CDK12 condensation in nuclear speckles confers sensitivity to cyclin K molecular glue degraders

Ye, K.; He, Q.; Cheng, Y.; Zhang, M.; Mu, H.; Cai, M.-C.; Zhou, S.; Xiang, H.; Hou, Y.; Li, Y.; Zang, Y.; Lv, J.; Cheng, L.; Xiang, L.; Zhao, D.; Zhang, Y.; Yin, X.; Di, W.; Shen, P.; Zhuang, G.; Tan, L.

doi:10.1101/2025.03.31.646293

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bioRxiv · 10.1101/2025.03.31.646293

CDK12 condensation in nuclear speckles confers sensitivity to cyclin K molecular glue degraders

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Abstract

Transcriptional machinery often operates in the configuration of biomolecular condensates, presenting emerging opportunities to develop therapies targeting transcriptionally addicted malignancies. In this study, we discovered that cyclin-dependent kinase 12 (CDK12), a key regulator of transcription elongation, formed dynamic liquid-like droplets within nuclear speckles, a process enhanced by high CDK12 expression and CDK12 inhibitor treatment. Recognizing this unique property, we rationally designed ZSQ253, a modular cyclin K molecular glue degrader that coupled binding moieties for both CDK12 and DDB1. By promoting phase separation-driven assembly and subsequent proteasomal degradation of the CDK12-cyclin K complex, ZSQ253 interfered with oncogenic transcription and demonstrated potent antitumor capability. Further structure-guided optimization yielded HQY1428, a derivative with a multi-site gluing effect and improved drug activity. Given the frequent genomic co-amplification of CDK12 and ERBB2 across diverse human cancers, we showed that combining HQY1428 with HER2 inhibitors provided synergistic therapeutic benefits. Collectively, our findings establish CDK12 condensation within nuclear speckles as an exploitable vulnerability, and introduce a novel mechanism of action underlying cyclin K molecular glue degraders.

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Ye, K., He, Q., Cheng, Y., Zhang, M., Mu, H., Cai, M.-C., Zhou, S., Xiang, H., Hou, Y., Li, Y., Zang, Y., Lv, J., Cheng, L., Xiang, L., Zhao, D., Zhang, Y., Yin, X., Di, W., Shen, P., Zhuang, G., Tan, L.. 2025-04-01. CDK12 condensation in nuclear speckles confers sensitivity to cyclin K molecular glue degraders. https://doi.org/10.1101/2025.03.31.646293

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