Chimeric Ligands for Induced Proximity (CLIP) platform for targeted proteome editing and upregulation of antigen presentation

Abstract UbiquiTx is developing a programmable, modular therapeutic platform for the direct modification of proteins of interest (POIs). Leveraging advances in artificial intelligence, protein engineering, and mRNA as a therapeutic modality, this platform allows for the engineering of enzymes to precisely recognize and ‘edit’ POIs by installing/removing post-translational modifications (PTMs). As one therapeutic application for this technology, UbiquiTx seeks to enhance the immune targeting of diseased cells through the upregulation of selective antigen presentation on the cell surface. T cells play a central role in immunosurveillance against viruses, other intracellular pathogens, and cancers by recognizing short peptides presented by major histocompatibility complex (MHC) class I molecules. These antigenic peptides are generated from proteins processed through the ubiquitin-proteasome system, then loaded onto MHC I molecules and transported to the cell surface for immunosurveillance. Global downregulation of antigen presentation on the cell surface is a major mechanism by which cells escape this immune surveillance, allowing diseased cells to proliferate. Thus, overcoming MHC-I downregulation and restoring antigen presentation represents a promising avenue for enhancing the efficacy of and patient response to immune-based therapies. UbiquiTx’s Chimeric Ligands for Induced Proximity (CLIPs) comprise a computationally designed guide peptide targeting a specific POI that is fused with a protein modification enzyme component. Preliminary data has provided compelling proof-of-concept, demonstrating the platform ability to design high-affinity peptide binders to POIs, that swap out modification enzymes and deliver CLIPs as an mRNA therapeutic using a lipid nanoparticle (LNP) vehicle. In this Phase I project, UbiquiTx will utilize the platform to upregulate the presentation of disease-associated peptide antigens by MHC-I, enhancing the immune surveillance of diseased cells. CLIPs will be designed and evaluated to promote the degradation of three key POIs: WT1, PRAME, and E7. WT1 is an intracellular, oncogenic transcription factor present in a wide range of leukemias and solid cancers, while PRAME is a cancer-testis antigen that provides a target for immunotherapy in acute myeloid leukemia. E7 is a human papillomavirus (HPV)-derived protein and target for the treatment of HPV-driven cancers. Evaluating these targets will demonstrate UbiquiTx’s platform modularity, ability to target proteins with variable expression, as well as degrade endogenous host- and virus-derived oncogenic proteins. The proposed Specific Aims are: 1. Develop and characterize ubiquitinase CLIPs (ubiCLIPs) for WT1, PRAME, and E7 and perform in vitro characterization to assess target engagement and protein degradation. 2. Evaluate WT1 antigen presentation and recognition by TCRm. UbiquiTx’s collaborator, Dr. David Scheinberg, will assess the effect of the top performing WT1 ubiCLIPs on peptide MHC (pMHC) presentation and recognition by TCRm in relevant cell lines; also, the effects on the immunopeptidome will be measured, with emphasis on target peptides and related proteins.