In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations
Abstract Aim: This study aimed to comprehensively assess the biocompatibility and toxicity profiles of poly(methyl methacrylate) (PMMA) and its monomeric unit, methyl methacrylate (MMA), crucial components in dental materials for interim prosthetic restorations. Methodology: Molecular docking was em...
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| Format: | Article |
| Language: | English |
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Springer
2024-06-01
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| Series: | Journal of Materials Science: Materials in Medicine |
| Online Access: | https://doi.org/10.1007/s10856-024-06799-7 |
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| author | Ravinder S. Saini Rayan Ibrahim H. Binduhayyim Vishwanath Gurumurthy Abdulkhaliq Ali F. Alshadidi Shashit Shetty Bavabeedu Rajesh Vyas Doni Dermawan Punnoth Poonkuzhi Naseef Seyed Ali Mosaddad Artak Heboyan |
| author_facet | Ravinder S. Saini Rayan Ibrahim H. Binduhayyim Vishwanath Gurumurthy Abdulkhaliq Ali F. Alshadidi Shashit Shetty Bavabeedu Rajesh Vyas Doni Dermawan Punnoth Poonkuzhi Naseef Seyed Ali Mosaddad Artak Heboyan |
| author_sort | Ravinder S. Saini |
| collection | DOAJ |
| description | Abstract Aim: This study aimed to comprehensively assess the biocompatibility and toxicity profiles of poly(methyl methacrylate) (PMMA) and its monomeric unit, methyl methacrylate (MMA), crucial components in dental materials for interim prosthetic restorations. Methodology: Molecular docking was employed to predict the binding affinities, energetics, and steric features of MMA and PMMA with selected receptors involved in bone metabolism and tissue development, including RANKL, Fibronectin, BMP9, NOTCH2, and other related receptors. The HADDOCK standalone version was utilized for docking calculations, employing a Lamarckian genetic algorithm to explore the conformational space of ligand-receptor interactions. Furthermore, molecular dynamics (MD) simulations over 100 nanoseconds were conducted using the GROMACS package to evaluate dynamic actions and structural stability. The LigandScout was utilized for pharmacophore modeling, which employs a shape-based screening approach to identify potential ligand binding sites on protein targets. Results: The molecular docking studies elucidated promising interactions between PMMA and MMA with key biomolecular targets relevant to dental applications. MD simulation results provided strong evidence supporting the structural stability of PMMA complexes over time. Pharmacophore modeling highlighted the significance of carbonyl and hydroxyl groups as pharmacophoric features, indicating compounds with favorable biocompatibility profiles. Conclusion: This study underscores the potential of PMMA in dental applications, emphasizing its structural stability, molecular interactions, and safety considerations. These findings lay a foundation for future advancements in dental biomaterials, guiding the design and optimization of materials for enhanced biocompatibility. Future directions include experimental validation of computational findings and the development of PMMA-based dental materials with improved biocompatibility and clinical performance. Graphical Abstract |
| format | Article |
| id | doaj-art-02a6fb2083b74c16b99fd30708f6163f |
| institution | Kabale University |
| issn | 1573-4838 |
| language | English |
| publishDate | 2024-06-01 |
| publisher | Springer |
| record_format | Article |
| series | Journal of Materials Science: Materials in Medicine |
| spelling | doaj-art-02a6fb2083b74c16b99fd30708f6163f2024-12-22T12:10:43ZengSpringerJournal of Materials Science: Materials in Medicine1573-48382024-06-0135111910.1007/s10856-024-06799-7In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorationsRavinder S. Saini0Rayan Ibrahim H. Binduhayyim1Vishwanath Gurumurthy2Abdulkhaliq Ali F. Alshadidi3Shashit Shetty Bavabeedu4Rajesh Vyas5Doni Dermawan6Punnoth Poonkuzhi Naseef7Seyed Ali Mosaddad8Artak Heboyan9Department of Dental Technology, COAMS, King Khalid UniversityDepartment of Dental Technology, COAMS, King Khalid UniversityDepartment of Dental Technology, COAMS, King Khalid UniversityDepartment of Dental Technology, COAMS, King Khalid UniversityDepartment of Restorative Dentistry, College of Dentistry, King Khalid UniversityDepartment of Dental Technology, COAMS, King Khalid UniversityDepartment of Chemistry, Warsaw University of TechnologyDepartment of Pharmaceutics, Moulana College of PharmacyDepartment of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha UniversityDepartment of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha UniversityAbstract Aim: This study aimed to comprehensively assess the biocompatibility and toxicity profiles of poly(methyl methacrylate) (PMMA) and its monomeric unit, methyl methacrylate (MMA), crucial components in dental materials for interim prosthetic restorations. Methodology: Molecular docking was employed to predict the binding affinities, energetics, and steric features of MMA and PMMA with selected receptors involved in bone metabolism and tissue development, including RANKL, Fibronectin, BMP9, NOTCH2, and other related receptors. The HADDOCK standalone version was utilized for docking calculations, employing a Lamarckian genetic algorithm to explore the conformational space of ligand-receptor interactions. Furthermore, molecular dynamics (MD) simulations over 100 nanoseconds were conducted using the GROMACS package to evaluate dynamic actions and structural stability. The LigandScout was utilized for pharmacophore modeling, which employs a shape-based screening approach to identify potential ligand binding sites on protein targets. Results: The molecular docking studies elucidated promising interactions between PMMA and MMA with key biomolecular targets relevant to dental applications. MD simulation results provided strong evidence supporting the structural stability of PMMA complexes over time. Pharmacophore modeling highlighted the significance of carbonyl and hydroxyl groups as pharmacophoric features, indicating compounds with favorable biocompatibility profiles. Conclusion: This study underscores the potential of PMMA in dental applications, emphasizing its structural stability, molecular interactions, and safety considerations. These findings lay a foundation for future advancements in dental biomaterials, guiding the design and optimization of materials for enhanced biocompatibility. Future directions include experimental validation of computational findings and the development of PMMA-based dental materials with improved biocompatibility and clinical performance. Graphical Abstracthttps://doi.org/10.1007/s10856-024-06799-7 |
| spellingShingle | Ravinder S. Saini Rayan Ibrahim H. Binduhayyim Vishwanath Gurumurthy Abdulkhaliq Ali F. Alshadidi Shashit Shetty Bavabeedu Rajesh Vyas Doni Dermawan Punnoth Poonkuzhi Naseef Seyed Ali Mosaddad Artak Heboyan In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations Journal of Materials Science: Materials in Medicine |
| title | In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations |
| title_full | In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations |
| title_fullStr | In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations |
| title_full_unstemmed | In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations |
| title_short | In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations |
| title_sort | in silico assessment of biocompatibility and toxicity molecular docking and dynamics simulation of pmma based dental materials for interim prosthetic restorations |
| url | https://doi.org/10.1007/s10856-024-06799-7 |
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