Endophytic fungi are a wealth of new bioactive metabolites with vast applications in drug discovery. The methyl alcohol extract obtained from the culture of the Phialophora verrucosa Medlar., the endophytic fungus of Senecio flavus (Asteraceae), was found to be cytotoxic to HepG2 and MCF-7 cell lines (IC50 of 20.01 and 28.44 μg/mL), respectively, compared to 5-flurouracil (IC50, 11.05 and 12.46). A chromatographic study led to the isolation of five polyketides; 3,6,7-trihydroxy-α-tetralone 1, 6-hydroxyisosclerone 2, 2,3-dihydro-8-hydroxy-2-methyl-benzopyran-1-one 3, altechromone A 4 and aloesol 5. Compounds 2, 4 and 5, are isolated for the first time from the genus Phialophora. Molecular docking analysis simulation was applied to evaluate the inhibitory activities of the isolated compounds against vascular endothelial growth factor receptor (VEGFR2), and cyclin-dependent kinases (CDKs), to illuminate the compounds responsible for the extract cytotoxic activity. Compounds 1 and 5 showed promising results and binding affinities to the examined enzymes. Manuscript profile