New Computational Protein Design Methods for De Novo Small Molecule Binding Sites

Book excerpt: Protein binding to small molecules is fundamental to many biological processes, yet it remains challenging to predictively design this functionality de novo. Current state-of-the-art computational design methods typically rely on existing small molecule binding sites or protein scaffolds with existing shape complementarity for a target ligand. Here we introduce new methods that utilize pools of discrete contacts observed in the Protein Data Bank between protein residues and defined small molecule ligand substructures (ligand fragments). We use the Rosetta Molecular Modeling Suite to recombine protein residues in these contact pools to generate hundreds of thousands of energetically favorable binding sites for a target ligand. These composite binding sites are built into existing scaffold proteins matching the intended binding site geometry with high accuracy. In addition, we apply pools of rotamers interacting with the target ligand to augment Rosetta's conventional design machinery and improve key metrics known to be predictive of design success. We demonstrate that our method reliably builds diverse binding sites into different scaffold proteins for a variety of target molecules. Our generalizable de novo ligand binding site design method will lay the foundation for versatile design of protein to interface previously unattainable molecules for applications in medical diagnostics and synthetic biology.