Advancing Protein Stabilization Therapeutic Development and DUBTAC Drug Discovery through Gene and Cell Engineering

Genetically modified cell models accelerate the development of safe and effective therapeutics, making them indispensable in the quest for new drugs. Through manipulation of cell line genetics, disease models can be faithfully replicated to screen and evaluate potential drug candidates. In particular, genetically engineered cell lines are essential for induced-proximity-based small-molecule drug discovery, enabling the expression of protein targets or disease-related proteins within cells. This facilitates the tracking of intracellular target engagement by protein ligands and monitoring changes in target abundance or modifications resulting from induced ternary complexes.

At Vicinitas Therapeutics, our vision centers around our proprietary Deubiquitinase Targeting Chimera (DUBTAC) platform, which aims to restore the levels of aberrantly degraded proteins that cause diseases, thereby conferring therapeutic benefits. To develop differentiated disease therapies based on our targeted protein stabilization platforms, cell lines are modified with lentivirus, transposon, and CRISPR to stably express specific proteins or variants involved in disease pathogenesis, such as tumor suppressors or mutated proteins causing genetic disorders. This allows us to study their effects, screen potential small-molecule drugs, and prevent their degradation.

Simultaneously, genetically engineered cell lines enable the utilization of multiple genetic and chemogenetic approaches to enforce proximity between target proteins and protein stabilization machinery. We employ a tagging system, iDimerize from Takara, which relies on FKBP-FRB-Rapamycin ternary, to stably express tagged protein targets and deubiquitinases in a selected tool cell line. By crossing the list of target proteins and deubiquitinases, we create a matrix that serves as a high-throughput assay system, capable of running hundreds of unique pairings concurrently. The resulting target stabilization and protein abundance change acts as a mimetic of induced proximity by future small-molecule DUBTACs. These proof-of-concept (PoC) studies play pivotal roles in early discoveries, aiding in target selection and validation.

Deubiquitinases reverse the effects of ubiquitination-dependent protein degradation via proteasome and lysosome, by cleaving the peptide or isopeptide bond between ubiquitin and its substrate protein. And a heterobifunctional molecule composed of target protein ligand, a linker, and a deubiquitinase recruiter ligand, facilitates the formation of an active ternary complex that leads to deubiquitination and restoration of target protein stability. Through genetic engineering of the cell model, we have developed cell-based assays that analyze the Mochenism-of-Action of DUBTAC and its chemogenetic mimetics. These assays utilize reporter cell lines and operate in heterogeneous systems that can be easily adapted into high-throughput workflows. They are able to quantify the intracellular target engagement or ligand binding, ubiquitination or deubiquitination, and ternary complex formation. These MoA studies provide a comprehensive understanding of DUBTAC function, guiding lead discovery and optimization of drug candidates.
By harnessing genetically engineered cell lines, the above approaches hold promise for drug discovery of diseases such as cancer and monogenic disorders, where the restoration of protein stability and function is crucial for therapeutic benefit. Vicinitas Therapeutics aims to overcome the challenge of targeting "undruggable" or intractable proteins, ultimately bringing about novel disease therapies that were previously inaccessible.

Learning Objectives:

• Vicinitas Therapeutics utilizes gene and cell engineering to develop differentiated disease therapies by stably expressing disease-related proteins and screening small-molecule drugs that prevent protein degradation.
• Genetically engineered cell lines facilitate induced-proximity-based small-molecule drug discovery by expressing disease-related proteins and tracking target engagement and ternary complex formation.