Les réactions de macrocyclisation sont souvent difficiles à réaliser du point de vue expérimental, puisque la dilution élevée nécessaire requiert un montage encombrant et la purification du mélange est souvent complexe en raison d’une mauvaise sélectivité de cyclisation. Ces raisons peuvent compliquer la planification des voies de synthèse, ce qui dissuade souvent les chimistes d’utiliser les macrocycles pour différentes applications. Dans les dernières années, notre groupe de recherche a développé une méthode nommée stratégie de séparation de phase. Il s’agit d’un nouveau protocole permettant de faire des réactions de macrocyclisation de façon monotope et dans un milieu beaucoup plus concentré, tout en évitant les réactions parasites d’oligomérisation, facilitant ainsi la purification des macrocycles obtenus. Cette thèse décrit le développement et l’application de stratégies permettant de surmonter les défis liés aux réactions de macrocyclisation. Dans la première partie de la thèse, le protocole de la stratégie de séparation de phase a pu être utilisé pour la synthèse de squelettes macrocycliques complexes, comme celui du produit naturel ivorenolide A (Chapitre 4) et celui de l’anti-viral vaniprevir (Chapitre 6). Ce protocole a permis de réaliser l’étape de macrocyclisation dans un milieu réactionnel 120 fois plus concentré, tout en maintenant un niveau de sélectivité de macrocyclisation élevé. Dans la deuxième partie de la thèse, le développement d’une nouvelle synthèse d’acétylures de soufre catalysée par un complexe de cuivre a permis la synthèse d’une librairie de macrocycles peptidiques (Chapitre 8). L’incorporation du motif acétylure de soufre a aussi permis la diversification de ce dernier afin de greffer plusieurs étiquettes bioactives. Pour terminer, l’étendue de la réaction intermoléculaire de la nouvelle réaction de formation de thioalcynes a été explorée (Chapitre 9). Ceci a permis la synthèse d’alcynes disubstitués par des hétéroatomes ainsi que la fonctionnalisation de peptides contenant une cystéine non protégée. Des études mécanistiques expérimentales et computationnelles de la nouvelle méthode de synthèse de thioalcynes ont aussi été réalisées. / Macrocyclization reactions can be problematic due to poor selectivity of cyclization versus oligomerization. As such, difficult purification of complex mixtures and/or the use of complex and cumbersome experimental setups are often necessary. The drawbacks can complicate synthetic pathways and deter chemists from exploring the unique chemical space of macrocycles. Our group has developed a new macrocyclization strategy called phase separation strategy, a protocol enabling one-pot macrocyclization reactions at much higher concentration. In the present thesis, the challenges associated with macrocyclization reactions are tackled by the development and the application of new strategies. First, the phase separation strategy protocol was used to synthesize the backbone of complex macrocycles like the natural product ivorenolide A (Chapter 4) and the antiviral vaniprevir (Chapter 6). With the use of the phase separation strategy protocol, macrocyclization reactions were performed at concentrations 120 times higher than traditional protocols while maintaining a high level of macrocyclization selectivity. Second, the development of a new copper-catalyzed synthesis of alkynyl sulfides for the synthesis of a macrocyclic peptide library is described (Chapter 8). The macrocyclic peptides were also tagged with several biomarkers by diversification of the resulting alkynyl sulfide motif. Finally, the scope of the intermolecular copper-catalyzed reaction was explored (Chapter 9). Using the method, bis-heteroatom substituted alkynes were synthesized and modification of unprotected cysteine sidechains was possible. Furthermore, the mechanistic reaction pathway of the new alkynyl sulfide synthesis was studied experimentally and computationally.

The work presented in this Thesis describes the design, synthesis and reactivity of a symmetric and various asymmetric Schiff-base macrocycles that are capable of forming a wedge-shaped “Pacman” conformation upon metal binding. Chapter One introduces catalysts for small molecule transformation as well as transition metal complexes of pyrrole-containing macrocycles. Further to this, Pacman systems, including previous work from Love and co-workers, and complexes capable of secondary coordination-sphere control will be discussed. Chapter Two details the design and synthesis of two asymmetric macrocycles that both contain one neutral and one N₄-donor imine-pyrrole binding pocket, H₂LP and H₂LNMe. The synthesis and characterisation of the series of complexes [M(LP)] and [M(LNMe)] (M = Pd, K₂, Co, VCl, TiCl, Mg, Fe and Mn) and their characteristics highlighted, including the formation of a supramolecular cyclic hexamer. Chapter Three presents the modification of the above ligands at the meso-group, the N-substituent and the non-pyrrolic binding pocket to give H2LFP and H₂LFNMe, H₂LNMes and H₂L(NH)NMe respectively. Palladium and cobalt complexes of these macrocycles were prepared and characterised. Chapter Four describes the design and synthesis of the ligand H₄LEt as well as the synthesis and characterisation of tin-alkyl and mononuclear calcium complexes of LEt, as well as the heterobimetallic complexes [SnMe₂(M)(THF)(LEt)] (M = Zn or Fe). The homobimetallic complexes [M₂(LEt)] (M = Co, Mg and NbCl) are also presented along with a magnesium-cubane structure of LEt in which the cubane is encapsulated by two, bowl-shaped macrocycles. Chapter Five provides a summary of the work presented in this thesis. Chapter Six describes the full experimental details and analytical data for all compounds synthesised in this work.

Cet ouvrage porte sur les macrocycles organiques. Une introduction générale sur les propriétés des macrocycles et leurs rôles dans la chimie des matériaux et le développment des médicaments est présentée en premier lieu pour expliquer notre intérêt particulier sur cette classe de molécules. Le premier chapitre parle d’une nouvelle conception des nanotubes supramoléculaires par auto-assemblage des macrocycles de forme persistante. Nous avons exploité la capacité d’auto-assembler des différents types de cyclopeptides de squelette rigidifié en structures nanotubulaires. Cette approche a aussi été bien étudiée par plusieurs groupes de recherche de la littérature. Une caractéristique commune dans toutes ces conceptions est le besoin des fonctions amides qui sont disposées à l’intérieur du macrocycle et responsables des ponts Hydrogènes intermoléculaires pour diriger l’auto-organisation en nanotubes. Cette approche fonctionnait bien mais trouve limitée dans le cas où la structure cyclique manque des motifs (en particulier les amides) responsables de l’auto-assemblage par exemple les structures π-conjuguées. Pour ce genre de molécules, l’incorporation des longues chaînes latérales alkyles en périphérie du cycle représente la méthode habituelle pour obtenir l’empilement efficace entre les molécules. Par contre, le matériau formé présente souvent un désordre moléculaire et une faible cristallinité. Nous proposons une meilleure conception pour stimuler la croissance unidimensionnelle en ajoutant les fonctions amides susceptibles des liaisons Hydrogène intermoléculaire en périphérie du cycle. La tribenzocyclyne (TBC) est choisie comme échafaudage pour examiner cette stratégie qui n’a jamais été appliquée et rapportée sur un système cyclique pour le même objectif. L’intensité et la directionnalité des interactions Hydrogène supporteraient l’auto-organisation efficace de ces dérivés de TBC en nanotubes comme manifestée par quelques calculs semi-empiriques. De différentes générations de TBC portant des amides latéraux ont été conçues, synthétisées et discutées pour améliorer la synthèse et pouvoir obtenir l’arrangement désiré des molécules. Afin de favoriser la compréhension sur les nanotubes supramoléculaires, une introduction sur la chimie supramoléculaire, les interactions non-covalentes et les différentes approches vers les nanotubes supramoléculaires est résumée en détail. Toujours concernant les marcocycles, le deuxième chapitre aborde la conception des nouveaux agonistes cycliques ciblant le récepteur opioïde δ (DOPr). Les résultats préliminaires obtenus par notre groupe ont permi de proposer une conformation de Leu-enképhaline (LENK), le ligand endogène activant le DOPr, qui est très probablement celle trouvée dans le site actif de DOPr. En basant sur ce modèle, nous voulons concevoir des macrocycles dont le squelette est fixé plus ou moins vers cette conformation active hypothétique en incorporant les espaceurs appropriés entre les pharmacophores. Les nouvelles molécules sont considérées comme candidats-agonistes sélectifs δ car la conception fixerait la conformation spécifique pour la liaison avec le DOPr au lieu des autres récepteurs opioïdes surtout le μ (MOPr). L’objectif à long terme de ce projet, qui est en collaboration avec le laboratoire du Professeur Louis Gendron, est d’obtenir les agonistes sélectifs δ puissants pour soulager les douleurs sévères et/ou chroniques avec les effets secondaires réduits ou éliminés. Ces effets indésirables constituent le problème majeur qui limite l’efficacité ou suspend la médication des agonistes opioïdes telles que la morphine dans le traitement de la douleur. Pour comprendre mieux l’arrivée des nouveaux macrocycles synthétisés et discutés dans ce chapitre, une introduction générale sur la douleur et les traitements actuels, les récepteurs opioïdes et leur rôle dans la modulation de la douleur est présentée en premier lieu. Les résultats préliminaires par notre groupe et les collaborations sont aussi résumées. Finalement, une concise annexe sur l’exploration d’une nouvelle conception de nanosphères supramoléculaires est ajoutée en dernier lieu. Ces nanocapsules résulteraient de l’auto-assemblage des dérivés de corannulène portant des amides latéraux, ce qui imitent la structure de la capside sphérique chez plusieurs virus.

In an effort to produce the tetrahedrally coordinated, catalytically active zinc center, three families of tris(2-pyridyl)methanol derivatives were synthesized and characterized. Zinc binding studies revealed that the binding behaviors of the ligands depended on the steric and electronic properties of the substituents on the pyridyl rings, as well as the functional group on the tertiary alcohol. A novel tris-pyridyl macrocyclic receptor was synthesized. The receptor possesses both hydrogen bond donors and acceptors. NMR titration experiments revealed that the receptor simultaneously bound both ammonium cation and the counter anion. The counter anion significantly influences the association between the receptor and the ammonium cation. Chiral ditopic macrocycles, which enantioselectively bind chiral ammonium cations, have also been synthesized. Their enantioselective binding properties, as well as the ditopic recognition properties were investigated

Madeirolide A (1) is a structurally novel polyketide natural product first isolated from the deep-sea sponge Leiodermatium sp. by Wright in 2009. Initial biological investigations of madeirolide A revealed potent inhibition of the fungal pathogen Candida albicans but failed to determine any appreciable cytotoxicity when tested against a limited range of cancer cell lines. The unusual bioactivity of madeirolide A coupled with uncertainty over the true stereostructure of the natural product makes it a compelling target for synthesis. This thesis discloses synthetic efforts towards the total synthesis of madeirolide A with an emphasis on the construction of the all-cis C21 - C27 eastern tetrahydropyran. Chapters 1 and 2 provide an introduction to the importance of natural products in drug discovery and outline the context of this project with details of the isolation and biological activity of madeirolide A. Previous synthetic efforts are also reviewed including those from within the group which formed the basis of the present studies. Chapter 3 describes the synthesis of a fully elaborated C1 - C11 fragment, building upon previously published work in the group. Specifically, it details the successful completion of a modified approach designed to avoid some of the major challenges previously encountered such as undesired migration of protecting groups and challenges in selectively installing an (E)-vinyl iodide. Chapter 4 discusses ongoing efforts towards the challenging C12 - C27 fragment of madeirolide A. The stereocontrolled synthesis of several linear C19 - C27 precursors is outlined, followed by details of screening reactions conducted to affect the desired oxy- Michael cyclisation. Additionally, extensive computational studies have been undertaken in an attempt to rationalise the frustrating lack of reactivity observed with the goal of developing a substrate suitably elaborated to cyclise. Finally, the asymmetric synthesis of the C13 - C17 subfragment is outlined, which will provide eventual access to the eastern tetrahydrofuran. Chapter 5 summarises the synthetic work carried out thus far and explores potential strategies for the future completion of the natural product with a focus on alternative disconnections of the eastern tetrahydropyran.

Les glycophanes sont des molécules cycliques, chirales contenant des sucres séparés par des segments hydrocarbonés. Ils sont considérés comme des hybrides de cyclophanes et de cyclodextrines. Ce travail concerne la synthèse de glycophanes symétriques à partir du D-glucal. Après la synthèse de O-glycosides insaturés et de bis-O-glycosides d'alkyle 2,3 insaturés par réarrangement de Ferrier, nous avons préparé des précurseurs bifonctionnels pour différentes réactions de macrocyclisation pour l'obtention de ces macrocycles à savoir les bis-ethers de propargyle pour la réaction de Glaser ; les azido-alcynes pour la réaction de Huisgen et les amino-acides de sucres pour le couplage peptidique. Les conditions de dilution ont permis d'obtenir des molécules-cages de symétrie C2 que nous avons déprotégées pour des essais de complexation.

Malaria is one of the major public health problems in the world. Approximately 500 million people are afflicted and almost 3 million people die from the disease each year. Of the four causative species Plasmodium falciparum is the most lethal. Due to the rapid spread of parasite resistance there is an urgent need for new antimalarial drugs with novel mechanisms of action. Several promising targets for drug intervention have been revealed. This thesis addresses the parasitic aspartic proteases termed plasmepsins (Plm), which are considered crucial to the hemoglobin catabolism essential for parasite survival. The overall aim was to identify inhibitors of the P. falciparum Plm I, II, and IV. More specific objectives were to attain activity against P. falciparum in infected erythrocytes and selectivity versus the most homologous human aspartic protease cathepsin D (Cat D). To guide the design process the linear interaction energy (LIE) method was employed in combination with molecular dynamics. Initial investigations of the stereochemical requirements for inhibition resulted in identification of an L-mannitol derived scaffold encompassing a 1,2-dihydroxyethylene transition state isostere with affinity for Plm II. Further modifications of this scaffold provided inhibitors of all three target plasmepsins (Plm I, II, and IV). Apart from the stereochemical analysis three major kinds of manipulation were explored: a) P1/P1′ and P2/P2′ side chain alterations, b) replacement of amide bonds by diacylhydrazine, 1,3,4-oxadiazole, and 1,2,4-triazole, and c) macrocyclization. Several inhibitors of Plm I and II with Ki values below 10 nM were discovered and one Plm IV selective inhibitor comprising two oxadiazole rings was found which represents the most potent non-peptide Plm IV inhibitor (Ki = 35 nM) reported to date. Some of the identified plasmepsin inhibitors demonstrated significant activity against P. falciparum in infected erythrocytes and all inhibitors showed a considerable selectivity for the plasmepsins over the human Cat D.

Peptidomimetics derived from the bioactive hexapeptide angiotensin IV (Ang IV, Val1-Tyr2-Ile3-His4-Pro5-Phe6) have been designed and synthesized. These peptidomimetics are aimed at inhibiting the insulin-regulated amino peptidase (IRAP), also known as the AT4 receptor. This membrane-bound zinc-metallopeptidase is currently under investigation regarding its potential as a target for cognitive enhancers. The work presented herein was based on stepwise replacement of the amino acid residues in Ang IV by natural and unnatural amino acids, non-peptidic building blocks, and also on the introduction of conformational constraints. Initially, we focused on the introduction of secondary structure mimetics and backbone mimetics. The C-terminal tripeptide His-Pro-Phe was successfully replaced by a γ-turn mimetic scaffold, 2-(aminomethyl)phenylacetic acid (AMPA), which was coupled via an amide bond to the carboxyl terminus of Val-Tyr-Ile. Substitution of Val-Tyr-Ile, Val-Tyr, Tyr-Ile and Tyr, respectively, by 4-hydroxydiphenylmethane scaffolds comprising a 1,3,5-substituted benzene ring as a central moiety unfortunately rendered peptidomimetics that were less potent than Ang IV. The subsequent approach involved the introduction of conformational constraints into Val-Tyr-Ile-AMPA by replacing Val and Ile by amino acid residues appropriate for disulfide cyclization or ring-closing metathesis. Chemically diverse structures encompassing an N-terminal 13- or 14-membered macrocyclic tripeptide and a C-terminal non-peptidic moiety were developed. Tyr2 and AMPA were modified to acquire further knowledge about the structure-activity relationships and, in addition, to improve the metabolic stability and reduce the polarity. Several of the compounds displayed a high capacity to inhibit IRAP and exhibited Ki values in the low nanomolar range. Hence, the new compounds were more than ten times more potent than the parent peptide Ang IV. Enhanced selectivity over the closely related aminopeptidase N (AP-N) was achieved, as well as improved stability against proteolysis by metallopeptidases present in the assays. However, additional investigations are required to elucidate the bioactive conformation(s) of the relatively flexible N-terminal macrocycles. The compounds presented in this thesis have provided important information on structure-activity relationships regarding the interaction of Ang IV-related pseudopeptides and peptidomimetics with IRAP. The best compounds in the series constitute important starting points for further discovery of Ang IV peptidomimetics suitable as tools in the investigation of IRAP and other potential targets for Ang IV. The literature presents strong support for the hypothesis that drug-like IRAP inhibitors would serve as a new type of future cognitive enhancers with potential use in the treatment of cognitive disorders, e.g. Alzheimer’s disease.

Hybrid macrocycles, which chimerically integrate multiple chemical compositions and architectures, provide an effective way to impart new properties to polymers that are not found in their linear or homocyclic analogues. This dissertation addresses the incorporation of hydrophilic blocks into hydrophobic polymer, as either a poly(dimethyl siloxane)-block-poly(oxyethylene) (PDMS-POE) tadpole with a hydrophobic head and a hydrophilic tail or as a diblock poly(styrene)-block-diethylene glycol (PS-DEG) hydrophobic-hydrophilic macrocycle. The supramolecular association properties of both kinds of cycles were studied: the PDMS-POE tadpoles in forming micelles, and the PS-DEG macrocycles in threading with linear polymer to form polyrotaxanes. For the PDMS-POE macrocycle, linear alpha,omega-dihydroxy PDMS was cyclized under dilute conditions with dichloromethylhydrosilane as a linking group to produce hydrosilane-functionalized cyclic PDMS. This was joined to alpha-methoxy,omega-allyl POE via a free radical hydrosilylation reaction to produce the hybrid tadpole macrocycle, which was analyzed by GPC, DSC, and 1H, 13C, and 29Si NMR spectroscopy. Supramolecular aggregation consisting of the formation of micelles under both polar and nonpolar conditions was studied by surface tensiometry and quasielastic light scattering. For the PS-DEG macrocycle, linear alpha,omega-dihydroxy PS was prepared by ATRP polymerization of styrene, followed by reaction with KOH to give hydroxyl endgroups. The linear PS was then cyclized under dilute conditions with diethylene glycol ditosylate, and the product was analyzed by GPC, MALDI-TOF MS, DSC, and 1H, 13C and DOSY NMR spectroscopy. The macrocycle was then statistically threaded with linear PS to give the supramolecular structure poly(styrene)-rotaxa-cyclo[poly(styrene)-block-diethylene glycol]. Characterization was performed with DOSY NMR to verify that the product was threaded, and 1H NMR was collected to determine that the product was 13% macrocycle by weight. DSC showed only one Tg, indicating that the linear and cyclic species were present in the same phase.

In efforts to search for tool compounds that are capable of probing normal and disease-associated biological processes, both quality and identity of the screening collection are very important. Towards this goal, diversity-oriented synthesis (DOS) has been explored for a decade, which aims to populate the chemical space with diverse sets of small molecules distinct from the traditional ones obtained via combinatorial chemistry. In the practice of DOS, macrocyclic ring-closing metathesis (RCM) reactions have been widely used. However, the prediction and control of stereoselectivity of the reaction is often challenging; chemical transformation of the olefin moiety within the product is in general limited. Chapter I of this thesis describes a methodology that addresses both problems simultaneously and thus extends the utility of the RCM reactions. By installing a silyl group at the internal position of one of the olefin termini, the RCM reaction could proceed with high stereoselectivity to afford the (E)-alkenylsiloxane regardless of the intrinsic selectivity of the substrate. The resulting alkenylsiloxane can be transformed to a variety of functionalities in a regiospecific fashion. The conversion of the (E)-alkenylsiloxanes to alkenyl bromides could proceed with inversion of stereochemistry for some substrates allowing the selective access of both the E- and Z-trisubstituted macrocyclic alkenes. It was also found that the silyl group could trap the desired mono-cyclized product by suppressing nonproductive pathways. Chapter II of this thesis describes the application of the concept of DOS in the area of fragment-based drug discovery. Most fragment libraries used to date have been limited to aromatic heterocycles with an underrepresentation of chiral, enantiopure, \(sp^3\)-rich compounds. In order to create a more diverse fragment collection, the build/couple/pair algorithm was adopted. Starting from proline derivatives, a series of bicyclic compounds were obtained with complete sets of stereoisomers and high \(sp^3\) ratio. Efforts are also described toward the generation of diverse fragments using methodology described in Chapter I. The glycogen synthase kinase \((GSK3\beta)\) was selected as the proof-of-concept target for screening the DOS fragments. / Chemistry and Chemical Biology