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<p>Among the persistent environmental pollutants with well-established toxic, mutagenic, and carcinogenic properties are Phenolic compounds and polycyclic aromatic hydrocarbons (PAHs). This study applied an in-silico framework to evaluate the predicted binding affinity of <i>Sphingomonas paucimobilis</i> protocatechuate 4,5-dioxygenase (LigAB; PDB ID: 1BOU) against selected phenolic derivatives and polycyclic aromatic hydrocarbons. Functional annotation via QuickGO confirmed its oxidoreductase and dioxygenase roles in aromatic ring cleavage. Binding site prediction using PrankWeb identified nine putative catalytic pockets. Nineteen environmentally relevant pollutants were retrieved from PubChem and subjected to molecular docking with LigAB using PyRx. Among them, dibenzo[a,h]anthracene (−&#xa0;8.8&#xa0;kcal/mol), benzo[a]pyrene (−&#xa0;8.2&#xa0;kcal/mol), and chrysene (−&#xa0;7.7&#xa0;kcal/mol) exhibited the strongest affinities, stabilized by π–π stacking, π–alkyl, and hydrogen bonding interactions as revealed by Discovery Studio. Toxicity profiling through ProTox 3.0 indicated moderate acute toxicity (LD<sub>50</sub> = 316&#xa0;mg/kg) for dibenzo[a,h]anthracene, alongside high hepatotoxic, mutagenic, and carcinogenic risks, underscoring the environmental urgency of its removal. Collectively, these findings highlight LigAB as a promising microbial biocatalyst for targeting recalcitrant polycyclic aromatic hydrocarbons and demonstrate the utility of computational pipelines for rapid enzyme–substrate screening in bioremediation research.</p>

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In silico evaluation of protocatechuate 4,5-dioxygenase for environmental detoxification of persistent organic pollutants

  • 期刊论文

  • 发表日期：

    2026年4月2日

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  • Muhammad Naveed,
  • Maryum Rasheed,
  • Maida Salah Ud Din,
  • Minahil Zahid,
  • Ayaz Ali Khan,
  • Mayasar I. Al Zaban,
  • Ashwag Shami,
  • Hayam A. Alwabsi

摘要

Among the persistent environmental pollutants with well-established toxic, mutagenic, and carcinogenic properties are Phenolic compounds and polycyclic aromatic hydrocarbons (PAHs). This study applied an in-silico framework to evaluate the predicted binding affinity of Sphingomonas paucimobilis protocatechuate 4,5-dioxygenase (LigAB; PDB ID: 1BOU) against selected phenolic derivatives and polycyclic aromatic hydrocarbons. Functional annotation via QuickGO confirmed its oxidoreductase and dioxygenase roles in aromatic ring cleavage. Binding site prediction using PrankWeb identified nine putative catalytic pockets. Nineteen environmentally relevant pollutants were retrieved from PubChem and subjected to molecular docking with LigAB using PyRx. Among them, dibenzo[a,h]anthracene (− 8.8 kcal/mol), benzo[a]pyrene (− 8.2 kcal/mol), and chrysene (− 7.7 kcal/mol) exhibited the strongest affinities, stabilized by π–π stacking, π–alkyl, and hydrogen bonding interactions as revealed by Discovery Studio. Toxicity profiling through ProTox 3.0 indicated moderate acute toxicity (LD50 = 316 mg/kg) for dibenzo[a,h]anthracene, alongside high hepatotoxic, mutagenic, and carcinogenic risks, underscoring the environmental urgency of its removal. Collectively, these findings highlight LigAB as a promising microbial biocatalyst for targeting recalcitrant polycyclic aromatic hydrocarbons and demonstrate the utility of computational pipelines for rapid enzyme–substrate screening in bioremediation research.