Molecular Recognition of Dental Resin Monomers by Salivary Proteins: Integrated Docking, DFT, Molecular Dynamics, and MM/PBSA Analysis
5 affiliations
- 1Department of Allied Dental Health Sciences COAMS King Khalid University Abha Saudi Arabia
- 2Department of Prosthodontics College of Dentistry King Khalid University Abha Saudi Arabia
- 3Department of Research Analytics Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University Chennai India
- 4Department of Prosthodontics Faculty of Stomatology Yerevan State Medical University after Mkhitar Heratsi Yerevan Armenia
- 5Department of Prosthodontics School of Dentistry Tehran University of Medical Sciences Tehran Iran
Abstract
An in silico investigation was performed to study the interactions between the commonly encountered resin monomers and the major salivary proteins. Bisphenyl diglycidylmethane (Bis-GMA), hydroxyethyl methacrylate (HEMA), and triethylene glycol dimethacrylate (TEGDMA) were assessed for molecular docking, density functional theory (DFT), molecular dynamics (MD), MM/PBSA binding free-energy calculations, and per-residue energy decomposition. α-amylase, lysozyme, and albumin emerged as critical predicted targets from the docking process. DFT calculations found Bis-GMA to possess the largest HOMO-LUMO gap (8.88 eV), suggestive of reduced electronic reactivity, and TEGDMA to have the smallest gap (5.56 eV) as well as the largest dipole moment (3.88 D), indicative of increased polarity. Mean solvent accessible surface areas (SASAs) determined through MD trajectories suggest a trend of increased conformational stability with Bis-GMA. More favorable mean MM/PBSA predicted binding free energies were calculated with Bis-GMA, especially with albumin (-24.53 ± 5.12 kcal/mol) and α-amylase (-17.63 ± 7.60 kcal/mol). Residue-decomposition heatmaps displayed mixed favorable and unfavorable contributions, which were interpreted descriptively. Recognition of monomers by salivary proteins appears to correlate with molecular dimensions, hydrophobicity, polarity, and electronic properties. These observations are preliminary calculations that require experimental evidence to reach clinical or functional conclusions.
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BibTeX
@article{saini2026molecular,
title = {{Molecular Recognition of Dental Resin Monomers by Salivary Proteins: Integrated Docking, DFT, Molecular Dynamics, and MM/PBSA Analysis}},
author = {Ravinder S. Saini and Fahad Hussain Alhamoudi and Rayan Ibrahim H. Binduhayyim and Abdulkhaliq Ali F. Alshadidi and Abdullah Hassan A. Alshehri and Abdulmajeed Okshah and Ahid Amer Alshahrani and Mohamed Saheer Kuruniyan and Vishwanath Gurumurthy and Masroor Ahmed Kanji and Artak Heboyan},
journal = {ChemistryOpen},
year = {2026},
month = nov,
doi = {10.1002/open.70332},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/open.70332},
note = {CC BY},
}
RIS
TY - JOUR
TI - Molecular Recognition of Dental Resin Monomers by Salivary Proteins: Integrated Docking, DFT, Molecular Dynamics, and MM/PBSA Analysis
AU - Ravinder S. Saini
AU - Fahad Hussain Alhamoudi
AU - Rayan Ibrahim H. Binduhayyim
AU - Abdulkhaliq Ali F. Alshadidi
AU - Abdullah Hassan A. Alshehri
AU - Abdulmajeed Okshah
AU - Ahid Amer Alshahrani
AU - Mohamed Saheer Kuruniyan
AU - Vishwanath Gurumurthy
AU - Masroor Ahmed Kanji
AU - Artak Heboyan
PY - 2026
DA - 2026/11/01
JO - ChemistryOpen
DO - 10.1002/open.70332
UR - https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/open.70332
AB - An in silico investigation was performed to study the interactions between the commonly encountered resin monomers and the major salivary proteins. Bisphenyl diglycidylmethane (Bis-GMA), hydroxyethyl methacrylate (HEMA), and triethylene glycol dimethacrylate (TEGDMA) were assessed for molecular docking, density functional theory (DFT), molecular dynamics (MD), MM/PBSA binding free-energy calculations, and per-residue energy decomposition. α-amylase, lysozyme, and albumin emerged as critical predicted targets from the docking process. DFT calculations found Bis-GMA to possess the largest HOMO-LUMO gap (8.88 eV), suggestive of reduced electronic reactivity, and TEGDMA to have the smallest gap (5.56 eV) as well as the largest dipole moment (3.88 D), indicative of increased polarity. Mean solvent accessible surface areas (SASAs) determined through MD trajectories suggest a trend of increased conformational stability with Bis-GMA. More favorable mean MM/PBSA predicted binding free energies were calculated with Bis-GMA, especially with albumin (-24.53 ± 5.12 kcal/mol) and α-amylase (-17.63 ± 7.60 kcal/mol). Residue-decomposition heatmaps displayed mixed favorable and unfavorable contributions, which were interpreted descriptively. Recognition of monomers by salivary proteins appears to correlate with molecular dimensions, hydrophobicity, polarity, and electronic properties. These observations are preliminary calculations that require experimental evidence to reach clinical or functional conclusions.
SN - 2191-1363
SN - 2191-1363
ER -