In vitro and in silico evaluation of a novel piperazine–tetrazole ligand against breast cancer cell lines: An integrated study of DFT, molecular docking, and molecular dynamics simulations

Abstract (4-(4-(1H-tetrazole-5-yl)benzyl)piperazin-1yl)(furan-2-yl)methanone (TBFM), a novel piperazine and tetrazole derivative, was synthesized through a two-step process. The structure of the synthesized compound was confirmed using ¹H NMR, LC-MS, and FTIR analyses.The compound’s cytotoxicity was evaluated against the MCF-7 breast cancer cell line using the MTT assay, with an IC50 value of 57.37 µM. Density Functional Theory (DFT) calculations showed a small energy gap of 0.172 eV, suggesting potentially higher biological activity. Further analysis, including non-covalent interaction (NCI) and electron localization function (ELF) studies, indicated that the tetrazole moiety contributes significantly to the molecule’s activity. Molecular docking was performed with 24 proteins from the MCF-7 cell line to explore TBFM’s binding interactions. Among these, proteins 1ZUA, 2SRC, 4RJ3, and 5IEV exhibited stronger interactions with TBFM, with 5IEV showing the highest docking score of -9.9 kcal/mol. The ADMET profile of TBFM was also assessed, revealing no violations of Lipinski's Rule of Five, indicating favourable drug-like properties. Molecular dynamics simulations were conducted for 100 ns to assess the stability of the protein–ligand complexes under near-physiological conditions. The root mean square deviation (RMSD) values for all four proteins werelow, suggesting stable complex formation. Principal component analysis (PCA) showed that the 1ZUA complex formed a compact, oval-shaped cluster. Additionally, Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) calculations estimated the binding free energy of TBFM with each protein, revealing that 2SRC had the highest binding energy among the analysed complexes. Overall, TBFM demonstrated stable binding interactions with all four proteins throughout the simulation period.