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<p>Phthalates, bisphenols, dioxins, and brominated flame retardants are among the persistent pollutants that have been brought into the environment by the rapid increase of xenobiotic chemicals. These pollutants represent serious threats to both the environment and human health. The need for sustainable alternatives is highlighted by the inefficiency and environmental harm of conventional disposal methods. In this study, we used computational methods to examine the biodegradation potential of dye-decolorizing peroxidase (DyP) from <i>Amycolatopsis japonica</i>. After obtaining the DyP protein sequence from NCBI and modeling it with AlphaFold, PROCHECK and ERRAT were used for structural validation. Complete catabolic modules for the breakdown of aromatic and halogenated chemicals were found by KEGG pathway analysis. Two possible active pockets were found using PrankWeb’s binding site prediction; Pocket 1 had the highest confidence score. Strong binding affinities were shown by molecular docking with 28 plasticizers and phenolic-derived xenobiotic compounds; the most promising substrates were naftalofos (–8.8&#xa0;kcal/mol), benzyl butyl phthalate (–8.4&#xa0;kcal/mol), and 2,3,7,8-Tetrachlorodibenzo-p-dioxin-P-Dioxin (–8.4&#xa0;kcal/mol). In the DyP active site, interaction analysis identified hydrophobic interactions and stable hydrogen bonds, especially involving Asp415, His323, and Arg348. These findings identify <i>Amycolatopsis japonica</i> DyP as a promising biocatalyst for xenobiotic degradation, giving structural and mechanistic insights for future enzyme engineering and scalable applications in biotechnology.</p>

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Exploring the biocatalytic potential of Amycolatopsis japonica DyP in degrading plasticizer and phenolic-derived xenobiotic compounds

  • 期刊论文

  • 发表日期：

    2026年2月9日

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  • Muhammad Naveed,
  • Ayesha Saleem,
  • Tariq Aziz,
  • Sadia Jabeen,
  • Sana Miraj Khan,
  • Maida Salah Ud Din,
  • Nantenaina Tombozara,
  • Mayasar I. Al-zaban,
  • Ashwag Shami,
  • Hayam A. Alwabsi

摘要

Phthalates, bisphenols, dioxins, and brominated flame retardants are among the persistent pollutants that have been brought into the environment by the rapid increase of xenobiotic chemicals. These pollutants represent serious threats to both the environment and human health. The need for sustainable alternatives is highlighted by the inefficiency and environmental harm of conventional disposal methods. In this study, we used computational methods to examine the biodegradation potential of dye-decolorizing peroxidase (DyP) from Amycolatopsis japonica. After obtaining the DyP protein sequence from NCBI and modeling it with AlphaFold, PROCHECK and ERRAT were used for structural validation. Complete catabolic modules for the breakdown of aromatic and halogenated chemicals were found by KEGG pathway analysis. Two possible active pockets were found using PrankWeb’s binding site prediction; Pocket 1 had the highest confidence score. Strong binding affinities were shown by molecular docking with 28 plasticizers and phenolic-derived xenobiotic compounds; the most promising substrates were naftalofos (–8.8 kcal/mol), benzyl butyl phthalate (–8.4 kcal/mol), and 2,3,7,8-Tetrachlorodibenzo-p-dioxin-P-Dioxin (–8.4 kcal/mol). In the DyP active site, interaction analysis identified hydrophobic interactions and stable hydrogen bonds, especially involving Asp415, His323, and Arg348. These findings identify Amycolatopsis japonica DyP as a promising biocatalyst for xenobiotic degradation, giving structural and mechanistic insights for future enzyme engineering and scalable applications in biotechnology.