Chronic oxidation linked diseases are on a rise and are one of the leading causes of death globally. Epidemiological evidence increasingly points towards consumption of fruits and vegetables as a preventive way to manage early stages of chronic oxidation linked diseases. Oxidation linked diseases are caused by excessive reactive oxygen species (ROS) generated by a disruption in cellular antioxidant homeostasis due to an overload of calories combined with stress, no excerise and a diet low in antioxidants. Phenolic compounds can not only act as antioxidants but also stimulate the activities of antioxidants enzyme through protective pathways which can help modulate cellular protection. The aim of this dissertation was to use probiotic fermentation to enhance the phenolic and antioxidant compounds in fruit systems which can form the basis of functional food design. The potential of these food systems for disease prevention was investigated in eukaryotic systems through understanding the role of critical metabolic pathways involed in prevention of oxidation linked chronic diseases. Based on structure-function rationale, antioxidant, anti-hyperglycemia and anti-hypertensive potential of phenolic compounds in tea and the effect of extraction time and different degrees of fermentation were investigated in in vitro models. Results indicated that the most fermented teas and a longer extraction time had the highest potential. Further these extracts also had higher H. pylori inhibition potential. Probiotic fermentation of fruit juices with L. helveticus was used to mobilize phenolics and improve biological functionality by maintaining a consistent phytochemical profile. Results indicated that total phenolic and antioxidant potential decreased with feremnetation. However α-glucosidase inhibitory activity and H. pylori inhibitory potential increased with fermentation. Investigation into the mechanism of H. pylori inhibition with fermented cherry extracts revealed inhibition of proline dehydrogenase as the likely mode of action. The potential of fermented apple extracts was further investigated as a phytochemical elicitor in eliciting phenolic and antioxidant response in germinating fava bean. The results indicated a stimulation of phenolic and antioxidant response likely through the stimulation of carbon flux through glycolytic pathways. In yeast, fermented apple extracts accelerated cell death in the presence of peroxide stress in pretreatment model whereas it provided protection against oxidative stress and prevented cell death in concurrent model. Chitosan oligosachharide treatment was investigated as a potential replacement of cancer causing diphenylamine treatment for scald reduction in Cortland apples. Although the treatment did not have any effect on scald reduction, it provides better protection in storage by stimulating phenolic and antioxidant response which related to better health relevant functionality.

<p> In four separate experiments, DL-[5-3H]/DL-[5-14C]ornithine, L-[5-3H]/DL- [5- 14C]ornithine, D-[5-3H]/DL- [5- 14C]ornithine and L-[2-3H]/L-[5- 14c]ornithine were administered to intact tobacco plants (Nicotiana tabacum). Nicotine, ornithine and proline were isolated in each of these experiments. In another experiment, R-[1-2H][l ,4-14C] putrescine was administered to intact tobacco plants and nicotine was isolated. The results of these experiments are consistent with the accepted mode of biosynthesis of nicotine from ornithine via putrescine (1,4-diaminobutane), N-methylputrescine, N-methyl-4-aminobutanal and N- methyl-1-pyrrolinium ion. The 3H:14c ratios of nicotine, the distribution of tritium within nicotine as established by chemical degradation and the distribution of deuterium within nicotine as established by 2H NMR are interpreted as showing that L-ornithine is the preferred enantiomer for nicotine biosynthesis, that the decarboxylation of L-ornithine to yield putrescine proceeds with retention of configuration at the reaction site, and that the oxidation of N-methylputrescine to N-methyl-4-aminobutanal proceeds with loss of the 4(S)hydrogen. </p> <p> Contrary to earlier reports, ornithine isolated in the 3H, 14C experiments had a changed 3:14c ratio from the ornithine which was fed. These results are interpreted as showing that L-ornithine is metabolised more rapidly than is D-ornithine in the tobacco plant. </p> <p> In all 3H, 14c experiments, proline was found to contain at least a small amount of tritium. In particular, when L-[2- 3H]/L-[5-14C] ornithine served as substrate, proline was found to contain 40 + 1% of the tritium, relative to 14C, that had been present in the feeding material. This result is interpreted as showing that, contrary to earlier reports, L-ornithine can be converted into proline via either a-keto-s-aminovaleric acid or glutamic semialdehyde. Together with the 3H: 14C ratios of proline in the other experiments, the results of this work are interpreted as showing that, when DL-ornithine serves as the substrate for proline biosynthesis in tobacco, 88 + 1% of the proline arises from D-ornithine via a-oxidation, 7 + 1% of the proline comes from L-ornithine via a-oxidation and 5 + 1% of the proline is produced from L-ornithine via s-oxidation. </p> / Thesis / Master of Science (MS)

No description available.

In the study of structurally restricted cyclic β-amino acids and peptides, methanopyrrolidine-5-carboxylic acids (MetPyr-5-acids), or 5-syn-carboxy-2-azabicyclo[2.1.1] hexanes, and derivatives were investigated. MetPyr-5-acids are a series of highly conformationally constrained β-proline derivatives, which belong to a novel category of β-amino acids utilized as building blocks for the synthesis of β-peptides. These β-peptides lack the backbone hydrogen bonds necessary for folding in the usual manner. Substituents and functional groups in this ring system were envisioned to impact the folding properties and functionalities of the corresponding β-peptides. In the present study, the analogues of MetPyr-5-acids with C6- substitutions were prepared, and the folding properties of their peptides were explored. To introduce different functionalities at C6 in MetPyr-5-acids, 6-syn-hydroxymethyl substituted derivatives were synthesized and were used as key intermediates. In the synthesis of this core structure, the major steps in their preparation included the Michael addition of benzyloxymethyl allyl amine to 3-butynone, followed by UV light irradiation of the diene to afford 5-acetyl-6-benzyloxymethyl-2-azabicyclo[2.1.1]hexane. Haloform (Br2/NaOH) oxidation of the acetyl group leads to the 6-substituted MetPyr-5-acid. Resolution of the racemate was achieved either by resolving (±)-6-syn-benzyloxymethyl-MetPyr-5-acid via a classical crystallization resolution method using (S)-(-)-α-methylbenzylamine, or by chiral preparative HPLC separation of (±)-6-syn-benzyloxymethyl-MetPyr-5-acid methyl ester. The absolute stereochemistry was confirmed by X-ray crystallography of a derivative. Novel analogs with a range of functionalities incorporated at the C6 position in MetPyr-5-acid were synthesized from 6-syn-hydroxymethyl-MetPyr-5-acid methyl ester, and include hydrophilic groups such as hydroxyl, amino, methyl ether, and hydrophobic groups, such as substituted phenyl groups and triazole. From the protected C6-substituted analogs of MetPyr-5-acids, peptide oligomers of C6-benzyloxymethyl-2,4-methanopyrrolidine-b-amino acid were prepared up to the length of octomer in high yields. This series of oligomers were characterized by circular dichroism (CD) and indicated enhanced order of folding uniformity for the tetramer and up, with increasing ordered folding for longer oligomers. The octomer exhibited minimal solvent effects, and was stable with increasing temperature up to 80 °C. Analysis by NMR of the iso-butyric amide capped monomer indicated a mixture of cis/trans conformation favoring the cis conformation. This was slightly different from the C6 unsubstituted iso-butyric amide derivative, which favored the trans conformation. For the dipeptide, the C6-benzyloxymethyl substitution increased the percentage of cis conformation of the dipeptide amide bond, but the major peptide had the trans conformation. This demonstrated that C6 substitutions could shift the cis/trans equilibrium towards the cis conformation. Longer oligomers showed ordered secondary folding structure as demonstrated by the increase in ellipticity per amino acid unit, but was too complicated to be determined by NMR analysis. Both the CD patterns and molecular model calculation predicted that the longer oligomers (tetramer and above) favor the trans conformation. This preference was driven by the backbone dipole effect. II. SYNTHESIS OF 2,2-DISUBSTITUTED PYRROLIDINE-3-CARBOXYLIC ACIDS Due to the perceived steric influence of 2,2-disubstitution in the pyrrolidine-3-carboxylic acid, it is believed that the adjacent amide/peptide bonds should result in a trans amide bond conformation. Because of the difficulty in introducing disubstitution at the hindered C2 position, the synthesis of such derivatives has not been successful. For this reason a new method was introduced to prepare novel derivatives, at the N- and C- termini of protected 2,2-dimethyl pyrrolidine-3-carboxylic acid, i.e., benzyloxycarbonyl protected 2,2-dimethylpyrrolidine-3-carboxylate. This procedure included the Michael addition of 2-nitropropane to dimethyl fumarate, followed by ring closure of the amino ester derived from reduction of the nitro ester providing the pyrrolidinone. Reduction of the pyrrolidinone to the pyrrolidine with borane finished 2,2-dimethylpyrrolidine-3-carboxylate in moderate overall yield. A preliminary set of two amides, iso-butyric amide and 3,5-dichlorobenzamide of this 2,2-dimethylpyrrolidine-3-carboxylate, were also prepared. NMR analysis of this pyrrolidine derivative suggested the amide bonds adopted the trans conformation. It was concluded that steric bulk of the 2,2-disubstitution favorably influenced the trans amide conformation. This demonstrated that trans amide conformation control of a β-proline amide was possible. / Chemistry

Binding to protein surfaces or shallow grooves with synthetic molecules poses a unique challenge, since this inherently requires large areas to facilitate interactions. Peptoids have been shown to interact with proteins, and combinatorial libraries of peptoids have been proven to be effective in discovering new ligands for protein binding. Unfortunately, most peptoids are flexible and lack the surface area required to compete with larger protein interactions. To combat these problems, we have created spiroligomers that have a rigid backbone, exhibit functionality comparable to proteins, and are resistant to proteases. To facilitate the rapid installment of spiroligomers into peptoid subunits, we required a more streamlined approach for functionalization of spiroligomers. To this end we applied a single-pot alkylation method, with which we installed over 25 unique functional groups onto different spiroligomer hydantoins. These spiroligomer hydantoins are spirocycles that possesses two stereocenters, of which we have complete control, as well as a protected proline amino acid. These new proline amino acids (enhanced prolines) have been incorporated into peptides via Fmoc-SPPS. Finally, we have functionalized these enhanced proline residues with another functional group and a protected primary amine, which allow for their use in peptoid synthesis. We developed methods to tether multiple spiroligomers together utilizing a peptoid backbone, as well as being able to incorporate spiroligomers into peptoid macrocycles. These spiroligomer-peptoid hybrids are large, diverse, and preorganized structures that have a large potential interacting surface area for binding to protein surfaces or shallow grooves. / Chemistry

Clostridioides difficile is a bacterial pathogen that causes pseudomembranous colitis and the majority of antibiotic-associated diarrheal cases. Broad-spectrum antibiotic usage disrupts the normal gut microbiota and thereby compromises colonization resistance, the main defense against C. difficile infection. Treatment options are limited to vancomycin, fidaxomicin, and the fecal microbiota transplant. Addressing the scarcity of these therapeutics, we documented two explorations in C. difficile drug discovery: (i) evaluation of antibacterial and toxin-suppressing activity of (+)-puupehenone and similar derivatives, and (ii) clarification of a discrepancy in the hypothesized mechanism of auranofin against C. difficile. A better understanding of how C. difficile colonizes and thrives in the gut can greatly benefit therapeutic development. Interestingly, C. difficile can scavenge nutrients such as amino acids and possibly even purines during infection. Amino acids including proline and glycine act as substrates for Stickland metabolism, a bioenergetics scheme that partially relies on enzymes containing selenium in the form of selenocysteine (e.g., D-proline reductase and glycine reductase). Purines such as xanthine and uric acid can be degraded by bacterial molybdenum hydroxylases harboring an uncharacterized form of selenium, though the role of these enzymes in C. difficile physiology is poorly understood. Selenium likely plays a key role in the scavenging of these nutrients during C. difficile infection. Our investigation of these selenium-dependent enzymes revealed two new findings in C. difficile biology: (i) a link between proline-dependent growth and D-proline reductase, characterized as an energy "addiction," and (ii) a previously uncharacterized selenium-dependent pathway involved in the catabolism of xanthine and uric acid. Overall, these physiological analyses of C. difficile provide promising candidates for therapeutics and key information regarding the organism's nutrient preferences.

Le présent projet a été réalisé dans le cadre d'une collaboration UniversitéIndustrie entre le laboratoire du professeur Robert Chênevert, à l'Université Laval et la compagnie OmégaChem, de Lévis. OmegaChem se spécialise dans la fabrication de dérivés d'acides aminés et de synthons chiraux pour l'industrie pharmaceutique. Dans le but de fournir à l'industrie pharmaceutique de nouveaux dérivés d'acides aminés, diverses pyrrolidines chirales non-racémiques apparentées à l'acide aminé proline ont été synthétisées. Ces pyrrolidines sont des dérivés a, p\ y-phosphoniques, ahydroxyphosphoniques et phosphoriques de la proline. Les dérivés de la proline peuvent éventuellement être incorporés à l'intérieur de peptides, augmentant ainsi leur biodisponibilité et leur résistance face aux peptidases

Les acides α-aminés non naturels forment une famille de composés incontournables pour la conception de peptidomimétiques. Plus précisément, l'utilisation du silicium comme isostère du carbone sur la chaîne latérale des acides α-aminés a été largement reportée dans la littérature, montrant alors l'importance d'une telle modification. En particulier, compte tenu du rôle fondamental que joue la proline dans la structuration des peptides, et des avantages que peut apporter le silicium, il nous a paru intéressant de nous centrer sur la silaproline. Après avoir mis au point une synthèse permettant la production de la silaproline à grande échelle, nous avons mis au point la préparation d'homopolypeptides de ce résidu particulier. Dans un premier temps des oligomères monodisperses de silaproline ont été synthétisés. L'étude structurale par RMN, CD et modélisation moléculaire a permis de confirmer la conformation préférentielle en hélice polyproline de type II (PPII). Ensuite la synthèse de polymères plus longs, obtenus par polymérisation de N-carboxyanhydrides a été développée. Ces nouveaux biopolymères ainsi préparés ont conduit à des mimes de PPII lipophiles. Enfin, une nouvelle voie de polymérisation, dans des conditions douces, par réaction d'esters, a été optimisée, permettant d'accéder facilement à des polypeptides. / Unnatural α-amino acids form a family of essential compounds for the design of peptidomimetics. More specifically, the use of silicon as an isostere of carbon on the side chain of α-amino acids has been widely reported in the literature, while demonstrating the importance of this modification. In particular, the fundamental role of proline in peptide structures, and the advantage of the silicon, promoted us to focus on the silaproline.After the development of a gram scale synthesis of silaproline, we prepared homopolypeptides of this particular residue. Firstly, monodisperse silaproline oligomers were synthesized. The structural study by NMR, CD and molecular modeling confirmed the conformational preference for polyproline type II helix (PPII). Then longer polymers were obtained by polymerization of N-carboxyanhydrides. These new biopolymers were prepared, leading to more lipophilic PPII mimics.Finally, a new way of polymerization by reacting esters under mild conditions has been optimized for easy access to polypeptides.

Objectifs : Les Récepteurs Couplés aux Protéines G (RCPG) constituent une grande famille ubiquitaire. Leur structure est caractérisée par sept hélices transmembranaires. Les déformations de ces hélices jouent un rôle majeur dans l’activation de ces récepteurs. La plupart de ces déformations sont liées à la présence de prolines conservées. Cependant, les prolines de l’hélice 2 et 5 des RCPG ne sont pas systématiquement présentes. De plus, la position de la proline dans l’hélice 2 est variable (2.58, 2.59 ou 2.60). Nous nous intéressons aux rôles des prolines des hélices 2 et 5 dans l’activation de deux RCPG : le récepteur de la thyrotropine (TSHR) et le récepteur 2 de la vasopressine (V2R). Méthodes : pour le TSHR et le V2R, nous concevons et caractérisons des mutants pour chaque position conservée de la proline dans l’hélice 2 et/ou 5, ainsi que des mutants sans proline. Résultats : Les mutants du TSHR n’ont pas le même comportement en termes d’expression, de glycosylation ou d’activité. La position la mieux tolérée, 2.59, nous permet de rapprocher le TSHR des récepteurs avec une proline en position 2.59 qui possèdent un renflement dans l’hélice 2. Pour l’hélice 5, les données expérimentales couplées à l’analyse des séquences et la modélisation moléculaire suggèrent une structure non renflée. Pour le V2R, le changement de position de la proline de l’hélice 2 est plus délétère que l’absence de proline dans cette hélice. La proline de l’hélice 5 est indispensable pour l’activité de ce récepteur. Conclusion : Les données obtenues sur le TSHR permettent de proposer un modèle avec une hélice 2 renflée et une hélice 5 non renflée et d’améliorer la modélisation de la cavité interne de ce récepteur, ce qui est essentiel pour le drug design. L’étude du V2R permet de proposer un modèle évolutif de ce récepteur et met en évidence sa spécificité par rapport à des récepteurs proches. / Objectives : Class A G-Protein-coupled receptors (GPCRs) constitute a large family of transmembrane receptors. Helical distortions play a major role in the overall fold and in the activation mechanism of these receptors. Most distortions are related to the presence of conserved proline residues. However, in helices TM2 and TM5, the presence of proline is not mandatory and the correlated mutation of these proline residues is observed in several GPCR sub-families. In addition, the position of the TM2 proline is variable (2.58 to 2.60). We are interested in the role of the TM2 and TM5 proline residues in the folding and activation mechanism of two GPCRs : the thyrotropin receptor (TSHR) and the vasopressin receptor type 2 (V2R). Methods : For both receptors, we engineered and characterized mutants with proline residues at different positions in TM2 and/or at position 5.50 in TM5, and without proline. Results : The expression, the glycolysation or the activity of TSHR mutants are differentially altered by changes in the proline pattern. The “best” mutant, TSHR P2.59, is consistent with a bulged structure for TM2. Experimental data in addition to sequences analysis and modeling suggest an unbulged structure for TM5. For V2R, the absence of proline in TM2 is better tolerated than ashift in the position. The TM5 proline is mandatory for the receptor activation. Conclusion : We suggest a model for TSHR with a bulged TM2 and an unbulged TM5. This should improve the modeling of the transmembrane cavity, which is fundamental for drug design. Our results on V2R suggest an evolutionary model for this receptor and enlighten its specificity compared to nearby receptors.

L'adénocarcinome canalaire pancréatique (ADKp) possède une architecture compacte, où les cellules tumorales forment des glandes emprisonnées dans un bouclier fibrotique, composé à 50% de collagènes. Ce bouclier empêche la vascularisation, limite l'apport en nutriments et oxygène. Beaucoup de cellules meurent, mais certaines survivent, en reprogrammant en particulier leur métabolisme. Ula plus étudiée est l'utilisation constitutive de la glycolyse, indépendamment de la présence d'oxygène (Effet Warburg). Nous montrons que la population hypoxique de l'ADKp dépend aussi de la dégradation de la glutamine, et que l'activité concomitante de la glycolyse et de la glutaminolyse entraîne la réactivation de la biosynthèse des hexosamines. Ces composés participent à la prolifération tumorale en stabilisant les transporteurs au glucose, ou des oncogènes. L'activité glycolytique intense des cellules hypoxiques permet la synthèse de lactate qui sert de ressource nutritive aux cellules oxygénées adjacentes aux cellules hypoxiques. Nous montrons que certaines cellules oxygénées sont capables de survivre au stress nutritif en dégradant le collagène (écophagie), en utilisant la proline qu'il contient. Les cellules tumorales captent et dégradent les fragments de collagènes pour survivre. Des traçages isotopiques de collagène marqué permettent d'appuyer que la proline internalisée provient du collagène matriciel. Cette proline est transformée en glutamate et fournit le cycle de Krebs pour favoriser la survie tumorale. Ces travaux montrent l'importance de l'étude de la reprogrammation métabolique dans l'ADKp, et le rôle de l'hypoxie ou du collagène dans la progression tumorale. / Pancreatic ductal adenocarcinoma (PDAC) has a compact architecture wherein the tumor cells are organized in glands and trapped in a fibrotic shield (stroma) made of up to 50% of collagen. This shield prevents blood supply, limits nutrients and oxygen intake. Many cells die, but some survive, and proliferate particularly by reprogramming their metabolism. The most studied metabolic reprogramming remains tumor cells addiction to glucose and the constitutive use of glycolysis, regardless of the presence of oxygen (Warburg effect). We show that the hypoxic population of PDAC also depends on glutamine degradation, and the concomitant activity of both glycolysis and glutaminolysis reactivates the hexosamine biosynthetic pathway. These compounds contribute to tumor proliferation by stabilizing glucose transporters, or oncogenes. The intense glycolytic activity of hypoxic cells allows the synthesis of lactate. Excreted in the microenvironment, it serves as a nutritive resource to oxygenic cells adjacent to the hypoxic population and enables their proliferation. We show that some oxygenated cells are also able to survive under nutrient stress by degrading collagen (ecophagy) and use proline it contains. Tumor cells intake and degrade collagen fragments to survive. Isotopic tracer experiments using labeled collagen support the idea that proline comes from the extracellular collagen. This proline is degraded and converted into glutamate, fueling the Krebs cycle for anaplerosis and promotes tumor survival. These studies therefore show the importance to study the metabolic reprogramming of PDAC, and the role of hypoxia or collagen matrix in tumor progression.