FROM EXPERIMENTAL DESIGN TO VALIDATED HITS: A COMPREHENSIVE WALK-THROUGH OF FRAGMENT LEAD IDENTIFICATION USING SURFACE PLASMON RESONANCE

The detection and characterization of fragment binding requires the use of technologies with extreme sensitivity to observe the binding interactions of low-affinity and low-molecular weight compounds to proteins. A number of methods have emerged capable of providing fragment hits to project teams including, but certainly not limited to, NMR, X-ray crystallography, and surface plasmon resonance (SPR). SPR-based biosensors are sufficiently sensitive and high throughput to provide complete fragment screens on libraries of several thousand compounds in just a few weeks per target. Biosensors provide quantitative binding information for ranking fragments by affinity and ligand efficiency and can support ongoing quantitative structure activity efforts during fragment hit-to-lead development. The combination of speed and binding quantitation makes SPR a valuable technology in pharmaceutical fragment-based drug discovery and development. Successful implementation of SPR biosensors in fragment efforts requires specialized methods for instrument preparation, assay development, primary compound handling, primary screening, confirmation testing, and data analysis. In this chapter, each of these topics is discussed in detail with general best practices for maintaining the highest throughput while maximizing data quality.