Discovery of a First-in-Class Murine Double Minute 2-Recruiting Positive Transcription Elongation Factor B PROTAC Degrader With Selective Antitumor Activity

Abstract

The positive transcription elongation factor b (P-TEFb) complex, composed of CDK9 and cyclin T isoforms (T1, T2a and T2b), is critical for gene transcription, positioning CDK9 as a very promising oncology target. However, the development of selective and clinically effective small-molecule CDK9 inhibitors has proven challenging. To overcome this limitation, we designed a series of highly efficient and selective P-TEFb degraders by conjugating the CDK9 inhibitor SNS032 with the mouse double minute 2 (MDM2) ligand RG7388. Our lead compound, 13 (dCDK9-010), recruits the MDM2 E3 ligase to induce proteasome-dependent degradation of CDK9 and all cyclin T isoforms across diverse cancer models. dCDK9-010 potently inhibits RNA polymerase II carboxy-terminal repeat domain phosphorylation and blocks MDM2-mediated p53 degradation, resulting in concurrent p53 pathway activation. This dual mechanism drives selective cytotoxicity in TP53 wild-type cancer cells, sparing TP53-mutant or nonmalignant cells. In murine xenograft models of lung cancer and Ewing sarcoma, intravenous dCDK9-010 administration significantly inhibited tumor growth while demonstrating an excellent safety profile. Collectively, this study establishes dCDK9-010 as a first-in-class, selective MDM2-recruiting P-TEFb degrader. By enabling the elimination of the entire P-TEFb complex, this MDM2-recruiting degradation strategy expands the toolkit for targeting CDK9 and represents a promising new therapeutic paradigm for TP53 wild-type cancers.

Keywords

anti-cancer / cyclin T / cyclin-dependent kinase 9 / mouse double minute 2 / positive transcription elongation factor B / proteolysis targeting chimera

References

[1] M. A. Toure, K. Motoyama, Y. C. Xiang, et al., “Targeted Degradation of CDK9 Potently Disrupts the MYC-Regulated Network,” Cell Chemical Biology 32, no. 4 (2025): 542–555.

[2] T. Z. Wu, J. L. Huang, X. K. Zhang, et al., “Rational Design of a Potent, Selective, and Metabolically Stable CDK9 Inhibitor to Counteract Osimertinib Resistance Through Mcl-1 Suppression and Enhanced BRD4 Co-Targeting,” Journal of Medicinal Chemistry 68, no. 4 (2025): 4929–4950.

[3] N. Puleo, H. Ram, M. L. Dziubinski, et al., “Identification of a TNIK-CDK9 Axis as a Targetable Strategy for Platinum-Resistant Ovarian Cancer,” Molecular Cancer Therapeutics 24, no. 4 (2025): 639–656.

[4] Z. Xu, Y. F. Geng, L. X. Guan, et al., “Discovery of a Highly Potent, Selective, and Stable D-Amino Acid-Containing Peptide Inhibitor of CDK9/Cyclin T1 Interaction for the Treatment of Prostate Cancer,” European Journal of Medicinal Chemistry 285 (2025): 117248.

[5] G. J. Hanna, G. M. Cote, R. Chugh, et al., “Safety and Efficacy of a Selective Inhibitor of Cyclin-Dependent Kinase 9 (KB-0742) in Patients With Recurrent or Metastatic Adenoid Cystic Carcinoma,” Cancer Research Communications 5, no. 5 (2025): 767–773.

[6] Z. B. Shao, K. He, Y. B. Su, and Z. Shi, “Crosslink Among Cyclin-Dependent Kinase 9, ATP Binding Cassette Transporter G2 and Beclin 1 in Colorectal Cancer,” World Journal of Gastrointestinal Oncology 16, no. 12 (2024): 4778–4781.

[7] X. Xie, B. Y. Zhang, D. H. Li, et al., “Suppression of Microtubule Acetylation Mediates the Anti-Leukemic Effect of CDK9 Inhibition,” Cancer Cell International 24, no. 1 (2024): 396.

[8] C. H. Luo, L. H. Hu, J. Y. Liu, et al., “CDK9 Recruits HUWE1 to Degrade RARα and Offers Therapeutic Opportunities for Cutaneous T-Cell Lymphoma,” Nature Communications 15, no. 1 (2024): 10594.

[9] T. M. Liang, L. L. Luo, X. R. Xu, et al., “CDK9 Inhibitor Elicits APC Through a Synthetic Lethal Effect in Colorectal Cancer Cells,” Genes & Disease 12, no. 1 (2025): 101220.

[10] C. Hu, L. Shen, F. Zou, et al., “Predicting and Overcoming Resistance to CDK9 Inhibitors for Cancer Therapy,” Acta Pharmaceutica Sinica B 13, no. 9 (2023): 3694–3707.

[11] C. Mo, N. Wei, T. Li, M. A. Bhat, M. Mohammadi, and C. Y. Kuang, “CDK9 Inhibitors for the Treatment of Solid Tumors,” Biochemical Pharmacology 229 (2024): 116470.

[12] R. Rahman, M. H. Rahaman, A. R. Hanson, et al., “CDK9 Inhibition Constrains Multiple Oncogenic Transcriptional and Epigenetic Pathways in Prostate Cancer,” British Journal of Cancer 131 (2024): 1092–1105.

[13] Y. Mori, Y. Akizuki, R. Honda, et al., “Intrinsic Signaling Pathways Modulate Targeted Protein Degradation,” Nature Communications 15, no. 1 (2024): 5379.

[14] W. X. Lv, X. J. Jia, B. W. Tang, et al., “In Silico Modeling of Targeted Protein Degradation,” European Journal of Medicinal Chemistry 289 (2025): 117432.

[15] W. G. Xiang, L. J. Zhao, X. Han, et al., “Discovery of ARD-1676 as a Highly Potent and Orally Efficacious AR PROTAC Degrader With a Broad Activity Against AR Mutants for the Treatment of AR Plus Human Prostate Cancer,” Journal of Medicinal Chemistry 66, no. 18 (2023): 13280–13303.

[16] X. Han, L. J. Zhao, W. G. Xiang, et al., “Discovery of ARD-2051 as a Potent and Orally Efficacious Proteolysis Targeting Chimera (PROTAC) Degrader of Androgen Receptor for the Treatment of Advanced Prostate Cancer,” Journal of Medicinal Chemistry 66, no. 13 (2023): 8822–8843.

[17] X. Han and Y. Sun, “PROTACs: A Novel Strategy for Cancer Drug Discovery and Development,” MedComm 4, no. 3 (2023): e290.

[18] X. Han, W. Wei, and Y. Sun, “PROTAC Degraders With Ligands Recruiting MDM2 E3 Ubiquitin Ligase: An Updated Perspective,” Acta Materia Medica 1, no. 2 (2022), 244-259.

[19] Y. B. Wang, M. M. Wang, L. Ma, et al., “Identification of a Potent and Selective CDK9 Degrader as a Targeted Therapeutic Option for the Treatment of Small-Cell Lung Cancer,” Journal of Medicinal Chemistry 68, no. 3 (2025): 2528–2550.

[20] H. J. Nie, B. F. Li, J. Y. Sun, et al., “Discovery of a Potent, Selective and Orally Bioavailable CDK9 Degrader for Targeting Transcription Regulation in Triple-Negative Breast Cancer,” Bioorganic Chem 153 (2024): 107876.

[21] K. Wang, M. X. Jiang, H. M. Liu, C. Meng, M. Y. Li, and H. B. Lu, “Discovery of Novel Co-Degradation CK1α and CDK7/9 PROTACs With p53 Activation for Treating Acute Myeloid Leukemia,” Bioorganic Chemistry 147 (2024): 107319.

[22] S. Y. Zheng, Y. Chen, Z. P. Zhu, et al., “Exploiting Targeted Degradation of Cyclins and Cyclin-Dependent Kinases for Cancer Therapeutics: A Review,” Journal of Zhejiang University-SCIENCE B 26, no. 8 (2025): 713–739.

[23] Y. P. Zeng, J. Xiao, Y. X. Xu, et al., “Degradation of Cyclin-Dependent Kinase 9/Cyclin T1 by Optimized Microtubule-Associated Protein 1 Light Chain 3 Beta-Recruiting Coumarin Analogs,” Journal of Medicinal Chemistry 66, no. 18 (2023): 12877–12893.

[24] J. C. Li, T. Liu, Y. L. Song, et al., “Discovery of Small-Molecule Degraders of the CDK9-Cyclin T1 Complex for Targeting Transcriptional Addiction in Prostate Cancer,” Journal of Medicinal Chemistry 65, no. 16 (2022): 11034–11057.

[25] Y. Zhong, J. Xu, H. Y. Cao, et al., “First ATG101-Recruiting Small Molecule Degrader for Selective CDK9 Degradation via Autophagy-Lysosome Pathway,” Acta Pharmaceutica Sinica B 15, no. 5 (2025): 2612–2624.

[26] M. E. Matyskiela, G. Lu, T. Ito, et al., “A Novel Cereblon Modulator Recruits GSPT1 to the CRL4CRBN Ubiquitin Ligase,” Nature 535, no. 7611 (2016): 252–257.

[27] J. Krönke, N. D. Udeshi, A. Narla, et al., “Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells,” Science 343, no. 6168 (2014): 301–305.

[28] T. Ito, H. Ando, T. Suzuki, et al., “Identification of a Primary Target of Thalidomide Teratogenicity,” Science 327, no. 5971 (2010): 1345–1350.

[29] G. E. Winter, D. L. Buckley, J. Paulk, et al., “Phthalimide Conjugation as a Strategy for in Vivo Target Protein Degradation,” Science 348, no. 6241 (2015): 1376–1381.

[30] D. Zhang, S. H. Baek, A. Ho, H. Lee, Y. S. Jeong, and K. Kim, “Targeted Degradation of Proteins by Small Molecules: A Novel Tool for Functional Proteomics,” Combinatorial Chemistry & High Throughput Screening 7, no. 7 (2004): 689–697.

[31] D. L. Buckley, I. Van Molle, P. C. Gareiss, et al., “Targeting the von Hippel-Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1α Interaction,” Journal of the American Chemical Society 134, no. 10 (2012): 4465–4468.

[32] G. Y. Tang, X. L. Cao, J. Q. Chen, et al., “Repurposing MDM2 Inhibitor RG7388 for TP53-Mutant NSCLC: A p53-Independent Pyroptotic Mechanism via ROS/p-p38/NOXA/Caspase-3/GSDME Axis,” Cell Death & Disease 16, no. 1 (2025): 452.

[33] R. K. Acharyya, L. Y. Huang, A. Aguilar, et al., “MD-4251: A First-in-Class Oral MDM2 Degrader Inducing Complete Tumor Regression With Single-Dose Administration,” Journal of Medicinal Chemistry 68, no. 13 (2025): 13249–13267.

[34] C. L. Wang, W. T. Liu, H. T. Guo, T. Lan, T. Y. Wang, and B. Wang, “The Intrabody Against Murine Double Minute 2 via a p53-Dependent Pathway Induces Apoptosis of Cancer Cell,” International Journal of Molecular Sciences 26, no. 11 (2025): 5286.

[35] H. Y. Liu, L. Jing, Y. X. Li, et al., “Lipid Droplet-Organized MDM2-Mediated P53 Degradation: A Metabolic Switch Governing Diet-Driven Tumor Progression,” Advanced Science 12, no. 32 (2025): 19.

[36] A. Goerg, G. Piendl, V. Albert, O. Ortmann, A. K. Wege, and G. Brockhoff, “Mdm2 Targeting via PROteolysis TArgeting Chimeras (PROTAC) Is Efficient in p53 Wildtype, p53-Mutated, and Abemaciclib-Resistant Estrogen Receptor-Positive Cell Lines and Superior to mdm2 Inhibition,” BMC Cancer 25, no. 1 (2025): 978.

[37] H. A. Al-Hussaniy, A. I. Oraibi, Z. S. Al-Tameemi, A. H. Alburghaif, M. A. Naji, and F. A. Naji, “The Association of KRAS and P53 Gene Mutations and MDM2 Expression With the Occurrence of Colorectal Cancer,” Current Cancer Drug Targets (2025), https://doi.org/10.2174/0115680096349198250407100724.

[38] Y. Huang, W. Li, Y. K. Zhou, et al., “Strategies for p53 Activation and Targeted Inhibitors of the p53-Mdm2/MdmX Interaction,” Cells 14, no. 8 (2025): 583.

[39] A. Yousuf and N. Khan, “Targeting MDM2-p53 Interaction for Breast Cancer Therapy,” Oncology Research 33, no. 4 (2025): 851–861.

[40] E. Aptullahoglu, M. Howladar, J. P. Wallis, et al., “Targeting the MDM2-p53 Interaction With Siremadlin: A Promising Therapeutic Strategy for Treating TP53 Wild-Type Chronic Lymphocytic Leukemia,” Cancers 17, no. 2 (2025): 274.

[41] J. Hines, S. Lartigue, H. Q. Dong, Y. M. Qian, and C. M. Crews, “MDM2-Recruiting PROTAC Offers Superior, Synergistic Antiproliferative Activity via Simultaneous Degradation of BRD4 and Stabilization of p53,” Cancer Research 79, no. 1 (2019): 251–262.

[42] A. Bricelj, C. Steinebach, R. Kuchta, M. Gutschow, and I. Sosic, “E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points,” Frontiers in Chemistry 9 (2021): 707317.

[43] A. R. Schneekloth, M. Pucheault, H. S. Tae, and C. M. Crews, “Targeted Intracellular Protein Degradation Induced by a Small Molecule: En Route to Chemical Proteomics,” Bioorganic & Medicinal Chemistry Letters 18, no. 22 (2008): 5904–5908.

[44] Q. Y. Zhao, T. L. Lan, S. Su, and Y. Rao, “Induction of Apoptosis in MDA-MB-231 Breast Cancer Cells by a PARP1-Targeting PROTAC Small Molecule,” Chemical Communications 55, no. 3 (2019): 369–372.

[45] B. S. Zhao and K. Burgess, “TrkC-Targeted Kinase Inhibitors and PROTACs,” Molecular Pharmaceutics 16, no. 10 (2019): 4313–4318.

[46] S. P. He, J. H. Ma, Y. X. Fang, et al., “Homo-PROTAC Mediated Suicide of MDM2 to Treat Non-Small Cell Lung Cancer,” Acta Pharmaceutica Sinica B 11, no. 6 (2021): 1617–1628.

[47] A. C. Qin, H. Jin, Y. Song, et al., “The Therapeutic Effect of the BRD4-Degrading PROTAC A1874 in Human Colon Cancer Cells,” Cell Death & Disease 11, no. 9 (2020): 805.

[48] M. P. Ficu, D. Niculescu-Duvaz, M. Aljarah, C. S. Kershaw, and C. J. Springer, “Hijacking the MDM2 E3 Ligase With Novel BRD4-Targeting Proteolysis-Targeting Chimeras in Pancreatic Cancer Cells,” Chembiochem 26, no. 13 (2025): e202500133.

[49] C. M. Olson, B. S. Jiang, M. A. Erb, et al., “Pharmacological Perturbation of CDK9 Using Selective CDK9 Inhibition or Degradation,” Nature Chemical Biology 14, no. 2 (2018): 163–170.

[50] L. Ma, L. Xie, Y. Wang, et al., “Discovery of dCDK9-202 as a Highly Potent and Selective PROTAC CDK9 Degrader With Strong in Vivo Antitumor Activity,” Journal of Medicinal Chemistry 68, no. 20 (2025): 21172–21186.

[51] R. K. Lin, J. Yang, T. Liu, et al., “Discovery of HyT-Based Degraders of CDK9-Cyclin T1 Complex,” Chemistry and Biodiversity 20, no. 8 (2023): e202300769.

[52] Y. Xiong, Y. Zhong, H. Yim, et al., “Bridged Proteolysis Targeting Chimera (PROTAC) Enables Degradation of Undruggable Targets,” Journal of the American Chemical Society 144, no. 49 (2022): 22622–22632.

RIGHTS & PERMISSIONS

2026 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.