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

Ainayat Ellah Saidi; Nebia Bouzidi; Mohammed Ziane; Mohammed Gherib; Chaimaa Rahila; Marius Mioc

doi:10.1080/07391102.2024.2301742

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

J Biomol Struct Dyn. 2024 Jan 10:1-20. doi: 10.1080/07391102.2024.2301742. Online ahead of print.

Authors

Ainayat Ellah Saidi¹, Nebia Bouzidi², Mohammed Ziane^{1

3}, Mohammed Gherib⁴, Chaimaa Rahila¹, Marius Mioc⁵

Affiliations

¹ Laboratory of Applied Hydrology and Environment, University of Ain Témouchent, Ain Témouchent, Algeria.
² Laboratory of physical chemistry of macromolécules and biological interfaces, departememt of biology sciences, faculty of sciences of nature and life, university Mustapha stambouli of mascara, mascara, Algeria.
³ Laboratory of Microbiology Applied to Food, Biomedical and the Environment (LAMAABE), Faculty of SNV/STU, University of Tlemcen, Tlemcen, Algeria.
⁴ Laboratory Sustainable Management of Natural Resources in Arid and Semi-Arid Zones, Department of SNV, Institute of Science and Technology, University Center Salhi Ahmed, Nâama, Algeria.
⁵ Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania.

PMID: 38197406
DOI: 10.1080/07391102.2024.2301742

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; dynamics simulation study; molecular docking.