Chemical proteomic mapping of reversible small molecule binding sites in native systems.

Reversible, non-covalent small molecule protein interactions are central to our understanding of biology and the development of therapeutics. Globally assessing all binding sites of a particular small molecule in a given system can be critical to defining mechanisms of action and assessing off-target effects. Emerging techniques to quantitatively map small molecule binding sites, largely driven by photoaffinity labeling (PAL) approaches, are expanding our knowledge of the ligandable proteome. Integrating small molecule binding site mapping with other technologies [e.g., structural modeling, artificial intelligence/machine learning (AI/ML)] will continue to improve our understanding of small molecule–protein interactions. The impact of small molecules in human biology are manifold; not only are they critical regulators of physiological processes, but they also serve as probes to investigate biological pathways and leads for therapeutic development. Identifying the protein targets of small molecules, and where they bind, is critical to understanding their functional consequences and potential for pharmacological use. Over the past two decades, chemical proteomics has emerged as a go-to strategy for the comprehensive mapping of small molecule–protein interactions. Recent advancements in this field, particularly innovations of photoaffinity labeling (PAL)-based methods, have enabled the robust identification of small molecule binding sites on protein targets, often in live cells. In this opinion article, we examine these advancements as well as reflect on how their strategic integration with other emerging tools can advance therapeutic development. The impact of small molecules in human biology are manifold; not only are they critical regulators of physiological processes, but they also serve as probes to investigate biological pathways and leads for therapeutic development. Identifying the protein targets of small molecules, and where they bind, is critical to understanding their functional consequences and potential for pharmacological use. Over the past two decades, chemical proteomics has emerged as a go-to strategy for the comprehensive mapping of small molecule–protein interactions. Recent advancements in this field, particularly innovations of photoaffinity labeling (PAL)-based methods, have enabled the robust identification of small molecule binding sites on protein targets, often in live cells. In this review article, we examine these advancements as well as reflect on how their strategic integration with other emerging tools can advance therapeutic development. [ABSTRACT FROM AUTHOR]