Combination of pharmacophore model development and binding mode analyses: identification of ligand features essential for IκB kinase-beta (IKKβ) inhibitors and virtual screening based on it.

Abstract IκB kinase β (IKKβ) is an important anti-cancer target that plays crucial role in activating the transcription factor NF-κB in response to various inflammatory stimuli. In order to discover novel IKKβ inhibitors, a 3D chemical-feature-based QSAR pharmacophore model was established. A homology model of IKKβ enzyme was also developed to study the binding mode of IKKβ and its inhibitors. The two models were consistent in predicting the binding conformation of IKKβ inhibitor. Based on the virtual screening using the pharmacophore model, 16 compounds from SPECS database were selected after multiple filtrations for biological test. Two compounds with IC 50 values lower than 10 μM were discovered.