Computational Exploration of Linoelaidic Acid Identified from GC–MS Profiling of <i>Lactiplantibacillus plantarum</i> YW11 with Safety Evaluation Against Bos taurus Milk Protein Allergens

Cow’s Milk Allergy (CMA) remains one of the most common food allergies, particularly in children, with several milk-derived proteins identified as the major allergens responsible for IgE-mediated hypersensitivity reactions, including [Formula: see text]-lactalbumin (Bos d 4), [Formula: see text]-lactoglobulin (Bos d 5), serum albumin (Bos d 6) and [Formula: see text]S1-casein (Bos d 9). Conventional therapies often carry limitations such as incomplete efficacy or safety concerns, necessitating the exploration of safer alternatives. This study aimed to evaluate probiotic-derived fatty acid metabolites, with a particular focus on linoelaidic acid, as potential therapeutic agents against milk allergens. A GC–MS profile of probiotic metabolites was constructed, followed by allergenicity screening of milk proteins. The allergen proteins were retrieved and subjected to molecular docking with identified fatty acids. Linoelaidic acid exhibited strong binding affinities (−8.4 kcal/mol to −9.1 kcal/mol) with major allergens and demonstrated stability across 100 ns MD simulations, suggesting potential for nutraceutical application. Molecular dynamics (100 ns) confirmed the structural stability and compactness of the docked complexes, supported by RMSD stabilization (0.7–0.9 nm for [Formula: see text]-lactalbumin, 0.6–0.7 nm for [Formula: see text]-lactoglobulin, 2.5 nm for [Formula: see text]S1-casein and 0.34 nm for serum albumin) and hydrogen bonding consistency ([Formula: see text]300 in [Formula: see text]S1-casein complex, [Formula: see text]1350 in serum albumin). Pharmacokinetic profiling through SwissADME demonstrated favorable drug-like properties, while ProTox-II analysis classified linoelaidic acid as nontoxic (Drug Class VI). These findings suggest that linoelaidic acid holds strong therapeutic potential for mitigating CMA. This study is based on computational predictions and requires experimental validation to confirm their biological relevance and therapeutic potential. Future prospects include in vitro and in vivo validation to confirm its immunomodulatory and clinical efficacy.