Computational Validation of Selected Compounds from the GC-MS Profile of Abies numidica Essential Oil and their Antibacterial Effects

Abstract

This work examined the chemical composition of the Algerian endemic tree Abies numidica (Pinaceae) and investigated the antibacterial potential of three major constituents of its essential oil-Santene, Linalyl acetate, and 2,6-Octadiene-2,6-dimethyl-as reported in previously published GC-MS data. Computational antibacterial screening was carried out by docking the selected compounds onto the bacterial proteins 5Z9N (Staphylococcus aureus) and 3AQC (Micrococcus luteus). Molecular docking demonstrated that the active compounds of the EO, including 2,6-Octadiene, 2,6-dimethyl (Cp3), Linalyl acetate (Cp2), and Santene (Cp1), interacted effectively with the active sites of bacterial proteins 5Z9N and 3AQC. Notably, Cp3 (2,6-Octadiene, 2,6-dimethyl) demonstrated the best overall affinity, outperforming both the native ligands and reference molecules with the binding energies for Cp3 (2,6-Octadiene, 2,6-dimethyl) were-4.8 kcal/mol (5Z9N) and-4.1 kcal/mol (3AQC), indicating stronger interactions. These compounds formed critical bonds with amino acids such as Ile78, Val71, and Ala47 (5Z9N) and Val76, Leu116, and Ala79 (3AQC), suggesting their role in disrupting bacterial function. Furthermore, ADMET and BOILED-Egg analyses further showed favorable drug-likeness, with all compounds meeting Lipinski’s criteria, exhibiting logP values below 4, and demonstrating suitable absorption and P-glycoprotein interaction profiles. Based on these results, we refer the antibacterial activity of the EO of Abies numidica, against the M. luteus and S. aureus, is suggesting to the presence of these compounds.