Predicting the structures of complexes between phosphoinositide 3-kinase (PI3K) and romidepsin-related compounds for the drug design of PI3K/histone deacetylase dual inhibitors using computational docking and the ligand-based drug design approach

- Predictions of PI3K-inhibitor complex was performed.
- Usefulness of the combination between docking and superposition was evaluated.
- The refinement of docking structures by MD simulations should be conducted.
- The bifurcated hydrogen bond plays important role in ligand recognition.
- The hydrophobic effects influence the inhibitory activities for PI3K.