Les petites molécules bioactives sont des acteurs clés dans la recherche biomédicale et les études de chimie biologiques, pour leur application potentielle comme sondes moléculaires pour enquêter les systèmes biologiques, et la possibilité de développer de nouveaux traitements puissants et sélectifs. Dans ce travail, nous avons exploré l'utilisation de plusieurs classes de petites molécules capables d'interférer avec des cibles biologiquement significatives, comme les acides nucléiques et les lysosomes, et déclencher des réponses biologiques. A partir de l'étoposide, l'un des agents anti-néoplasiques le plus employé en clinique, nous avons développé une nouvelle classe de petites molécules actives capables de cibler différemment les deux isoformes humaines de la topoisomérase II, TOP2A et TOP2B, qui jouent des rôles différents dans l'inhibition de la croissance des cellules cancéreuses, et le développement de tumeurs malignes secondaires. Dans un autre projet, nous avons utilisé une stratégie d'étiquetage « click in situ » pour enquêter sur la localisation subcellulaire d'un nouvel inhibiteur de la réaction d'échange nucléotidique des protéines Arf, un outil potentiel pour l'étude du trafic cellulaire et la signalisation liés a ces protéines. Enfin, nous avons étudié l'origine de l'efficacité d'un nouveau agent de ciblage du compartiment lysosomal: l'artesumycin, un hybride moléculaire des petites molécules bioactives la marmycine A et l'artésunate, qui possède une activité antiproliferative accrue en comparaison avec les deux produits naturels utilisés indépendamment. Nos résultats fournissent une précieuse contribution dans ces domaines de recherche. / Bioactive small molecules are key players in biomedical research and chemical biology studies given their potential application as molecular probes to investigate biological system, together with the possibility to develop new potent and selective therapeutics. In this work, we explored the use of several classes of small molecules able to interfere with therapeutically relevant targets, from nucleic acids to lysosomes, and evaluate ensuing biological responses. Starting from etoposide, one of the most clinically employed anti-neoplastic agents, we developed a new class of active small molecules able to differentially target the two human topoisomerase II isoforms, TOP2A and TOP2B, which have been shown to play different roles in inhibiting cancer cell growth and initiating secondary malignancies. In a separate project, we aimed to use an in situ click labelling strategies to investigate the subcellular localization of a new inhibitor of the nucleotide exchange reaction of Arf proteins, a potential tool for the study of Arf-related cellular trafficking and signalling. Finally, we studied the origins of the synergy displayed by the new lysosome targeting agent artesumycin, a molecular hybrid of the bioactive small molecules marmycin A and artesunate, which has been shown to possess enhanced antiproliferative activity in comparison to the two natural product used independently. Our results provide valuable contributions for future advances in these research areas.

Target-guided synthesis is an approach to drug discovery that uses the biological target as a template to direct synthesis of its own best inhibitors from small molecule fragments. The process bridges the gap between chemical synthesis of drug candidates and their biological binding assay, merging the two operations into a single process whereby the active site or a binding pocket within the structure of the biological target directly controls the assembly of the best inhibitor in situ. Two different approaches to target-guided synthesis, the thermodynamic approach, making use of reversible reactions, and the kinetic approach, which uses an irreversible reaction, have been employed to discover novel, isoform selective inhibitors of the glutathione transferase (GST) enzyme family – possible drug targets in cancer and parasitic disease treatments. The thermodynamic approach described in this thesis uses the aniline-catalysed reversible acyl hydrazone formation reaction to create a dynamic covalent library of bivalent ligands designed to bind the dimeric structure of GST. In the presence of GST one of the bivalent ligands was selectively amplified at the expense of the other library members. This ligand was shown, via biological assays, to be a specific inhibitor for one isoform of GST, the mu isoform mGSTM1-1. A kinetic approach has also been investigated as a way to identify novel bivalent GST inhibitors utilising the Huisgen 1, 3 dipolar cycloaddition reaction. An azide and alkyne fragment library was designed to bind across the dimeric GST structure. The inhibitor structures are therefore bivalent, containing two anchoring fragments known to bind to the GST active site, linked by a triazolopeptide spacer. The triazole provides the click chemistry disconnection, enabling rapid in situ screening of candidate alkyne and azide fragments for inhibitor discovery. Whilst the in situ reaction with GST yielded inconclusive results, a number of the triazole products were found to have low nanomolar inhibitory activity towards GST.

Le développement de nouveaux antibiotiques est un enjeu majeur de santé publique. Etant donné, le fort potentiel des aminoglycosides en tant qu’antibiotique, ces composés ont attisé l’intérêt de plusieurs groupes de recherche. Cependant, leur usage est encore très limité, malgré leur ancienneté, du fait de leur toxicité et du développement toujours croissant des mécanismes de résistances aux aminoglycosides. Afin de mieux appréhender les problèmes inhérents à leur utilisation, il est crucial de mieux comprendre leur action sur les différentes cibles cellulaires, et d’étudier leur interaction avec leur cible moléculaire (ARN et protéine). En plus de leur pouvoir antibiotique, les aminoglycosides sont également des ligands universels pour des ARN, capables d’interagir spécifiquement avec notamment les ARN du VIH-1 suivants : DIS, TAR, RRE. L’élaboration d’aminoglycosides modifiés présente un énorme avantage car le domaine d’application, et en conséquence les retombées, sont grandes. Néanmoins, la complexité structurale de ces molécules est un frein majeur, la fonctionnalisation chimiosélective est indispensable mais malheureusement peu décrite dans la littérature. Dans le cadre de ce travail, nous avons développé deux types d’approches pour cibler le DIS et/ou le site A du ribosome bactérien. La première originale, mais risquée se base sur le concept de click in situ. La seconde approche est traditionnelle et est basée sur la fonctionnalisation sélective de certaines positions clés des aminoglycosides. / The development of new antibiotics is a major public health issue. Given the high potential of aminoglycosides as antibiotics, these compounds have aroused great interest in many research groups. However, despite their maturity, their use is still limited because of their toxicity and the increasing development of resistance mechanisms to aminoglycosides. To better understand the problems inherent to their use, it is crucial to understand their action a cellular level, and to study the interactions with their molecular targets (RNA and protein). In addition to their antibiotic power, aminoglycosides are also universal ligands for several RNAs, capable of specific interactions with RNAs of HIV-1: DIS, TAR and RRE. The elaboration of modified aminoglycosides presents a huge advantage because the domain of application, and therefore the benefits, are important. Nevertheless, the structural complexity of these molecules is a major constraint, chemoselective functionalization is essential but unfortunately poorly described in the literature.In this work, we developed two approaches to target the DIS and/or the A site of the bacterialribosome. The first one, unique but challenging is based on the concept of in situ click chemistry. The second approach is conventional and is based on the selective functionalization of some keypositions of aminoglycosides.

My Ph.D. research consists of two components: discovery of novel macrolide antibiotics and methodology development of N-sulfinyl metallodienamines. To tackle bacterial resistance, new antibiotics are desperately needed. My research objective is to address this need by designing, synthesizing, and evaluating novel macrolide antibiotics based on the best-in-class drug candidate, solithromycin. The drug discovery including following three projects: 1) Synthesis of solithromycin analogs wherein the desosamine sugar has been replaced with an acyclic amino alcohol surrogate; 2) In cellulo Click chemistry wherein the bacterial cell serves as the reaction vessel and the ribosome catalyzes the formation of triazole cycloadducts by testing different combinations of azide and alkyne fragments. One of the mechanisms of resistance to macrolide antibiotics is exemplified by methylation of A2058 by the methyltransferase encoded in erm genes. Methylation or dimethylation of A2058 leads to a steric clash with the macrolides and reduces the affinity of the macrolide for the ribosome. Thus, the bacterial resistant can be relieved via disrupting steric clashes between desosamine and A2058 residues. In 2017, I started a new project looking at the scope of the acyclic domino Michael/Mannich reaction to prepare chiral cyclohexenes developed by a previous group member, Dr. Vijay Chatare. This reaction is highly regioselective and stereoselective. Recent research showed that this reaction could be utilized on acroleins, acrylates and unsaturated ketones. Thus, we applied this useful methodology towards the concise total synthesis of (+)-ibogamine. / Chemistry

Antibiotic resistance has become and will continue to be a major medical issue of the 21st century. If not addressed, the potential for a post-antibiotic era could become a reality, one that the world has not been familiar with since the early 1900’s. Multidrug-resistant hospital-acquired bacterial infections already account for close to 2 million cases and 23,000 deaths in the United States, along with 20 billion dollars of additional medical spending each year. The CDC released a report in 2013 regarding the seriousness of antibiotic resistance and providing a snapshot of costs and mortality rates of the most serious antibiotic resistant bacteria, which includes 17 drug resistant bacteria, such as carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococcus and Staphylococcus aureus, and multidrug-resistant Acinetobacter and Pseudomonas aeruginosa. The development of antibiotic resistance is part of bacteria’s normal evolutionary process and thus impossible to completely stop. To ensure a future where resistant bacteria do not run rampant throughout society, there is a great need for new antibiotics and accordingly, methods to facilitate their discovery Macrolides are a class of antibiotics that target the bacterial ribosome. Since their discovery in the 1950’s medicinal chemistry has created semi-synthetic analogues of natural product macrolides to address poor pharmacokinetics and resistance. Modern X-Ray crystallography has allowed the chemist access to high resolution images of the bacterial ribosome bound to antibiotics including macrolides which has ushered in an era of structure-based design of novel antibiotics. These crystal structures suggest that the C-4 methyl group of third generation ketolide antibiotic telithromycin can sterically clash with a mutated rRNA residue causing loss of binding and providing a structural basis for resistance. The Andrade lab hypothesized that the replacement of this methyl group with hydrogen would alleviate the steric clash and allow the antibiotic to retain activity. To this end, the Andrade lab set out on a synthetic program to synthesize four desmethyl analogues of telithromycin by total synthesis that would directly test the steric clash hypothesis and also provide structure-activity relationships about these methyl groups which have not been assessed in the past. Following will contain highlights of the total synthesis of (-)-4,8,10-didesmethyl telithromycin, (-)-4,10-didesmethyl telithromycin, and (-)-4,8-desmethyl telithromycin and my journey toward the total synthesis of (-)-4-desmethyl telithromycin Traditional combinatorial chemistry uses chemical synthesis to make all possible molecules from various fragments. These molecules then need to be purified, characterized, and tested against the biological target of interest. While high-throughput assay technologies (i.e., automation) has streamlined this process to some extent, the process remains expensive when considering the costs of labor, reagents, and solvent to synthesize, purify, and characterize all library members. Unlike traditional combinatorial chemistry, in situ click chemistry directly employs the macromolecular target to template and synthesize its own inhibitor. In situ click chemistry makes use of the Huisgen cycloaddition of alkyne and azides to form 1,2,3-triazoles, which normally reacts slowly at room temperature in the absence of a catalyst. If azide and alkyne pairs can come together in a target binding pocket the activation energy of the reaction can be lowered and products detected by LC-MS. Compounds found in this way generally show tighter binding than the individual fragments. Described in the second part of this dissertation is the development of the first in situ click methodology targeting the bacterial ribosome. Using the triazole containing third generation ketolide solithromycin as a template we were able to successfully show that in situ click chemistry was able to predict the tightest binding compounds. / Chemistry