A Bacillus amyloliquefaciens serine protease reduces ELISA-detectable epitopes of major indoor allergens: Computational modeling of the Fel d 1 binding interface.

Indoor allergens from pets and dust mites are persistent biological pollutants that pose significant risks to human health, yet effective and environmentally sustainable control strategies remain limited. Here, we isolated Bacillus amyloliquefaciens Ba2501, which secretes a subtilisin-family serine protease. Whole-cell co-culture assays demonstrated that Ba2501 reduces ELISA-detectable epitopes of three major indoor allergens-Fel d 1 (cat), Can f 1 (dog), and Der p 1 (dust mite). ELISA signals of Der p 1 and Fel d 1 became nearly undetectable within 48-72 h (99.86% and 100% reduction, respectively), while Can f 1 showed a more gradual decrease (67.83% at 72 h). To gain structural insights, we focused on Fel d 1 as a model and performed molecular docking, 200 ns molecular dynamics simulations, and MMPBSA analysis. The subtilisin-Fel d 1 complex exhibited a large buried interface (2392 Å2) stabilized by a salt bridge, short hydrogen bonds, and hydrophobic contacts. Residue-wise energy decomposition identified key interfacial residues driving the interaction. These findings provide a structural basis for protease-mediated allergen recognition and identify B. amyloliquefaciens Ba2501 as a promising candidate for developing environmentally sustainable, enzyme-based strategies to mitigate indoor allergen exposure and improve indoor air quality.