There are many applications of small organic compounds, e.g. as drugs or as tools to study biological systems. Once a compound with interesting biological activity has been found, medicinal chemists typically synthesize small libraries of compounds with systematic differences to the initial “hit” compound. By screening the new ensemble of compounds for their ability to perturb the biological system, insights about the system can be gained. In the work presented here, various ways to synthesize small libraries of ring-fused 2‑pyridones have been developed. Members of this class of peptidomimetic compounds have previously been found to have a variety of biological activities, e.g. as antibacterial agents targeting virulence, and as inhibitors of the aggregation of Alzheimer b‑peptides. The focus in this work has been to alter the core skeleton, the central fragment, of the previously discovered biologically active 2‑pyridones and evaluate the biological effects of these changes. Several new classes of compounds have been constructed and their preparations have included the development of multi-component reactions and a method inspired by diversity-oriented synthesis. Some of the new compounds have been evaluated for their effect on the fibrillation of different amyloid proteins. Both the Parkinson-associated amyloid protein a-synuclein and the bacterial protein CsgA that is involved in bacterial biofilm formation are affected by subtle changes of the compounds’ central fragments. This is an example of the usefulness of central-fragment alterations as a strategy to probe structure-activity relationships, and the derived compounds may be used as tools in further study of the aggregation of amyloid proteins.

Important information on the bioactive conformation of biologically active peptides may be obtained by studies of rigid peptides or well-defined secondary structure mimetics incorporated into pseudopeptides. The structural requirements for the interaction of angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe) with its AT1 and AT2 receptors were the subject of this study. The main objectives of this work were to synthesize secondary structure mimetics and incorporate these into Ang II. Ang II has been suggested to adopt a turn conformation around Tyr4 when interacting with its AT1 receptor. Therefore, two γ- and one β-turn mimetic scaffolds based on the benzodiazepine structure were synthesized and decorated with side chains. The scaffolds replaced the turn region around Tyr4. Most of the pseudopeptides obtained after incorporation into Ang II exhibited high AT2/AT1 selectivity and nanomolar affinity to the AT2 receptor. One pseudopeptide encompassing a β-turn mimetic also displayed AT1 receptor affinity. We hypothesized that the position of the guanidino group of the arginine residue and the N-terminal end, in relation to the tyrosine side chain, was critical for AT2 receptor affinity. Conformational evaluation of the pseudopeptides revealed that in all the compounds with AT2 receptor affinity the arginine side chain and the N-terminal end could reach common regions, not accessible to the inactive compound. It is proposed that Ang II has a more extended bioactive conformation when binding to the AT2 receptor than when binding to the AT1 receptor. Furthermore, in a Gly scan of Ang II only replacement of the arginine residue reduced the affinity for the AT2 receptor considerably. Some N-terminal modified Ang II analogues were also synthesized and it was concluded that truncated Ang II analogues interact with the AT2 receptor differently than Ang II. Three of the synthesized pseudopeptides were evaluated in AT2 receptor functional assays and were found to act as agonists.

Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogeneous peptides with new physicochemical and pharmacological properties. The β-hairpin motif has been shown to be involved in numerous physiological processes, among others in regulation of eucariotic gene transcription. This thesis addresses the design, synthesis and conformational analysis of photoswitchable β-hairpin mimetics. The developmental work included the establishment of an improved procedure for cross coupling of aryl halides with terminal alkynes. Microwave mediated Sonogashira couplings in closed vessels were optimized under homogeneous and solid-phase conditions furnishing excellent yields for a large variety of substrates within 5 – 25 minutes. In addition, microwave heating was shown not to have any non-conventional effect on the reaction rate. Furthermore, the most important factors affecting β-hairpin stability were evaluated. Studies of tetrapeptide and decapeptide analogues revealed the essential role of the β-turn in initiation of hairpin folding. Moreover, hydrogen bonding was shown to be the main interchain stabilizing force, whereas hydrophobic interactions were found to be relatively weak. Nevertheless, hydrophobic packing appears to provide an important contribution to the thermodynamic stability of β-hairpins. Photoswitchable peptidomimetics were prepared by incorporation of various stilbene moieties into tetra- and decapeptides. Synthesis, photochemical isomerisation and spectroscopic conformational analysis of the compounds were performed.

Despite the unfavorable pharmacokinetic properties associated with peptides, they are still of great interest in drug development due to a multitude of interesting biological functions. The development of peptidomimetics strives to maintain or improve the biological activity of a peptide concurrently with removing the unwanted properties. This thesis describes two synthetic approaches to peptidomimetics with particular emphasis on secondary structure mimetics. First the design, synthesis and evaluation of two beta-turn mimetics incorporated in the endorphin Leu-enkephalin is presented. The beta-turn mimetics were stabilized by replacement of the intramolecular hydrogen bond with an ethylene bridge, and the amide bond between Tyr and Gly was replaced with an ether linkage. Linear analogues of the two mimetics were also synthesized. The peptidomimetics and their linear analogues were evaluated in a competitive binding assay at two opiate receptors, my and delta. One of the cyclized beta-turn mimetics was found to be a delta receptor antagonist with an IC50 value of 160 nM. Second a synthetic strategy to a beta-strand mimetic using 2-fluoro-4-iodopyridine as scaffold is described. The synthesis involved a Grignard exchange reaction on the pyridine scaffold using an amino acid derivative as electrophile followed by an SNAr reaction using an amine as nucleophile. The synthesis of a tripeptidomimetic of Leu-Gly-Gly and attempts to introduce chiral building blocks at the C-terminal, as well as studies towards elongated mimetics are presented. Two additional studies deal with the synthesis of two classes of potential thrombin inhibitors based on the pyridine scaffold. The first class contain pyridine as central fragment (P2 residue) substituted with a para-amidinobenzylamine group as P1 residue and various benzoyl groups as P3 residues. Three potential thrombin inhibitors were synthesized and found to be microM inhibitors in an enzymatic assay. In the second class, the pyridine ring serves as P3 residue. This class also lacks a strongly basic group in the P1 position. A small library of eight compounds were synthesized and evaluated in the enzymatic assay. Unfortunately, these compounds lacked inhibitory activity.

This thesis focuses on the design and synthesis of inhibitors targeting Mycobacterium tuberculosis ribonucleotide reductase (RNR) and hepatitis C virus (HCV) NS3 protease; enzymes that have been identified as potential drug targets for the treatment of tuberculosis and hepatitis C, respectively. Small peptides have been recognized as inhibitors of these enzymes. However, the use of peptides as drugs is limited due to their unfavorable properties. These can be circumvented by the development of less peptidic molecules, often referred to as peptidomimetics. When this work was initiated, only a few inhibitors targeting M. tuberculosis RNR had been identified, whereas the HCV NS3 protease was an established drug target. Therefore, early peptidomimetic design strategies were applied to inhibitors of RNR while the NS3 protease inhibitors were subjected to modifications in a later stage of development. It has previously been shown that peptides derived from the C-terminus of the small subunit of M. tuberculosis RNR can compete for binding to the large subunit, and thus inhibit enzyme activity. To investigate the structural requirements of these inhibitors, different series of peptides were evaluated. First, peptides from an N-terminal truncation, an alanine scan and a designed library were synthesized and evaluated to examine the importance of the individual amino acid residues. Then, a set of N-terminally Fmoc-protected peptides was evaluated, and it was found that the N-terminal group improved the affinity of the peptides even when the length of the compounds was reduced. Furthermore, potential inhibitors of less peptidic character were generated by the introduction of a benzodiazepine-based scaffold. To further reduce the peptidic character and investigate the binding properties of HCV NS3 protease inhibitors, a series of tripeptides incorporating a β-amino acid was synthesized. Inhibition was evaluated and docking studies were performed to understand how the structural changes affected inhibitory potency. The results illustrated the importance of preserving the hydrogen bonding network and retaining electrostatic interactions in the oxyanion hole between inhibitor and protein.

The Signal Transducer and Activator of Transcription-3 (Stat3) is a transcription factor that is required for transformation by a number of oncogenes, while a constitutively active form of Stat3 alone is sufficient to induce neoplastic transformation. It was previously demonstrated that cell to cell adhesion causes a dramatic increase in the activity of Stat3 in both normal and tumour cells. This hinted for the first time at the possibility that the role of Stat3 may differ upon cellular confluence. To examine such a mechanism, it is important to evaluate the effect of Stat3 downregulation at different time-points relative to confluence. To examine this, two different approaches for Stat3 downregulation were used: (1) the introduction of high levels of peptidomimetics analogs, which block the Stat3-SH2 domain by using a technique of in situ electroporation. (2) Treatment with two platinum compounds that inhibit Stat3 binding to activated receptors and DNA. The results demonstrated that Stat3 downregulation in vSrc or TAg transformed mouse fibroblast cells or in breast carcinoma lines, induced apoptosis which was more pronounced post-confluence at the time of its peak activity. In contrast, in sparsely growing normal mouse fibroblasts, Stat3 inhibition induced merely a growth retardation. However, in densely growing normal fibroblasts, Stat3 inhibition induced apoptosis. At least in part, apoptosis induced by Stat3 inhibition was mediated by p53, as shown by the resistance to cell death by Stat3 downregulation in colon carcinoma cells, HCT116, where the p53 gene is ablated. Overall, our observations point to the possibility that constitutive activation of Stat3 may lead to tumourigenesis by downregulating wt-53 in cancers that do not have p53 mutations. As a result, targeting Stat3 in cancers with wt-p53 may be a promising therapeutic approach for restoring p53 function, thereby inducing p53-mediated apoptosis. Next, we examined the effect of constitutively activated Stat3 as an oncogene. Stat3C expression in rat F111 fibroblasts induced anchorage independence, but to a lower degree compared to other oncogenes, such as vSrc. Surprisingly Stat3C expression increased gap junction intercellular communication, despite the fact that other oncogenes such as vSrc or vRas effectively block gap junctions. / Thesis (Ph.D, Pathology & Molecular Medicine) -- Queen's University, 2009-04-26 01:09:21.654

Ces travaux s’articulent autour de dérivés saccharidiques de type exo-glycals ou C-glycosides pour lesquels de nouvelles méthodologies synthétiques ainsi que des applications dans le domaine de la biologie ont été développées. Dans un premier temps, l’addition de nucléophiles soufrés et carbonés sur le carbone anomérique de différents exo-glycals activés a été réalisée, permettant un accès efficace à de nouveaux S-glycosides tertiaires ainsi qu’à des γ-glycoamino acides anomériques. Ces derniers ont été utilisés pour l’élaboration de peptides linéaires mixtes α/γ dont les propriétés de structuration ont ensuite été étudiées par RMN, IR, CD et modélisation moléculaire. De nouvelles plates-formes glycopeptidiques multifonctionnelles ont été préparées par cyclisation de ces peptides. Dans un second temps, le développement de peptidomimétiques ciblant le récepteur neuropiline-1, impliqué dans l’angiogenèse tumorale, a été entrepris. En s’appuyant sur des études de modélisation moléculaire, certains composés ont montré une bonne affinité pour le récepteur NRP-1 et l’un des composés a montré des propriétés prometteuses pour l’inhibition de la formation de tubules / This work is focused on the development of new synthetic pathways for exo-glycals functionalization and synthesis of bioactive compounds. The first part of this manuscript describes the efficient preparation of new tertiary S-glycosides and γ-glycoamino acids via Michael addition of thiols derivatives and carbanions on anomeric carbon of exo-glycals. The obtained γ-glycoamino acids were then incorporated in α/γ mixed peptides and their structural properties were studied by NMR, IR, CD and molecular modelling studies. Furthermore, cyclic multivalent platforms were built by intramolecular cyclization of these entities. The second part of the manuscript concerns the elaboration of peptidomimetics targeting neuropilin-1 receptor, implicated in tumor angiogenesis. Based on molecular modeling studies, some compounds showed interesting binding affinity for NRP-1 receptor and one of them displayed promising properties toward inhibition of tubule formation

The human papillomavirus (HPV) has been a “companion” of humanity for as long as humanity has existed. The migration of peoples around the globe has given rise to more than 170 different types of the virus, which cause a variety of conditions. All five genera of HPV infect epithelial cells in the body, but only the Alphapapillomaviruses infect the genital mucosa. Most infections are benign and typically regress to subclinical within two years, but persistent infections can cause precancerous lesions. HPV types 16 and 18 are among the highest risk and account for the majority of cervical cancer, and more than 90% of all other HPV-related cancers. While the two vaccines, Gardasil and Cervarix, have been successfully implemented in the US market and some European and Asian countries, complete world penetrance has been burdened by multiple factors, including financial constraints and social norms. Treatments for established papillomas are invasive (cryosurgery, conization, etc.) and advanced malignant HPV-related tumors have been targeted with chemo- and radiotherapy with varied success. The high morbidity and long-term effects of current treatment options make clear the need for easy-to-administer, low-cost therapies, which can specifically treat both early and advanced HPV-associated cancers.<div><br></div><div>The hallmark of HPV tumors is the inactivation of p53, an evasion strategy key to the progression of HPV- derived cancers. Through an interaction between the viral protein E6 and the E3 ubiquitin ligase E6AP, p53 is polyubiquitinated and targeted for proteasomal degradation, allowing infected cells to bypass their own defense mechanisms. This work explores interruption of the association between E6 and E6AP as an opportunity to combat the infection and resulting malignancies.<br></div><div><br></div><div>In the first part of this project, disruption of the E6-E6AP interactions is pursued through the development of helical stabilized peptidomimetics of the LxxLL motif, which E6AP uses for E6 recognition and binding. Several reports have indicated that targeting the E6 binding groove is a viable means for disrupting the interaction. However, reported peptides were not cell permeable or optimized for α-helicity and proteolytic resistance (for reference, the LxxLL motif is an α-helix when bound). To address this challenge a peptide stabilization strategy was applied, which uses an all-hydrocarbon chain to connect two non-adjacent residues and enforce α-helicity. Results from in silico simulations and biochemical assay with these new stapled peptides showed that affinity for E6, α-helicity, and cell permeability can all be improved with the installment of the proper staple.<br></div><div><br></div><div>The second question examined by this work is whether fragment-based drug design can be successfully employed to derive new small-molecule inhibitors of the formation of the E6-E6AP complex. From a design perspective, the significant challenge was to define discreet binding hot-spots capable of accommodating fragments with reasonable affinity, which can then be linked together into a complete ligand. Using existing structural knowledge of the E6 protein and computational hot-spot searching tools, three previously-unidentified regions (sub-pockets) on E6 were discovered, which are near but not directly engaged by either the E6AP motif or p53. Using high-throughput in silico and biochemical screening, three sets of sub-pocket specific fragments were defined and elaborated into larger molecules with two different scaffolds. As a result, the work herein presents a stepwise approach to targeting the E6-E6AP protein-protein interaction – the discovery of new binding hot spots, the identification of site-specific fragments, and the design of complete molecules with versatile scaffold.<br></div>

Le cancer de l’ovaire représente la quatrième cause de décès par cancer chez la femme. En France, près de 4 500 nouveaux cas par an sont diagnostiqués, avec plus de 3000 décès chaque année. Ce cancer reste longtemps silencieux : un diagnostic souvent tardif, et le développent d’une chimiorésistance qui touche jusqu'à 75 % des patientes, expliquent le fort taux de mortalité et une survie à 5 ans estimée à moins de 45 %. Les mécanismes responsables du développement de la chimiorésistance sont nombreux. Aujourd’hui, un fort intérêt est porté au développement de nouvelles stratégies de traitement en ciblant les protéines cellulaires inhibitrices de l’apoptose (mort cellulaire programmée). Deux familles de protéines jouent un rôle cruciale dans la régulation de l’apoptose : la famille Bcl-2 et la famille IAP. Nous nous sommes intéressés à la synthèse de petites molécules abiotiques, appelées foldamères. Ces composés sont capables de perturber les interactions entre les protéines anti-apoptotiques des familles Bcl-2 ou IAP, surexprimées dans le cancer de l’ovaire, et leurs partenaires biologiques (pro-apoptotiques). Ceci permet de libérer les protéines pro-apoptotiques et rétablir l’apoptose dans les cellules cancéreuses. Ce travail de thèse a permis la conception, la synthèse, la caractérisation et l’évaluation biologique de molécules inhibitrices des protéines anti-apoptotiques Mcl-1 et Bcl-xL de la famille Bcl-2, et de possibles inhibiteurs de la protéine XIAP de la famille IAP. / Ovarian cancer is the 4th leading cause of cancer death in women. In France, nearly 4,500 new cases per year are diagnosed, with more than 3,000 deaths each year. This cancer remains silent for a long time: late diagnosis and chemoresistance development for up to 75% of patients, explain the high mortality rate and the 5-year survival estimated at less than 45%. Mechanisms responsible for the development of drug resistance are numerous. Today, there is a strong interest in the development of new treatment strategies by targeting cellular proteins that inhibit apoptosis (programmed cell death). Two families of proteins play a crucial role in the regulation of apoptosis: the Bcl-2 family and the IAP family. We are interested in the synthesis of small abiotic molecules, called foldamers. These compounds are able to disrupting the interactions between the anti-apoptotic proteins of the Bcl-2 or IAP families, overexpressed in ovarian cancer, and their biological (pro-apoptotic) partners. This releases the pro-apoptotic proteins and restores apoptosis in the ovarian cancer cells. This PhD work allowed the design, synthesis, characterization and biological evaluation of inhibitors of Mcl-1 and Bcl-xL anti-apoptotic proteins of Bcl-2 family, and the development of possible inhibitors of the XIAP protein of IAP family.

L’intérêt des composés organiques fluorés est de nos jours de plus en plus important en raison de leur large domaine d’application (agrochimie, nucléaire, matériaux, chimie médicinale…). Par exemple, en chimie médicinale, la présence d’un ou plusieurs atomes de fluor au sein de biomolécules conduit très souvent à une amélioration de leur profil thérapeutique. Par ailleurs, le cyclopropane, le plus petit et le plus tendu des cycloalcanes, permet également de modifier les caractéristiques pharmacologiques de composés biologiques de par sa géométrie inhabituelle. En effet, la rigidification structurale apportée par ce motif influe sur la biodisponibilité d’une biomolécule en améliorant sa sélectivité et son affinité pour un récepteur biologique. Dans ce contexte, nous avons choisi d’associer les propriétés remarquables de l’atome de fluor à la contrainte structurale du cyclopropane dans le but d’élaborer deux nouvelles classes de fluoropeptidomimétiques.Tout d’abord, nous nous sommes intéressés à la modification de la chaîne latérale d’acides aminés naturels en développant la synthèse des analogues cyclopropaniques fluorés de la méthionine, de la leucine, de la lysine et de l’arginine. Nous avons ensuite appliqué l’un de nos acides aminés cyclopropaniques fluorés à la synthèse totale de l’analogue fluoré d’un inhibiteur de la sérineprotéase NS3/4A, le TMC 435.Enfin, dans le but de proposer une voie de synthèse générale permettant l’accès aux pseudopeptides fluorés comportant un monofluorocyclopropane à la place du lien peptidique, nous avons développé une nouvelle stratégie basée sur une étape d‘addition nucléophile de réactifs organométalliques sur des N-(tert-butanesulfinyl)-α-fluoroimines chirales. / Fluoroorganic compounds are increasingly popular owing to their wide range of applications. For instance, in the field of medicinal chemistry, fluorinated molecules often lead to an improvement of the therapeutic profile compared to non-fluorinated derivatives. Besides, with its unique bonding properties, the cyclopropane ring provides unusual physical and pharmacological properties to structures that incorporate it. Indeed, the structural constraint provided by the cyclopropane ring clearly alters the selectivity and the affinity for a binding site. In this context, we decided to combine the cyclopropane and the fluorine atom to develop two new classes of peptidomimetics. First, we focused on the modification of the side chain of natural aminoacids (methionine, leucine,lysine and arginine) and the synthesis of fluorinated cyclopropyl analogues was achieved. Then, we applied our strategy to the synthesis of the fluorinated analogue of the TMC 435, a NS3/4A serine protease inhibitor involved in the replication cycle of Hepatitis C virus. Finally, in our project aiming at proposing a general method to access pseudopeptides featuring a fluorinated cyclopropane moiety as the peptide bond isostere, we develop a new strategy based on the nucleophilic addition of organometallic reagents to N-(tert-butanesulfinyl)-α-fluoroimines. This methodology allows us to control the asymmetric center on the N-terminal side of the peptide.