Targeting CDK7-dependent transcriptional addiction with novel, orally available small molecule inhibitor shows efficacy in pancreatic cancer models

Purpose: Many cancers are addicted to oncogenic super-enhancers that drive expression of oncogenes such as Myc. Super-enhancers are a class of regulatory regions that are associated with a strong enrichment of transcriptional coactivators (MED1, BRD4) and chromatin marks (H3K27Ac). Importantly, majority of super-enhancers depend on the ability of cyclin-dependent kinase 7 (CDK7) to initiate transcription by phosphorylating the C-terminal domain of RNA Pol II. Recent reports have shown that high level of CDK7 is associated with poor prognosis in breast, gastric, ovarian cancer, pancreatic, SCLC and AML cancers. Targeting transcriptional machinery of super-enhancer binding proteins is an active therapeutic strategy and we have focused our efforts on developing a selective and reversible small molecule inhibitor of CDK7. Methods: With the application of in-house fragment library screening utilizing the crystal structure of hCDK7 (PDB: 1UA2) and iterative optimization within the ATP binding pocket, candidate criteria, and synthesis led to the identification of lead CDK7 inhibitor TGN-1062. In vitro kinase assays were performed using ADP-GloTMkinase assay kit (Promega). Cell viability assays were performed in a panel of cancer cell lines using CellTiter-Glo assay kit (Promega). RNA Pol II phosphorylation and total c-Myc protein levels were determined by Western Blotting. Results: Here we report the identification of novel, orally available reversible CDK7 inhibitor TGN-1062, through fragment-based and CDK7 kinase screening strategies. TGN-1062 demonstrated promising selectivity against CDK7 with an IC50 of 33 nM (Ki=19 nM) and IC50 values were 6- and 23- fold higher for CDK2 and CDK5, respectively. Our in vitro studies showed that pancreatic cancer cell lines were sensitive to TGN-1062 with GI50 of less than 0.4 µM. In addition, phosphorylation of RNA Pol II and expression of c-Myc were suppressed by TGN-1062 in the MiaPaca2 pancreatic cancer cells. Mouse pharmacokinetic analysis of TGN-1062 demonstrated an oral bioavailability of 62.5%. Further optimization within TGN-1062 series led to the discovery of TGN-1069 that retained the potency against CDK7 with an IC50 of 38 nM (Ki=22 nM) and showed a selectivity of 64- and 122- fold towards CDK2 and CDK5, respectively. Conclusion: In summary, we have developed a novel reversible, selective and an orally available inhibitor of CDK7. The preclinical lead candidate TGN-1069 is currently under investigation for kinome profiling, super-enhancer binding protein activities, ADME-Tox and efficacies. Citation Format: Trason Thode, Zhaoliang Li, Alexis Weston, Raffaella Soldi, Mohan Rao Kaadige, Hariprasad Vankayalapti, Sunil Sharma. Targeting CDK7-dependent transcriptional addiction with novel, orally available small molecule inhibitor shows efficacy in pancreatic cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-107.