“Integrating experimental and In silico approaches to elucidate the potential role of Lignin Peroxidase in crude oil biodegradation by Phanerochaete chrysosporium ”

Crude oil contamination remains a major environmental concern due to the persistence and toxicity of polycyclic aromatic hydrocarbons (PAHs). This study integrated experimental biodegradation assays, GC–MS profiling, principal component analysis (PCA), molecular docking, and molecular dynamics simulation to evaluate the role of lignin peroxidase (LiP) in crude oil biodegradation by Phanerochaete chrysosporium. Over a 21-day incubation period, total petroleum hydrocarbon (TPH) concentration decreased from an initial value of 510 mg/L to 82.6 ± 4.8 mg/L after P. chrysosporium treatment, representing an apparent removal efficiency of 83.8%. After correction for abiotic losses observed in the sterile control, fungal-mediated TPH biodegradation was estimated at 73.0%, indicating substantial biological contribution to hydrocarbon removal. Increased ligninolytic enzyme activities accompanied this reduction, with maximum activities recorded on Day 14 for laccase (∼4.2 U/mL), manganese peroxidase (∼3.9 U/mL), and lignin peroxidase (∼3.6 U/mL). CO2 evolution increased from approximately 8 to 42 mg/100 mL, while pH declined from 7.2 to 6.2, indicating active mineralization and metabolic transformation of hydrocarbons. GC–MS analysis showed substantial reduction in individual PAHs after degradation, including phenanthrene, naphthalene, chrysene, pyrene, and fluoranthene. PCA further associated hydrocarbon reduction with increased enzymatic activity, particularly LiP. Molecular docking revealed favorable LiP–PAH interactions, with docking scores ranging from −9.651 kcal/mol for Benzo[a]pyrene to −5.122 kcal/mol for Naphthalene. Key interacting residues included PHE46, PHE265, LEU173, HIS176, and ARG43, suggesting hydrophobic stabilization, π–π stacking, and hydrogen-bond contributions within the catalytic pocket. “The findings demonstrate that P. chrysosporium effectively degraded crude oil hydrocarbons and suggest that lignin peroxidase may contribute to PAH transformation under the tested conditions, although further enzyme-specific investigations are required for confirmation.”