Investigation of Specific Binding Proteins to Photoaffinity Linkers for Efficient Deconvolution of Target Protein

Photoaffinity-based
target identification has received recent attention
as an efficient research tool for chemical biology and drug discovery.
The major obstacle of photoaffinity-based target identification is
the nonspecific interaction between target identification probes and
nontarget proteins. Consequently, the rational design of photoaffinity
linkers has been spotlighted for successful target identification.
These nonspecific interactions have been considered as random events,
and therefore no systematic investigation has been conducted regarding
nonspecific interactions between proteins and photoaffinity linkers.
Herein, we report the protein-labeling analysis of photoaffinity linkers
containing three photoactivatable moieties: benzophenone, diazirine,
and arylazide. Each photoaffinity linker binds to a different set
of proteins in a structure-dependent manner, in contrast to the previous
conception. The list of proteins labeled by each photoaffinity linker
was successfully used to eliminate the nonspecific binding proteins
from target candidates, thereby increasing the success rate of target
identification.