Chemical Ligand Space of Cereblon

The protein Cereblon serves as a substrate receptor of a ubiquitin Ligase complex that can be tuned toward different target proteins by cereblon-binding agents. This approach to targeted protein degradation is exploited in different clinical settings and has sparked the development of a growing number of thalidomide derivatives. Here, we probe the chemical space of Cereblon binding beyond such derivatives and work out a simple set of chemical requirements, delineating the metaclass of Cereblon effectors. We report co-crystal structures for a diverse set of compounds, including commonly used pharmaceuticals, but also find that already minimalistic cereblon-binding moieties might exert teratogenic effects in zebrafish. Our results may guide the design of a post-thalidomide generation of therapeutic Cereblon effectors and provide a framework for the circumvention of unintended Cereblon binding by negative design for future pharmaceuticals.