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<p>Herein, conformational, molecular, and spectral properties of the GNA nucleotides containing cytosine, thymine and uracil in both free and metalated forms were investigated for the first time using aqueous-phase DFT. Binding characteristics of the metal-GNA scaffolds with KRAS protein were further examined through docking and molecular dynamics simulations. Experimentally observed conformers, taken as reference structures, were found slightly more stable than theoretically obtained geometries, with comparable ΔE, ΔH, ΔG, and dipole moments suggesting possibilities of their coexistence. Metal association alters the electronic landscape of GNA conformers, resulting in reduced orbital gaps and increased electrophilicity, consistent with ESP maps. Simulated FT-IR spectra show shifts in ν(C═O) and δ(NH<sub>2</sub>) modes for cytosine systems, while spectral shifts are largely influenced by the position of CH<sub>3</sub> group in thymine conformers. Docking and MD simulations revealed persistent ligand interactions with ASP30, VAL29, GLU31 residues, including multiple hydrogen bonding. Consistent RMSD, RMSF, and MM/PBSA based free energy estimation (ΔG<sub>Binding</sub> ≈ − 10.2&#xa0;kcal/mol) suggests stable ligand–protein association. Collectively, these results highlight valuable insights into the structural aspects of GNA nucleotides, their metal complexes and metal-mediated GNA–KRAS interactions.</p>

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Conformational, molecular, spectral and binding properties of Zn(II)-coordinated glycol nucleic acid monophosphate: a DFT, docking and molecular dynamics assessment

  • 期刊论文

  • 发表日期：

    2026年4月27日

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  • Mwikwm Basumatary,
  • Phulung Basumatary,
  • Satyajit Barman,
  • Gunajyoti Das

摘要

Herein, conformational, molecular, and spectral properties of the GNA nucleotides containing cytosine, thymine and uracil in both free and metalated forms were investigated for the first time using aqueous-phase DFT. Binding characteristics of the metal-GNA scaffolds with KRAS protein were further examined through docking and molecular dynamics simulations. Experimentally observed conformers, taken as reference structures, were found slightly more stable than theoretically obtained geometries, with comparable ΔE, ΔH, ΔG, and dipole moments suggesting possibilities of their coexistence. Metal association alters the electronic landscape of GNA conformers, resulting in reduced orbital gaps and increased electrophilicity, consistent with ESP maps. Simulated FT-IR spectra show shifts in ν(C═O) and δ(NH2) modes for cytosine systems, while spectral shifts are largely influenced by the position of CH3 group in thymine conformers. Docking and MD simulations revealed persistent ligand interactions with ASP30, VAL29, GLU31 residues, including multiple hydrogen bonding. Consistent RMSD, RMSF, and MM/PBSA based free energy estimation (ΔGBinding ≈ − 10.2 kcal/mol) suggests stable ligand–protein association. Collectively, these results highlight valuable insights into the structural aspects of GNA nucleotides, their metal complexes and metal-mediated GNA–KRAS interactions.