A defined structural unit enables de novo design of small-molecule-binding proteins.
Polizzi, N.F., DeGrado, W.F.(2020) Science 369: 1227-1233
- PubMed: 32883865 
- DOI: https://doi.org/10.1126/science.abb8330
- Primary Citation of Related Structures:  
6W6X, 6W70, 6X8N - PubMed Abstract: 
The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.
Organizational Affiliation: 
Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. nicholas.polizzi@ucsf.edu william.degrado@ucsf.edu.