Abstract 3225: Profiling the DNA regulome to discover direct inhibitors of the brachyury transcription factor

Abstract

Abstract Background: The human genome encodes more than 1,600 transcription factors (TFs), along with additional cofactors, chromatin regulators, and structural proteins that collectively execute the regulatory instructions encoded within the nuclear DNA. Dysfunctions of these proteins, collectively known as the Regulome, are known to drive multiple conditions such as cancer, autoimmune conditions, and fibrosis. Despite their importance, many of these proteins are considered undruggable due to challenges in modeling their activity in vitro. Methods: We have addressed these shortcomings by implementing a live-cell Regulome profiling approach that quantifies the global activity of TFs without the need for cell manipulation or genome engineering, called TF-Scan. The technology coupled rapid, automated purification of the DNA-bound proteome coupled to scalable Data Independent Acquisition (DIA) quantitative mass spectrometry proteomics and machine learning. Results: We completed a screen of covalent compounds across 8 tissue types to discover hotspot sites on TFs that control their DNA-binding activity. A chordoma cell line was included in this screen. The screen identified compounds capable of binding to and disrupting the activity of several previously undruggable transcription factors, including brachyury. Hit validation and hit-to-lead medicinal chemistry resulted in a covalent chemical probe for brachyury, with activity in cell line models of chordoma. Conclusion: Phenotypic drug discovery in live, unmodified human cells with systematic regulome profiling enables the discovery of compounds that disrupt previously undruggable targets by multiple mechanisms of action. Citation Format: Alexander Joel Federation, Yang Gao, Brian McEllin, Tonibelle Gatbonton-Schwager, Andrea Gutierrez, Julia Robbins, Bodhi Hueffmeier, Erin Broderick, Daniele Canzani, William Fondrie, Lindsay Pino. Profiling the DNA regulome to discover direct inhibitors of the brachyury transcription factor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3225.