Structure-Guided Discovery of a Bis-Pyridyl Diamine-Based Dual CDK7/9 Inhibitor with In Vitro and In Vivo Antitumor Efficacy in Glioblastoma Multiforme

Glioblastoma multiforme (GBM) is a lethal and fast-growing brain Cancer that is difficult to treat with standard medical interventions. GBM tumors often overexpress cyclin-dependent kinase 9, in complex with cyclin T1, and thus, it represents a promising target for therapeutic intervention. In this study, we employed a structure-based virtual screening approach for a curated library of 6,059 bis-pyridyl compounds from PubChem to identify potential CDK9/T1 inhibitors. Subsequent in vitro ADP-Glo assay led to the identification of GNE-3511 as a potent CDK9/T1 inhibitor with an IC₅₀ of 0.064 μM. GNE-3511 also inhibited CDK7/cyclin H with an IC₅₀ of 0.12 μM. In U-87 MG and T98G glioblastoma cells, GNE-3511 exhibited cytotoxicity with a GI₅₀ of 3.4 and 5.0 μM, inducing G2/M phase cell cycle arrest and promoting early Apoptosis. Treatment with GNE-3511 significantly reduced the expression of the anti-apoptotic markers Bcl-2, Survivin and drug resistance markers (ABCB1 and ABCG2) in a dose-dependent manner, and downregulated glioma stem cell population/markers (CD44, CD90⁺, or CD133⁺ and BMI-1) and sphere formation abilities. Oral administration of GNE-3511 at 20 mg/kg (twice daily) demonstrated significant anti-tumor efficacy and improved survival in both U-87 MG and T98G xenograft/orthotopic mouse models. Collectively, these findings highlight GNE-3511 as a promising lead candidate for the development of GBM therapeutics.