. The synthesis of the pyrrolo[3,2-e][1,4]diazepin-2-one library was achieved on Wang resin. The side chain of Tyr was mimicked using tyramine, Lys and Orn were used as the basic amino acid component, and the side chain of Trp was replicated using biphenyl (as in urocontrin) 1-naphthyl and 2-naphthyl groups that were introduced by employing their respective aldehydes in a Pictet-Spengler reaction, which furnished unsaturated and saturated S- and R-pyrrolo[3,2-e][1,4]diazepin-2-ones. Evaluation of the biological activity of the pyrrolo[3,2-e][1,4]diazepin-2-ones on the UT receptor was performed in vitro and ex vivo. Tests in vitro measured binding in CHO-cells which expressed UT by employing hUII-125I as radiolabeled control. In rat aorta, ex vivo tests measured capacity to induce contraction, or modulate the contractions induced by hUII and URP. Certain R-pyrrolo[3,2-e][1,4]diazepin-2-ones caused an up to 50% reduction of the radioactive signal of hUII-125I. Pyrrolo[3,2-e][1,4]diazepin-2-ones exhibited little activity ex vivo; however, they modulated contractions induced by hUII and URP. For example, the saturated R-analog possessing lysine and a biphenyl side chain inhibited completely hUII-induced contractions of the aorta at 14 µM with a pKb of 5.54 at 4 µM, without influencing URP-induced contractions. Pyrrolo[3,2-e][1,4]diazepin-2-ones were selective for the urotensinergic system and inactive on the related receptor endothelin-1. Pyrrolo[3,2-e][1,4]diazepin-2-ones represent the first small molecules that can differently modulate the biological activities of UII and URP, and offer interesting potential as tools for studying the urotensinergic system.