The cellular protein lens epithelium-derived growth factor, or transcriptional coactivator p75 (LEDGF/p75), plays a crucial role in HIV integration. The protein–protein interactions (PPIs) between HIV-1 integrase (IN) and its cellular cofactor LEDGF/p75 may therefore serve as targets for the development of new anti-HIV drugs. In this work, a structure-based pharmacophore model for potential small-molecule inhibitors of HIV-1 IN–LEDGF/p75 interaction was developed using the LigandScout software. The 3D model obtained was used for virtual screening of our in-house chemical database, CHIME, leading to the identification of compound CHIBA-3002 as an interesting hit for further optimization. The rational design, synthesis and biological evaluation of four derivatives were then carried out. Our studies resulted in the discovery of a new and more potent small molecule (7, CHIBA-3003) that is able to interfere with the HIV-1 IN–LEDGF/p75 interaction at micromolar concentration, representing one of the first compounds to show activity against these specific PPIs. Docking simulations were subsequently performed in order to investigate the possible binding mode of our new lead compound to HIV-1 IN. This study is a valid starting point for the identification of anti-HIV agents with a different mechanism of action from currently available antiviral drugs.