A pharmacophore model of PI3Ka inhibitors was built using the DiscoveryStudio 2.0 package. Pharmacophore-based screening (PBS) retrieved a series of novel morpholino–quinoxalines as PI3Ka inhibitors, as exemplified by 1a (PI3Ka IC50: 0.44 mM). All target compounds showed good in vitro cytotoxicity against tested human cell lines. A pharmacophore mapping analysis and docking study indicated that both the morpholino group and the sulfonyl group contributed significantly to the potent PI3Ka inhibitory activity and cytotoxicity of the compounds.