Antibacterial of Dibenzo-p-Dioxi-2,8-Dicarboxylic Acid Against Pathogenic Oral Bacteria E. faecalis ATCC 29212 Peptide Pheromones: Quorum Sensing of in vitro and in silico Study

Abstract

Background

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.

Aim

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.

Materials and Methods

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.

Results

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).

Conclusion

It is proposed that compound 1 has a good activity to inhibit E. faecalis through its peptide pheromones in the QS system.

Keywords:

• oral bacteria
• quorum sensing
• peptide pheromones
• PrgQ
• PrgX
• PrgZ
• CcfA

Acknowledgments

The authors are grateful to Universitas Padjadjaran. This research was supported by Academic Leadership Grant 2019–2020 from Universitas Padjadjaran, Sumedang Indonesia.

Disclosure

The authors report no conflicts of interest in this work.