Designing Binding Pockets on Protein Surfaces using the A* Algorithm

The in-silico design of ligands binding to the protein surface instead of deep binding pockets is still a great challenge. Often no appropriate binding pockets are available in the apo experimental structures and standard virtual screening techniques will fail. Here, we present two new algorithms for designing tailored ligand binding pockets on the protein surface that account for protein backbone and side chain flexibility. At first, the protein surface is scanned for potential pocket positions using a program named PocketScanner. This program minimizes the protein energetically in the presence of generic pocket spheres representing the new binding pockets whose positions remain fixed. The side chains of the relaxed protein conformations are then further refined by a second program named PocketBuilder. PocketBuilder identifies all residues within a given radius of the pocket positions and searches for the best combination of side chain rotamers using the A* algorithm. Given multiple protein conformations as input, PocketBuilder identifies those that lead to the best results, namely protein conformations of low energy that possess binding pockets with desired properties. The approach was tested on the proteins BCL-XL, IL-2, and MDM2 which are involved in protein-protein interactions and hence represent challenging drug targets. Although the native ligand binding pocket was not or only partly open in the apo crystal or NMR structures, PocketScanner and PocketBuilder successfully generated conformations with pockets into which a known inhibitor could be docked in a nativelike orientation for two out of the three test systems. For BCL-XL, the docking scores were even similar to those obtained in re-docking experiments to the inhibitor bound crystal structure.