Phosphoinositide-3-kinase-delta (PI31 delta) is a key regulator in the process of IgE mediated mast cell degranulation, which directly induces allergic diseases, such as asthma. This study is aimed at discovery of natural PI3K delta inhibitors from Chinese medicine and evaluating their anti-mast cell degranulation activity. A combined virtual screening based on 3D pharmacophore model and molecular docking was used to screen for bioactive ingredients directly targeting PI3K delta . Then, an in vitro kinase inhibition assay was conducted to evaluate the PI3K delta inhibitory activity of the virtual screening hits. Subsequently, a beta-fihexosaminidase release assay was performed to verify the anti-mast cell degranulation activity of the active compounds. Finally, ginkgoneolic acid was identified as a P1310 inhibitor (IC50= 2.49 mu M) and exhibited anti-mast cell degranulation activity in vitro (IC50 = 2.40 mu M). Docking studies showed that Glu826, Val827 and Val828 were key amino acid residues for PI3K delta inhibitory activity. Ginkgoneolic acid may be a potential lead compound for developing effective and safe PI3K delta-inhibiting drugs. (C) 2018 Published by Elsevier Inc.