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

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.

The larvae (wireworms) of some click beetle genera inhabit the soil in agricultural land and are crop pests. In the UK, a pest complex of Agriotes species, A. obscurus, A. sputator and A. lineatus, has been identified as the cause of the majority of damage. However, studies on their ecology are lacking, despite knowledge of this being important for the development of sustainable risk assessment and pest management strategies, in part due to the morphologically cryptic nature of wireworms. The ecology of economically important click beetle species was investigated, focusing on UK Agriotes species. The relationship between sex pheromone trapped male Agriotes adults and wireworms, identified using a molecular tool (T‐RFLP), was influenced by sampling method, and some environmental variables significantly correlated with species distributions. Scale of sampling influenced the observed distribution of wireworms and other soil insect larvae. Other wireworm species were trapped together with Agriotes species, but mitochondrial 16S rRNA sequences could not be matched to those of other UK species. Sequences from Canadian wireworm samples revealed possible cryptic species. Differences in adult movement rates were found in laboratory tests (A. lineatus > A. obscurus > A. sputator). Molecular markers (AFLPs) were developed to assess dispersal in adult male Agriotes but further protocol optimisation is required. The results show the importance of identifying wireworms to species for assessing adult and wireworm distributions, since the Agriotes pest complex may not be present or as 3 widespread as previously assumed. Sex pheromone trapping of adults may not be appropriate for risk assessment as the relationship between aboveground adult and belowground wireworm species distribution is not straightforward. The differences observed in Agriotes species’ ecology have implications for the implementation of pest management strategies. The techniques used here can be applied in future studies to provide information on other economically important click beetle species worldwide.

The recovery of the selected biological material in affinity-based separations relies on reversing the biological interaction responsible for the binding. General elution methods which are independent of the bioaffinity interaction have attracted increasing attention. The first three chapters of this thesis describe the development of a novel “click” functionalised azobenzene-based linker for affinity-independent elution protocols and the preliminary affinity studies using this linker. Ligands functionalised with a bioorthogonal propargyl label were readily attached to the terminal azide of the linker using the copper(I) catalysed Huisgen cycloaddition (or "click" reaction). Following separation, the linker was cleaved under mild non-denaturing conditions using Na2S2O4. In the last three chapters a novel approach towards the synthesis of the 4-methyl proline fragment of the cytotoxic natural product bisebromoamide (a potential affinity target) is proposed. For the pyrrolidine ring construction an enamide-olefin ring-closing metathesis (RCM) approach has been attempted. The installation of the required absolute stereochemistry has been achieved using a phase-transfer catalyst for the enantioselective alkylation of Schiff bases derived from glycine esters.

Peptide nucleic acids (PNAs) were used as encoding tags to enable the analysis of peptide libraries by PNA/DNA hybridisation onto DNA microarrays. This allowed entire peptide libraries to be organised and sorted in a two dimensional format whereby all library members could be interrogated and analysed on a one-byone basis. In this thesis, PNA-encoded peptide libraries, generated by split-and-mix library synthesis, were screened for a variety of functions. Peptide sequences identified from the screening of a PNA-encoded library were analysed in detail as the first specific substrates for chymopapain. A new PNAencoded library consisting of D-amino acids was synthesised and screened with a number of proteases in attempts to identify novel/unusual substrates. PNA-encoded libraries were also used in the screening of peptide libraries for other activities. Thus substrates for catalyst-free Hüisgen cycloaddition were identified following the reaction between an alkyne modified peptide library and azidofluorescein, while cell-penetrating peptides were identified by hybridization of an internalized encoded library onto a DNA microarray.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

L’utilisation de peptides ou de protéines radiomarquées au fluor-18, comme radiotraceurs pour l’imagerie par Tomographie par Emission de Positons (TEP) est en plein essor. C’est ainsi que l’objectif de notre travail a été de concevoir et de synthétiser de nouveaux groupements prosthétiques de nature glucidique, analogues du 2-Fluoro-2-[18F]désoxy-D-glucose ([18F]FDG). La particularité de ces derniers, est qu’ils sont porteurs de motifs azides afin de les lier de façon simple et efficace à des biomolécules fonctionnalisées par des groupements alcynes via la réaction de Huisgen ou réaction de « click chemistry ». Le premier objectif de ce travail a été d’étudier la position idéale d’introduction du motif azide sur le FDG, soit sur la position C-1, soit sur la position C-6. Deux stratégies de synthèse différentes ont été développées pour aboutir à deux générations de précurseurs de marquage et à leurs références froides, permettant ainsi d’évaluer l’étape d’incorporation du fluor-18. Le second objectif a été d’introduire un groupement propargyle sur la phénylalanine, la cystéine et le glutathion afin de réaliser le couplage par click chemistry avec le meilleur groupement prosthétique obtenu. / The use of peptides or proteins labeled with fluorine-18, as agents for Positron Emission Tomography (PET) is a rapidly growing field. Thus, the objective of our work was to create and to synthesize new glycosyl prosthetic groups, which are analogs of 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG). The particularity of these compounds is their azide moiety which enables a simple and efficient ligation with alkynylated amino acids via a Huisgen type reaction or “click Chemistry”. The first goal was to study the ideal position for the introduction of the azide moiety on the sugar, either at the C-1 or C-6 position. In order to evaluate the incorporation of fluorine-18, two different strategies were developed to obtain two generations of labeled precursors and cold references. The second objective was to synthesize alkynylated phenylalanine, cysteine and gluthation derivatives to test the “click Chemistry” ligation method with the best prosthetic group.

The objective of this project was to prepare alkyne-functionalized polymer latexes using surfactant-free emulsion polymerization, and then functionalize these polymer latexes with three quaternary ammonium azides via Cu(I)-catalyzed azide/alkyne cycloaddition (CuAAC) in order to produce antimicrobial polymer latexes. Three quaternary ammonium azides with different linear alkyl chain lengths (C4, C8 and C12) were successfully synthesised in high yield ( > 70%) using established procedures, and their purity determined by elemental analysis, Fourier transform infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy. Alkyne-functionalized polymer latexes were prepared via surfactant-free emulsion polymerization using 2,2'-azobis(2-methylpropionamidine)dihydrochloride (AIBA) as initiator, [2-(methaccryloyloxy)ethyl]trimethylammonium chloride (MATMAC) as cationic comonomer, propargyl methacrylate (PMA) to provide the alkyne groups, and for some latexes, ethylene glycol dimethacrylate (EGDMA) as crosslinking comonomer. The effects of temperature and the concentrations of AIBA, MATMAC, PMA and EGDMA on monomer conversion, the rate of polymerization, particle diameter and colloidal stability have been investigated. The studies showed that the very high rates of polymerization were due to high values of the number of radicals per particle (in the range 3-2300). The observations also determined that the reaction conditions required to produce small particles (diameter of 150-350 nm) of narrow size distribution were: 75 oC reaction temperature, AIBA at 0.2 wt% to the total mass of monomer, MATMAC level of smaller or equal to 12 mol% to total monomer (including MATMAC), and EGDMA level of < 2.0 mol% to total monomer (excluding EGDMA). Three series of alkyne-functionalized polymer latexes have been synthesised using these conditions: non-crosslinked (NCL), crosslinked (CL) and core-shell (CS). All the latex particles were functionalized with the three quaternary ammonium azides by CuAAC. Zeta potential analysis, FTIR and Raman spectroscopy analysis confirmed the success of the click reactions. The quantitative analysis of FTIR and Raman spectra showed similar values of conversion of click reaction for both NCL and CL particles, indicating NCL and CL particles have similar swellability. The data also showed that significantly higher click reaction conversions were achieved for CS particles (around 60%) than for NCL/CL particles (less than 40%), which indicates that the click reaction only occurred at the surface of particles and that a higher proportion of alkyne groups are located on the surface of CS particles than on NCL/CL particles. The antimicrobial properties of all QAAs, MATMAC, NCL, CL and CS polymer latexes against E. coli bacteria (ATCC 25922) have been investigated using a modified liquid microdilution method in M9 medium, which was shown not to affect latex colloidal stability. It was found that all the polymer latexes showed much higher antimicrobial activities (MIC 6.5-75 µg ml-1) than many antimicrobial polymers reported recently in the literature (MIC 100-2000 µg ml-1); (Ganewatta, M.S. and C.B. Tang, Controlling macromolecular structures towards effective antimicrobial polymers. Polymer, 2015. 63: p. A1-A29). Polymer latexes with clicked-on QAAs showed significantly higher antimicrobial activities than the original latexes. The magnification of the increase in antimicrobial properties of CS particles after click reaction (~3.5 times) was greater than for NCL/CL particles (~2.5 times), showing that a larger amount of QAAs have been clicked onto the surface of CS particles than NCL/CL particles and that the clicked-on QAAs enhance the antimicrobial activity significantly.

Cumarinas são metabólitos secundários de plantas encontrados majoritariamente nas espécies das famílias Asteraceae, Rutaceae e Umbeliferae. Quimicamente, são compostos fenólicos, formados pela fusão de um benzeno e de um anel α-pirona, chamados de benzopironas. Elas apresentam diversas propriedades farmacológicas, associadas com baixa toxicidade. Nosso grupo de pesquisa sintetiza cumarinas pela reação de Pechmann, que ocorre através da condensação de um fenol com um β-cetoéster, na presença de um ácido de Bronsted ou Lewis. Um dos trabalhos mais recentes foi a síntese de 6-metil-4-clorometilcumarinas com um IC50 menor do que 1,6 μM para atividade antitripanocida. Em outro trabalho, um grupo de compostos de híbridos cumarina-triazol foi sintetizado e apresentou potencial atividade como agente antitumoral. Baseado nesses trabalhos, foi planejado a síntese de análogos da 6-metil-4-clorometilcumarina via condensação de Pechmann, com diferentes substituintes na posição 6, obtidos através das reações de click chemistry, no intuito de aumentar a atividade antioxidante desses compostos. Assim, para obter esses compostos, foi realizada uma condensação de Pechmann com hidroquinona e 4-cloroacetoacetato de etila. Após, uma eterificação de Williamson com brometo de propargila foi feita. Finalmente, a reação de click chemistry foi realizada sob irradiação de micro-ondas com diversas azidas previamente sintetizadas no laboratório, conduzindo à obtenção de diversos análogos da 6-metil-clorometilcumarina que foram avaliados quanto a viabilidade celular através ensaio do MTT (brometo de 3-(4,5-dimetiltiazol-2-il)-2,5-difeniltetrazólio). Também foi testada a sua capacidade antioxidante pelo método do DCFH-DA (diacetato de 2’,7’ –diidroclorofluoresceína). Dessa maneira, sob as condições reacionais utilizadas neste trabalho, foi possível sintetizar 12 compostos inéditos com rendimentos entre 9 e 61%. Os ensaios biológicos preliminares indicaram que os compostos sintetizados apresentam potencial atividade antioxidante e algumas moléculas tiveram potencialidade como agente citotóxico. / Coumarins are secondary plant metabolites typically found in species of the Asteraceae, Rutaceae and Umbeliferae families that demonstrate diverse pharmacological properties associated with low toxicity to humans. Chemically, they are phenolic compounds characterized by the fusion of benzene with an α-pyrone ring, yielding the benzopyrone nucleus. Our research group usually synthesizes coumarins by the Pechmann reaction, through the condensation of phenols with β-ketoesters catalyzed by Bronsted or Lewis acids. One of the most recent works performed at our laboratory describes the synthesis of 6-methyl-4-chloromethylcoumarins with an IC50 of 1.6 μM concerning the anti-trypanocidal activity. Another work described the syntheses of coumarin-triazole hybrids with potential activity as anticancer agents. Based on the previous works, it was designed the synthesis of 4-chloromethylcoumarins via Pechmann condensation with several substituents at the position 6 of the coumarin ring through click chemistry reactions to improve their antioxidant activities. The synthesis of the coumarins started with Pechmann condensation using hydroquinone and ethyl 4-chloroaceacetate followed by functionalization of the phenolic hydroxyl with propargyl bromide via Williamsom ether synthesis. Subsequently, the click chemistry reactions were performed under microwave irradiation using different organic azides previously synthesized at our laboratory, yielding several 6-substituted-4-chloromethylcoumarin analogues which were evaluated for cell viability through MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Their antioxidant capacity was also tested by the DCFH-DA (2’,7’–diihydrochlorofluorescin diacetate) method. Therefore, under the reaction conditions used in this study, it was possible to synthesize 12 novel compounds with yields between 9 and 61%. Preliminary biological assays indicated that the compounds synthesized have potential antioxidant activity and some molecules had potential as an antitumor agent.

This master thesis report describes the work of evaluating the approach of using an eye-tracker and machine learning to generate an interaction model for clicks. In the study, recordings were done from 10 participants using a quiz application, and machine learning was then applied. Models were created with varying quality from a machine learning view, although most models did not work well for interaction. One model was created that enable correct interaction 80\% of the time, although the specific circumstances for success were not identified. The conclusion of the thesis is that the approach works in some cases, but that more research needs to be done to evaluate general suitability, and approaches to make it work reliably.