Molecular identification of the blaOXA gene in Bacillus cereus and AI-driven optimization of natural phytochemicals for foodborne illness treatment.

The rise of antibiotic-resistant Bacillus cereus strains, particularly those carrying the blaOXA gene encoding oxacillinase-type β-lactamase, has significantly limited treatment options for foodborne illnesses. This study aimed to identify blaOXA-positive Bacillus cereus from environmental samples and evaluate AI-optimized phytochemicals as novel inhibitors of the blaOXA enzyme. Soil-derived bacterial isolates were identified via 16S rRNA gene amplification and Sanger sequencing. Antibiotic susceptibility was assessed using the disc diffusion method. The blaOXA gene was amplified and sequenced, followed by phylogenetic analysis. The blaOXA protein was modeled using AlphaFold3 and validated by the Ramachandran plot and ERRAT. Thirty phytochemicals were screened using molecular docking against blaOXA protein. Piperine emerged as the top candidate and was optimized using the WADDAICA AI tool. AI-modified derivatives were evaluated through docking, ADMET, toxicity, density functional theory (DFT), molecular dynamics (MD) simulations, and pharmacophore analysis. The isolated strain MBBL37 was confirmed as B. cereus (NCBI Accession: PVO14952.1), resistant to ampicillin and cefoxitin. The blaOXA gene (632 bp; Accession: PV535213.1) showed phylogenetic similarity with Enterobacter and E. coli, suggesting potential horizontal transfer. The predicted blaOXA protein demonstrated high stereochemical reliability (87.8% residues in favored regions; ERRAT score: 100%). Piperine showed the best natural docking score (- 6.9 kcal/mol), while the AI-optimized compound 2 exhibited superior binding (- 7.3 kcal/mol) compared to standard antibiotics (e.g., cefotaxime, - 6.5 kcal/mol). MD simulations confirmed complex stability, and DFT analysis showed a favorable energy gap (0.20 a.u). AI-modified Piperine showed improved pharmacokinetics, reduced CYP interactions, and lower toxicity. However, these findings are based on in silico analyses and require further validation through in vitro and in vivo studies to confirm biological activity, safety, and therapeutic potential.