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Research Article


Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach

Irwan Susanto, Fachrul R. Mahendra, Roni Ridwan, Komang G. Wiryawan, Erika B. Laconi, Anuraga Jayanegara.


Abstract
Background:
Silage technology ensures year-round feed for ruminants, and phytobiotics like tannin, saponin, and cumin can enhance preservation by maintaining nutritional content and inhibiting decay.

Aim:
This study evaluates the efficacy of secondary metabolites from tannin, saponin, and cumin essential oil as inhibitors of amino acid deamination in silage, focusing on their binding affinity and stability with Glutamate dehydrogenase (GDH).

Methods:
Molecular docking and dynamics simulations were used to study protein conformational changes at the atomic level. The spoilage bacterium Clostridium sp., which contaminates silage, expresses GDH, an enzyme linked to amino acid deamination. Molecular screening was conducted using AutoDock Vina (v1.1.2) with GDH receptors from Clostridium sp. (PDB: 1BGV).

Results:
Punicalagin, a tannin metabolite, showed the lowest affinity energy value as a deamination inhibitor, at -16.3 kcal/mol. Within the saponin group, Theasapogenol B displayed an affinity energy value reaching -11.4 kcal/mol, and cumin includes alpha-hederin, which has an affinity energy value reaching -11.3 kcal/mol for GDH inhibition. The smaller the affinity energy value, the greater the effectiveness in preventing deamination, indicating stronger inhibitory potential. Furthermore, the molecular dynamics data indicated that punicalagin, a metabolite from tannins, exhibited increased efficacy and measurable conformational stability as a deamination inhibitor.

Conclusion:
The secondary metabolites punicalagin (from tannins), Theasapogenol B (from saponins), and alpha-hederin (from cumin essential oil) showed optimal efficacy as deamination inhibitors in silage. Punicalagin demonstrated more optimal and stable results as a deamination inhibitor.

Key words: Deamination; Glutamate dehydrogenase; Molecular dynamic; Silage; Secondary metabolite.


 
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How to Cite this Article
Pubmed Style

Susanto I, Mahendra FR, Ridwan R, Wiryawan KG, Laconi EB, Jayanegara A. Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. Open Vet. J.. 2025; 15(11): 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40

Web Style

Susanto I, Mahendra FR, Ridwan R, Wiryawan KG, Laconi EB, Jayanegara A. Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. https://www.openveterinaryjournal.com/?mno=252796 [Access: November 30, 2025]. doi:10.5455/OVJ.2025.v15.i11.40

AMA (American Medical Association) Style

Susanto I, Mahendra FR, Ridwan R, Wiryawan KG, Laconi EB, Jayanegara A. Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. Open Vet. J.. 2025; 15(11): 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40


Vancouver/ICMJE Style

Susanto I, Mahendra FR, Ridwan R, Wiryawan KG, Laconi EB, Jayanegara A. Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. Open Vet. J.. (2025), [cited November 30, 2025]; 15(11): 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40


Harvard Style

Susanto, I., Mahendra, . F. R., Ridwan, . R., Wiryawan, . K. G., Laconi, . E. B. & Jayanegara, . A. (2025) Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. Open Vet. J., 15 (11), 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40


Turabian Style

Susanto, Irwan, Fachrul R. Mahendra, Roni Ridwan, Komang G. Wiryawan, Erika B. Laconi, and Anuraga Jayanegara. 2025. Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. Open Veterinary Journal, 15 (11), 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40


Chicago Style

Susanto, Irwan, Fachrul R. Mahendra, Roni Ridwan, Komang G. Wiryawan, Erika B. Laconi, and Anuraga Jayanegara. "Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach." Open Veterinary Journal 15 (2025), 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40


MLA (The Modern Language Association) Style

Susanto, Irwan, Fachrul R. Mahendra, Roni Ridwan, Komang G. Wiryawan, Erika B. Laconi, and Anuraga Jayanegara. "Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach." Open Veterinary Journal 15.11 (2025), 5838-5857. Print. doi:10.5455/OVJ.2025.v15.i11.40


APA (American Psychological Association) Style

Susanto, I., Mahendra, . F. R., Ridwan, . R., Wiryawan, . K. G., Laconi, . E. B. & Jayanegara, . A. (2025) Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach. Open Veterinary Journal, 15 (11), 5838-5857. doi:10.5455/OVJ.2025.v15.i11.40


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