Identification and characterization of molecular targets of natural products by mass spectrometry

Abstract

Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule-targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry-based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small-molecule affinity selection combined with mass spectrometry is a successful strategy to "fish" cellular targets from the entire proteome. Mass spectrometry-based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products-protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high-throughput strategies that provide low-resolution structural information of non-covalent natural product-protein complexes. In this review, we provide an overview on the applications of mass spectrometry-based techniques in the identification and characterization of natural product-protein interactions, and we describe how these applications might revolutionize natural product-based drug discovery.

A High-Efficiency Cellular Extraction System for Biological Proteomics

“…4–5 Recently, mass spectrometry proteomics has also been used to improve the sensitivity of drug target discovery 6–7 and analysis of protein-protein interactions. 8 Due to the requirement of purified molecular species for analysis, all of these methods depend on the efficiency of cell disruption and protein extraction techniques that maintain native protein activity and structure.…”

Approaches to Target Profiling of Natural Products

“…As a classical method for the purification of proteins, affinity chromatography has been applied to the identification of the targets of bioactive small organic molecules [65][66][67][68]. Although it is applicable to small molecules that are able to be derivatised without disrupting its bioactivity [69,70], the method suffers from the problems of the steric hindrance and hydrophobic environment induced by nonspecific binding.…”

Identifying the Cellular Targets of Bioactive Small Molecules with Activity-Based Probes

“…Recent advances in MS methodology have made it a powerful technology in protein characterization [95,96]. Molecular weight (MW) determination of the target protein can most easily be accomplished using either electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI).…”