Predicting and overcoming resistance to CDK9 inhibitors for cancer therapy

Chen Hu; Lijuan Shen; Fengming Zou; Yun Wu; Beilei Wang; Aoli Wang; Chao Wu; Li Wang; Jing Liu; Wenchao Wang; Qingsong Liu

doi:10.1016/j.apsb.2023.05.026

Predicting and overcoming resistance to CDK9 inhibitors for cancer therapy

Acta Pharm Sin B. 2023 Sep;13(9):3694-3707. doi: 10.1016/j.apsb.2023.05.026. Epub 2023 May 26.

Authors

Chen Hu^{1

2}, Lijuan Shen^{1

3}, Fengming Zou^{1

2}, Yun Wu^{1

2}, Beilei Wang^{1

2}, Aoli Wang^{1

2}, Chao Wu⁴, Li Wang^{1

2}, Jing Liu^{1

3

2}, Wenchao Wang^{1

3

2}, Qingsong Liu^{1

3

2

5}

Affiliations

¹ Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
² Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
³ University of Science and Technology of China, Hefei 230026, China.
⁴ Tarapeutics Science Inc., Bengbu 233000, China.
⁵ Precision Medicine Research Laboratory of Anhui Province, Hefei 230088, China.

Abstract

Abnormally activated CDK9 participates in the super-enhancer mediated transcription of short-lived proteins required for cancer cell survival. Targeting CDK9 has shown potent anti-tumor activity in clinical trials among different cancers. However, the study and knowledge on drug resistance to CDK9 inhibitors are very limited. In this study, we established an AML cell line with acquired resistance to a highly selective CDK9 inhibitor BAY1251152. Through genomic sequencing, we identified in the kinase domain of CDK9 a mutation L156F, which is also a coding SNP in the CDK9 gene. By knocking in L156F into cancer cells using CRISPR/Cas9, we found that single CDK9 L156F could drive the resistance to CDK9 inhibitors, not only ATP competitive inhibitor but also PROTAC degrader. Mechanistically, CDK9 L156F disrupts the binding with inhibitors due to steric hindrance, further, the mutation affects the thermal stability and catalytic activity of CDK9 protein. To overcome the drug resistance mediated by the CDK9-L156F mutation, we discovered a compound, IHMT-CDK9-36 which showed potent inhibition activity both for CDK9 WT and L156F mutant. Together, we report a novel resistance mechanism for CDK9 inhibitors and provide a novel chemical scaffold for the future development of CDK9 inhibitors.

Keywords: Acquired resistance mutations; BAY1251152; CDK9 inhibitors; Single nucleotide polymorphisms; Transcription.