Predicting and overcoming resistance to CDK9 inhibitors for cancer therapy

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.

Ligand- and structure-based pharmacophore modeling, docking study reveals 2-[[4-[6-(isopropylamino) pyrimidin-4-yl]-1H-pyrrolo[2,3-b] pyridin-6-yl] amino] ethanol as a potential anticancer agent of CDK9/cyclin T1 kinase

Objective: CDK9/Cyclin T1 kinase is a protein kinase, indirectly involved in the cell cycle progression in the form of transcription elongation, CDK9 specific inhibitors may be a potential alternative treatment not only for cancer but also other life-threatening diseases. Materials and Methods: Ligand-based and structure-based pharmacophore model was developed for discovering of the new anticancer agents. These models used as three-dimensional query for virtual screening against the chemical structure databases such as Maybridge HitFinder, MDPI, and ZINC. Subsequently, the potential hit compound was filtered by the ADMET and docking score. Results: After applying all filtration, 11 hits were found as potential hits based on good docking scores as well as good ADMET properties. Compound 2-[4-[6-(isopropylamino) pyrimidin-4-yl]-1H-pyrrolo[2,3-b] pyridin-6-yl] amino] ethanol was found to be most potent among all the potential hits. These hits could be used as an anticancer agent in near future. Conclusions: So many advances in the treatment of death leading diseases have been made over the past few decades, However, looking for the development in this research ligand-based and structure-based pharmacophore modeling was done, hit1 2-[4-[6-(isopropylamino) pyrimidin-4-yl]-1H-pyrrolo[2,3 b] pyridin-6 yl] amino] ethanol was found to be more potent and selective. It is understandable that these hits could be as selective and potent anticancer agents of cyclin-dependent kinase complex

Advances in research on a novel antitumor target CDK9 and its inhibitors / 中国药科大学学报

The cyclin-dependent protein kinase 9 (CDK9) is a member of the family of cyclin-dependent protein kinases.Different from other CDKs,CDK9 mainly works on the transcription regulation and has no affects on the cell cycle progress.There are many kinds of CDK9 inhibitors in the clinical research.The detailed structure and action mechanism of CDK9,its difference of protein structure from other CDKs,several selective or nonselective CDK9 inhibitors,as well as their structure-activity relationship (SAR) are discussed in this paper.

Design and discovery of novel small-molecule inhibitor of CDK9 / 中国药理学通报

Aim To look for novel small-molecule inhibitors of CDK9 through structure-based virtual screening and biological activity determination.Methods Homology modeling of CDK9 was based on the 3-D structure of other cyclin-dependent kinase family members,and then virtual screening by DOCK(molecular docking)of database of small molecule was carried on.MTT method was used in inhibition of tumor cell growth in vitro,while Western blot was used for further study of molecular mechanisms.Results From the top 1000 compounds with the best DOCK energy score,27 compounds were selected for biological assay based on the diversity of chemical structure and functional group.12 of 27 selected compounds showed significantly inhibition activity on tumor cell proliferation,and only one compound in 12 with half-maximum inhibition concentration(IC50)values less than 20 ?mol?L-1 named C-21 was selected for further molecular mechanism study.The western blotting data showed C-21 compound could effectively inhibit CDK9 from phosphorylating large subunit C-terminal of RNA polymerase Ⅱ in a dose-dependent manner.Conclusions Through homology modeling,virtual screening by computer,determination of biological activity and experimental studies of molecular mechanism,a new promising lead compound targeted for CDK9 was found and confirmed.