Recent Developments in Designing Compact Biological Photoprobes

Abstract

Identification and characterization of small molecule–protein interactions are common needs for both basic science and drug discovery programs. Photoaffinity probe molecules (photoprobes) have been used for more than 40 years to label the targets of small molecules, but identification of those targets has remained challenging. Recently, renewed interest in the use of photoprobes has been spurred by the advent of modern mass spectrometry methods that facilitate target identification. In addition, development of new chemoselective labeling reactions (i.e., “click chemistry” approaches) now enables facile purification of photocrosslinked complexes for analysis. Photoprobe technology is being applied for a variety of purposes, including identifying the direct binding partner(s) of a small molecule, obtaining information about the nature of the ligand binding site in the absence of a three-dimensional structure, determining whether ligand binding occurs through a primary or allosteric site, and investigating the specificity determinants of ligand binding. In this chapter, we discuss a selection of compact photoprobes that have been reported in the past 10 years. The chapter describes photoprobes containing each of the three common photoactivatable functional groups—aryl azide, benzophenone, and diazirine. We highlight the molecular design strategies that have yielded functional photoprobes, including compact construction, choice of photoactivatable functional groups, use of tags for chemoselective labeling, and linker design. We conclude by discussing remaining challenges that stand in the way of widespread adoption of photoprobe reagents.