Structure-based design of enzyme inhibitors and receptor ligands

With the ongoing progress in protein crystallography and NMR, structure-based drug design is adopting increasing importance in the search for new drugs. Modeling starts from the 3D structure of a target protein in order to construct molecules which are complementary to a binding site, in their geometry as well as in the pattern of their physicochemical properties around the molecules. The rational design process is accompanied by 3D structure determinations of different ligand-protein complexes. Most often, significantly improved binding affinities of the ligands are observed after several cycles of 3D structure determinations, the design of compounds with appropriate structural modifications, synthesis, and testing of the new drug candidates. As an alternative, pharmacophore models are derived from the 3D structures of active analogs. A risk with lead structure optimization by structure-based design is the neglect of other important biological properties, such as bioavailability and metabolic stability. Recent applications of structure-based design, as well as success stories in the search for new, potent and selective HIV protease inhibitors, thrombin inhibitors, neuraminidase inhibitors and integrin receptor antagonists, are reviewed.