Abstract 3011: Novel CDK12 inhibitors with preclinical anti-tumor activity and best-in-class profile on HER2 low breast cancer patient samples
Authors: Chandan Seth Nanda, Maria New, Angela Velentza-Almpani, Julio Martinez-Torres, Nourdine K. Bah, Niamh A. Leonard, Farah A. Sangkolah, Keqian K. Nan, Eleonora Peerani, Duleek Ranatunga
Journal: Cancer Research (2025)

Abstract CDK12 is an oncogenic ATP-dependent kinase that participates in transcriptional regulation by directly phosphorylating RNApol-II when in complex with cyclin K. Overexpression or amplification of CDK12 is associated with hyper-transcription including upregulation of DNA damage repair enzymes (e.g., RAD51) which then interact with BRCA1, BRCA2 and modulate genomic instability (CDK12 directly phosphorylates cycE1 in the pre-replication complex) and induce uncontrolled cellular proliferation. Immunohistochemistry (IHC) experiments have shown high expression of CDK12 in multiple solid tumors and is associated with poor prognosis. Genomic or chemical inhibition of CDK12 reduces cancer cell proliferation in vitro and in vivo. A series of novel CDK12 inhibitors were designed, synthesized and screened in a panel of efficacy, selectivity, safety/toxicity, target engagement and functional assays. PB301, PB316, PB325 and PB338 were identified as lead reversible inhibitors exhibiting high on-target potency and low off-target inhibition (non-transcriptional CDKs e.g., CDK2, CDK4, CDK6). For instance, PB325 and PB301 were, respectively, ∼800x and 16x more potent than SY-143 (a selective CDK12/13 inhibitor) in 2D cell proliferation assays on a panel of cancer cell lines (e.g., IC50 of 0.1nM for PB325, 5nM for PB301 and 81nM for SY-143 on CAL51 cell line). Moreover, in efficacy assays, the median IC50 for PB316 was 42.99nM (n=7 cell lines), 66.4nM (n=10 patient-derived organoids) and 51.25nM (N=10 primary breast microtumors). Based on this, 50nM was chosen as the CDK12i dose to be tested as an exploratory drug (monotherapy and combo therapy) using fresh ex vivo tissue samples from patients enrolled in the observational clinical trial PEAR-TNBC (NCT05435352) to identify potential combination drug partners and compare drug efficacy to standard-of-care neoadjuvant therapies. Using in vivo models, good bioavailability, plasma and tissue distribution was observed in PK/PD studies upon oral dosing for all the lead compounds in Balb/c mice and key biomarkers like RNApol-II pSer2 and RAD51 showed significant decrease upon successful inhibition of CDK12 in vitro and in vivo. Moreover, our novel compounds demonstrated efficacy in reducing tumor burden in xenografted Balb/c mice (SUM149PT cell line) with once/twice-daily oral dosing. In summary, we identified a novel series of CDK12 inhibitors which have drug-likeness and high therapeutic potential in solid tumors. Our lead compounds have been assessed and carefully selected using our precision medicine platform to highlight drug molecules that can treat fresh tumor samples as a monotherapy and in combination with standard of care therapeutics. These molecules will be investigated further to nominate a development candidate and commence IND-enabling studies. Citation Format: Chandan Seth Nanda, Maria New, Angela Velentza-Almpani, Julio Martinez-Torres, Nourdine K. Bah, Niamh A. Leonard, Farah A. Sangkolah, Keqian K. Nan, Eleonora Peerani, Duleek Ranatunga. Novel CDK12 inhibitors with preclinical anti-tumor activity and best-in-class profile on HER2 low breast cancer patient samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3011.