Le paludisme, maladie infectieuse due à des parasites du genre Plasmodium, reste mortel et préoccupant dans les régions intertropicales d’Afrique, d’Asie et d’Amérique. Les phénomènes de résistance des parasites aux différentes générations de traitements représentent un problème majeur, auxquels s’ajoutent le coût des traitements et donc l’accès aux soins pour les populations les plus défavorisées. Il est ainsi urgent de trouver de nouvelles cibles et de développer de nouveaux agents antipaludiques agissant via des mécanismes originaux. La cible étudiée lors de ces travaux de thèse est la leucyl aminopeptidase bimétallique de P. falciparum, notée PfA-M17. Elle a récemment émergé comme potentielle cible antipaludéenne et jouerait un rôle essentiel à la croissance et à la survie du parasite. Elle serait impliquée dans la dernière étape du catabolisme de l’hémoglobine lors du cycle érythrocytaire du parasite. Ces travaux se sont concentrés sur la conception, la synthèse et l’évaluation d’inhibiteurs sélectifs de PfA-M17. En s’inspirant de travaux antérieurs menés au laboratoire et d’expériences de modélisation moléculaire, des analogues benzocycloheptanes trisubstitués ont été conçus pour inhiber sélectivement PfA-M17. Une voie de synthèse diastéréosélective partant de l’acide D-isoascorbique a été mise au point et a permis d’accéder à des analogues cycloheptanes et cyclohexanes trisubstitués. Cette voie de synthèse a aussi été étudiée afin d’obtenir des analogues benzocycloheptanes trisubstitués. / Malaria is an infectious disease due to Plasmodium parasites, still causing numerous deaths in intertropical areas of Africa, America and Asia. Existing treatments face problems of high cost and resistance, hence the need to discover new targets and to develop new compounds. This work focused on a recent antimalarial target, a bimetallic leucyl aminopeptidase, named PfA-M17. Inhibition of this aminopeptidase shows it is essential for parasite survival and growth. PfA-M17 may be involved in the last step of hemoglobin digestion during the intraerythrocytic cycle of the parasite. This study concerned the design, the synthesis and the evaluation of selective PfA-M17 inhibitors. Trisubstituted benzocycloheptane analogs were designed as PfA-M17 inhibitors, based on previous works performed in our team and based on molecular modelling. A diastereoselective pathway was developed from D-isoascorbic acid and gave trisubstituted cycloheptanes and cyclohexanes analogs. This pathway was also studied in order to get the trisubstituted benzocycloheptane scaffolds.

Les chiffres des statistiques du cancer colorectal en France et dans le mondemontrent la nécessité de développement de plateformes technologiques plus rapides,sensibles et spécifiques pour assurer le diagnostic du cancer. Un diagnostic rapide va ainsiaider à améliorer l’état de santé et réduire le temps d’attente des résultats qui peut être ungrand facteur de stress pour les patients. L’analyse des biomarqueurs dans le sang, lesurines et autres fluides corporels est l’une des méthodes appliquées pour la détectionprécoce de la maladie. Dans le cadre de ce projet des nucléosides urinaires ont été identifiéscomme biomarqueurs pour le cancer colorectal. Financée par l’Agence Nationale de laRecherche (ANR), à travers le projet CancerSensor (programme TECSAN), cette thèse s’estdéroulée au sein de l’équipe MDA (Microsystèmes de Détection Acoustique) du laboratoireIMS. Dans le cadre de ce projet, nous avons proposé une solution technologique dedétection et de suivi de biomarqueurs du cancer colorectal. Notre choix de la stratégie dedétection s’est porté sur les polymères à empreintes moléculaires comme élément dereconnaissance des biomarqueurs. Celui-ci sera associé à un transducteur acoustique àondes de Love mis au point lors de travaux précédents au sein de l’équipe MDA. Lebiocapteur ainsi développé va cibler les nucléosides mis en évidence pour le cancercolorectal. / Colorectal cancer statistics in France and all over the world demonstrate theneed for fast, sensitive and specific technological platforms development for cancerdiagnosis. A rapid diagnosis will improve the patients’ health status and reduce the resultswaiting time which could be a great stress factor. Biomarkers analysis in blood, urine andother body fluids is recognized as one of the applied methods for early cancer detection. Inframe of this project, urinary nucleosides have been identified as colorectal cancerbiomarkers. Funded by the National Research Agency (ANR), through the cancer sensorproject (TECSAN program), this thesis was carried out in IMS laboratory. Hence, a colorectalcancer biomarkers detection and monitoring technological solution has been proposed. Inour detection strategy, Molecularly Imprinted Polymers (MIP) has been identified asbiomarker recognition element. The MIP layer has been associated to Love Wave acoustictransducer. This biosensor will sense the identified colorectal cancer nucleosides.

Les systèmes bioélectroniques tels que les biopiles enzymatiques nécessitant souvent l'utilisation des assemblages moléculaires complexes comprenant le cofacteur de l'enzyme, des agents de couplage et des médiateurs électrochimiques. Afin de les simplifier, nous avons remplacé ces différents partenaires par 13 analogues simples à synthétiser après identification par criblage in silico. Le noyau aromatique est couplé à un noyau aromatique et puis un médiateur électrochimique est couplé à celui-ci. Les produits sont des poudres de couleurs variées (rose, rouge). Le rendement de la première étape est de 83% avec une pureté d'environ 92%. Le rendement de la seconde étape est compris entre 45% et 65% avec une pureté de 97%. Ces analogues ont été caractérisés chimiquement (RMN, spectrométrie de masse) et électrochimiquement (voltammétrie cyclique et spectroélectrochimie). Les activités de deux enzymes, la formiate déshydrogénase (FDH) et l'alcool déshydrogénase de foie de cheval (HLADH), et d'un catalyseur organométallique, le [Cp*Rh(bpy)(H2O)]2+, ont été évaluées avec ces analogues. De faibles activités ont été observées en présence de l'HLADH avec 4 analogues et en présence de la FDH avec un seul analogue. Au contraire aux enzymes, la réduction d'un médiateur a pu été confirmée en présence du catalyseur [Cp*Rh(bpy)(H2O)]2+ par voltammétrie cyclique. La FDH native n'est pas adaptée à fonctionner avec ces nouveaux substrats solubles dans un LI, le [MMIm][Me2PO4]. Une FDH tolérante (N187S/T321S) au [MMIm][Me2PO4] précédemment obtenue par évolution dirigée a été donc étudiée en isolant les simples mutants N187S et T321S. Le double mutant N187S/T321S et le simple mutant N187S sont 4 fois plus actifs en solution aqueuse et en présence de LI. Des analyses par spectroscopie de fluorescence ont montré que la simple mutation N187S favorise la stabilité du dimère de FDH en modifiant le pKa de l'acide aminé E163. Celui-ci est impliqué dans la thermostabilité et la tolérance des FDHs aux LIs / Bioelectrical systems, such as enzymatic biofuel cells, often require a molecular construction complex comprising the enzyme cofactor, intermediary molecules and electrochemical mediators. In order to simplify them, we have replaced these different partners by 13 analogs that are simple to synthesize after identification by screening in silico. The nicotinamide ring is coupled to an aromatic moiety and an electrochemical mediator is then coupled to it as well, resulting in various colored powders (pink, red). The first step' s yield is around 83% with a purity of approximately 92%. The second step's yield is comprised between 45% and 65% with a purity of 97%. The analogs were characterized chemically (NMR, mass spectrometry) and electrochemically (cyclic voltammetry, spectroelectrochemistry). The activities of two enzymes, the formate dehydrogenase (FDH) and the horse liver alcohol dehydrogenase (HLADH), and an organometallic catalyst, [Cp*Rh(bpy)H2O]2+, were evaluated with these analogs. Weak activities were observed for 4 analogs using the HLADH and 1 analog using the FDH. Unlike the enzymes, the reduction of a conjugated mediator was confirmed with the catalyst [Cp*Rh(bpy)H2O]2+ using cyclic voltammetry. The wild type FDH is not adapted to function with these new substrates, which can be solubilized in an IL such as [MMIm][Me2PO4]. An FDH (N187S/T321S) shown to be tolerant to [MMIm][Me2PO4], and obtained previously by directed evolution, was studied by isolating the two single mutants, N187S and T321S. The double mutant N187S/T321S and the mutant N187S are 4 times more active in aqueous solution and in [MMIm][Me2PO4]. Fluorescence spectroscopy analyses showed that the single mutation N187S favorises FDH dimer stability by modifying the pKa of the amino acid E163. The latter is involved in FDH thermal stability and tolerance in ILs

The glycoprotein hormone family comprising of Luteinizing Hormone (LH), Chorionic Gonadotropin (hCG), Follicle Stimulating Hormone (FSH) and Thyroid Stimulating Hormone (TSH) plays important role in reproduction and overall physiology of the organism. These hormones are heterodimeric molecules consisting of an identical α subunit non-covalently associated with the hormone-specific β subunit. Both subunits of all these hormones are N-glycosylated. In addition, hCGβ subunit also has four O-linked oligosaccharides located at the C-terminus of the polypeptide(1). The α and β subunits of all these hormones contain five and six disulfide bonds respectively and the crystal structures of hCG and hFSH indicate that both subunits of the hormones belong to the cystine knot family of proteins(2-4). Although the β subunits are hormone specific, there are distinct similarities in these subunits with the 12 cysteines conserved in all these subunits (1). These hormones, because of their unique structural features have proved to be important models for structure–function relationship studies of complex dimeric glycoproteins. Folding of subunits during biosynthesis, role of glycosylation in folding pathways and in vitro and in vivo bioactivity of the hormone, as well as, identification of domains important for subunit association, receptor binding and subsequent signal transduction have been topics of active investigations. The receptors of these hormones belong to the family of G-protein coupled receptors (GPCR) and have unique hormone specific exodomain not present in other members of the GPCR family and characteristic seven transmembrane domains followed by a C terminal domain(5). Primary structure analysis of Glycoprotein hormone receptors family revealed sequence conservation, maximum homology being observed in the transmembrane domain (TMD)(6). Significant homologies could be observed in the hormone specific extracellular domains (ECD) also (7). Despite these homologies, the receptors exhibit exquisite specificity with very low cross reactivity with other members of the hormone family (8). Elucidation of the molecular details of the contacts between the hormone and the receptors has not been achieved so far. Various approaches have been employed to delineate the residues or domains of both hormone and receptors involved in interaction. These include testing of chimeras or mutants of hormones or receptors for changes in activity (9-12), chemical modifications(13) and competition with peptides from either hormones (14) or receptors (15). Polyclonal and monoclonal antibodies against glycoprotein hormones and various fragments of their receptors have been used to determine the role of different domains of both in binding and response (6, 16, 17). However, till date there is no consensus on the specific mechanisms by which the glycoprotein hormone docks onto its receptor. It was proposed that the initial contact between the hormone and the receptor occurs through high affinity binding of the hormone specific β subunit to the Leucine rich regions of the ECD that results in conformational changes in both hormone, as well as, the receptor and brings hormone/ECD complex closer to the TMD of the receptor. The secondary, relatively lower affinity interactions between the hormone and the receptor then take place through common α subunit and exoloops of TMD of the receptor resulting in signal generation (18, 19). Recently a different kind of model has been proposed which suggests that the hormone does not make any direct contacts with the TMD of the receptor. The signal is transduced by the change in contacts between ECD and TMD brought about by hormone’s interaction with ECD(8, 20). The present study was initiated with an overall objective of understanding the molecular details of the hormone receptor interactions of this family, particularly hCG- LH receptor interactions. Two different approaches were employed for this purpose; the first, direct approach being structure elucidation of the members of the glycoprotein hormone family while the second approach uses antibodies against hCG as tools to probe into hormone-receptor interactions. The results obtained using these two approaches have been consolidated in the present thesis and are organized as follows. Chapter 1 is an extensive review of the literature and it builds background for the present work while the exact aim and scope of the present work have been defined in Chapter 2. Chapter 3 describes cloning, expression and purification of recombinant glycoprotein hormones hLH, hCG and single chain derivative of hCG. The Chapter 4 gives details of the molecular aspects of hCG-LH receptor interaction dissected using hCG monoclonal antibodies (MAbs). Chapter 5 discusses implications of the observations made in the present study and states the future directions envisaged. There are a number of endocrinopathies associated with abnormal levels of glycoprotein hormones and treatments of such disorders often demand large quantities of either agonists or antagonists of the hormones. The structure-function relationship studies should help in identifying domains/residues important for subunit interaction, receptor binding, and signal transduction, which would also allow engineering of agonists and antagonists of hormone action. However, structure determination of the glycoprotein hormone family using X-ray crystallography has proved to be a difficult task and it is believed that the heterogeneity in glycosylation is the primary reason for this low success rate in the process of crystallization. The first crystal structure of hCG was that of completely deglycosylated hCG but such a molecule displays antagonistic behavior(2, 3). Use of NMR spectroscopy, the alternate method commonly used for structure determination is often limited by the availability of large quantities of biologically active hormones free of any contaminants. Large quantities of LH, hCG and FSH are also required for treatment of infertile patients suffering from gonadotropin deficiency. The first goal of the present study was thus to produce and purify biologically active recombinant hCG and hLH. Owing to the inherent features of glycoprotein hormones and their potential therapeutic applications, the recombinant expression of these hormones is an important goal from both basic research, as well as, commercial point of view. Considering the above mentioned features it is clear that the expression system used for the hyperexpression of these glycoprotein hormones should also serve as a model system for investigating structure–function relationships and folding of subunits during biosynthesis, in addition to providing sufficient quantities of the hormones for clinical applications. It has been demonstrated that N-linked glycosylation during biosynthesis facilitates protein folding and conformational maturation of glycoprotein hormone subunits into an assembly-competent, biologically active form (21). Therefore, the ideal recombinant expression system should also be able to glycosylate the protein during biosynthesis. The Pichia pastoris yeast expression system was chosen for hyperexpression of glycoprotein hormones as it blends the advantages of both bacterial and mammalian expression systems. Earlier, expression of biologically active hCG and the subunits of hCG and bovine FSH using Pichia pastoris expression system has been reported from the laboratory (22, 23). Chapter 3 (section 3.3.1) of the thesis describes hyperexpression of hLH. The expression of these heterologous proteins was scaled up using fermentation procedures to fulfill the requirements of large quantities of hormones for various applications. Purification of Pichia expressed hormones turned out to be a complex task as large quantity of the hormone was secreted out in the fermentation medium (10litre volume) that was of high ionic strength. Of several different strategies attempted for concentration and partial purification of recombinant hCG, hydrophobic interaction chromatography (HIC) using Phenyl Sepharose matrix emerged as the most efficient technique as a first step of purification. Subsequently, cation exchange chromatography using SP- Sepharose matrix yielded completely purified biologically active recombinant hCG (section 3.3.2). The preliminary data also suggested that Pichia cells express a biologically active form of hCG which appeared to be less glycosylated and of lower molecular weight. Using the same protocol purification of hLH, as well as, single chain derivative of hCG, phCGαβ was achieved (section 3.3.3). These recombinant proteins were characterized extensively using various biochemical, as well as, immunological criteria and were shown to be similar to their natural counterparts with respect to their ability to bind LH receptor and to transduce signal as judged by radioreceptorassays and in vitro bioassays respectively. The hydrophobic interaction chromatography proved an important starting point for purification of all the other members of the glycoprotein hormone family expressed using Pichia pastoris expression system. With the availability of purified, biologically active recombinant hCG in large quantities it was now possible to make attempts towards structure elucidation using NMR spectroscopy. The structure determination of such complex proteins by NMR spectroscopy is made relatively easier by labeling the proteins with magnetically more active, stable isotopes of carbon and nitrogen, 13C and 15N respectively however the cost is often prohibitively high. The Pichia pastoris expression system offers simple means of labeling the proteins as the cells can be grown on simple salts of carbon and nitrogen such as 13C labeled methanol, 15N labeled ammonium chloride or ammonium sulphate. The Chapter 3 also gives a brief account of the preliminary attempts made to label the recombinant hCG with 15N and the structural studies carried out with the carbohydrate moieties of the recombinant hCG using solution NMR spectroscopy. This work was carried out in collaboration with the laboratory of Prof. J.P Kamerling of the University of Utrecht, Netherlands and the efforts are currently underway to elucidate the complete structure of the Pichia expressed hCG. The common feature of receptors and antibodies against the ligand is that both display very specific, high affinity binding towards the ligand. Hence, it is logical to speculate that the antigen binding regions of the antibodies that inhibit hormone binding and/or response, exhibit homology with distinct domains of the receptor. By identifying the epitopes recognized by such antibodies, it should be possible to predict contact points between the hormone and the receptor. In the present study, this hypothesis has been tested using monoclonal antibodies (MAbs) against hCG recognizing different epitopes in the hormone molecule and having different effects on hormone binding and response (Chapter 4). These MAbs were classified as α subunit specific, β subunit specific or heterodimer specific depending on their abilities to bind either subunit in addition to the hormone itself. Interestingly, it was observed that the hCGβ subunit specific MAbs, as well as, heterodimer specific MAbs inhibited hCG receptor binding and hence the response generated by hCG, while the hCGα subunit specific MAbs inhibited only response to the hormone without interfering in binding (Section 4.3.1). To dissect out these interactions further the epitopes recognized by these antibodies on hCG molecule were determined (Section 4.3.2), single chain fragment variable (ScFv) were generated from each of these antibodies and it was shown that these ScFv retain the functionality of the original antibody (Section 4.3.3). Further, the amino acid sequence of each antibody was determined (Section 4.3.4) and finally shown that the antigen binding domains of antibodies show homology to the distinct regions of the LH receptor on sequence alignments between the two using three different programs (4.3.5). The hCGβ subunit specific MAb 52/28' displayed distinct homology with the ECD of LH receptor while the α subunit specific MAb C10 showed regions homologous to TMD of the receptor and the heterodimer specific MAb E12 was found to be similar to the hinge region of the receptor. This clearly indicates that the β subunit of hCG is in close contact with ECD of the receptor while the α subunit makes contacts with the TMD of receptor. The present study thus supports the existing model of hormone receptor interactions, which states that the hormone first binds to the exodomain of the receptor mainly through its β subunit while the integrity of the α subunit is critical for signaling. (24, 25). Also, the observations made in the present study exhibit an interesting possibility of antigen antibody complexes being used as surrogate models for gaining insights into hormone receptor complex. Further, it has been reported that hCG has immunocontraceptive potential(26). Active and passive immunization studies with hCG in primates and humans have demonstrated the possibility of controlling fertility by the antibodies capable of neutralizing hCG. This forms the basis for female contraceptive vaccine that has undergone Phase II clinical trials in India. The MAb E12 characterized in the present study displayed highly specific binding to heterodimeric hCG exclusively without showing any cross reactivity with hLH (Section 4.3.1). The epitope mapping analysis revealed that this antibody recognizes a unique discontinuous epitope present only in the heterodimeric hCG and is distinct from the unique C-terminal extension of hCGβ absent in hLHβ (Section 4.3.2). The MAb, IgG or its recombinant single chain fragment variable (ScFv), inhibited response to hCG, but not to hLH (4.3.3). Thus, the epitope recognized by this MAb is an ideal candidate antigen for immunocontraception. The MAb E12 can also be used for passive immunization in case of emergency contraception. Another potential application of hCG specific antibodies is in homing and the treatment of tumors that secrete hCGβ subunit. The hCGβ subunit specific MAbs used in the present study 52/12 and 52/28' that inhibited hCG receptor binding as well as response generated by hCG can be used in treating such tumors. The functional ScFvs generated from these MAbs in the present study can be made use of on humanization. Thus, the present study has yielded some important molecules for therapeutic applications besides providing a new platform for structure-function relationship studies of the complex glycoprotein hormones.

A key element of hydrologic routing models is the storage-discharge relationship assumed to follow a certain mathematical form, usually a linear or a power function, the parameters of which are calibrated based on existing inflow-outflow data. While this assumption simplifies the model calibration process, it also constrains the models to operate by this function throughout their flow range. In view of the complex and nonlinear river flow behavior, this approximation undoubtedly introduces errors. This research presents a new hydrologic river routing approach that is not limited by the above assumption. River reaches are modeled as cascades of interacting conceptual reservoirs, with storage-discharge functions identified by the data. A novel parameter estimation approach has been developed to identify these functions and all other model parameters based on control theory concepts. After calibration, these functions indeed exhibit different mathematical forms at different regions of their active variation range. The new approach is applied and successfully demonstrated in real world reservoir and river routing applications from the Nile River Basin. A Bayesian forecasting scheme was also developed that uses the new approach to generate flow forecasts with explicit uncertainty characterization.

Peptides have assumed considerable importance in pharmaceutical industry and vaccine research. Understanding the structural features of these peptide molecules can be effective not only in mimicking natural proteins but also in the design of new biomaterials. Polypeptide sequences consisting of twenty genetically coded amino acids possess structural flexibility, which makes the predictions difficult. However, the introduction of non-protein amino acids into the peptide chain restricts the available range of backbone conformations and acts as stereochemical directors of polypeptide chain folding. Such conformationally rigid residues allow the formation of well defined structures like helices, strands etc, which further assemble into super secondary structural motifs by flexible linkages. Crystal structure determination of the oligopeptides by X-ray diffraction gives insight into the specific conformational states, modes of aggregation, hydrogen bond interactions, solvation of peptides and various weakly polar interactions involving the side chains of aromatic residues (Phe, Trp and Tyr). In β-, γ- and higher ω-amino acids, due to the insertion of one or more methylene groups between the N- and Cα-atoms into the peptide backbone the accessible conformational space is greater than the α-amino acids. The β-, γ-, δ-…. amino acid residues belong to the family of ω-amino acids. Extensive research in the field of β-peptides, which have been experimentally verified or theoretically postulated, has assigned several helices, turns and sheets. The use of ω-amino acid residues in conjunction with α-residues permits systematic exploration of the effects of introducing additional backbone atoms into well-characterized α-peptide structures. The observation of new families of hydrogen bonded motifs in the hybrid peptides containing α- and ω-amino acids are the recent interest in this regard. This thesis reports results of X-ray crystallographic studies of eighteen designed peptides and four protected ω-amino acids listed below. Within brackets are given the abbreviations used for the sequences (Symbol U represents Aib). The ω-amino acids reported in this thesis are: (S)-β3-HAla (β3-homoalanine), (R)-β3-HVal, (S)-β3-HVal (β3-homovaline), (S)-β3-HPhe (β3-homophenylalanine), (S)-β3-HPro (β3-homoproline), βGly (β-homoglycine), γAbu (gamma aminobutyric acid) and δAva (delta aminovaleric acid). 1. Boc-Leu-Trp-Val-OMe (LWV), C28H42N4O6 2. Ac-Leu-Trp-Val-OMe (Space group P21) (LWV1), C25H36N4O5 3. Ac-Leu-Trp-Val-OMe (Space group P212121) (LWV2), C25H36N4O5 4. Boc-Leu-Phe-Val-OMe (LFV), C26H41N3O6 5. Ac-Leu-Phe-Val-OMe (LFV1), C23H35N3O5 6. Boc-Ala-Aib-Leu-Trp-Val-OMe (AULWV), C35H54N6O8 7. Boc-Trp-Trp-OMe (WW), C28H32N4O5 8. Boc-Trp-Aib-Gly-Trp-OMe. (WUGW), C34H42N6O7 9. Boc-Leu-Trp-Val-Ala-Aib-Leu-Trp-Val-OMe (H8AU), C57H84N10O11 10. Boc-(S)-β3-HAla-NHMe (BANH), C10H20N2O3 11. Boc-(R)-β3-HVal-NHMe (BVNH), C12H24N2O3 12. Boc-(S)-β3-HPhe-NHMe (BFNH), C16H24N2O3 13. Boc-(R)-β3-HVal-(R)-β3-HVal-OMe (BVBV), C18H34N2O5 14. Boc-(R)-β3-HVal-(S)-β3-HVal-OMe (LVDV), C18H34N2O5 15. Boc-(S)-β3-HPro-OH (BPOH), C11H19N1O4 16. Boc-Leu-Phe-Val-Aib-(S)-β3-HPhe-Leu-Phe-Val-OMe (UBF8), C60H88N8O11 17. Piv-Pro-Gly-NHMe (PA1), C13H23N3O3 18. Piv-Pro-βGly-NHMe (PB1), C14H25N3O3 19. Piv-Pro-βGly-OMe (PBO), C14H24N2O4 20. Piv-Pro-δAva-OMe (PDAVA), C16H28N2O4 21. Boc-Pro-γAbu-OH (BGABU), C14H24N2O5 22. Boc-Aib-γAbu-OH (UG), C13H24N2O5 23. Boc-Aib-γAbu-Aib-OMe (UGU), C18H33N3O6 The thesis is divided into seven chapters. Chapter 1 gives a general introduction to the stereochemistry of polypeptide chains and the secondary structure classification: helices, β-sheets and β-turns followed by an overview of different types of weakly polar interactions involving the side chains of aromatic amino acid residues. This section also provides a brief overview of the conformational analysis of β-, γ- and higher ω-amino acid residues in oligomeric β-peptides and in α,ω-hybrid peptides. A brief discussion on X-ray diffraction and solution to the phase problem is also presented. Chapter 2 describes the crystal structures of the peptides, Boc-Leu-Trp-Val-OMe (LWV), the two polymorphs of Ac-Leu-Trp-Val-OMe (LWV1 and LWV2), Boc-Leu-Phe-Val-OMe (LFV), Ac-Leu-Phe-Val-OMe (LFV1) and Boc-Ala-Aib-Leu-Trp-Val-OMe (AULWV), in order to explore the nature of interactions between aromatic rings, specifically the indole side chain of Trp residues [1]. Peptide LWV adopts a type I β-turn conformation, stabilized by an intramolecular 4→1 hydrogen bond. Molecules of LWV pack into helical columns stabilized by two intermolecular hydrogen bonds, Leu(1)NH…O=CTrp(2) and Indole NH…O=CLeu(1). The superhelical columns further pack into the tetragonal space group P43 by means of a continuous network of indole - indole interactions. The peptide Ac-Leu-Trp-Val-OMe crystallized in two polymorphic forms: P21 (LWV1) and P212121 (LWV2). In both forms, the peptide backbone is extended and the crystal packing shows anti-parallel β-sheet arrangement. Similarly, extended strand conformation and anti-parallel β-sheet formation are also observed in the Phe containing analogs, LFV and LFV1. The pentapeptide AULWV adopts a short stretch of 310-helix. Analysis of aromatic - aromatic and aromatic - amide interactions in the structures of peptides LWV, LWV1 and LWV2 are reported along with the examples of 12 Trp containing peptides from the Cambridge Structural Database. The results suggest that there is no dramatic preference for the orientation of two proximal indole rings. In Trp containing peptides specific orientations of the indole ring, with respect to the preceding and succeeding peptide units, appear to be preferred in β-turns and extended structures. Crystal parameters LWV: C28H42N4O6; P43; a = 14.698(1) Å, b = 14.698(1) Å, c = 13.975(2) Å; Z = 4; R = 0.0737, wR2 = 0.1641. LWV1: C25H36N4O5; P21; a =10.966(3) Å, b = 9.509(2) Å; c = 14.130(3) Å, β = 104.94(1)°; Z = 2; R = 0.0650, wR2 = 0.1821. LWV2: C25H36N4O5; P212121; a = 9.533(6) Å, b = 14.148(9) Å, c = 19.53(1) Å, Z = 4; R = 0.0480, wR2 = 0.1365. LFV: C26H41N3O6; C2; a = 31.318(8) Å, b = 10.022(3) Å, c = 9.657(3) Å, β = 107.41(1)°; Z = 4; R = 0.0536, wR2 = 0.1328. LFV1: C23H35N3O5; P212121; a = 9.514(8) Å, b = 13.56(1) Å, c = 20.04(2) Å, Z = 4; R = 0.0897, wR2 = 0.1960. AULWV: C35H54N6O8.2H2O; P21; a = 9.743(3) Å, b = 22.807(7) Å, c = 10.106(3) Å, β = 105.73(2)°; Z = 2; R = 0.0850; wR2 = 0.2061. Chapter 3 describes the crystal structures of three peptides containing Trp residues at both N- and C-termini of the peptide backbone: Boc-Trp-Trp-OMe (WW), Boc-Trp-Aib-Gly-Trp-OMe (WUGW) and Boc-Leu-Trp-Val-Ala-Aib-Leu-Trp-Val-OMe (H8AU). Peptide WW adopts an extended conformation and the molecules pack into an arrangement of parallel β-sheet in crystals, stabilized by three intermolecular N-H…O hydrogen bonds. The potential hydrogen bonding group NE1H of Trp(1), which does not take part in hydrogen bonding interaction with an oxygen acceptor participate in an intermolecular N-H…π interaction. Peptide WUGW adopts a folded structure, stabilized by a consecutive type II-I’ β-turn conformation. The crystal of WUGW contains a stoichiometric amount of chloroform in two distinct sites each with an occupancy factor of 0.5 and the structure provides examples of N-H…π, C-H…π, π…π, N-H…Cl, C-H…Cl and C-H…O interactions [2]. The molecular conformation of H8AU reveals a 310-helix. The crystal structure of H8AU reveals an interesting packing motif in which helical columns are stabilized by side chain - backbone hydrogen bond involving the indole NH of Trp(2) as donor and C=O group of Leu(6) as acceptor of a neighboring molecule, which closely resembles the hydrogen bonding pattern obtained in the tripeptide LWV [1]. Helical columns also associate laterally and strong interactions are observed between the Trp(2) and Trp(7) residues on neighboring molecules [3]. The edge-to-face aromatic interactions between the indoles suggest a potential C-H…π interaction involving the CE3H of Trp (2) Crystal parameters WW: C28H32N4O5; P212121; a = 5.146(1) Å, b = 14.039(2) Å, c = 35.960(5) Å; Z = 4; R = 0.0503, wR2 = 0.1243. WUGW: C34H42N6O7.CHCl3; P21; a = 12.951(5) Å, b = 11.368(4) Å, c = 14.800(5) Å, β = 101.41(2)°; Z = 2; R = 0.1095, wR2 = 0.2706. H8AU: C57H84N10O11; P1; a = 10.494(7) Å, b = 11.989(7) Å, c = 13.834(9) Å, α = 70.10(1)°, β = 82.74(1)°, γ = 78.96(1)°; Z = 1; R = 0.0855, wR2 = 0.1965. Chapter 4 describes the crystal structures of four protected β-amino acid residues, Boc-(S)-β3-HAla-NHMe (BANH); Boc-(R)-β3-HVal-NHMe (BVNH); Boc-(S)-β3-HPhe-NHMe (BFNH); Boc-(S)-β3-HPro-OH (BPOH) and two β-dipeptides, Boc-(R)-β3-HVal-(R)-β3-HVal-OMe (BVBV); Boc-(R)-β3-HVal-(S)-β3-HVal-OMe (LVDV). Gauche conformations about the Cβ-Cα bonds (θ ~ ± 60°) are observed for the β3-HPhe residue in BFNH and all four β3-HVal residues in the dipeptides BVBV and LVDV. Trans conformations (θ ~ 180°) are observed for β3-HAla residues in both independent molecules in BANH and for the β3-HVal and β3-HPro residues in BVNH and BPOH, respectively. In all these cases except for BPOH, molecules associate in the crystals via intermolecular backbone hydrogen bonds leading to the formation of sheets. The polar strands formed by β3-residues aggregate in both parallel (BANH, BFNH, LVDV) and anti-parallel (BVNH, BVBV) fashion. Sheet formation accommodates both the trans and gauche conformations about the Cβ - Cα bonds [4]. Crystal parameters BANH: C10H20N2O3; P1; a = 5.104(2) Å, b = 9.469(3) Å, c = 13.780(4) Å, α = 80.14(1)°, β = 86.04(1)°, γ = 89.93(1)°; Z =2; R = 0.0489, wR2 = 0.1347. BVNH: C12H24N2O3; P212121; a = 8.730(2) Å, b = 9.741(3) Å, c = 17.509(5) Å; Z = 4; R = 0.0479, wR2 = 0.1301. BFNH: C16H24N2O3; C2; a = 20.54(1) Å, b = 5.165(3) Å, c = 16.87(1) Å, β = 109.82(1)°; Z = 4; R = 0.0909, wR2 = 0.1912. BVBV: C18H34N2O5; P212121; a = 9.385(2) Å, b = 11.899(2) Å, c = 19.199(4) Å; Z = 4; R = 0.0583, wR2 = 0.1589. LVDV: C18H34N2O5; P212121; a = 5.170(4) Å, b = 10.860(8) Å, c = 37.30(3) Å; Z = 4; R = 0.0787, wR2 = 0.1588. BPOH: C11H19N1O4; P1; a = 5.989(2) Å, b = 6.651(2) Å, c = 8.661(3) Å, α = 70.75(1)°, β = 77.42(1)°, γ = 86.98(1)°; Z = 1; R = 0.0562, wR2 = 0.1605. Chapter 5 describes a new class of polypeptide helices in hybrid sequences containing α-, β- and γ-residues. The molecular conformation in crystals determined for the octapeptide Boc-Leu-Phe-Val-Aib-(S)-β3-HPhe-Leu-Phe-Val-OMe (UBF8) reveals an expanded helical turn in the hybrid sequence (ααβ)n. A repetitive helical structure composed of C14 hydrogen bonded units is observed. Using experimentally determined backbone torsion angles for the hydrogen bonded units formed by hybrid sequences, the energetically favorable hybrid helices have been generated. Conformational parameters are provided for C11, C12, C13, C14 and C15 helices in hybrid sequences [5]. Crystal parameters UBF8: C60H88N8O11; P212121; a = 12.365(1) Å, b = 18.940(2) Å, c = 27.123(3) Å; Z = 4; R = 0.0625, wR2 = 0.1274. Chapter 6 describes the crystal structures of five model peptides Piv-Pro-Gly-NHMe (PA1), Piv-Pro-βGly-NHMe (PB1), Piv-Pro-βGly-OMe (PBO), Piv-Pro-δAva-OMe (PDAVA) and Boc-Pro-γAbu-OH (BGABU). A comparison of the structures of peptides PA1 and PB1 illustrates the dramatic consequences upon backbone homologation in short sequences. The molecule PA1 adopts a type II β-turn conformation in the crystal state, while in PB1, the molecule adopts an open conformation with the β-residue being fully extended. The peptide PBO, which differs from PB1 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the crystal state. In peptide PDAVA, the observed conformation resembles that determined for PB1 and PBO, with the δAva residue being fully extended. In peptide BGABU, the molecule undergoes a chain reversal, revealing a β-turn mimetic structure stabilized by a C-H…O hydrogen bond [6]. Crystal parameters PA1: C13H23N3O3; P1; a = 5.843(1) Å, b = 7.966(2) Å, c = 9.173(2) Å, α = 114.83(1)°, β = 97.04(1)°, γ = 99.45(1)°; Z = 1; R = 0.0365, wR2 = 0.0979. PB1: C14H25N3O3.H2O; P212121; a = 6.297(3) Å, b = 11.589(5) Å, c = 22.503(9) Å; Z = 4; R = 0.0439, wR2 = 0.1211. PBO: C14H24N2O4.H2O; P212121; a = 6.157(2) Å, b = 11.547(4) Å, c = 23.408(8) Å; Z = 4; R = 0.050, wR2 = 0.1379. PDAVA: C16H28N2O4.H2O; P21212; a = 11.33(1) Å, b = 25.56(2) Å, c = 6.243(6) Å; Z = 4; R = 0.0919, wR2 = 0.2344. BGABU: C14H24N2O5; P61; a = 9.759(2) Å, b = 9.759(2) Å, c = 29.16(1) Å; Z = 6; R = 0.0773, wR2 = 0.1243. Chapter 7 describes the crystal structures of a dipeptide, Boc-Aib-γAbu-OH (UG) and a tripeptide, Boc-Aib-γAbu-Aib-OMe (UGU) containing a single γAbu residue in each sequence. The structure of UG forms a reverse turn stabilized by a 10-membered intramolecular C-H…O hydrogen bonded ring. The peptide UGU crystallized in the triclinic space group P⎯1 with two molecules in the asymmetric unit resulting in a parallel assembly of sheets in crystals. Notably, the insertion of a single Aib residue at the C-terminus drastically changes the overall conformation of the structures. Crystal parameters UG: C13H24N2O5; P21/c; a = 16.749(3) Å, b = 5.825(1) Å, c = 16.975(3) Å; β = 111.82(1); Z = 4; R = 0.0507; wR2 = 0.1294. UGU: C18H33N3O6; P⎯1; a = 9.576(6) Å, b = 13.98(1) Å, c = 17.83(1); α = 85.31 (1); β = 77.46 (1); γ = 71.39 (1); Z = 4; R = 0.0648; wR2 = 0.1837.

Clopidogrel is an antiplatelet drug prescribed to prevent stent thrombosis after a percutaneous coronary intervention (PCI). Previous evidence suggests that some widely prescribed statins may inhibit the antiplatelet effects of clopidogrel via competitive metabolism of its activating enzyme cytochrome P450 3A4 (CYP3A4). / The objective was to investigate the possibility of an interaction post-PCI between statins and clopidogrel. / We carried out a population-based cohort study identifying 10,491 patients using clopidogrel post-PCI (2001-2004). The outcome was a composite of death of any cause, myocardial infarction, unstable angina, repeat revascularization, and cerebrovascular events. We found that co-prescription of CYP3A4-metabolized statins (hazard ratio (HR) 0.95, 95% confidence interval (CI) 0.79-1.15), or non-CYP3A4-metabolized statins (HR 0.82, 95% CI 0.63-1.07) with clopidogrel was not associated with increase in adverse outcomes. / We observed no evidence of interaction between clopidogrel and statins in a large population cohort of PCI patients, suggesting unlikelihood of an important interaction.

The active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25D), is a key calcium (Ca++) regulatory hormone. It is also associated with functions unrelated to Ca++ homeostasis. Here, special attention is paid towards the anticancer properties of 1,25D. 1,25D strongly inhibits the growth of well-differentiated head and neck squamous cell carcinoma (HNSCC) derived cell lines. However, advanced, less differentiated, HNSCC cell lines (e.g. SCC4) are partially resistant to 1,25D. Resistance to nuclear receptor (NR) agonists is a common event that occurs in other NR-related treatments. For example, some leukemias develop resistance to the usually effective retinoic acid (RA) treatment. However, treating RA-resistant cells with HDAC inhibitors (HDACi) sensitizes them to RA. Thus, this study aims to investigate how treatment with TSA, an HDACi, would affect the response of SCC4 cell lines to 1,25D. We found that TSA had a variety of effects on 1,25D-regulated gene expression. Combined treatment with 1,25D and TSA increased the expression of cell-cycle regulating proteins, but also enhanced the downregulation of key target genes. Given the potential of the 1,25D/HDACi combination in combating cancers, two chimeric compounds, each containing parts of 1,25D and an HDACi, were synthesized in collaboration with Dr. James Gleason (Dept. of Chemistry, McGill). These 1,25D analogs have the HDACi-like structure replacing the 1,25D side chain. Both compounds proved to be agonists of the vitamin D receptor. Moreover, the TSA-substituted compound, called triciferol, effectively induced a-tubulin as well as histones acetylation. This study underlines the potential of combining 1,25D and TSA in cancer treatment, and reveals that bi-functional 1,25D analogs can be produced with potentially enhanced therapeutic activity.

5-Bromo-2'-deoxyuridine (BrdU), a thymidine analogue, is genotoxic and teratogenic. The exposure of mouse embryos to BrdU at doses that cause malformations induces oxidative stress and an embryonic stress response characterized by an increase in c-Fos dependent AP-1 DNA binding. The goal of this thesis was to test the hypothesis that development is disturbed at sites where BrdU is incorporated into DNA, triggering oxidative stress and c-Fos induction. Gestation day 9 CD-1 mice were treated with BrdU and embryos were obtained for immunolocalization of BrdU, 8-oxoguanine, a biomarker for oxidative stress, and c-Fos. BrdU incorporation into DNA was dispersed throughout the embryo. In contrast, the staining for 8-oxoguanine and c-Fos were highest in the neuroepithelium. BrdU incorporation was not affected by the pre-administration of N-acetyl-cysteine (NAC), an anti-oxidant, although both 8-oxoguanine and c-Fos staining were decreased. Thus, the response of the embryo to insult is tissue specific.

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