Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps
Abstract Resistance-nodulation-cell devision (RND) efflux pump variants have attracted a great deal of attention for efflux of many antibiotic classes, which leads to multidrug-resistant bacteria. The present study aimed to discover the interaction between the RND efflux pumps and antibiotics, find...
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| Format: | Article |
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Nature Portfolio
2022-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-20278-5 |
| _version_ | 1818026020746297344 |
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| author | Hooria Seyedhosseini Ghaheh Mohammad Sadegh Damavandi Parisa Sadeghi Ahmad Reza Massah Taravat Hamidi Asl Azhar Salari-Jazi Seyed Hossein Hejazi |
| author_facet | Hooria Seyedhosseini Ghaheh Mohammad Sadegh Damavandi Parisa Sadeghi Ahmad Reza Massah Taravat Hamidi Asl Azhar Salari-Jazi Seyed Hossein Hejazi |
| author_sort | Hooria Seyedhosseini Ghaheh |
| collection | DOAJ |
| description | Abstract Resistance-nodulation-cell devision (RND) efflux pump variants have attracted a great deal of attention for efflux of many antibiotic classes, which leads to multidrug-resistant bacteria. The present study aimed to discover the interaction between the RND efflux pumps and antibiotics, find the conserved and hot spot residues, and use this information to target the most frequent RND efflux pumps. Protein sequence and 3D conformational alignments, pharmacophore modeling, molecular docking, and molecular dynamics simulation were used in the first level for discovering the function of the residues in interaction with antibiotics. In the second level, pharmacophore-based screening, structural-based screening, multistep docking, GRID MIF, pharmacokinetic modeling, fragment molecular orbital, and MD simulation were utilized alongside the former level information to find the most proper inhibitors. Five conserved residues, containing Ala209, Tyr404, Leu415, Asp416, and Ala417, as well as their counterparts in other OMPs were evaluated as the crucial conserved residues. MD simulation confirmed that a number of these residues had a key role in the performance of the efflux antibiotics; therefore, some of them were hot spot residues. Fourteen ligands were selected, four of which interacted with all the crucial conserved residues. NPC100251 was the fittest OMP inhibitor after pharmacokinetic computations. The second-level MD simulation and FMO supported the efficacy of the NPC100251. It was exhibited that perhaps OMPs worked as the intelligent and programable protein. NPC100251 was the strongest OMPs inhibitor, and may be a potential therapeutic candidate for MDR infections. |
| first_indexed | 2024-12-10T04:25:22Z |
| format | Article |
| id | doaj.art-d7cdd54df86b41aba192c27d692e6fd6 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-10T04:25:22Z |
| publishDate | 2022-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-d7cdd54df86b41aba192c27d692e6fd62022-12-22T02:02:17ZengNature PortfolioScientific Reports2045-23222022-09-0112112010.1038/s41598-022-20278-5Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumpsHooria Seyedhosseini Ghaheh0Mohammad Sadegh Damavandi1Parisa Sadeghi2Ahmad Reza Massah3Taravat Hamidi Asl4Azhar Salari-Jazi5Seyed Hossein Hejazi6Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical SciencesDepartment of Microbiology, School of Medicine, Isfahan University of Medical SciencesDepartment of Microbiology, School of Medicine, Isfahan University of Medical SciencesDepartment of Chemistry, Shahreza Branch, Islamic Azad UniversitySkin Diseases and Leishmaniasis Research Center, Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical SciencesDepartment of Drug Development and Innovation, Behban Pharmed LotusSkin Diseases and Leishmaniasis Research Center, Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical SciencesAbstract Resistance-nodulation-cell devision (RND) efflux pump variants have attracted a great deal of attention for efflux of many antibiotic classes, which leads to multidrug-resistant bacteria. The present study aimed to discover the interaction between the RND efflux pumps and antibiotics, find the conserved and hot spot residues, and use this information to target the most frequent RND efflux pumps. Protein sequence and 3D conformational alignments, pharmacophore modeling, molecular docking, and molecular dynamics simulation were used in the first level for discovering the function of the residues in interaction with antibiotics. In the second level, pharmacophore-based screening, structural-based screening, multistep docking, GRID MIF, pharmacokinetic modeling, fragment molecular orbital, and MD simulation were utilized alongside the former level information to find the most proper inhibitors. Five conserved residues, containing Ala209, Tyr404, Leu415, Asp416, and Ala417, as well as their counterparts in other OMPs were evaluated as the crucial conserved residues. MD simulation confirmed that a number of these residues had a key role in the performance of the efflux antibiotics; therefore, some of them were hot spot residues. Fourteen ligands were selected, four of which interacted with all the crucial conserved residues. NPC100251 was the fittest OMP inhibitor after pharmacokinetic computations. The second-level MD simulation and FMO supported the efficacy of the NPC100251. It was exhibited that perhaps OMPs worked as the intelligent and programable protein. NPC100251 was the strongest OMPs inhibitor, and may be a potential therapeutic candidate for MDR infections.https://doi.org/10.1038/s41598-022-20278-5 |
| spellingShingle | Hooria Seyedhosseini Ghaheh Mohammad Sadegh Damavandi Parisa Sadeghi Ahmad Reza Massah Taravat Hamidi Asl Azhar Salari-Jazi Seyed Hossein Hejazi Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps Scientific Reports |
| title | Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps |
| title_full | Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps |
| title_fullStr | Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps |
| title_full_unstemmed | Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps |
| title_short | Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps |
| title_sort | targeting and ultrabroad insight into molecular basis of resistance nodulation cell division efflux pumps |
| url | https://doi.org/10.1038/s41598-022-20278-5 |
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