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. 2024 Jun 4;35(1):28.
doi: 10.1007/s10856-024-06799-7.

In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations

Ravinder S Saini  1 , Rayan Ibrahim H Binduhayyim  1 , Vishwanath Gurumurthy  1 , Abdulkhaliq Ali F Alshadidi  1 , Shashit Shetty Bavabeedu  2 , Rajesh Vyas  1 , Doni Dermawan  3 , Punnoth Poonkuzhi Naseef  4 , Seyed Ali Mosaddad  5   6 , Artak Heboyan  7   8   9
Affiliations

In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations

Ravinder S Saini et al. J Mater Sci Mater Med. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. .
Chemical visualization. a 2D structure of MMA. b 2D structure of PMMA. c Minimized 3D structure of MMA. d Minimized 3D structure of PMMA
Fig. 2
Fig. 2
Molecular docking simulation results. a The 3D perspective of the TRAP: MMA complex. b The 2D perspective of the TRAP: MMA complex. c The 3D perspective of TRAP: PMMA complex. d The 2D perspective of TRAP: PMMA complex
Fig. 3
Fig. 3
Molecular dynamics (MD) simulation results. a RMSD of top 5 MMA complexes. b RMSF of top 5 MMA complexes. c RMSD of top 5 PMMA complexes. d RMSF of top 5 PMMA complexes
See this image and copyright information in PMC

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