Identifying the target proteins of bioactive small molecules is a key step in understanding mode-of-action of the drug and addressing the underlying mechanisms responsible for a particular phenotype. Proteomics has been successfully used to elucidate the target protein profiles of unmodified and ligand-modified bioactive small molecules. In the latter approach, compounds can be modified via click chemistry and combined with activity-based protein profiling. Target proteins are then enriched by performing a pull-down with the modified ligand. Methods that utilize unmodified bioactive small molecules include the cellular thermal shift assay, thermal proteome profiling, stability of proteins from rates of oxidation, and the drug affinity responsive target stability (DARTS) determination (or read-out). This review highlights recent proteomic approaches utilizing data-dependent analysis and data-independent analysis to identify target proteins by DARTS. When combined with liquid chromatography/tandem mass spectrometry, DARTS enables the identification of proteins that bind to drug molecules that leads to a conformational change in the target protein(s). In addition, an effective strategy is proposed for selecting the target protein(s) from within the pool of analyzed candidates. With additional complementary methods, the biologically relevant target proteins that bind to the small bio-active molecules can be further validated.
Bibliographical noteFunding Information:
H.-Y.H. and T.Y.K. contributed equally to this work. This work was supported by grants from the National Research Foundation of Korea, funded by the Korean government (MSIP; 2015K1A1A2028365, 2015M3A9B6027818, 2016K2A9A1A03904900, 2018M3A9C4076477) and the Brain Korea 21Plus Project in the Republic of Korea and ICONS (Institute of Convergence Science), Yonsei University; as well as the Berta Kamprad Foundation, Lund, Sweden; and KNN121510 by the National Research, Development and Innovation Office of Hungary.
All Science Journal Classification (ASJC) codes
- Molecular Biology