The impact of crystallization conditions protein constructs and space groups on structure based drug design

Orly Dym

Abstract

The 3D structure of apo proteins and proteins with inhibitors provide the basis for structure-based drug design studies and is also utilized in docking procedures to search for more potent drug. Specific examples for drug design of Acetyl Cholinesterase (AChE) and Phosphotriesterase (PTE) using X-ray crystallography will be presented. Comparative analysis between the computational docking drug design approach and the AChE crystal structures reviled that the position of the ligands within the active-site gorge of the enzyme is influenced by the crystallization conditions. Spectroscopic evidence and thermal stability results supported such a difference in ligand positioning. These results have implications for structure-based drug design using docking procedures. We also analyzed nineteen crystal structures of the apo and several phosphonate (OP) analogs bound to few highly evolved PTE variants. In addition to providing insights into the binding modes of OPs into the active site of the different PTE variants, the data reveal the importance of tags used for protein expression, the ‘choice of the appropriate’ crystallization conditions, the protein constructs and the space groups and their implications for structure-based drug design.