Recently, it has emerged from the international scientific literature that quorum sensing (QS) is a promising way for the effective treatment of diseases caused by pathogenic bacteria. One of the crucial proteins in the QS system of Gram-positive bacteria is the pheromone. Some research has reported secondary metabolites from natural products capable of attenuating bacteria through the interruption of the quorum sensing system. One of the Indonesian herbal plants containing bioactive compounds is Sarang Semut ( Myrmecodia pendans). A phenolic compound, dibenzo- p-dioxin-2,8-dicarboxylic acid, has been isolated from this plant which had antibacterial activity against Enterococcus faecalis. However, the molecular mechanism of it has not been known.
The study in question aimed to predict the molecular action of the compound M. pendans against some proteins that act as a signal in the mediated QS of Gram-positive bacteria, called pheromones, including PrgQ, PrgX, PrgZ, and CcfA.
The methods used in this in silico study were ligand-protein docking and virtual screening that were performed by some software and programs. The compound 1 and some positive controls act as ligand were subject binding to PrgQ, PrgX, PrgZ, and CcfA as proteins target, the ligands were free for blind docking. A framework was presented potency of phenolic compounds to inhibit the protein’s target from its affinity binding scores.
It was found thatcompound 1 was potential to inhibit all of the tested protein and gave the highest binding affinity to PrgX (−9.2 kcal.mol −1; the site at Phe59B, Phe59B, Asn63A, and Asn63B residue) and PrgZ (−7.4 kcal.mol −1; the site at Leu4B, Thr65A, Thr82A. Gln81A, and Val5B residue).