Selection and Characterization of Small Molecules That Bind the HIV-1 Frameshift Site RNA

Abstract

HIV-1 requires a −1 translational frameshift to properly synthesize the viral enzymes required for replication. The frameshift mechanism is dependent upon two RNA elements, a seven-nucleotide slippery sequence (UUUUUUA) and a downstream RNA structure. Frameshifting occurs with a frequency of ~5%, and increasing or decreasing this frequency may result in a decrease in viral replication. Here, we report the results of a high-throughput screen designed to find small molecules that bind to the HIV-1 frameshift site RNA. Out of 34,500 compounds screened, 202 were identified as positive hits. We show that one of these compounds, doxorubicin, binds the HIV-1 RNA with low micromolar affinity (K d = 2.8 μM). This binding was confirmed and localized to the RNA using NMR. Further analysis revealed that this compound increased the RNA stability by approximately 5 °C and decreased translational frameshifting by 28% (±14%), as measured in vitro.Twenty-five years after its initial identification, human immunodeficiency virus type 1 (HIV-1) continues to be a major health concern across much of the world. Although many anti-HIV-1 drugs have been developed, the virus is often able to evade these therapies owing to its high mutation rate. In addition to new classes of drugs being designed against the traditional targets (protease and reverse transcriptase) (1,2), recent research has focused on targeting the −1 programmed translational frameshift that occurs between the gag and pol reading frames (3)(4)(5)(6)(7)(8). This frameshift allows for translation of the pol genes (encoding the protease, reverse transcriptase, and integrase enzymes) in the form of a Gag-Pol fusion polyprotein via the evasion of a stop codon located at the end of the gag gene. Without this frameshift, only the Gag polyprotein (matrix, capsid, nucleocapsid, and p6 structural proteins) will be produced. The structural and enzymatic proteins are found in approximately a 20:1 molar ratio as a result of a frameshift efficiency of approximately 5% (9-15). This stoichiometry is required for appropriate packaging of virus particles, and an increase or decrease in the frameshift efficiency has been found to significantly decrease the production of infectious virions (4,15,16).The frameshift event is programmed by two cis-acting RNA elements between the gag and pol genes: a seven-nucleotide slippery sequence (UUUUUUA) and a highly conserved stemloop structure immediately downstream (9,17). This stem-loop structure has been shown to induce ribosomal pausing, which is required for frameshifting, and its stability has been correlated with the efficiency of ribosomal frameshifting (18,19). At the base of the stem-loop, the frameshift site RNA contains a conserved GGA bulge. This sequence has been hypothesized to interact with the translational machinery during frameshifting (20), by virtue of its predicted positioning near the mRNA entrance channel, which is located 13-15 nucleotides of the P site codon (21). Due to the distance the mRNA must traverse through the r...

Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity

“…Although both the proteolytic processing of HIV-1 proteins and a normal intracellular Gag/Gag-Pol ratio are required for RNA dimerization, the formation of stable RNA dimers is not essential for the packaging of HIV-1 genomic RNA (18). The importance of maintaining Gag/Gag-Pol levels for viral infectivity has encouraged the exploration of various approaches attempting to discover small molecules that could modulate HIV-1 frameshift efficiency (19)(20)(21)(22)(23)(24)(25).…”

Dynamic Motions of the HIV-1 Frameshift Site RNA

“…RNA for NMR was transcribed in vitro using purified His 6 -tagged T7 RNA polymerase and synthetic DNA oligonucleotides (IDT), as previously described (69,71,74). 13 C/ 15 N-labeled RNA was prepared using 13 C/ 15 Nlabeled rNTPs (Cambridge Isotope Laboratories).…”

“…Fluorescence measurements were performed in triplicate similar to those previously described (71). Briefly, the 2-aminopurine substituted RNAs (HIV-1 G33-2AP, G34-2AP, and A35-2AP) were excited at 309 nm and emission was measured at 360 nm with a Varian Cary Eclipse Fluorescence spectrometer.…”

“…Here, we investigate the dynamics of the HIV-1 frameshift site (FS) RNA (63,(68)(69)(70)(71)(72). During translation of the FS, the RNA switches from a 3-helix junction structure to a 2-helix junction via ribosome-mediated remodeling of the RNA secondary structure (63).…”

Ribosomal Frameshift Signals in Viral Genomes

“…This demonstrates how our lack of understanding of how specific stimulatory elements facilitate frameshifting makes antiviral design difficult. Marcheschi et al, (2009) replaced the guanosine in the HIV FSS purine bulge with a fluorescent analog, 2-aminopurine. By measuring fluorescence they were able to monitor the stability of the HIV stem-loop as different compounds were applied.…”