Direct affinity screening chromatography–mass spectrometry assay for identification of antibacterial agents from natural product sources

A direct affinity screening – mass spectrometry assay, coupled to liquid chromatography, is presented as a tool for natural product drug discovery. Using the assay, fractionated extracts from a Caribbean gorgonian coral were shown to contain a new chemical entity (NCE) which binds to a mimic of the Gram positive bacterial cell wall (lysine–d-alanine–d-alanine). Conditions for observation of a specific noncovalent complex between the NCE and the target mimic using electrospray ionization-mass spectrometry were validated in a series of positive and negative control experiments, which featured flow injection analysis-based titrations. While the structural identity of the NCE could not be determined due to limited sample quantities, this work provides proof-of-principle for such an approach to potentially accelerate drug discovery from natural product sources.

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► Novel affinity mass spectrometry assay for natural product drug discovery.
► Assay based on monitoring complex formation with a target ligand mimic.
► Lysine–d-alanine–d-alanine used as Gram positive target ligand.
► Potential antibacterial compound tracked through fractionation of coral extract.