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From a biomedical standpoint, how do the authors account for the biological complexity of the oral environment, such as enzymatic degradation, salivary interactions, and microbial biofilm formation, which may significantly influence the long-term biocompatibility and mechanical integrity of these materials? Would the absence of in vitro or in vivo validation risk oversimplifying these interactions and overestimating the clinical utility of the proposed formulations?
In the Molecular docking simulations section (page 3), the authors state: “Importantly, in this step, the simulations were carried out without including specific receptors, which allowed for a more comprehensive and open-ended exploration of the intermolecular interactions.”
This approach represents a significant and potentially critical deviation from standard molecular docking practice. Molecular docking is fundamentally a technique to predict the preferred orientation and binding affinity of a ligand to a target/receptor with a known binding site. The scoring functions in docking software (like HADDOCK) are parameterized and validated for such ligand-receptor interactions, accounting for shape complementarity, electrostatic potentials, and desolvation effects within a defined binding pocket.
Without a defined receptor or binding site, what structural frame of reference was used to calculate the “binding energy”? The reported energies (e.g., -37.6 kcal/mol for TEGDMA-SiO2-TRIS) are exceptionally high for non-covalent interactions between small molecules and fillers in a solvent-free vacuum simulation. Are these energies representative of dimerization energies, adsorption energies onto a surface, or something else?
How were the “active residues” and “passive residues” defined for the ligands (monomers, fillers, agents) in the absence of a receptor? In HADDOCK, these definitions typically refer to residues on the receptor and ligand involved in the interface.
The correlation analyses (Fig. 1B) and subsequent conclusions about the role of van der Waals and desolvation energies in “adhesion strength” are based on these docking outputs. If the docking protocol does not accurately model the physical context of adhesion (e.g., a monomer interacting with a functionalized filler surface or a tooth mineral substrate), can these correlations and the resulting predictions be considered reliable?