Application of HIV-1 viral protein R-derived-peptides as new E3 ligase-binding components of BRD4 degraders

Abstract

Proteolysis targeting chimeras (PROTACs) have become a new modality for drug development of particular importance for cancer chemotherapy. PROTACs are composed of a ligand that binds to the protein of interest (POI) tethered by a linker to a ubiquitin E3 ligase-binding motif. These molecules can degrade the POI by ubiquitination and subsequent digestion using the ubiquitin-proteasome system (UPS). Although more than six hundred E3 ligases are encoded in human genome, only a small number are currently utilized by PROTACs. Because the expression levels and activities of E3 ligases vary among the cell lines, it can be advantageous to develop PROTACs that utilize new E3 ligase-binding components. In our current work we report new E3 ligase-binding ligands that employ viral protein R (Vpr), an accessory protein of the human immunodeficiency virus type-1 (HIV-1). Vpr can bind to both the E3 ligase complex, Cul4A-DDB1-DCAF1 and host proteins, such as UNG2 and facilitate host protein degradation via the UPS. We envisioned that Vpr fragments may function in PROTACs as new E3 ligase-binding ligands. Herein, we designed, synthesized and evaluated bromodomain 4 (BRD4)-targeting PROTACs (BRD4-PROTACs) that employ a well-known BRD4 inhibitor (JQ1) as a warhead and Vpr-derived peptides as the E3 ligase-binding ligands. We successfully demonstrate that the Vpr-derived peptides can function as E3 ligase-targeting ligands for PROTAC development. We also evaluated PROTACs based on the HIV-1 latency-reversing activity of JQ-1. The chemical degraders are less effective than the parent inhibitor as a latency-reversing agent (LRA). However, the low cytotoxicity of the new peptidic PROTACs allowed the compounds to be tolerated at high does, leading to potent LRA activity.