Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biochemistry and Biophysics, 2016
Human Immunodeficiency Virus Type 1(HIV-1) has a genome of only nine thousand bases. This
small genomic space means the virus can only encode for a few proteins and must use an
alternate process to achieve the regulation necessary to propagate the virus. Instead the virus uses
structured RNA in the viral messenger RNA to regulate translation. One such regulatory RNA,
the frameshift stimulatory signal (FSS), encodes for a -1 programmed ribosomal frameshifting
event (PRF). This PRF causes a shift from the open reading frame encoding for gag (structural
proteins) to the reading frame encoding for pol (viral enzymes), resulting in the translation of
gag-pol, a large poly-protein. This frameshift occurs 5-10% of the time in all HIV-1 isolates, and
deviation from this frequency causes a decrease in virion production and virion infectivity. The
mechanism of frameshifting is not well understood. The lack of knowledge combined with the
potential of altering this process as a novel therapeutic strategy makes the HIV-1 FSS RNA an
attractive target against which to develop molecular probes. In this work I describe two chemical
modifications that improve a previously described peptide-based molecule that binds the HIV-1
FSS RNA. The first is amide N-methylation. This was found to increase permeability of these
compounds by as much as 4 fold, increase the binding affinity for the FSS RNA by 60 fold, and
increase the efficacy of these compounds in a pseudotyped infectivity assay by 4 fold. The
second modification was substitution of the olefin bioisotere for a triazole. Incorporation of the
triazole had a large effect on the acute cellular toxicity of these compounds, reducing the LD50
by >5 Fold, and increasing the therapeutic index by >5 fold.