Natural products have embedded molecular recognition and can be considered as useful library components for screening against protein targets. The basis of natural product binding to proteins can be explained by the similarity of biosynthetic enzyme substrate interactions and protein-natural product interactions. Secondary metabolites from natural sources, such as plants, animals, and microorganisms, are evolved by natural selection and encoded to bind specific proteins to exert a wide range of biological functions. Native mass spectrometry using electrospray ionization Fourier transform mass spectrometry is a tool for dereplication and metabolomics analysis. Thus, molecular weight ID from ligand-protein complexes by electrospray ionization Fourier transform mass spectrometry allowed rapid dereplication. Mass guided isolation and NMR identification of hits confirmed the mass accuracy of the ligand in the ligand-protein MS complexes. Seven common hits were identified as apigenin 6- C- β- D-glucoside 8- C- α- L-arabinoside, sweroside, 4′,5-dihydroxy-7-methoxyflavanone-6- C-rutinoside, loganin acid, 6- C-glucosylnaringenin, biochanin A 7- O-rutinoside and quercetin 3- O-rutinoside. Based on molecular weight common hits were detected binding to all four proteins. Native mass spectrometry detection of ligand-protein complexes allowed rapid detection of natural product binders of apo and calcium-bound S100A4 (a member of the metal binding protein S100 family), T cell/transmembrane, immunoglobulin (Ig), and mucin protein 3, and T cell immunoreceptor with Ig and ITIM (immunoreceptor tyrosine-based inhibitory motif) domains precursor protein from extracts and fractions.
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