LC-MS/MS-based metabolic profiling and in silico molecular modeling revealed a quorum sensing inhibitor from Embelia ribes Burm. f. fruits

Abstract

Embelia ribes Burm f. (ER) fruits are consumed as condiments and commonly used as antimicrobial agents. However, the molecule that inhibits quorum sensing (QS), a bacterial communication mechanism that ensures sufficient cell density and regulates the gene expression responsible for virulence, was unknown. Here, we identified ER's anti-QS molecule and its mechanism. Initially, crude extracts of ER fruits from dimethyl sulfoxide (DMSO), n-hexane, and methanol were screened against the Agrobacterium tumefaciens (At) biofilm, an indicator of effective QS. Interestingly, only the methanolic extract-treated At culture showed biofilm disruption. Further fractionations of the methanolic extract using high performance liquid chromatography (HPLC) and examination of each fraction's biofilm disruption ability identified the active-molecule-containing fraction. Liquid chromatography and tandem mass spectrometry analysis identified five compounds specific to the active fraction, where quinic acid (QA) was predominant. QA application could inhibit biofilm formation independently or complemented with an inactive fraction. Molecular modeling and molecular dynamics simulations showed that the allosteric stable binding of QA with the receptor protein TraR reduces the fluctuations in the DNA-binding domain. Moreover, the QA application also reduced the virulence of At. Our study suggests that QA from ER fruit inhibits biofilm formation and virulence of At by allosteric modification of TraR that impairs DNA recognition essential for biofilm development.