In silico and in vitro studies: investigating the chemical composition, DFT, molecular docking, and dynamic simulation of Satureja candidissima (Munby) Briq essential oil as a potential antibacterial agent

Abstract

This study aimed to investigate the chemical composition and antibacterial properties of the essential oil (EO) derived from the aerial parts of Satureja candidissima (Munby) Briq (SC), as well as the mechanisms of interaction between SCEO chemical components and target proteins related to antibacterial activity mechanisms using a molecular docking approach, and for more accuracy molecular dynamic simulation and DFT calculations were carried out. The GC–MS technique was used to analyze the chemical composition of SCEO. The results showed that SCEO contained various chemical compounds, with pulegone being identified as the major component (53.26%). The results also indicated the presence of (+)-menthone (11.02%), borneol (4.43%), 2-cyclohexen-1-one, 3-methyl-6-(1-methylethylidene) (2.50%), and 3-octanol (2.09%). The study revealed that the SCEO displayed antibacterial activity against all tested gram-positive bacteria. To further understand the mechanism behind its antibacterial activity, in silico molecular docking studies were performed. The results indicated that the antibacterial effect of SCEO compounds could be due to the combination with enoyl-[acyl-carrier-protein] reductase [NADPH] FabI (PDB ID: 4ALL) in a variety of ways. The molecular dynamics simulation analysis yielded favorable outcomes for the docked complex involving 1H-cycloprop[e]azulen-7-ol, decahydro-1,1,7-trimethyl-4-methylene, and 1,4,7-tetramethyldecahydro-1H-cyclopropa[e]azulen-4-ol with enoyl-[acyl-carrier-protein] reductase [NADPH]. Geometry optimization, coupled with Density Functional Theory (DFT), can be employed to assess the importance of quantum chemical descriptors in elucidating potential antibacterial activity. Quantum descriptors were computed based on E_HOMO and E_LUMO. The results of this study provide important insights into the potential use of Satureja candidissima (Munby) Briq EO as antibacterial agent.

Communicated by Ramaswamy H. Sarma

Keywords:

• Essential oil
• Satureja candidissima (Munby) Briq
• antibacterial properties
• molecular docking
• dynamics simulation study

Acknowledgment

A.E. SAIDI extends gratitude to Dr. Ahmed M. Sayed, Dr. Hafiz Muzzammel Rehman, and Dr. Vijay Kumar Vishvakarma for their invaluable guidance, significantly enhancing the quality of the study.

Author contributions

A.e.S. contributed to sample collection,M.G. and N.B. handled the extraction of the essential oil, and N.B. performed GC-MS analysis. M.Z. and C.R. contributed to the in vitro antibacterial study. A.e.S. was involved in data interpretation, analysis, manuscript draft preparation, in silico molecular dynamic simulation, and DFT. Both A.e.S. and M.M. conducted molecular docking. M.M., M.Z., and N.B. supervised the work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Publicly available datasets and tools were employed for this study.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.