Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 1% of the population in the western world. It is characterised by a tissue specific attack of cartilage in peripheral joints. Collagen induced arthritis (CIA) is one of the most commonly used animal models for (RA), with similar symptoms and histopathology. CIA is induced by immunisation of mice with type II collagen (CII), and the immunodominant part was previously found to be located between residues 256-270. This thesis describes the interaction between the MHC molecule, glycopeptide antigens from CII and the T cells that is essential in development of CIA. The glycopeptide properties for binding to the mouse MHC molecule Aq have been studied, as well as interaction points in the glycopeptide that are critical for stimulation of a T-cell response. The thesis is based on five studies. In the first paper the minimal glycopeptide core, that is required for binding to the Aq molecule while still giving a full T cell response was determined. The second paper studied the roles of amino acid side-chains and a backbone amide bond as T-cell contact points. In the third paper the hydrogen bond donor-acceptor characteristics of the 4-OH galactose hydroxyl group of the glycopeptide was studied in detail. In the fourth paper we established a structure activity relationship (QSAR model) for (glyco)peptide binding to the Aq molecule. Finally, the stereochemical requirements for glycopeptide binding to the Aq molecule and for T-cell recognition was studied in the fifth paper. The study was performed using collagen glycopeptide analogues, which were synthesised on solid phase. Amide bond and hydroxyl group isosteres were introduced for study of hydrogen bond donor-acceptor characteristics. Statistical methods were used to design a representative peptide test set and in establishing a QSAR model. The results give a deeper understanding of the interactions involved in the ternary MHC-glycopeptide-T cell complex. This information contributes to research directed towards finding new treatments for RA.

Mannheimia haemolytica (M. haemolytica)-induced bovine respiratory disease causes millions of dollars in economic losses to Canadian cattle industry. Contemporary management strategies built around the use of antimicrobials are proving to be increasingly unavailing and lead to drug residues in meat which may contribute to the development of multi drug resistant bacteria. Many M. haemolytica vaccines are effective in stimulating antibody responses but studies of vaccina-tion in young calves and the cattle exposed to M. haemolytica (high-risk cattle) have shown poor vaccine efficacy. Antimicrobial peptides (AMPs) may help in the management of respiratory disease caused by M. haemolytica while minimizing the risk of drug residues in animal-derived food products. AMPs are positively charged molecules that can kill bacteria primarily through the electrostatic interactions with the anionic bacterial lipid bilayer. Since the primary target of AMPs is the bac-terial surface charge, which is evolutionarily conserved, the development of resistance towards AMPs seems less likely. These peptides hold potential to replace or reduce the use of antibiotics. Human β-Defensin 3 (HBD3) and Microcin J25 (MccJ25) are cationic peptides that have shown good activity against many Gram-negative bacteria. Five peptides, namely native HBD3, three synthetic HBD3 analogues (28 amino acid, 20AA, and 10AA), and MccJ25 were selected for microbicidal activity against M. haemolytica. Three C-terminal analogues of HBD3 with all cysteines replaced with valines were manually synthesized using solid phase peptide synthesis (SPPS). In all the three analogue, replacement of cysteine with valine rendered them linear and increased their antibacterial activity. Minimum Bactericidal concentration (MBC) assays were performed with the final inoculum size of 1-5x105 cells/ml, with the exception of the 10AA analogue which was incubated with 104 cells/ml final inoculum size. The antimicrobial assay showed that M. haemolytica was intermediately sensitive to HBD3, 28AA and 20AA analogue with an MBC of 50 µg/ml. MccJ25 had limited effect with an MBC greater than 100 µg/ml. The MBC value of 6.3 µg/ml achieved with the 10AA analogue is likely a result of lower final inoculum size. AMPs have several immunomodulatory functions, and these peptides can act as chemoattractant, induce cytokine release that in turn leads to chemotaxis of monocytes and neutrophils. Since neutrophils play an important role in the pathogenesis of BRD, the chemotactic effect of HBD3, 20AA and 28AA peptides on bovine neutrophils was studied using Boyden chamber. Peripheral blood neutrophils isolated from normal healthy cattle showed chemotaxis towards HBD3 and 20AA peptides (P<0.05) but not towards 28AA analogue. Co-incubation of neutrophils with any of the peptides did not affect their chemotaxis towards N-formyl-L-methionyl-L-leucyl-phenylalanine (fMLP). Based on these data, it can be concluded that HBD3 and its analogues showed antimicrobial ef-fects against M. haemolytica but MccJ25 had limited microbicidal activity against M. haemolytica. While HBD3 and 20AA analogue were chemotactic for bovine peripheral blood neutrophils, none of the peptides inhibited fMLP-induced migration of neutrophils. These peptides hold potential for further in vivo testing to develop them for use to manage M. haemolytica-induced respiratory disease in cattle.

High-resolution magic angle spinning (HRMAS) NMR spectroscopy is used to study solid samples that are normally difficult to analyze due to broadening of peaks. Solid-phase peptide synthesis can bind peptides to an insoluble resin that can be analyzed with HRMAS NMR spectroscopy. A combination of HRMAS NMR and IRMPD spectroscopy, along with computational chemistry, was applied to analyze and evaluate the structure of resin-bound glutathione. Two-dimensional 1H-1H NMR experiments such as COSY, TOCSY, and ROESY were employed to assign and predict the structure of the resin-bound peptide. IRMPD results were used along with calculated protonated structures and spectra to evaluate the conformation of the peptide. The experimental spectrum was compared to the spectra and structures of the protonated species to hypothesize the most favoured structure. Molecular mechanics, molecular dynamics and DFT calculations were implemented to collect structures that best resembled the free and resin-bound glutathione peptide. The results from these methods were compared to determine the structure that is most probable for the glutathione peptide. A semi-folded conformation is the structure the resin-bound GSH most preferred as concluded from the NMR and DFT results. The IRMPD results were analyzed as separate from the resin-bound experiments and suggested protonated GSH had a folded conformation. FK-13 was another peptide synthesized using the solid-phase peptide synthesis technique. The peptide was synthesized using a modified technique different from conventional methodology used in the past. The peptide was also analyzed using COSY, TOCSY, and ROESY to confirm that the synthesis was done correctly and hypothesize a structure. The low substitution of the peptide on the resin gave rise to minimal NOE interactions, but there was some evidence suggesting that the synthesis was successful and the peptide adopted a cyclic conformation. These initial results are useful for future analyses and conformational studies of this resin-bound peptide. Further work needs to be done for both peptides to explore the structures in more detail. The explicit model of solvation should be used to explore the effect of solvent molecules on the conformation of the glutathione peptide as opposed to the implicit model that PCM provides. FK-13 could be synthesized better so that a higher substitution is achieved and better NMR results are obtained. The IRMPD results obtained by the McMahon group can then be compared to the NMR results and computational calculations can be performed to obtain realistic structures of the peptide.

Plants are exposed to a wide range of biotic and abiotic stresses that hinder their growth and reduce crop productivity. In their adaptive response, plants use signaling molecules that are trafficked throughout the plant. This research focuses on the chemical synthesis and assessment of analogs of the plant signal phytosulfokine (PSK, a sulfated pentapeptide), its delivery to plants and its observation using a fiber-optic fluorescence microscope. PSK regulates growth, cell expansion, heat tolerance, and tissue longevity. Analogs of PSK were synthesized using solid-phase peptide synthesis. Pure PSK and TAMRA-labeled PSK were delivered into the wild-type Arabidopsis thaliana Col-0 and a transgenic line expressing PSKR-GFP (PSK receptor – green fluorescent protein). PSKR-GFP could be detected in imaging experiments, but no internalization was observed upon treatment with PSK. Successful implementation of a microscopic approach suited for live plants opens a path to understanding how plants signal and adapt under different stress conditions.

Background: The COVID-19 pandemic is caused by the SARS-CoV-2 virus, which enter the host cells through interactions between the receptor-binding domain (RBD) on the S-protein and the ACE-2 receptor on the host cell. A novel type of vaccine strategy is peptide vaccines, with great potential as a faster and more selective approach to conventional vaccine development. This study focuses on the possibility of generating an antibody response through synthetic peptides harboring B cell epitopes.  Aim: This project aims to investigate the potential of immunogenic peptides to generate an antibody response when used as synthetically produced peptides. As proof-of-concept, the project studies the interactions between previously identified monoclonal antibodies with defined B cell epitopes and the corresponding peptide sequences.  Method: The interactions are evaluated by different ELISA experiments. The candidate peptides are additionally investigated on their binding to polyclonal serum with established S reactive antibodies. Furthermore, the project includes synthesis of one peptide by solid phase peptide synthesis. Results: The ELISA experiments presented no interaction between the synthetic peptides and the monoclonal antibodies or human sera.  Conclusion: The project fulfilled its aim to study the interaction between the B cell epitopes and the monoclonal antibodies. However, no binding was observed. Despite the many advantages in production and stability, development of B cell epitope vaccines come with many challenges. Future will entail if synthetic peptides harboring B cell epitopes can be used as vaccines, or if peptide vaccines will be a focus when a T cell response is to be induced.

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Depuis la découverte du Virus de l'Immunodéficience Humaine (VIH) au début des années 80, la recherche de nouvelles molécules anti-VIH demeure un challenge important pour la communauté scientifique. Les effets secondaires liés à l'usage d'inhibiteurs de la réplication virale, la découverte des récepteurs et la compréhension du mécanisme d'entrée du virus dans la cellule hôte ont encouragé la recherche sur de nouveaux inhibiteurs ciblant l'entrée virale. A ce jour, l'Enfuvirtide est le seul inhibiteur d'entrée approuvé en tant qu'inhibiteur de fusion. Bien que ce composé soit un antiviral puissant, il présente néanmoins de sérieuses limitations, son mode d'administration (injection sous cutanée deux fois par jour) et l'émergence de résistances, le classent en agent rétroviral de seconde classe. Une approche alternative est la génération de D-peptides inhibiteurs de fusion, résistants aux protéases et prometteurs pour le développement et l'identification d'une nouvelle classe de médicaments anti-VIH. Basée sur cette dernière approche, cette thèse est consacrée à la synthèse et à l'étude d'analogues peptidiques en tant qu'inhibiteurs de fusion du VIH. Tout d'abord, des études de modélisation associées à la synthèse d'analogues peptidiques ont permis de mettre en évidence et de comprendre les caractéristiques essentielles responsables de l'activité des D-peptides. Ensuite, des études de relations structure-activité, à partir de séquences modifiées, ont conduit à l'obtention de nouveaux analogues peptidiques inhibiteurs de fusion actifs. Enfin, dans le but de réduire la nature peptidique et par conséquent d'améliorer les propriétés pharmaceutiques, des macrocycles peptidiques ont été conçus, et une nouvelle stratégie de synthèse de peptides cycliques a été développée. / Since the discovery of the Human Immunodeficiency Virus (HIV) at the beginning of the 1980's, the search for new anti-HIV molecules remains an important challenge for the scientific community. Secondary effects associated with viral replication inhibitors, the discovery of receptors and the understanding of the mechanism of the viral entry makes HIV viral entry one of the most promising target for HIV drug development. To date, Enfurvitide is the only approved entry inhibitor as HIV fusion inhibitor. Although highly effective, Enfurvirtide has several serious limitations including high dosing requirements, the administration by injection, and the emergence of resistant strains. An alternative approach that has shown considerable potential is the generation of new D-peptides HIV fusion inhibitors expected to be resistant to proteolytic degradation and useful for the development and the identification of a new class of anti-HIV drugs with improv ed bioavailability.Based on this approach, the present work is dedicated to the synthesis and the study of peptide analogs as HIV fusion inhibitors. First, modeling studies and the synthesis of peptide analogs were devoted to point out and to understand the key elements responsible for the activity of the reference D-peptides. Then, structure activity relationship studies based on different modifications sequences led to the discovery of active peptide analogues as HIV fusion inhibitors. In another approach, in order to decrease peptide nature and consequently to improve the pharmaceutical properties, reduced cyclic peptides were designed. Finally, a novel strategy for cyclic peptide synthesis was developed.