Structure Based Drug Design

The field of structure-based drug design is a rapidly growing area in which many successes have occurred in recent years. The explosion of genomic, proteomic, and structural information has provided hundreds of new targets and opportunities for future drug lead discovery. This review summarizes the process of structure-based drug design and includes, primarily, the choice of a target, the evaluation of a structure of that target, the pivotal questions to consider in choosing a method for drug lead discovery, and evaluation of the drug leads. Key principles in the field of structure-based drug design will be illustrated through a case study that explores drug design for AmpC β-lactamase.

In structure-based drug design, the three-dimensional structure of a drug target interacting with small molecules is used to guide drug discovery. "Structure-based drug design represents the idea that you can see exactly how your molecule interacts with its target protein," says Raymond Salemme, founder, president, and chief scientific officer of Three-Dimensional Pharmaceuticals in Exton, Pa. This structural information can be obtained with X-ray crystallography or nuclear magnetic resonance spectroscopy (NMR). Ideally, these two techniques complement one another. However, most companies that are specializing in structure-based drug design focus on only one method of structure determination, at least initially.

Originally, structure-based drug design was equated with de novo design or building a molecule from the ground up. The active site of the protein was a space to be filled with a molecule that complemented it in terms of shape, charge, and other binding components.

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