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.