Abstract Chordoma is a rare cancer arising from embryonic notochord remnants, most often in the sacrum and cervical spine. Although surgery and radiation are standard treatments, complete removal is frequently not possible and recurrence is common, leaving patients without effective targeted therapies. A defining molecular hallmark of chordoma is the aberrant reactivation of the transcription factor (TF) Brachyury (TBXT), a developmental regulator normally silenced in adult tissues. TBXT functions as a lineage-survival factor, driving tumor initiation and progression and establishing itself as both a diagnostic marker and compelling therapeutic target.However, TFs like TBXT are inherently difficult to drug due to their structural disorder and dependence on chromatin context. To overcome these barriers, we developed TF-Scan, a proteome-wide mass spectrometry platform that directly quantifies TF chromatin occupancy in live cells, enabling functional assessment and therapeutic targeting of TFs that were previously considered undruggable.Using TF-Scan, we discovered TAL61, a first-in-class covalent small-molecule hit that selectively binds TBXT and displaces it from chromatin. We initiated an iterative medicinal chemistry campaign, generating multiple analog series with improved covalent engagement, potency, and drug-like properties. Lead compounds strongly suppressed TBXT-dependent transcriptional programs and showed potent cytotoxicity in TBXT-expressing chordoma cell lines while sparing TBXT-negative controls. In vivo, optimized analogs produced robust tumor growth inhibition in UCH1 xenografts and the CF-365 patient-derived xenograft model, with excellent tolerability and durable pharmacodynamic activity.Transcriptomic analyses of TCGA, cBioPortal, and CRO datasets revealed aberrant TBXT expression in subsets of NECs, including Merkel Cell Carcinoma and Small Cell Lung Cancer. Ongoing work using cancer cell lines and patient-derived organoids is defining TBXT dependency in these diseases, suggesting that TBXT may serve as a broader lineage survival factor.Together, these results establish TF-Scan as a powerful TF drug discovery- platform and demonstrate the feasibility of pharmacologically targeting TBXT. Our covalent inhibitors show potent, selective antitumor activity in chordoma and point to new therapeutic opportunities in neuroendocrine cancers lacking targeted treatments. Citation Format: Gaelle Mercenne, Brian McEllin, Julia Robbins, Lindsay Pino, Gavin Hirst, Alexander Joel Federation. Targeting Brachyury with small molecules: A new therapeutic paradigm for chordoma and neuroendocrine carcinomas abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 432.
Mercenne et al. (Fri,) studied this question.