The present study aimed to investigate the decolorization of various commercial dyes by azoreductases (AzrBmH21, AzrBmH22/3, and AzrBmH24/5) through bioinformatics means, comprising molecular docking, molecular dynamics simulation, and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA). Therefore, four commercial dyes, namely acid orange 7, cresol red, methylene blue, and malachite green, were selected as potential targets for degradation by the above said azoreductases derived from Bacillus megaterium H2. The prediction of ligand binding or catalytic sites for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 were performed using a machine learning algorithm based on the Prank Web and DeepSite chemoinformatic tool. This analysis revealed that several amino acids of AzrBmH2 interacted with the tested dyes, indicating the presence of distinct ligand-binding sites for AzrBmH2-dye complexes. Likewise, the binding affinity for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 ranged from − 9.4 to − 5.5 kcal/mol, − 9.2 to − 5.4 kcal/mol, and − 9.0 to − 5.4 kcal/mol, respectively, with each complex stabilized at a minimum of 0–5 hydrogen bonds. MD simulations revealed stable AzrBmH2-dye complexes with RMSD and RMSF values ranging from 0.15 to 0.42 nm and 0.05 to 0.48 nm, respectively, with Rg values between 1.75 and 1.88 nm. MM-PBSA calculations indicated that the AzrBmH2–dye complexes, except for AzrBmH2–malachite green, exhibited the lowest binding energy (− 191.05 ± 7.08 to 314.19 ± 6.88 kcal/mol), with prevalent hydrophobic interactions (− 268.25 ± 12.25 to − 418.92 ± 29.45 kcal/mol) through van der Waals forces. Therefore, this study was able to highlight the potential role of enzymes, specifically azoreductases from Bacillus megaterium H2, in predicting the decolorization of commercial dyes. These findings could contribute to our understanding of the azoreductases’ mechanisms in bioremediation and for biotechnological applications.

本研究旨在通过生物信息学手段，包括分子对接、分子动力学模拟和分子力学泊松-玻尔兹曼表面积（MM-PBSA）研究偶氮还原酶（AzrBmH21、AzrBmH22/3和AzrBmH24/5）对各种商业染料的脱色作用。 ）。因此，选择四种商业染料，即酸性橙7、甲酚红、亚甲基蓝和孔雀石绿作为上述源自巨大芽孢杆菌H2的偶氮还原酶降解的潜在靶标。使用基于 Prank Web 和 DeepSite 化学信息学工具的机器学习算法预测 AzrBmH21、AzrBmH22/3 和 AzrBmH24/5 的配体结合或催化位点。该分析表明 AzrBmH2 的几个氨基酸与测试的染料相互作用，表明 AzrBmH2-染料复合物存在不同的配体结合位点。同样，AzrBmH21、AzrBmH22/3 和 AzrBmH24/5 的结合亲和力范围分别为 - 9.4 至 - 5.5 kcal/mol、- 9.2 至 - 5.4 kcal/mol 和 - 9.0 至 - 5.4 kcal/mol。复合物稳定在至少 0-5 个氢键。MD 模拟显示稳定的 AzrBmH2-染料复合物，RMSD 和 RMSF 值分别为 0.15 至 0.42 nm 和 0.05 至 0.48 nm，Rg 值在 1.75 至 1.88 nm 之间。MM-PBSA 计算表明，除 AzrBmH2-孔雀石绿外，AzrBmH2-染料复合物表现出最低的结合能（− 191.05 ± 7.08 至 314.19 ± 6.88 kcal/mol），具有普遍的疏水相互作用（− 268.25 ± 12.25 至 − 418.92） ± 29.45 kcal/mol) 通过范德华力。因此，本研究能够强调酶（特别是来自巨大芽孢杆菌H2 的偶氮还原酶）在预测商业染料脱色方面的潜在作用。这些发现可能有助于我们了解偶氮还原酶在生物修复和生物技术应用中的机制。