Selective inhibition of CDK9 in triple negative breast cancer

Abstract

Targeted therapy for triple-negative breast cancers (TNBC) remains a clinical challenge due to tumour heterogeneity. Since TNBC have key features of transcriptionally addicted cancers, targeting transcription via regulators such as cyclin-dependent kinase 9 (CDK9) has potential as a therapeutic strategy. Herein, we preclinically tested a new selective CDK9 inhibitor (CDDD11-8) in TNBC using cell line, patient-derived organoid, and patient-derived explant models. In vitro, CDDD11-8 dose-dependently inhibited proliferation (IC50 range: 281–734 nM), induced cell cycle arrest, and increased apoptosis of cell lines, which encompassed the three major molecular subtypes of TNBC. On target inhibition of CDK9 activity was demonstrated by reduced RNAPII phosphorylation at a CDK9 target peptide and down-regulation of the MYC and MCL1 oncogenes at the mRNA and protein levels in all cell line models. Drug induced RNAPII pausing was evident at gene promoters, with strongest pausing at MYC target genes. Growth of five distinct patient-derived organoid models was dose-dependently inhibited by CDDD11-8 (IC50 range: 272–771 nM), including three derived from MYC amplified, chemo-resistant TNBC metastatic lesions. Orally administered CDDD11-8 also inhibited growth of mammary intraductal TNBC xenograft tumours with no overt toxicity in vivo (mice) or ex vivo (human breast tissues). In conclusion, our studies indicate that CDK9 is a viable therapeutic target in TNBC and that CDDD11-8, a novel selective CDK9 inhibitor, has efficacy in TNBC without apparent toxicity to normal tissues.

Discovery of Orally Bioavailable and Potent CDK9 Inhibitors for Targeting Transcription Regulation in Triple-Negative Breast Cancer

“…Despite several significant advancements in targeting CDKs as novel approaches and promising treatment options against TNBC (Figure B,C; compound 1 – 6 − ), there remains a shortage of CDK9 modulators specifically designed for TNBC treatment, and most of these inhibitors either exhibit only moderate potency or target other subtypes of CDKs (especially CDK2, a cell cycle-related CDK with 40% sequence identity to CDK9). − For example, dinaciclib (also named SCH727965 or MK-7965), which progressed into three TNBC-related clinical trials (phase 1 or phase 2; ClinicalTrials.gov ID: NCT00732810, NCT01624441, NCT01676753), have similar inhibitory activity against CDK2 and CDK9 (IC 50 = 1 and 4 nM, respectively); fadraciclib (CYC065), being tested in an ongoing clinical trial on advanced solid tumors, including TNBC (phase 1/2; ClinicalTrials.gov ID: NCT04983810), also targets both CDK2 and CDK9 (IC 50 = 5 and 26 nM, respectively) . Indeed, off-target inhibition might result in side effects and unexpected toxicity, thereby narrowing the therapeutic window and compromising the potential for developing targeted therapeutics; principally, the development of selective inhibitors offers various benefits, including providing specific insight into the mechanism of action, refining patient selection criteria, and facilitating the establishment of a specific therapeutic window .…”

“…Indeed, our recent research demonstrates that selectively targeted degradation of CDK9 via Proteolysis Targeting Chimeras (PROTACs) can also effectively downregulate the downstream target MCL 1 - at the transcriptional level, leading to apoptosis in TNBC cells . While this endeavor is still at an early stage, recent studies by others and us have suggested that disrupting CDK9 activity led to effective inhibition of proliferation in both in vitro and in vivo TNBC models, ,− highlighting that targeting CDK9 holds promise for TNBC treatment.…”