In-silico molecular docking and molecular dynamic simulation of γ-elemene and caryophyllene identified from the essential oil of Kaempferia galanga L. against biofilm forming proteins, CrtM and SarA of Staphylococcus aureus

Abstract

Medicinal plants play an important role as antimicrobials by inhibiting various key targets of diverse microorganisms. A major antimicrobial component of plants is its essential oil, which are increasingly being studied for their antimicrobial properties as well as for their potential role in the inhibition of biofilm formation. In the present study, essential oil from Kaempferia galanga L was isolated resulting in the identification of eleven compounds. Of these, two of the compounds, γ-elemene and caryophyllene were found to dock with the target proteins, CrtM and SarA of Staphylococcus aureus, which are essential for the formation of biofilm. γ-elemene demonstrated the best binding affinity with CrtM with binding energy of −8.1 kcal/mol whereas caryophyllene and its derivative isocaryophyllene showed the best binding with SarA with binding energy −6.1 kcal/mol. ADMET study of the compounds also revealed that the compounds are non-toxic and can be used as probable compounds for inhibition of biofilms. Molecular dynamic simulation studies revealed high affinity of binding and stability of the molecules with their targets. PCA analysis helped in identifying the principal motions occurring within a trajectory that are essential in inducing conformational changes.

Communicated by Ramaswamy H. Sarma

Keywords:

• Antibiotic resistance
• antimicrobial activity
• biofilm
• essential oil
• Kaempferia galanga L
• molecular docking
• molecular dynamics and simulation
• Staphylococcus aureus

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors acknowledge the support received from the authority of the Assam Royal Global University for their support in purchase of laboratory equipment and chemicals.