Abstract 6981: Discovery and optimization of purine-based CDK11 inhibitors for the treatment of Ewing’s sarcoma

Abstract RNA splicing, the process of intron removal from pre-mRNA, is a fundamental step in gene expression regulation mediated by the spliceosome. In Ewing’s sarcoma, driven by the EWS-FLI1 fusion transcription factor, splicing is essential for generating in-frame fusion transcripts. Cyclin-dependent kinase 11 (CDK11) has been identified as a bona fide kinase responsible for phosphorylating SF3B1, a core component of the U2 snRNP. Both CDK11 and SF3B1 are crucial for EWS-FLI1 pre-mRNA maturation, with inhibition of either impairing splicing and disrupting downstream oncogenic target expression, revealing key therapeutic vulnerabilities in Ewing’s sarcoma. These vulnerabilities offer novel therapeutic strategies to target EWS-FLI1-driven malignancy. We have employed structure-based drug design to develop a novel series of purine-based CDK11 inhibitors. Subsequently, machine learning-based quantitative structure activity relationship (QSAR) modeling was employed to optimize the dataset by identifying key structural features correlated with CDK11 activity, enabling a more focused refinement of the inhibitor series. Differential scanning fluorimetry confirmed preferential binding of one series of stereoisomers, indicating a potential for enhanced selectivity across the kinome. Furthermore, radiometric kinase assays further validated the inhibition of CDK11 functional activity. Biochemical and cell-based assays, including NanoBRET target engagement and CellTiter-Glo viability assays were performed to triage compounds. These efforts aim to identify potent and selective CDK11 inhibitors, ultimately advancing our understanding of CDK11's role in Ewing’s sarcoma and its therapeutic potential. Citation Format: Nada Elkholy, Pompom Ghosh, Hannah Walker-Mimms, Luxin Sun, Dylan Grassie, Ernst Schonbrunn, Derek Duckett, Andrii Monastyrskyi. Discovery and optimization of purine-based CDK11 inhibitors for the treatment of Ewing’s sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6981.