Chemical synthesis of base-modified ribonucleosides as novel antiviral agents

by Harki, Daniel Allen.

ii RNA viruses exist in nature as a population of genetic variants termed a quasispecies. This inherent genomic variability permits the rapid evolution of a virus population in response to changing environmental conditions, reestablishing a new population of viruses that have adapted to their surroundings. The development of antiviral drug resistance is propagated through this mechanism. To maintain this high degree of genomic adaptability, RNA viruses exist on the edge of “error catastrophe.” Slight increases in the relative mutation frequencies of RNA virus genomes can surpass the tolerated error threshold yielding viral inviability or “lethal mutagenesis.” The antiviral drug ribavirin was recently demonstrated to function as an antiviral lethal mutagen. Following intracellular phosphorylation to the 5’triphosphate, this antiviral nucleotide is misincorporated into the viral (poliovirus) RNA genome by the promiscuous viral RNA-dependent RNA polymerase (RdRP). Once present in the viral genome, ribavirin templates the misincorporation of the pyrimidines C and U during multiple rounds of replication. The degenerate templating specificity of ribavirin enhances the frequency of A ? G and G ? A transition mutations, forcing the virus into error castrophe and loss of viability. Efforts towards the development of novel antiviral lethal mutagens are described throughout this thesis. Chapter one provides an overview of the lethal mutagenesis strategy, citing many of the pioneering accomplishments in the iii development of this antiviral drug discovery approach. Chapter two describes the development of a “universal base” ribonucleoside designed to be misincorporated opposite all four RNA bases. A structural comparison between this analogue (3-NPN) and the antiviral drug ribavirin is presented. The third chapter of this thesis expands on the development of universal base ribonucleosides and examines a series of substituted indoles and azaindoles for antiviral activity. One particular compound, termed 5-NINDN, functions as a universal base by misincorporating opposite all four RNA bases when utilized as a substrate for poliovirus and coxsackievirus RdRPs. Chapter four examines a family of 5-substituted cytidine derivatives, structurally inspired by 5-hydroxy-2’deoxycytidine, a lethal mutagen for HIV. Two analogues from this series were shown to possess good antiviral activities against poliovirus and coxsackievirus, with 5-nitrocytidine surpassing the observed antiviral activity for ribavirin. The final chapter, Chapter five, is split among two studies. The first section describes basic strategies for nucleotide synthesis, focusing on efforts directed towards an efficient synthesis of ribavirin triphosphate and pyrazofurin triphosphate. The second part describes the biochemical evaluation of a 4-nitroimidazole ribonucleoside analogue.