Multitarget affinity/specificity screening of natural products: finding and characterizing high-affinity ligands from complex mixtures by using high-performance mass spectrometry.
In this work we describe a high-throughput screening approach based on electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR) that rapidly interrogates the noncovalent interaction between RNA-based drug targets and components derived from a bacterial natural product library. The screening process detects molecules present in the natural product library that bind to a synthetic RNA target that mimics the prokaryotic 16S rRNA A-site, while simultaneously measuring specificity for the synthetic A-site target using a control RNA target that lacks the critical structural element of the A-site construct. This screening approach known as multitarget affinity/specificity screening (MASS) demonstrated the expected binding of paromomycin from a fractionated natural product library derived from Streptomyces rimosus sp. paromomycinus. A new molecule was observed to bind with specificity to the 16S A-site RNA construct. MS/MS characterization of this species yielded partial structural information suggesting it is an aminoglycoside consisting of a paromomycin core with one or more modified rings. This work demonstrates the tremendous utility of MASS for screening natural product fractions against macromolecular targets.
D001483:Base Sequence; D001688:Biological Products; D004926:Escherichia coli / Q000235:genetics; D009690:Nucleic Acid Conformation; D010303:Paromomycin / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry; D021241:Spectrometry, Mass, Electrospray Ionization; D013302:Streptomyces / Q000737:chemistry*
D001688:Biological Products; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D010303:Paromomycin