Structure Based Identification of Potential BBB Permeable Natural Compound Inhibitors Targeting RUNX1-CBFβ in Glioblastoma Multiforme

• Systematic screening of phytochemicals for BBB permeability. • Virtual screening identified dual RUNX1/CBFβ inhibitors for GBM therapy. • Crinasiatine exhibits superior binding vs controls in both targets. • MM-GBSA calculations validate strong binding thermodynamics. • Natural lignad derivatives show promise as CNS-penetrant anticancer agents. Glioblastoma multiforme remains the most lethal primary brain malignancy with median survival of 12-15 months, where the RUNX1-CBFβ heterodimeric transcriptional complex drives mesenchymal glioblastoma pathogenesis through orchestrating proliferation, invasion, stemness, and therapeutic resistance. However, no central nervous system-penetrant inhibitors targeting this critical protein-protein interaction have been developed due to blood-brain barrier (BBB) restrictions and the challenge of targeting transcription factor complexes. We conducted systematic computational screening of 736 anticancer and antitumor phytochemicals through sequential pharmacokinetic profiling using Lipinski’s Rule of Five, Veber’s rules, and BBB permeability prediction via SwissADME, followed by toxicity assessment using ProTox-II and multi-platform ADMET profiling integrating DeepPK for P-glycoprotein efflux, hERG, and AMES assessment. BBB-permeable candidates underwent molecular docking against RUNX1 and CBFβ interfaces and the preformed heterodimeric complex, 500-nanosecond molecular dynamics simulations, and MM-GBSA binding free energy calculations. RUNX family selectivity was assessed via comparative docking against RUNX2 and RUNX3, and off-target profiling was performed using SwissTargetPrediction. We identified four BBB-permeable dual-target candidates: Tylophorinine, Crinasiatine, Sanguinarium, and Austrobailignan-1; demonstrating superior binding affinities exceeding control molecules, and stable trajectories throughout simulations. Crinasiatine emerged as the highest-priority lead with binding free energies of -5.39 kcal/mol for RUNX1 and -14.34 kcal/mol for CBFβ, exceptional hydrogen bonding, lowest structural fluctuations, stable heterodimeric complex engagement confirmed by 500 ns complex MD, and a GBM-relevant off-target profile. These computational findings identify BBB-permeable phytochemical candidates targeting RUNX1-CBFβ heterodimerization, warranting experimental validation through binding confirmation and cell-based assays.