Antraciclinas estão entre os mais eficazes quimioterápicos contra o cancer. São fármacos glycosídicos compostos pelo carboidrato daunosamina ligado a uma aglicona hidróxi antraquinona, e atuam por intercalação ao DNA, geração de estresse oxidative e envenenamento de topoisomerase II. Apesar de sua utilidade terapêutica, multirresistência e cardiotoxicidade grave são importantes limitações decorrentes do tratamento com antraciclinas, estimulando a descoberta de novos análogos, por exemplo através de glicodiversificação. Este trabalho objetivou explorar azido glicosídeos, a serem combinados com agliconas de antraciclinas para gerar novos glicosídeos. Em uma estratégia semi-sintética, daunorrubicinona e doxorrubicinona protegida foram glicosiladas com doadores 2-azido glucosídicos e -galactosídicos, além de glicais. Uma varredura de metodologias de glicosilação envolveu cloretos, imidatos e tioglicosídeos, sendo os promotores com melhores rendimentos HgO/HgBr2 (4-52%) e TMSOTf (38-41%); para glucais e galactais, catalisadores de Au(I) and Cu(I) forneceram moderados rendimentos (15-46%), mas o sistema mais eficiente foi o organocatalisador de tiouréia e ácido fosfórico (18-95%). A clivagem dos grupos de proteção foi desafiadora, dificultando e atrasando a obtenção dos glicosídeos livres. Mediante desproteção, os glicosídeos obtidos incluíram glucosídeo 49 (13%), 2-azido glucosídeo 51 (34%), 2-desóxi glucosídeo 58 (11%) e 2-desóxi galactosídeo 61 (85%), todos com o esqueleto de daunorrubicina. Em ensaios de proliferação celular, os glicosídeos 61? e 61? foram testados em linhagens de células tumorais humanas HeLa, MDA-MB-231 e MCF-7 e um modelo de células sadias (HDF), com IC50 na faixa de 27.1 a 74.6 ?M para o anômero ?, e superior a 250 ?M para o anômero ?. Estudos preliminares com cardiomiócitos humanos derivados de células-tronco induzidas foram inconclusivos para estabelecer um modelo experimental de toxicidade cardíaca. / Anthracyclines are ranked among the most effective chemotherapeutics against cancer. They are glycoside drugs comprised by the aminosugar daunosamine linked to a hydroxyanthraquinone aglycone, and act by DNA-intercalation, oxidative stress generation and topoisomerase II poisoning. Regardless of their therapeutic value, multidrug resistance and severe cardiotoxicity are important limitations arising from anthracycline treatment, prompting the discovery of novel analogues, for instance through glycodiversification. This work aimed to exploit azido glycosides, to be combined with anthracycline aglycone and generate novel glycosides. In a semi-synthesis approach, both daunorubicinone and protected doxorubicinone were glycosylated with conveniently functionalised 2-azido glucosyl and galactosyl donors, as well as glycals. A screening of glycosylation protocols involved glycosyl chlorides, imidates and thioglycosides with the most successful promoters being HgO/HgBr2 (4-52% yield) and TMSOTf (38-41%); for glucals and galactals, Au(I) and Cu(I) catalysts gave moderate yields (15-46%), but thiourea-phosphoric acid was the most efficient catalyst system (18-95%). Cleavage of protecting groups proved challenging, hampering and delaying the obtention of free glycosides. Upon deprotection, the glycosides obtained included glucoside 49 (13%), 2-azido glucoside 51 (34%), 2-deoxyglucoside 58 (11%), and 2-deoxygalactoside 61 (85%), all with the daunorubicin scaffold. In cell proliferation assays, glycosides 61? and 61? were tested against human cancer cell lines HeLa, MDA-MB-231 and MCF-7 and a model of healthy cells (HDF), with IC50 in the range of 27.1 to 74.6 ?M for the ? anomer, and higher than 250 ?M for the ? anomer. Preliminary studies with human cardiomyocytes derived from induced pluripotent stem cells were inconclusive to establish a cardiac toxicity experimental model.

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. / The aim of this work was the design and synthesis of symmetrical glycophanes from D-glucal. Glycophanes may be considered as sugar-cyclophanes hybrids. Having prepared unsaturated O-glycosides and unsaturated alkyl bis-2,3-O-glycosides by a Ferrier rearrangement, we synthetized bifunctional precursors for various reactions of macrocyclization: propargyl-ethers for the reaction of Glaser; azido-alkynes for the reaction of Huisgen and sugar amino-acids for the peptide coupling. The conditions of dilution allowed us to obtain C2 symmetric molecule-cages which were deprotected for complexation purposes.

Heparan sulphate (HS) is critical for embryonic development with involvement in a myriad of biological processes, centrally mediating morphogenic movements and facilitating the specification and differentiation of tissues. Complicated by its structural micro-heterogeneity along with expression on numerous different proteoglycan cores, the plethora of roles for HS in biology and their underlying mechanisms have not yet been fully defined. The discovery and characterisation of new reagents and methods for modification of HS expression and/or structure will aid efforts in elucidating the structure and activity of this glycosaminoglycan. Until now, azido sugars have been utilised as labelling reagents for various types of glycosylation, including N-glycans, O-linked mucin-type glycosylation and O-GlcNAcetylation of proteins. Incorporation of the unnatural azido sugar into the glycan of interest inserts a chemically reactive abiotic azide for subsequent detection via Staudinger ligation or click chemistries. However, to our knowledge, application of these azido sugars has not been explored for glycosaminoglycans. A metabolic labelling approach using Ac4GalNAz yields UDP-GalNAz and UDP-GlcNAz (Boyce et al., 2011), ready to target CS/DS and HS, respectively. We hypothesised that HS synthesis might be altered in the presence of UDP-GlcNAz due to the location of the azide on the acetyl group and the potential for interference with endogenous N-deacetylase-N-sulphotransferase biosynthetic enzyme activity. In mammalian cell culture (Chinese hamster ovary cells), treatment with Ac4GalNAz led to a decrease in total HS abundance accompanied by significant increases in 6-O-sulphation within the chains. Incorporation of a radiolabelled metabolic precursor revealed that average HS chain length was decreased in azido sugar-treated CHO cells. The modifications to HS were dose-dependent and HS inhibition was transient. Following removal of Ac4GalNAz from cell culture, HS expression returned to baseline levels within 24 hours. Previous work from the Bertozzi group has demonstrated the utility of Ac4GalNAz for visualising GalNAc- and O-GlcNAc-modified proteins in vivo. Using Xenopus, we were able to show that treatment of fertilised eggs with Ac4GalNAz decreased the abundance of HS in a similar way to that seen in vitro, with an associated impact on embryonic development. Embryonic axial elongation was impaired, with defective myotomal development and aberrant axonal patterning along the trunk and tail. Posterior somite cell nuclei were disorganised, with loss of distinct chevron patterning and skeletal muscle development was impaired with muscle fibres spanning some of the somite boundaries. Removal of the inhibitor partially rescued tail extension defects, as well as muscle development, but not axonal patterning. Therefore, these experiments illustrate a novel application for Ac4GalNAz as a soluble and reversible inhibitor of HS synthesis for in vitro and in vivo studies. The observed potential for control of inhibition via time- and dose-dependent effects enables targeted and selective inhibition of HS and potentially provides a powerful new inhibitor for the study of HS-mediated events.

Current methods for studying RNA binding proteins (RBPs) combine the use of ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) to analyze RNA-protein interactions. An underexplored alternative approach is using site-specific incorporation of photoactivatable non-canonical amino acids (ncAAs) to enhance the crosslinking efficiency of many CLIP protocols. This thesis describes the incorporation of the photo-crosslinking unnatural amino acid p-azido-L-phenylalanine (AzF) into the Hepatitis C Virus (HCV) non-structural protein 3 helicase (NS3h) for photo-crosslinking and in vitro analysis of the potential binding sites found within the HCV RNA genome. From the five potential sites identified from the NS3h crystal structure for AzF incorporation, two sites, E503AzF and Q580AzF, allowed for nucleic acid photo-crosslinking with fluorescently labelled DNA substrates. We further tested if these mutations adversely affected NS3h and binding activity through a molecular beacon helicase assay and fluorescence polarization methods. We found that E503AzF unexpectedly had a faster unwinding rate than wild type (WT) NS3h and managed to have a similar binding affinity to the tested DNA substrate. Finally, we found that there was a 5-fold increase in the photo-crosslinking efficiency of nucleic acids for E503AzF NS3h mutant compared to our WT NS3h at 254 nm UV light. We are currently working on methods for our CLIP-based protocol to ensure quality RNA footprint generation and purification from photo-crosslinked NS3h. Other work contained in this thesis consists of using Prevotella sp. P5-125 Cas13b (PspCas13b), a clustered regularly interspaced short palindromic repeats (CRISPR) RNA-targeting system, which has been previously shown to knockdown viral RNA and mRNA through designable guide CRISPR RNA (crRNA). Here we incorporated the photo-crosslinking ncAA AzF into PspCas13b to irreversibly bind the crRNA in an attempt to enhance knockdown efficiency and longevity of viral and mRNA targets. We were able to design a crRNA that produced significant knockdown targeting the luciferase mRNA of a luciferase rennilla reporter system. When targeting an HCV subgenomic replicon luciferase reporter system, knockdown was not observed. Additionally, the WT PspCas13b had photo-crosslinking to the bound crRNA and requires further optimization for future use.

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

There are multiple mechanisms by which DNA can become damaged. Such damage must be repaired for the cell to avoid ill-health consequences. Homologous recombination (HR) is a means of repairing one specific type of damage, a double-strand break (DSB). This complex pathway includes the Rad51-DNA nucleoprotein filament as its primary machinery. Current methodology for studying HR proteins includes the use of fluorescently labeled DNA to probe for HR dynamics. This technique limits the number of proteins that can be involved in experimentation, and often only works as an end reporter. The work here aims at improving upon standard techniques by creating two fluorescent protein probes. The first probe was developed by directly attaching a fluorophore to Saccharomyces cerevisiae Rad51 with the use of click chemistry and the incorporation of unnatural amino acids. This probe could function as a primary reporter on the formation and dissociation of the Rad51-DNA filament in the presence of pro- and anti- HR mediator proteins. The second probe was created by labeling the exterior cysteine residues of Plasmodium falciparum single strand DNA binding protein (SSB) with a fluorophore via maleimide chemistry. This probe acts as a secondary reporter for HR dynamics by signaling for when free single stranded DNA (ssDNA) is available.

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.

The goal of our research is to generate cryopreservation agents derived from antifreeze glycoproteins. One postulated mechanism of cell cryo-injury is ice recrystallization. It is known that simple saccharides and cryopreservation agents (DMSO) display ice recrystallization inhibition (IRI). This study assessed the cytotoxicity and cryopreservation ability of these sugars in relation to their IRI. It was determined that compounds with greater IRI have increased cytotoxicity yet confer cryoprotection. To further investigate how structure is affecting IRI activity, several galactopyranoside derivatives were synthesized. A series of deoxy and α-Callyl- deoxy galactopyranoses were prepared. Testing determined that removal of any hydroxyl group removes IRI. 3-deoxy-β-thiophenyl galactose was also synthesized and had surprisingly better IRI than β-thiophenylgalactose. Also, 6-azido galactose had similar IRI to 6-deoxy galactose. Lastly, a series of β- thioalkylgalactosides was synthesized and testing gave contradicting results which suggest that predicting IRI based on hydrophilicity is more complicated than initially hypothesized.

The goal of our research is to generate cryopreservation agents derived from antifreeze glycoproteins. One postulated mechanism of cell cryo-injury is ice recrystallization. It is known that simple saccharides and cryopreservation agents (DMSO) display ice recrystallization inhibition (IRI). This study assessed the cytotoxicity and cryopreservation ability of these sugars in relation to their IRI. It was determined that compounds with greater IRI have increased cytotoxicity yet confer cryoprotection. To further investigate how structure is affecting IRI activity, several galactopyranoside derivatives were synthesized. A series of deoxy and α-Callyl- deoxy galactopyranoses were prepared. Testing determined that removal of any hydroxyl group removes IRI. 3-deoxy-β-thiophenyl galactose was also synthesized and had surprisingly better IRI than β-thiophenylgalactose. Also, 6-azido galactose had similar IRI to 6-deoxy galactose. Lastly, a series of β- thioalkylgalactosides was synthesized and testing gave contradicting results which suggest that predicting IRI based on hydrophilicity is more complicated than initially hypothesized.

The goal of our research is to generate cryopreservation agents derived from antifreeze glycoproteins. One postulated mechanism of cell cryo-injury is ice recrystallization. It is known that simple saccharides and cryopreservation agents (DMSO) display ice recrystallization inhibition (IRI). This study assessed the cytotoxicity and cryopreservation ability of these sugars in relation to their IRI. It was determined that compounds with greater IRI have increased cytotoxicity yet confer cryoprotection. To further investigate how structure is affecting IRI activity, several galactopyranoside derivatives were synthesized. A series of deoxy and α-Callyl- deoxy galactopyranoses were prepared. Testing determined that removal of any hydroxyl group removes IRI. 3-deoxy-β-thiophenyl galactose was also synthesized and had surprisingly better IRI than β-thiophenylgalactose. Also, 6-azido galactose had similar IRI to 6-deoxy galactose. Lastly, a series of β- thioalkylgalactosides was synthesized and testing gave contradicting results which suggest that predicting IRI based on hydrophilicity is more complicated than initially hypothesized.