De novo design of a protein fold for small-molecule binding through aromatic π stacking

De novo protein design typically relies on known scaffolds and extensive screening, limiting access to small-molecule binders. In this study, investigators used a motif-guided generative approach to build proteins around a minimal aromatic pi-stacking motif targeting doxorubicin, an anthracycline anticancer drug. Initial experimental testing of twelve designs yielded a doxorubicin binder, and two additional design cycles improved scaffold stability and binding affinity, ultimately producing an 85-residue protein with a dissociation constant of 85 nM.