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

Silage technology ensures year-round feed for ruminants, and phytobiotics, such as tannin, saponin, and cumin, can enhance ruminant survival by maintaining nutritional content and inhibiting decay.

This study evaluated 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).

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

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, including alpha-hederin, 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.

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 optimal and stable results as a deamination inhibitor.