The purpose of the proposed studies is to understand the HIV-1 frameshift (FS) mechanism and to learn how it can be targeted with small, drug-like molecules. The HIV-1 FS site is a highly conserved genomic RNA structure located between the gag and pol reading frames. Its purpose is to stimulate a -1 FS that is required for expression of the Pol genes, which are in the -1 reading frame relative to Gag. We have solved the structure of the HIV-1 FS RNA, both alone and in complex with small drug-like molecules. We will use high throughput screens to identify small molecules that bind to and modulate the HIV-1 FS RNA, both in vitro and in vivo. The best small molecule ligands will be identified as lead compounds. The structures of the HIV-1 FS RNA in complex with lead compounds will be solved, in order to understand the basis for their modes of action. From this information, novel second generation compounds will be developed with improved affinity, specificity and potency. Additionally, we will investigate the FS mechanism, which is currently not well understood. Elucidation of the FS mechanism will provide a better understanding of this essential feature of the viral life cycle, which is utilized by all retroviruses. Finally, we will investigate the structure and function of the entire HIV-1 genomic FS domain, which has been recently identified and is hypothesized to function in slowing the kinetics of translation prior to the FS.
More than 30 million people are infected with Human immunodeficiency virus (HIV), the causative agent of AIDS. Results of the proposed studies will elucidate how HIV stimulates translational frameshifting, a critical step in the viral replication cycle. Small drug-like molecules that inhibit viral replication by targeting this mechanism will be developed.
|Butcher, Samuel E; Jan, Eric (2016) tRNA-mimicry in IRES-mediated translation and recoding. RNA Biol 13:1068-1074|
|Garcia-Miranda, Pablo; Becker, Jordan T; Benner, Bayleigh E et al. (2016) Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity. J Virol 90:6906-6917|
|Vander Meulen, Kirk A; Horowitz, Scott; Trievel, Raymond C et al. (2016) Measuring the Kinetics of Molecular Association by Isothermal Titration Calorimetry. Methods Enzymol 567:181-213|
|Hilimire, Thomas A; Bennett, Ryan P; Stewart, Ryan A et al. (2016) N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA. ACS Chem Biol 11:88-94|
|Mouzakis, Kathryn D; Dethoff, Elizabeth A; Tonelli, Marco et al. (2015) Dynamic motions of the HIV-1 frameshift site RNA. Biophys J 108:644-54|
|Au, Hilda H; Cornilescu, Gabriel; Mouzakis, Kathryn D et al. (2015) Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. Proc Natl Acad Sci U S A 112:E6446-55|
|Yin, Kaifeng; Hacia, Joseph G; Zhong, Zhe et al. (2014) Genome-wide analysis of miRNA and mRNA transcriptomes during amelogenesis. BMC Genomics 15:998|
|Low, Justin T; Garcia-Miranda, Pablo; Mouzakis, Kathryn D et al. (2014) Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry 53:4282-91|
|Moser, Ann B; Hey, Jody; Dranchak, Patricia K et al. (2013) Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells. Lipids Health Dis 12:10|
|Mouzakis, Kathryn D; Lang, Andrew L; Vander Meulen, Kirk A et al. (2013) HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome. Nucleic Acids Res 41:1901-13|
Showing the most recent 10 out of 29 publications