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<p>Knowledge of the structural aspects of di- and tri-peptides is vital to the understanding of folding mechanisms of proteins as well as their structure–function relationships. The current work examines how different side-chains of C-terminal entities may affect the physicochemical profiles of seven dipeptides that contain N-terminal <i>N</i>-formylmethionine. Computations are performed in gas, implicit and explicit water environments using B3LYP function augmented with 6–311 +  + G(d,p) basis set to obtain relevant information on structural, electronic, vibrational, DNA-docking, and ADMET properties of dipeptides to figure out the effects of solvation and C-terminal side-chain’s identity on structural as well as molecular characteristics of the peptides. H-bonded interactions between the formyl group and the amide planes are found to be crucial in regulating the peptides’ gas and solvent (aqueous) phase conformational characteristics about the <i>ψ</i> dihedrals. Intermolecular H-bonding due to explicitly introduced water molecules show significant influence on geometries linked to amide planes and vibrational frequencies of dipeptides, providing reinforcement to previous theoretical and experimental findings. Docking investigations show that the peptides bind to DNA minor grooves via H-bonds.</p> Graphical abstract <p></p>

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First-principles structural, molecular docking, and ADMET studies on dipeptides containing N-terminal N-formylmethionine: a study in gas, implicit and explicit solvents

  • 期刊论文

  • 发表日期：

    2025年5月12日

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  • Shilpi Mandal Das,
  • Satyajit Barman,
  • Gunajyoti Das

摘要

Knowledge of the structural aspects of di- and tri-peptides is vital to the understanding of folding mechanisms of proteins as well as their structure–function relationships. The current work examines how different side-chains of C-terminal entities may affect the physicochemical profiles of seven dipeptides that contain N-terminal N-formylmethionine. Computations are performed in gas, implicit and explicit water environments using B3LYP function augmented with 6–311 +  + G(d,p) basis set to obtain relevant information on structural, electronic, vibrational, DNA-docking, and ADMET properties of dipeptides to figure out the effects of solvation and C-terminal side-chain’s identity on structural as well as molecular characteristics of the peptides. H-bonded interactions between the formyl group and the amide planes are found to be crucial in regulating the peptides’ gas and solvent (aqueous) phase conformational characteristics about the ψ dihedrals. Intermolecular H-bonding due to explicitly introduced water molecules show significant influence on geometries linked to amide planes and vibrational frequencies of dipeptides, providing reinforcement to previous theoretical and experimental findings. Docking investigations show that the peptides bind to DNA minor grooves via H-bonds.

Graphical abstract