In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins

Gizem Köprülülü Küçük; Tuğba Kaman; Ahmed Badri Abed; Safiye Elif Korcan; Muhsin Konuk

doi:10.21448/ijsm.1791584

In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins

Abstract

Acinetobacter baumannii is a highly pathogenic, multidrug-resistant bacterium, posing a significant clinical challenge. Targeting key proteins such as OmpA and LigA offers potential for novel antimicrobial strategies. In this study, we evaluated the antimicrobial activity of Origanum vulgare essential oil against A. baumannii strains and investigated the mechanism by which the main components (carvacrol, beta-caryophyllene, gamma-terpinene, thymol, and p-cymene) in the supplement have an antimicrobial effect on A. baumannii using computational techniques. Amino acid sequences for OmpA and LigA were obtained from NCBI and modeled in 3D using Swiss-Model, AlphaFold, and GalaxyWeb. Ligands were sourced from PubChem, and models were evaluated with PROCHECK and ERRAT, while active binding sites were identified through Consurf analysis. Protein-ligand docking was performed using HDOCK and AutoDock Vina, with interactions analyzed via the PLIP tool. The MIC values for Origanum vulgare were determined following CLSI guidelines, using emulsified oils and bacterial inocula in 96-well plates, incubated at 37°C for 24 hours, with MIC defined as the lowest concentration showing no growth, measured at 450 nm absorbance. For OmpA, HDOCK identified thymol (-95.53) and carvacrol (-93.58) as the top-scoring ligands, whereas AutoDock Vina highlighted γ-terpinene (-5.6) and p-cymene (-5.4). For LigA, carvacrol (-112.21) and thymol (-111.73) showed the strongest HDOCK binding, while AutoDock Vina favored p-cymene (-7.0) and carvacrol (-6.9). The lowest MIC against the A13 strain was observed with a 1/64 dilution of Origanum vulgare oil, while 1/16 and 1/32 dilutions inhibited other strains. These results support the potential of these essential oils as antimicrobial agents.

Keywords

References

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Details

Primary Language

English

Subjects

Microbiology (Other)

Journal Section

Research Article

Authors

Gizem Köprülülü Küçük ^*
0000-0001-6667-4532
Türkiye

Tuğba Kaman
0000-0002-5885-0193
Türkiye

Ahmed Badri Abed
0000-0002-7803-7917
Türkiye

Safiye Elif Korcan
0000-0001-7875-5516
Türkiye

Muhsin Konuk
0000-0002-6651-718X
Türkiye

Early Pub Date

August 3, 2026

Publication Date

September 2, 2026

Submission Date

September 26, 2025

Acceptance Date

March 22, 2026

Published in Issue

Year 2026 Volume: 13 Number: 3

DOI

https://doi.org/10.21448/ijsm.1791584

IZ

https://izlik.org/JA25KP89UJ

Cite

RIS / Bibtex

APA

Köprülülü Küçük, G., Kaman, T., Abed, A. B., Korcan, S. E., & Konuk, M. (2026). In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins. International Journal of Secondary Metabolite, 13(3), 760-788. https://doi.org/10.21448/ijsm.1791584

AMA

1.Köprülülü Küçük G, Kaman T, Abed AB, Korcan SE, Konuk M. In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins. Int. J. Sec. Metabolite. 2026;13(3):760-788. doi:10.21448/ijsm.1791584

Chicago

Köprülülü Küçük, Gizem, Tuğba Kaman, Ahmed Badri Abed, Safiye Elif Korcan, and Muhsin Konuk. 2026. “In Vitro and Bioinformatics Evaluation of Origanum Vulgare Oil Against Acinetobacter Baumannii Proteins”. International Journal of Secondary Metabolite 13 (3): 760-88. https://doi.org/10.21448/ijsm.1791584.

EndNote

Köprülülü Küçük G, Kaman T, Abed AB, Korcan SE, Konuk M (September 1, 2026) In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins. International Journal of Secondary Metabolite 13 3 760–788.

IEEE

[1]G. Köprülülü Küçük, T. Kaman, A. B. Abed, S. E. Korcan, and M. Konuk, “In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins”, Int. J. Sec. Metabolite, vol. 13, no. 3, pp. 760–788, Sept. 2026, doi: 10.21448/ijsm.1791584.

ISNAD

Köprülülü Küçük, Gizem - Kaman, Tuğba - Abed, Ahmed Badri - Korcan, Safiye Elif - Konuk, Muhsin. “In Vitro and Bioinformatics Evaluation of Origanum Vulgare Oil Against Acinetobacter Baumannii Proteins”. International Journal of Secondary Metabolite 13/3 (September 1, 2026): 760-788. https://doi.org/10.21448/ijsm.1791584.

JAMA

1.Köprülülü Küçük G, Kaman T, Abed AB, Korcan SE, Konuk M. In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins. Int. J. Sec. Metabolite. 2026;13:760–788.

MLA

Köprülülü Küçük, Gizem, et al. “In Vitro and Bioinformatics Evaluation of Origanum Vulgare Oil Against Acinetobacter Baumannii Proteins”. International Journal of Secondary Metabolite, vol. 13, no. 3, Sept. 2026, pp. 760-88, doi:10.21448/ijsm.1791584.

Vancouver

1.Gizem Köprülülü Küçük, Tuğba Kaman, Ahmed Badri Abed, Safiye Elif Korcan, Muhsin Konuk. In vitro and bioinformatics evaluation of Origanum vulgare oil against Acinetobacter baumannii proteins. Int. J. Sec. Metabolite. 2026 Sep. 1;13(3):760-88. doi:10.21448/ijsm.1791584