Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification

Abstract

Natural products are an important source of new drugs for the treatment of various diseases. However, developing natural productbased new medicines through random moiety modification is a lengthy and costly process, due in part to the difficulties associated with comprehensively understanding the mechanism of action and the side effects. Identifying the protein targets of natural products is an effective strategy, but most medicines interact with multiple protein targets, which complicate this process. In recent years, an increasing number of researchers have begun to screen the target proteins of natural products with chemical proteomics approaches, which can provide a more comprehensive array of the protein targets of active small molecules in an unbiased manner. Typically, chemical proteomics experiments for target identification consist of two key steps: (1) chemical probe design and synthesis and (2) target fishing and identification. In recent decades, five different types of chemical proteomic probes and their respective target fishing methods have been developed to screen targets of molecules with different structures, and a variety of protein identification approaches have been invented. Presently, we will classify these chemical proteomics approaches, the application scopes and characteristics of the different types of chemical probes, the different protein identification methods, and the advantages and disadvantages of these strategies.

Identifying bioactivity of pseudo-natural products using the Cell Painting assay

“…Initially, it was attempted to identify the target by compound-centric chemical proteomics (CCCP), 43,44 a technique where the molecule in question is immobilized (e.g. on magnetic beads) via a spacer.…”

Quantitative Chemical Proteomics Reveals Resveratrol Inhibition of A549 Cell Migration Through Binding Multiple Targets to Regulate Cytoskeletal Remodeling and Suppress EMT

“…In recent years, quantitative chemical proteomics approaches have been widely applied to identify the protein targets of active small molecules to elucidate their mechanism of action and side effects ( Cheng et al, 2014 ; Wang et al, 2014 ; Wang et al, 2016a ). The approach utilizes a probe, which is structurally similar to its parent molecule and retains the pharmacological activity of interest, to interact with the protein targets in living cells or cell lysates ( Chen et al, 2020 ). Then, the probe-protein complexes are enriched with affinity technology.…”

Click and Release Chemistry for Activity‐Based Purification of β‐Lactam Targets

“…This approach enables detection of known PBPs but present limitations concerning the identification of unknown targets since it only provides information on the electrophoretic mobility of the protein‐dye adduct. This limitation has been addressed by the use of biotinylated azido‐containing dyes for streptavidin affinity pull‐down purification followed by mass spectrometry analysis [15,16] . Selective penicillin‐binding protein imaging probes have also been described using fluorescent β‐lactams, [17] such as fluorescent cephalosporins [18] .…”

“…This limitation has been addressed by the use of biotinylated azido-containing dyes for streptavidin affinity pull-down purification followed by mass spectrometry analysis. [15,16] Selective penicillin-binding protein imaging probes have also been described using fluorescent βlactams, [17] such as fluorescent cephalosporins. [18] Of note, fluorescent β-lactams were also used as fluorogenic molecular probes for the detection of β-lactamases in vitro or in living bacteria.…”