Chimeric Ligands for Induced Proximity (CLIP) platform for targeted proteome editing to treat severe alcoholic hepatitis

Abstract UbiquiTx is advancing a modular platform technology called chimeric ligands for induced proximity (CLIPs) to induce posttranslational modifications to proteins of interest that will help address the critical need for novel therapeutics. There is a critical need to leverage novel bioactive molecules that can achieve targeted protein modification, including addition and removal of ubiquitin to de-stabilize or stabilize proteins, respectively. It would be particularly advantageous to apply bioactive molecules to address alcoholic hepatitis (AH), a severe form of alcoholic liver disease that causes such severe damage to liver that the liver’s regenerative capacity is diminished. Current treatment for AH is corticosteroids, which is not an effective or long-term option. Although liver transplant is the most effective way to address AH, the organ donation list is long and many AH patients die while waiting for transplant. However, nuclear erythroid 2-related factor 2 (Nrf2), a regulator of anti-inflammatory and antioxidant gene expression, has become a therapeutic target of great interest for the treatment/prevention of liver diseases. The dysregulation of Nrf2 is correlated with chronic liver disease, and its activation has been shown to modulate gene expression to prevent oxidative and inflammatory disease in studies with ethanol induced hepatotoxicity in mice. UbiquiTx’s CLIPs comprise a computationally designed target recognition domain fused with a protein modification enzyme component of choice (e.g., ligases, kinases, deubiquitinates). This novel platform can be used to program the localization, binding, turnover, and activation of disease-relevant proteins currently considered “undruggable” by existing therapeutic modalities. In this Phase I SBIR project, UbiquiTx will develop and test deubiquitinating CLIPs (dubCLIPs) with the goal of enhancing Nrf2 activity through stabilization as a novel therapy for AH. To achieve this goal, the following aims will be completed: 1. Identify and optimize dubCLIPs that target and stabilize Nrf2 levels through a combination of in silico and in vitro approaches. Multiple AI/ML designed peptides will be designed and screened, then their binding will be validated to identify, characterize and optimize lead dubCLIPs consisting of the right guide peptide, linker, and deubiquitinase enzyme. Target binding activity (kinetics/affinity), effects on Nrf2 levels, downstream effects on antioxidant responsive genes (ARGs), and potential off-target effects in vitro will be evaluated. The potency, amplitude and duration of effect of the Nrf2-stabilizing dubCLIPs in cellular models of oxidative stress will also be determined to identify the top leads to advance. 2. Demonstrate in vivo target engagement for lead dubCLIP Nrf2 stabilizers. mRNAs encoding the lead dubCLIPs from Aim 1 will be packaged in lipid nanoparticles and administered to healthy mice to assess the pharmacokinetic (PK) parameters of dubCLIPs, including the stability and half-lives of the dubCLIP mRNA and protein in the target tissue and the in vivo levels of Nrf2 stabilization, downstream ARGs, and off-target effects.