A detail investigation of CT-DNA/BSA binding of new palladium complex by experimental techniques along with molecular docking and molecular dynamic simulations

Abstract

Abstract A novel mononuclear palladium complex, [Pd(dach)(SSA)], where dach and SSA are diaminocyclohexane and sulfosalicylic acid ligands, respectively, has been synthesized and identified utilizing analytical and spectral methods. DFT calculations, namely geometry optimization, MEP, HOMO-LUMO and NBO analysis, have been conducted at B3LYP level by aug-ccpVTZ-PP and 6-311G(d,p) basis sets. By employing MTT assay, the cytotoxicity activity of the aforesaid compound was examined on K562 cell line, which revealed a proper activity compared to cisplatin. To ascertain the lipophilicity of the newly made compound, the partition coefficient measurement was accomplished, which follows the order of cisplatin < Pd(II) complex. Next, investigation of binding properties of the studied compound with DNA of calf thymus and BSA were done by spectroscopic (CD, fluorescence emission and electronic adsorption) and non-spectroscopic (viscosity measurements, DNA gel electrophoresis, molecular docking and molecular dynamics simulation) methods. Data obtained from UV-Vis studies indicate non–intercalative mutual action. Fluorescence quenching mechanism of the two biomolecules by metal complex is static and the calculated thermodynamic parameters suggests the hydrogen bonding to the DNA and BSA. Further, docking simulation indicated that the studied compound fits into the groove of DNA and the BSA site I. The stability of metal compound-DNA/-BSA in the presence of H2O solvent and over the time were validated via molecular dynamics simulation.