Abstract

Although there is no shortage of potential drug targets, there are only a handful known low molecular weight inhibitors of protein-protein interactions (PPIs). One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, we developed a novel pharmacophore-based interactive screening technology that builds on the role anchor residues, or deeply buried hot spots, have in PPIs, and redesigns these entry points with anchor-biased virtual multicomponent reactions, delivering tens of millions of readily synthesizable novel compounds. Application of this approach to the MDM2 /p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors. Our unique open-access technology promises to both expand chemical space and develop new probes to study protein function by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure.