Synthesis And Characterization Studies Of Nucleoside Analogues: Chemical Probes With Photochemically Controlled Properties And Phosphoramidate Pronucleotides As Antiviral Agents

Abstract

Nucleosides are fundamental building blocks of life that play crucial roles in various biological processes. Beyond their role as genetic material, nucleosides have also gained significant attention in chemical biology and therapeutic development. Nucleoside-based drugs have emerged as effective therapeutic agents for the treatment of a diverse array of diseases, including cancer and viral infections, with over twenty nucleoside-based therapeutics gaining Food and Drug Administration (FDA)-approval. This thesis will focus on the development of nucleoside analogues as chemical biology tools that become bioactive with light and provide insights into the development of broad-spectrum antiviral agents.Chapter 2 will discuss the development of photochemically responsive nucleoside analogues that generate abasic sites photolysis. The previously developed Catch and Release DNA Decoy (CRDD) technology was expanded with the development of nitro-functionalized pyrimidine mimics that photochemically depurinate, similar to their 7-nitroindole (7-NI) predecessor. Four nucleobases that mimic the endogenous pyrimidines were investigated: 2-nitroimidazole (2-NI), 2-nitrobenzene (2-NB), 2-nitropyrrole (2-NP) and 3-nitropyrrole (3-NP). The synthesis of the nucleosides and their incorporation into DNA, as well as their ability to photochemically depurinate are described. Chapter 3 discusses a novel synthesis towards the phosphoramidite of GS-441524, the nucleoside precursor of the FDA-approved drug remdesivir, as well as RNA containing the nucleoside precursor GS-441524, to enable mechanistic studies of viral polymerases with RNA-incorporated remdesivir. Chapter 4 presents a structure-activity relationship study based on the previously reported 3ʹ-deoxy-3ʹ,4ʹ-didehydro-cytidine-prodrug (ddhCPD), which produces significant antiviral activity in West Nile and Zika virus infection models. The synthesis, antiviral evaluation, and cell viability of 3ʹ-deoxy-3ʹ,4ʹ-didehydro-nucleosides and prodrugs encompassing the natural nucleobases adenine, guanine, hypoxanthine, thymine, and uracil are examined. Appendix A introduces the design and synthesis of 3ʹ-deoxy-3ʹ,4ʹ-didehydro-cytidine-lipid prodrug (ddhCLPD) for efforts to specifically target lung tissue. Appendix B examines inhibitors of the receptor binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2 using biolayer interferometry (BLI). Through the development of our designed assay, several DNA aptamers and peptides were screened against the RBD of the spike protein of SARS-CoV-2 and SARS-CoV.