Predicting and overcoming resistance to CDK9 inhibitors for cancer therapy

Area of Science:

• Oncology
• Molecular Biology
• Drug Discovery

Background:

• Cyclin-dependent kinase 9 (CDK9) is crucial for cancer cell survival and is a target for anti-cancer drugs.
• Limited knowledge exists regarding drug resistance mechanisms to CDK9 inhibitors.

Purpose of the Study:

• To investigate acquired drug resistance to a selective CDK9 inhibitor in Acute Myeloid Leukemia (AML).
• To identify the molecular mechanisms underlying CDK9 inhibitor resistance.
• To discover novel therapeutic strategies to overcome CDK9 inhibitor resistance.

Main Methods:

• Established a resistant AML cell line using a CDK9 inhibitor (BAY1251152).
• Utilized genomic sequencing and CRISPR/Cas9 gene editing to identify and validate the CDK9 L156F mutation.
• Assessed the impact of the mutation on inhibitor binding, protein stability, and catalytic activity.
• Screened for novel compounds effective against both wild-type and mutant CDK9.

Main Results:

• Identified a novel CDK9 kinase domain mutation, L156F, conferring resistance to both ATP-competitive inhibitors and PROTAC degraders.
• The L156F mutation causes steric hindrance, impairing inhibitor binding and altering CDK9 protein stability and activity.
• Discovered a novel compound, IHMT-CDK9-36, with potent inhibitory activity against both wild-type and L156F mutant CDK9.

Conclusions:

• Reported a new mechanism of drug resistance mediated by the CDK9 L156F mutation.
• Demonstrated that the L156F mutation confers resistance to various CDK9 inhibitors.
• Presented IHMT-CDK9-36 as a promising chemical scaffold for developing next-generation CDK9 inhibitors effective against resistant mutations.