Adventures in small molecule fragment screening by x-ray crystallography

Abstract

Since its conception in the early 1990s, fragment-based drug discovery (FBDD) has become established as a powerful tool for identifying new, chemically tractable pharmacophores. Unlike traditional methods that focus primarily on initial potency, FBDD stresses efficiency of binding and exploration of a highly diverse chemical space. Small fragment library sizes (~ 1,000 compounds) and the weak binding affinity of fragments have spurred the use of biophysical methods not readily applicable to screening of traditional compound libraries (greater than 100,000 compounds). X-ray crystallography is a powerful, yet under-appreciated, biophysical method for systematic identification of small molecule binding and discovery of potential inhibitory sites in a macromolecular target. Indeed, due to tremendous improvements in methodologies and technologies involved in X-ray data collection and analysis, it is now possible to collect data on a complete fragment library for a given macromolecular target during a single trip to a current generation synchrotron. Here we highlight some key insights and innovations learned from fragment screening campaigns targeting influenza and HIV-1 polymerases.