Doctor of Philosophy, Case Western Reserve University, 2023, Chemistry

Positive Strand RNA (PSR) viruses, such as coronaviruses and enteroviruses, cause serious health and economic threats worldwide, as seen with the COVID-19 pandemic. This has drawn attention to the importance of identifying new antivirals and molecular targets in RNA viruses. The multifunctionality of PSR genomes make them desirable targets for therapeutic intervention. Here, we present a class of antivirals that can inhibit SARS-CoV-2 replication in vitro by targeting conserved viral RNA structures at the 5'-end. Specifically, stem loops (SLs) 1, 4, 5a, and 6 of the viral 5'-region have shown a degree of binding with dimethyl amiloride molecules as determined by NMR structural analysis. These results open the door to potentially develop specific small molecules against SARS-CoV-2 and related coronaviruses. Upon investigating SL6, interesting structural dynamics features were observed at the budge region when exposed to different temperatures. From various Nuclear Magnetic Resonance (NMR) and single angle x-ray scattering (SAXS) experiments, experimental restrains were obtained in order to generate a 3D structure of SL6 using molecular dynamics simulations. In SARS-CoV-2, stem-loop 3, which contains the transcriptional regulatory sequence, was proven to bind to the host Unwinding Protein 1 (UP1) using electrophoretic mobility shift assay (EMSA), isothermal titration chromatography (ITC), and NMR, which possibly suggests that UP1 participates in the mechanism of transcription of sub-genomic RNA. In addition, another PSR virus, Enterovirus A71 (EV-A71), which is the etiological agent of the hand, foot, and mouth disease, has caused severe morbidity and high mortality rates in children for decades. Thus, understanding the mechanisms by which EV-A71 replicates within the cellular environment can bring to light efficient drug targets for viral inhibition. The 5'-untranslated region (5'-UTR) of the RNA genome is the control hub of viral replication and transcription in EV- (open full item for complete abstract)

Committee: Blanton S. Tolbert (Advisor); Fu-Sen Liang (Committee Chair); Thomas Gerken (Committee Member); Robert Salomon (Committee Member); Divita Mathur (Committee Member) Subjects: Biochemistry; Biophysics; Chemistry; Virology