Abstract B047: Discovery of a covalent inhibitor targeting PAX8-driven ovarian cancer

Abstract The paired box (PAX) family of transcription factors plays critical roles in embryonic development but is largely silenced in most adult tissues. Among them, PAX8 has emerged as a lineage-specific oncogenic driver in uterine and ovarian cancers – tumor types characterized by high incidence, limited therapeutic options, and poor clinical outcomes. Genetic knockout and knockdown studies have consistently demonstrated strong anti-tumor activity across diverse ovarian cancer cell lines, firmly establishing PAX8 as a as a critical dependency in these malignancies. As a lineage-restricted transcription factor, PAX8 regulates the expression of critical oncogenes such as FGF18 and CCNA2, and its elevated activity correlates with poor patient prognosis, highlighting its potential as a compelling therapeutic target with a favorable safety profile due to its limited expression in normal adult tissues. Despite its therapeutic potential, PAX8 has long been considered “undruggable” due to the absence of well-defined small-molecule binding pockets and its dependence on DNA binding for function. To overcome this challenge, we applied BridGene’s proprietary IMTAC™ (Isobaric Mass Tagged Affinity Characterization) platform and identified PAX8 covalent binders targeting PAX8 in live cell screening. This approach led to the discovery of a hit compound, which was further optimized through structure–activity relationship (SAR) studies to yield BGP-31609 with enhanced potency, selectivity, and drug-like properties. BGP-31609 irreversibly binds to a single, functionally critical cysteine residue within the DNA-binding domain of PAX8, thereby providing a novel, targeted mechanism of action against this historically undruggable transcription factor. In a series of biochemical and cellular assays, BGP-31609 demonstrated robust on-target activity with minimal off-target concern. It showed dose-responsive inhibition of DNA binding in Electrophoretic mobility shift assay (EMSA), and inhibited PAX8 driven transcription activity in TPO-luciferase reporter assay, while has minimum effects in ERK driven SRE-luciferase reporter assay. In viability assays, it selectively reduced growth of PAX8-high OVCAR3 cells, while showing no effect on PAX8-negative A549 cells. Gene expression analysis by qPCR revealed suppression of PAX8 target genes in OVCAR3 cells. Together, these findings establish BGP-31609 as a mechanistically validated hit compound that covalently binds PAX8 at a single site and impairs its transcriptional function and tumor cell proliferation. BridGene is actively advancing BGP-31609 to further enhance its potency, selectivity, and druggability, aiming for a novel therapy for PAX8-dependent cancers. Citation Format: Yining Hao, Steve Luo, Maryam Quraishi, Ian Wang, Vivian Zhang, Monica M. Kangussu-Marcolino, Rajani Ravishankar, Iris Dong, Jingyu Dong, Anna Chen, Ning Deng, Ping Cao, Shirley Guo. Discovery of a covalent inhibitor targeting PAX8-driven ovarian cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr B047.