Targeting HIV transcription with RNA-binding small molecules

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Summary Combination antiretroviral therapy (cART) in current use is able to suppress HIV-1 to undetectable levels (<50 copies/mL), but unable to eliminate the provirus in latent CD4+ T cells. Thus, patients must remain under cART indefinitely or risk viral rebound if therapy is discontinued. The available anti-HIV drugs do not prevent transcription from provirus nor inhibit viral release from cellular reservoirs. A new class of anti-HIV drugs targeting transcription could buttress current cART due to its potential to block viral reactivation in latently infected CD4+ T cells, resulting in a state of deep-latency, followed by the continuous decay of this latent pool of cells over time. Eradication of the latent HIV reservoir could be achieved by employing disruptors of HIV’s TAR secondary structure, which would prevent binding of the Tat protein and other host factors required for transcription. We propose to identify small molecules that specifically bind and disrupt the apical loop or side bulge in HIV’s TAR hairpin that result in inhibition of the trans- activation of the viral promoter and virus replication. Vironika LLC has developed new methods and assays to identify small molecules which interact with structured viral RNA. For example, Vironika has developed applications of Homogeneous Time-Resolved Fluorescence (HTRF immunoassay), Alpha Screen (Donor/Acceptor beads) and thermocycler-based Fluorescence Resonance Energy Transfer (FRET), which enable high-throughput screening (HTS) of small molecules to identify inhibitors of HSV and EBV latent infection. Libraries containing novel and proprietary small molecules with potential for new medicinal chemistry will be screened using an RNA probe representing the TAR hairpin. Cell-based assays will be used to investigate the antiviral activity of selected hit compounds. The product that ultimately results from this proposal is a small molecule that selectively binds and disrupts the secondary structure of HIV’s TAR, thereby inhibiting the binding of TAT and/or P-TEFb which are required for viral expression. Safe, efficacious, small molecule agents targeting HIV TAR/Tat or TAR/P-TEFb interaction would inevitably change current clinical practice and possibly enable global control of this disease.