A new small molecule that directly inhibits the DNA binding of NF-κB

Abstract Nuclear factor-κB (NF-κB) has been considered as a good target for the treatment of many diseases. Although a lot of NF-κB inhibitors have already been reported, many of them have several common problems. Thus, we attempted to identify novel NF-κB inhibitors to be unique lead compounds for creating new pharmaceuticals. In the present study, we screened our chemical library for compounds that directly inhibit the DNA binding of NF-κB by using fluorescence correlation spectroscopy (FCS). Consequently, we identified a promising compound, 4,6-dichloro- N -phenyl-1,3,5-triazin-2-amine, referred to as NI241. It mediated a dose-dependent inhibition of the DNA binding of NF-κB p50. Its analogues also showed dose-dependent inhibition and their inhibitory effects were altered by the substituents on the N -phenyl group. Furthermore, we predicted the binding mode of NI241 with p50 in silico. In this model, NI241 forms three hydrogen bonds with Tyr60, His144, and Asp242 on p50, which are important amino acid residues for the interaction with DNA. These results suggest that NI241 with structural novelty may serve as a useful scaffold for the creation of new NF-κB inhibitors by rational optimization.