As they make up DNA and RNA, nucleosides are considered the key to life. Synthetic nucleosides also constitute many drugs that treat viral infections and cancer. As a result, more efficient methods to access these crucial molecules would have implications that extend beyond a synthetic chemist's benchtop and into medicinal chemistry and medical research. One of the most challenging steps in the synthesis of nucleosides is the glycosylation step between the acceptor heterocycle (nucleobase) and the saccharide-based donor. Often to obtain satisfactory yield of this step with good regio- and stereochemical control the extensive use of protecting groups must be employed to squelch reactivity at unwanted reactive groups. Consequently, this process of protection−glycosylation−deprotection is laborious, inefficient, and often requires the use of toxic reagents. It would be, therefore, highly welcomed if new methodology to effect this glycosylation step was designed that reduces or removes the need to use protecting groups, but would still provide nucleosides in good yield, regio- and stereoselectively. Herein, this thesis presents my efforts into achieving this end. By employing modified Mitsunobu conditions, I determined that it is possible to directly glycosylate a nucleobase with D-ribose to afford...

Systematic discontinuation of long-term treatment with nucleos(t)ide analogues (NAs) is one strategy to increase functional cure rates in patients with chronic hepatitis B e antigen (HBeAg)-negative hepatitis B. Currently, available study results are heterogeneous; however, long-term hepatitis B surface antigen (HBsAg) loss rates of up to 20% have been reported in prospective trials. This review proposes criteria that can be used when considering NA discontinuation in patients with chronic hepatitis B virus (HBV). Discontinuing NA treatment frequently results in a virologic and biochemical relapse that runs through different phases: the lag phase, reactivation phase, and consolidation phase. The HBV-DNA flares observed during the reactivation phase are often transient and most likely represent a trigger for inducing a long-term immune control by specific CD8+ T cells, and therefore do not need immediate interventions but close follow-up evaluation. Low HBsAg levels at the time of treatment cessation predict a positive long-term response to NA discontinuation associated with a higher likelihood of HBsAg clearance. Other host and viral biomarkers are currently under evaluation that may prove to be helpful to further characterize the population that may benefit most from the finite NA treatment concept. Potential harmful biochemical flares during the reactivation phase need to be identified early and can be effectively terminated by reintroducing NA treatment. Hepatic decompensation represents a risk to patients with cirrhosis undergoing NA discontinuation. Therefore, the finite NA approach should only be considered after excluding advanced fibrosis and cirrhosis and if a close follow-up of the patient and supervision by an experienced physician can be guaranteed. Conclusion: For selected patients, NA discontinuation has become a powerful tool to achieve control over HBeAg-negative HBV infections. Its significant effect represents a challenge to novel treatment approaches, but it may also serve as their enhancer.

Among many putative genetic risk variations reported to date, the ApoE4 allele remains the most common genetic risk factor for late-onset AD, and is associated with both an increase in incidence and a decrease in age of clinical onset. The majority of ApoE is produced in the: 1) central nervous system (CNS) by astrocytes to transport lipids between cells and modulate the inflammatory response; and 2) liver, where it facilitates lipid uptake into peripheral tissues via low-density lipoprotein (LDL) receptors. Consistent with its dual roles, genetic knockout of ApoE increases the risk for atherosclerosis, but it also dramatically improves AD phenotypes in mouse models. Antisense oligonucleotide (ASO) based modulation of CNS ApoE has only marginal effects on AD phenotypes, suggesting that post-embryonic silencing of ApoE is not a viable therapeutic strategy. However, the recent development of novel CNS siRNA chemical structures enables widespread distribution and potent target silencing throughout the brain. Using this technology, we demonstrate that liver and brain ApoE pools are spatially and functionally distinct, and that complete silencing of brain, not liver, ApoE results in robust reduction of amyloid plaque formation, without impacting systemic cholesterol. Furthermore, RNAseq analysis shows minimal off target effects of the siRNAs and identifies immune modulation and metabolic alterations as potential mechanisms behind ApoE’s role in plaque formation and clearance. Moving forward, these results build upon the rationale to modulate ApoE expression and provide the technology necessary to further evaluate the impact ApoE silencing in AD and other neurodegenerative diseases

Recently the Peterson lab discovered a promising anticancer adenosine derivative-- 2´,3´-bis-O-tert-butyldimethylsilyl-5´-deoxy-5´-[N-(methylcarbamoyl)amino]-N6-(N-phenylcarbamoyl)adenosine. This compound showed selective toxicity against human colon cancer cells in vitro with LC50's = 6--10 µM. It was hypothesized that the lead compound exerted its cytotoxic effects by interacting with a protein kinase. A systematic Structure Activity Relationship (SAR) was undertaken in an attempt to increase the kinase-binding affinity of the lead compound. Many regions of the lead compound were examined: the N6-phenyl urea moiety, the 5´-N-methyl urea group, the 2´,3´-bis-O-TBS groups, the nucleobase, and the ribose sugar. Results of these studies produced some promising new derivatives. In particular, one analogue exhibited potent cancer cell growth inhibition with an average GI50 of 0.58 μM (NCI-60). In addition, another compound showed selective toxicity for the non-small cell adenocarcinoma cell line NCI-H522 with an LC50 of 10 nM. Efficient methods for the preparation of a wide variety of N6-aryl and -alkyl substituted derivatives were developed. One versatile route involved the installation of an N6-ethoxy carbonyl and subsequent displacement with an alkly- or arylamine. Synthetic routes for the preparation of of a variety of 2´,3´-bis-O-acylated analogues were also developed. Nucleoside mono-, di-, and triphosphate bioisosteres in which the phosphoester or phosphoanhydride have been replaced by an unnatural functional group have been extensively investigated. A simple and efficient method was developed for the preparation of carbamoyl analogues of nucleoside mono-, di-, and triphosphate surrogates. This method uses a modified version of the Kočovský reaction to install mono-, di-, and triphosphate mimics in good to excellent yields (ave = 75%).

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Cationic polymers have shown potential as gene delivery vectors due to their ability to condense DNA and protect it from cellular and restriction nucleases. Dendrimers are hyperbranched macromolecules with precisely defined molecular weights and highly symmetric branches stemming from a central core. The nanosize, tunable surface chemistries and ease of surface functionalization has made dendrimers an attractive alternative to conventional linear polymers for DNA delivery applications. The commercially available, cationic dendrimer poly(amidoamine) or PAMAM is the most widely studied dendrimer for use as a gene delivery vector. The aim of this dissertation is to provide an increased understanding of the packaging and forces within PAMAM–DNA complexes. In Chapter 4, we will discuss the effect of molecular chain architecture on DNA-DNA intermolecular forces by examining DNA condensed by low generation (G0 & G1) PAMAM and comparing them to comparably charged linear arginine peptides. Using osmotic stress coupled with X-ray scattering, we are able to determine the structure and forces within dendrimer-DNA complexes, or dendriplexes. We show that PAMAM–DNA assemblies display significantly different physical behavior than linear cation–DNA assemblies. In Chapter 5, we examine the role of pH on condensation in these same low generation PAMAM-DNA complexes. PAMAM dendrimers have both terminal primary amines and internal tertiary amines with different pKas of approximately 9 and 6, respectively. We show changes in the pH at condensation greatly influence the resulting packaging as well as the resulting phase behavior for PAMAM dendriplexes. In Chapter 6, we examine the packaging of DNA by G4 PAMAM as a function of the percent zwitterionic modification. Many cationic polymers, including PAMAM, have shown high transfection efficiency in cell culture and potential for in vitro and in vivo applications, but its development is hindered by cytotoxicity in many cell lines and tissues. We hypothesize that zwitterionic PAMAM (zPAMAM) represent a new means to tune polymer-DNA interactions through PAMAM surface charge potentially enhancing intracellular unpackaging while reducing cellular toxicity. These zPAMAM complexes are currently under investigation for their potential as safer and more efficient materials for DNA delivery.

RNA nanotechnology is an emerging field that holds great promise for advancing drug delivery and materials science. Recently, RNA nanoparticles have seen increased use as an in vivo delivery system. RNA was once thought to have little potential for in vivo use due to biological and thermodynamic stability issues. However, these issues have been solved by: (1) Finding of a thermodynamically stable three-way junction (3WJ) motif; (2) Chemical modifications to RNA confer enzymatic stability in vivo; and (3) the finding that RNA nanoparticles exhibit low immunogenicity in vivo. In vivo biodistribution and pharmacokinetics are affected by the physicochemical properties, such as size, shape, stability, and surface chemistry/properties, of the nanoparticles being delivered. RNA has an inherent advantage for nanoparticle construction as each of these properties can be finely tuned. The focus of this study is as follows: (1) Construction of diverse size and shape RNA nanoparticles with tunable physicochemical properties; (2) Investigation of the effect that size, shape, and nanoparticle properties have on in vivo biodistribution; (3) Development of drug encapsulation and release mechanism utilizing RNA nanotechnology; and (4) Establishment of large-scale synthesis and purification methods of RNA nanoparticles. In (1), RNA triangle, square, and pentagon shaped nanoparticles were constructed using the phi29 pRNA-3WJ as a core motif. Square nanoparticles were constructed with sizes of 5, 10, and 20 nanometers. The RNA polygons were characterized by AFM to demonstrate formation of their predicted geometry per molecular models. Furthermore, the properties of RNA polygons were tuned both thermodynamically and chemically by substitution of nucleic acid type used during nanoparticle assembly. In (2), the biodistribution of RNA nanosquares of diverse sizes and RNA polygons of diverse shapes were investigated using tumor models in nude mice. It was found that increasing the size of the nanosquares led to prolonged circulation time in vivo and higher apparent accumulation in the tumor. However, it was observed that changing of shape had little effect on biodistribution. Furthermore, the effect of the hydrophobicity on RNA nanoparticles biodistribution was examined in mouse models. It was found that incorporation of hydrophobic ligands into RNA nanoparticles causes non-specific accumulation in healthy organs, while incorporation of hydrophilic ligands does not. Lower accumulation in vital organs of hydrophobic chemicals was observed after conjugation to RNA nanoparticles, suggesting RNA has the property to solubilize hydrophobic chemicals and reduce accumulation and toxicity in vital organs. In (3), a 3D RNA nanoprism was constructed to encapsulate a small molecule fluorophore acting as a model drug. The fluorophore was held inside the nanoprism by binding to an RNA aptamer. The ability of the stable frame of the nanoprism to protect the fragile aptamer inside was evidenced by a doubling of the fluorescent half-life in a degrading environment. In (4), a method for large-scale in vitro synthesis and purification of RNA nanoparticles was devised using rolling circle transcription (RCT). A novel method for preparing circular double stranded DNA was developed, overcoming current challenges in the RCT procedure. RCT produced more than 5 times more RNA nanoparticles than traditional run-off transcription, as monitored by gel electrophoresis and fluorescence monitoring. Finally, large-scale purification methods using rate-zonal and equilibrium density gradient ultracentrifugation, as well as gel electrophoresis column, were developed.

Cela fait plus de quarante ans que la plupart des modifications des ARNt ont été découvertes mais ce n’est que récemment que les gènes correspondants ont pu être identifié. La modification N6-threonylcarbamoyl adénosine (t6A) est universelle et se trouve à la position 37, adjacente de l’anticodon, dans de nombreux ARNt. Les quatre gènes responsables de la synthèse de cette modification chez les bactéries furent découverts par des approches de génomique comparative mais uniquement deux de ces gènes sont universels, TsaC/Sua5 et TsaD/Kae1/Qri7. Des travaux récents ont révélé qu'il existait différentes voies enzymatiques pour la synthèse de cette modification selon domaine de la vie, les organelles et les espèces considérés. L'étude de ces variations est toujours en cours de caractérisation.Ce travail a identifié quatre autres protéines requises pour la synthèse de t6A dans les ARNt cytoplasmiques de levure (Bud32, Pcc1, Cgi121 et Gon7) et établi que seuls Sua5 et Qri7 sont requis pour modifier les ARNt mitochondriaux. La même enzyme, Sua5, effectue la première étape de la synthèse de t6A à la fois dans le cytoplasme et les mitochondries. Cette protéine peut être localisée dans les deux compartiments grâce à l’utilisation de sites d’initiation de la traduction différents. Cette étude a montré qu’une machinerie de synthèse minimale est requise pour la synthèse de t6A dans les mitochondries, potentiellement similaire à la machinerie présente dans le dernier ancêtre commun. Les rôles de cette modification complexe in vivo semblent également varier. Par exemple, t6A est indispensable chez les procaryotes, mais pas dans la levure. Les causes des phénotypes pléïotropes observés lors de la diminution ou l'absence de t6A ne sont pas encore entièrement comprises. Nous avons pu élucider certains des rôles joués par la modification t6A, en effectuant une analyse globale des erreurs de traduction observées en absence de cette modification par analyse des profils ribosomaux. Par exemple, il semble que la présence de t6A permet aux ARNt rares de concurrencer plus efficacement les ARNt abondants. La complexité et la diversité des voies de synthèse combiné à l’importance fonctionnelle et évolutive de cette modification ont fait de t6A une “décoration” des ARNt particulièrement fascinante à étudier. / The modification of tRNA has a rich literature of biochemical analysis going back more than 40 years; however, the genes responsible for the modifications have only been recently identified. Comparative genomic analysis has allowed for the identification of the genes in bacteria, and subsequent characterization of the enzymes, responsible for the modification N6-threonylcarbamoyladenosine (t6A) located at position 37, adjacent to the anticodon of tRNAs. While the modification is present in all domains of life, only two of the four enzymes responsible for biosynthesis machinery are conserved. In Eukaryotes, both cytoplasmic and mitochondrial tRNAs are modified with t6A, and previously only the two universally conserved members of the cytoplasmic t6A synthesis pathway, TsaC/Sua5 and TsaD/KaeI/Qri7 were known. Recent progress on deciphering the t6A synthesis pathways has revealed that different solutions have been adopted in different kingdoms, species, and organelles, and these variant pathways are still being characterized.This investigation identified the other four proteins required for cytoplasmic synthesis (Bud32, Pcc1, Cgi121, Gon7), and determined that only Sua5 and Qri7 are required for mitochondrial synthesis of t6A in yeast. The same enzyme, Sua5, performs the first step of t6A synthesis in both the cytoplasm and the mitochondria. It is targeted to both the cytoplasm and the mitochondria through the use of alternative, in-frame AUG translational start sites. This study showed that a minimum synthesis machinery is responsible for mitochondrial t6A, implicating a core set of enzymes from the LUCA.The roles of this complex modification in vivo also seem to vary. For example, t6A is essential in prokaryotes, but not in yeast. The causes of the observed pleiotropic phenotypes triggered by the reduction or absence of t6A synthesis enzymes are not yet fully understood. This work used ribosome profiling to map all translation errors occurring when t6A was absent. By examining ribosomal occupancy of every codon, this work indicates that t6A is helping rare tRNAs compete with high copy tRNAs. The complexity and diversity of the t6A pathway combined with the functional and evolutionary importance of this modification have made t6A a particularly fascinating “decoration” of tRNA to study.

Les analogues synthétiques des nucléosides naturels constituant des acides nucléiques occupent une place importante dans le domaine du médicament comme principes actifs antiviraux ou anticancéreux. Ces nucléosides agissent comme « prodrogues » en perturbant la biosynthèse des acides nucléiques viraux ou des cellules cancéreuses après phosphorylation. Dans la recherche de nouveaux médicaments antiviraux, nous avons cherché à synthétiser de nouveaux analogues des nucléosides naturels, les 2-désoxy-adénosine et -guanosine, et de l’aciclovir et de ses dérivés (vanciclovir, ganciclovir…) qui sont très utilisés dans le traitement de l’Herpès. Des premiers travaux en série adénine et guanine, n’ont pas permis d’obtenir les dérivés cycliques recherchés dans lesquels la base et la chaîne latérale introduite en position 9 de la base sont liés par un atome d’oxygène se trouvant en position 8 pour former un nouveau cycle. Quatre analogues cycliques en série guanine ont été synthétisés dans lesquels la base et la chaîne latérale en position 8 sont liés soit par un hétéroatome (préparés par réaction de substitution nucléophile), soit par une liaison carbone-carbone (préparés par réaction radicalaire) et sont en cours d’évaluation antivirale. / The synthetic analogues of the natural 2’-deoxyribonucleosides, linked by phosphodiester groups in nucleic acids, constitute major classes of antiviral and anticancer drugs. Such nucleosides act as “prodrugs” disturbing the biosynthesis of nucleic acids after phosphorylation. Searching for new antiviral drugs, the aim of this work was the synthesis of new modified nucleosides analogues of 2’-deoxyadenosine and -guanosine also analogues of aciclovir and its derivatives (vanciclovir, ganciclovir…) widely used for Herpes treatment. In the first works in adenine and guanine series, the cyclic analogues in which the base and a side chain introduced at position 9 of the base are linked at position 8 by an oxygen atom could not be obtained. Four cyclic analogues in the guanine series were prepared in which the base and the 9-side chain are linked at position 8 are either linked by a heteroatom (synthesized by nucleophilic substitution) or by a carbon-carbon bond (synthesized by free radical reaction). The evaluation of the antiviral activity of these compounds is underway.