Research Progress and Applications of Target Discovery Strategies for Natural Products
Natural products, characterized by structural diversity and broad biological activities, have become a major source for drug discovery and lead compound identification. However, unclear targets have seriously hindered the research and development of many natural products, making target identification a critical bottleneck and a major focus in this field. In recent years, extensive efforts have been devoted to the discovery of natural product targets, and a relatively systematic methodological framework has gradually been established. According to whether chemical modification is required, current target identification strategies for natural products can be broadly classified into two categories: labeled and label-free approaches. This review systematically summarizes the major target identification techniques within these two strategic frameworks, with particular emphasis on their underlying principles, technical advantages, limitations, applicable scenarios, and representative applications, in order to provide references and insights for mechanistic studies and target discovery of natural products. The labeled strategies include activity-based protein profiling (ABPP), specific pupylation as identity reporter (SPIDER), and proteolysis-targeting chimeras (PROTAC). The label-free strategies include cellular thermal shift assay (CETSA), thermal proteome profiling (TPP), drug affinity responsive target stability (DARTS), limited proteolysis mass spectrometry (Lip-MS), stable isotope labeling by amino acids in cell culture (SILAC), and stability of proteins from rate of oxidation (SPROX). SILAC and other quantitative proteomics methods are often combined with the above strategies to improve the reliability of target screening and differential protein analysis. Each strategy has its own advantages, limitations, and scope of application. This review analyzes the characteristics, limitations, applicable ranges, and optimization directions of each technique, providing a reference for natural product target discovery.