Elucidation of protein functions on the basis of structure–activity relationships can reveal
the mechanisms of homeostasis functions in life and is one of the greatest interests of
scientists. In the human body, many proteins are activated and/or inactivated by ligands to
maintain homeostasis. Understanding the mechanism of molecular interactions between
small bioactive ligands and proteins is an important step in rational drug design and
discovery. !
Photoaffinity labeling, which is one of the most familiar approaches for chemical biology
analysis, was initiated using diazocarbonyl derivatives in 1962 (Singh et al., 1962). Many
researchers have subsequently tried to establish alternative approaches for the direct
identification of target proteins for the bioactive small ligands. These approaches are based
on the affinity between the ligand and the target protein (Figure 1). Several reviews are
published for the recent applications of photoaffinity labeling (Tomohiro et al., 2005;
Hashimoto & Hatanaka, 2008).
To archive photoaffinity labeling, researchers have to prepare photoaffinity labeling ligands.
The native ligands must be modified by photoreactive compounds (photophores) by organic
synthesi