Rapid-Kinetics Degron Benchmarking Reveals Off-Target Activities and Mixed Agonism-Antagonism of MYB Inhibitors

Attenuating aberrant transcriptional circuits holds great promise for the treatment of numerous diseases, including cancer. However, development of transcriptional inhibitors is hampered by the lack of a generally accepted functional cellular readout to characterize their target specificity and on-target activity. We benchmarked the direct gene-regulatory signatures of six agents reported as inhibitors of the oncogenic transcription factor MYB against targeted MYB degradation in a nascent transcriptomics assay. The inhibitors demonstrated partial specificity for MYB target genes but displayed significant off-target activity. Unexpectedly, the inhibitors displayed bimodal on-target effects, acting as mixed agonists-antagonists. Our data uncover unforeseen agonist effects of small molecules originally developed as TF inhibitors and argue that rapid-kinetics benchmarking against degron models should be used for functional characterization of transcriptional modulators. ### Competing Interest Statement A. Koehler is a founder, board of directors/SAB member and/or consultant for 76Bio, AstraZeneca, Enveda Biosciences, Flagship Pioneering, Kronos Bio, MS2Array, Nested Therapeutics, ORIC Pharmaceuticals, Photys Therapeutics, Vicinitas Therapeutics; received grant/research support from Bayer, GSK, Janssen, Ono, Pfizer; a significant stockholder in 76Bio, Invaio Sciences, Kronos Bio, Nested Therapeutics, Photys Therapeutics, Sigilon Therapeutics, Vicinitas Therapeutics. K. Stegmaier has funding from Novartis Institute of Biomedical Research, consults for and has stock options in Auron Therapeutics, and has consulted for Kronos Bio and AstraZeneca on topics unrelated to this work. B. Nabet is an inventor on patent applications related to the dTAG system (WO/2017/024318, WO/2017/024319, WO/2018/148440, WO/2018/148443 and WO/2020/146250). K. Eagle has consulted for Flare Therapeutics in support of their work on small molecules targeting TFs. All other authors declare no potential conflict of interest.