Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes
Abstract 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-...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2024-02-01
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| Series: | Environmental Sciences Europe |
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| Online Access: | https://doi.org/10.1186/s12302-024-00853-5 |
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| author | Habeebat Adekilekun Oyewusi Roswanira Abdul Wahab Kolajo Adedamola Akinyede Ghadeer M. Albadrani Muath Q. Al-Ghadi Mohamed M. Abdel-Daim Basiru Olaitan Ajiboye Fahrul Huyop |
| author_facet | Habeebat Adekilekun Oyewusi Roswanira Abdul Wahab Kolajo Adedamola Akinyede Ghadeer M. Albadrani Muath Q. Al-Ghadi Mohamed M. Abdel-Daim Basiru Olaitan Ajiboye Fahrul Huyop |
| author_sort | Habeebat Adekilekun Oyewusi |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-07T15:15:19Z |
| format | Article |
| id | doaj.art-9f0d7b1c2bf449a0bea351b6322a6a7a |
| institution | Directory Open Access Journal |
| issn | 2190-4715 |
| language | English |
| last_indexed | 2024-03-07T15:15:19Z |
| publishDate | 2024-02-01 |
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| series | Environmental Sciences Europe |
| spelling | doaj.art-9f0d7b1c2bf449a0bea351b6322a6a7a2024-03-05T17:58:21ZengSpringerOpenEnvironmental Sciences Europe2190-47152024-02-0136112010.1186/s12302-024-00853-5Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyesHabeebat Adekilekun Oyewusi0Roswanira Abdul Wahab1Kolajo Adedamola Akinyede2Ghadeer M. Albadrani3Muath Q. Al-Ghadi4Mohamed M. Abdel-Daim5Basiru Olaitan Ajiboye6Fahrul Huyop7Department of Biosciences, Faculty of Science, Universiti Teknologi MalaysiaDepartment of Chemistry, Faculty of Science, Universiti Teknologi MalaysiaDepartment of Science Technology, Biochemistry unit, The Federal PolytechnicDepartment of Biology, College of Science, Princess Nourah Bint Abdulrahman UniversityDepartment of Zoology, College of Science, King Saud UniversityDepartment of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical CollegePhytomedicine and Molecular Toxicology Research Laboratory, Department of Biochemistry, Federal University Oye-EkitiDepartment of Biosciences, Faculty of Science, Universiti Teknologi MalaysiaAbstract 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.https://doi.org/10.1186/s12302-024-00853-5AzoreductasesBacillus megateriumDegradationSynthetic dyesMolecular dockingMolecular dynamics simulation |
| spellingShingle | Habeebat Adekilekun Oyewusi Roswanira Abdul Wahab Kolajo Adedamola Akinyede Ghadeer M. Albadrani Muath Q. Al-Ghadi Mohamed M. Abdel-Daim Basiru Olaitan Ajiboye Fahrul Huyop Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes Environmental Sciences Europe Azoreductases Bacillus megaterium Degradation Synthetic dyes Molecular docking Molecular dynamics simulation |
| title | Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes |
| title_full | Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes |
| title_fullStr | Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes |
| title_full_unstemmed | Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes |
| title_short | Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes |
| title_sort | bioinformatics analysis and molecular dynamics simulations of azoreductases azrbmh2 from bacillus megaterium h2 for the decolorization of commercial dyes |
| topic | Azoreductases Bacillus megaterium Degradation Synthetic dyes Molecular docking Molecular dynamics simulation |
| url | https://doi.org/10.1186/s12302-024-00853-5 |
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