Chemical Probes of Escherichia coli Uncovered through Chemical-Chemical Interaction Profiling with Compounds of Known Biological Activity

SummaryWhile cell-based screens have considerable power in identifying new chemical probes of biological systems and leads for new drugs, a major challenge to the utility of such compounds is in connecting phenotype with a cellular target. Here, we present a systematic study to elucidate the mechanism of action of uncharacterized inhibitors of the growth of Escherichia coli through careful analyses of interactions with compounds of known biological activity. We studied growth inhibition with a collection of 200 antibacterial compounds when systematically combined with a panel of 14 known antibiotics of diverse mechanism and chemical class. Our work revealed a high frequency of synergistic chemical-chemical interactions where the interaction profiles were unique to the various compound pairs. Thus, the work revealed that chemical-chemical interaction data provides a fingerprint of biological activity and testable hypotheses regarding the mechanism of action of the novel bioactive molecules. In the study reported here, we determined the mode of action of an inhibitor of folate biosynthesis and a DNA gyrase inhibitor. Moreover, we identified eight membrane-active compounds, found to be promiscuously synergistic with known bioactives.

► Chemical-chemical interaction profiling with known bioactives provides functional information on the mode of action of novel antibacterial compounds
► Chemical-chemical interaction profiling facilitates the identification of nonselective molecules through promiscuously synergistic fingerprints
► The approach was validated with the determination of the mechanism of action of two novel antibacterial compounds
► Compound MAC-0038968 is an inhibitor of dihydrofolate reductase, while MAC-0003199 is a novel DNA gyrase inhibitor