Virtual screening by 2-D fingerprints, shape and docking for discovering new chemotypes of activator protein-1 inhibitors

Abstract

Activator protein-1 Fos/Jun proteins bind to cognate DNA and regulate gene expression. Small-molecule inhibitors targeting activator protein-1 DNA binding have been developed in the past decades for therapeutic applications. Recent structural and in silico studies suggest a putative inhibitor binding pocket on the activator protein-1 structure, and computational modeling suggests a consensus binding mode of three classes of known small-molecule inhibitors. Here, virtual screening of two-dimensional fingerprints, shape, and docking was performed in search of novel chemotypes of activator protein-1 inhibitors. A standard score (Z3-score) coalescing top-ranked ligands from the three methods was used and the top-scoring ligands were clustered by similarity. A representative ligand from each large cluster was evaluated using metadynamics simulations and molecular mechanics calculations. Representative hits showed diverse chemotypes and their modeled binding pose on activator protein-1 reproduced key interactions with binding site residues. Communicated by Ramaswamy H. Sarma