AI Summary & Key Takeaways
AI InsightThis study contributes a comparative theoretical perspective for the relationship between small chemical derivatives of some compounds and DNA structures, and demonstrates that chemical hardness and electronic descriptors predict DNA binding behavior.
📌 3 Key Takeaways
Abstract
We performed extensive in silico studies using molecular docking methods and density functional theory (DFT) to study structurally diverse small chemical derivatives binding and interacting on the B-DNA dodecamer (1BNA) target. Chemically different molecules such as alcohols, amines, halogenated compounds, silane derivatives, hydrocarbons and heteroatom containing species, were examined for their affinity as well as their interactions to the DNA framework. Molecular docking calculations using Glide scoring functions were applied along with the binding energies and Glide scores, Coulombic interactions as well as van der Waals contributions to ligand efficiency. It was observed that small polar compounds and heteroatom-containing derivatives showed better affinity for binding to the 1BNA structure due to favorable electrostatic interactions and the hydrogen bonding contributions. In contrast nonpolar hydrocarbon derivatives exhibited weaker affinities, which also suggested that they were not well-fit for the polar DNA-binding environment. Conceptual DFT descriptors such as HOMO–LUMO energies, energy gap (ΔE), chemical hardness (η), softness (σ), electronegativity (χ), and electrophilicity index (ω) based on docking analysis were then used to assess the reactivity and stability of the investigated derivatives. The chemical hardness analysis of the extracted compounds revealed that molecules having lower hardness and smaller HOMO–LUMO gaps showed greater tendency to interact between the organic molecule & DNA structure, indicating improved electron transfer capability and higher chemical reactivity. On the contrary, those having highly rigid and chemically hard molecules showed weak binding interactions. The docking and chemical hardness analysis indicated a correlation between electronic properties and binding affinity toward B-DNA. This study contributes a comparative theoretical perspective for the relationship between small chemical derivatives of some compounds and DNA structures, and demonstrates that chemical hardness and electronic descriptors predict DNA binding behavior.