A New Paradigm for HIV Treatment: Targeted Degradation of HIV Reverse Transcriptase via the Ubiquitin-Proteasome Pathway

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PROJECT SUMMARY/ABSTRACT In accordance with RFA-AI-19-072, Novel Therapeutics Directed to Intracellular HIV Targets, we propose using targeted protein degradation (TPD) against the essential HIV reverse transcriptase (RT). The RFA states “Controlling protein function by controlling intracellular protein levels has evolved as a promising and novel therapeutic strategy. This can be achieved by the targeted degradation of intracellular proteins thru the ubiquitin- proteasome pathway.” Heterobifunctional targeted protein degraders (TPDs) are being actively pursued as enhancers of proteasomal destruction of proteins specifically associated with several cancers. Such agents offer advantages over traditional occupancy-based inhibitors including a unique catalytic mechanism of action, greater target selectivity, and a reduced probability for resistance development. Surprisingly, this promising therapeutic modality has only recently been applied to antiviral drug discovery through a successful Telapravir-based TPD effective against the wild type and resistant forms of the HCV protease. Analysis of reported HIV-1 drug-bound structures suggests that the essential viral RT should be readily adaptable to targeted protein degradation. The potent and clinically used HIV-1 RT inhibitor (RTI), Rilpivirine (RPV) binds the RT site in Gag-Pol and also allosterically inhibits p66/p51 RT function by binding the non-nucleoside-RTI (NNRTI) Binding Pocket (NNIBP) on the p66 subunit. RPV is amenable to conjugation with linkers and ubiquitin E3 ligase recruiting ligands to serve in the design and preparation of prototype HIV-1 RT TPDs. The OBJECTIVE of this study is to show proof-of-concept of a new inhibitory mechanism by which HIV-1 RT can be targeted for degradation, impairing HIV infectivity and replication. Importantly, due to TPDs’ unique mechanism of action, even a low- affinity RT/TPD interaction will likely lead to effective target degradation. Thus, we pose the HYPOTHESIS that RPV-based TPDs will not only augment inhibition against HIV-1 with RTI-sensitive RT but will remain effective against RTI-resistant RT variants. Ultimately, this approach can reduce resistance development and potentially extend regimen lifetimes in the fight against HIV disease. The objective of AIM 1 is to design and prepare RPV- based TPDs built on state-of-the-art computational methods and predictive physicochemical properties currently accepted for in vivo active TPDs. In AIM 2, we will screen the two series of TPDs for antiviral activity in complementary in vitro models of HIV-1 single-round infection (in the TZM-bl assay), and of replication (in primary CD4+ T lymphocytes). The IMPACT of the discovery of targeted HIV-1 RT degraders that limit infectivity and replication through a mechanism distinct from occupancy-based HIV-1 RTIs will be the identification of agents that are effective against RTI-resistant HIV strains and that limit RTI susceptibility to viral resistance development. Grandly, this research will demonstrate that TPD approaches can be superior in the treatment of HIV disease and will set the stage for the advancement of TPDs against other HIV targets with improvements in the prevention of resistance development and with concomitant enhanced clinical treatment outcomes.