Virtual Selection by Molecular Docking and Activity Evaluation of Key Antibiofilm Components in Essential Oil of Green Sichuan Pepper (Zanthoxylum armatum DC.) against Bacillus amyloliquefaciens

Abstract

To explore the key antibiofilm components of green Sichuan pepper essential oil (GPEO) against the spoilage microorganism Bacillus amyloliquefaciens and their intracellular targets, a molecular structure database of GPEO components and a collection of the molecule structures of target proteins related to the biofilm formation of B. amyloliquefaciens were created based on related literature data, and the CB-DOCK2 servicer was used to perform molecular docking of the active components of GPEO to biofilm formation-related target proteins. Furthermore, the key antibiofilm components of GPEO were selected based on their docking affinity and their potential targets were explored. Finally, in vitro experiments and crystal violet staining were conducted to confirm the antibiofilm effects of two key active components of GPEO, caryophyllene oxide and β-caryophyllene, against B. amyloliquefaciens. Molecular docking results showed that 24 volatile components of GPEO had different affinities to 58 targets associated with the biofilm formation of B. amyloliquefaciens, among which β-caryophyllene and caryophyllene oxide could tightly bind to ComP and RapC through intermolecular forces such as hyperconjugation, hydrophobic interaction and van der Waals force, forming a stable conformation. In vitro experiments showed that the minimal inhibitory concentrations (MICs) of caryophyllene oxide and β-caryophyllene against the biofilm of B. amyloliquefaciens were 6.0 and 2.0 mg/mL, respectively. Both compounds interfered with the swimming motility of this bacterium, reduced the initial cell adhesion and auto-aggregation ability, and altered the cell surface hydrophobicity. These results provide feasible strategies to help decipher the intracellular molecular mechanisms related to the biological activity of plant essential oil.

Keywords

• molecular docking; biofilm; green sichuan pepper essential oil; bacillus; caryophyllene oxide; β-caryophyllene