Integrated experimental and computational study of oxime-based derivatives: Antiproliferative evaluation, gene expression, DNA minor groove binding, detailed DFT, docking, and molecular dynamics analyses
Computational Biology and Chemistry, cilt.124, 2026 (SCI-Expanded, Scopus)
- Yayın Türü: Makale / Tam Makale
- Cilt numarası: 124
- Basım Tarihi: 2026
- Doi Numarası: 10.1016/j.compbiolchem.2026.109085
- Dergi Adı: Computational Biology and Chemistry
- Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, Chimica, Compendex, MEDLINE, zbMATH
- Anahtar Kelimeler: CT-DNA, DFT, Dynamic simulation, Fluorescence quenching, MTT assay, QPCR
- Süleyman Demirel Üniversitesi Adresli: Evet
Özet
In this study, two oxime-based compounds, DAG and DAF, were synthesized and investigated using experimental, spectroscopic, biological, and computational approaches. The biological potential of the compounds was evaluated using MTT assays in normal HUVEC cells and HeLa cervical cancer cells. While both molecules exhibited low cytotoxicity toward normal cells, they demonstrated dose- and time-dependent antiproliferative activity against HeLa cells, with DAF showing slightly lower IC50 values compared to DAG. Gene expression analysis further revealed upregulation of pro-apoptotic markers (CASP3 and CASP8) and downregulation of the anti-apoptotic gene BCL-2, suggesting the involvement of caspase-dependent apoptotic pathways, particularly in DAF-treated cells. The interaction of DAG and DAF with CT-DNA was explored using fluorescence spectroscopy, molecular docking, and molecular dynamics simulations. Fluorescence quenching studies indicated a static quenching mechanism and suggested a groove-binding mode rather than classical intercalation. Binding constant analysis revealed moderate DNA affinity, and DAF exhibited stronger interaction. Docking simulations supported minor groove binding stabilized mainly by hydrogen bonding interactions, while 150 ns MD simulations confirmed structural stability of the ligand+DNA complexes. DFT calculations provided insight into electronic structure, frontier molecular orbitals, charge distribution, MEP/ESP surfaces, RDG analysis, ELF, LOL, and quantum reactivity descriptors. ADME–Tox predictions confirmed compliance with Lipinski's RO5, acceptable solubility and lipophilicity, and absence of predicted toxicity risks. The results identify DAF as a promising DNA-interacting anticancer candidate with favorable pharmacokinetic and safety profiles.