Studies of DNA- and HSA-binding properties of new nano-scale green synthesized Ni (II) complex as anticancer agent using spectroscopic methods, viscosity measurement, molecular docking, MD simulation and QM/MM

Abstract

Herein, we synthesized a new nano-scale Schiff base Ni(II) complex in water as a green solvent and at ambient temperature. The compound was characterized using FT-IR and elemental analysis. Also, its molecular structure was determined by single crystal X-ray diffraction technique. The MTT assay results indicated that the anticancer activity of the compound is affected by its size. Finally, binding ability of the nano-scale Ni(II) Schiff base complex with calf thymus DNA and human serum albumin was investigated using combination of experimental (UV–Vis, fluorescence, circular dichroism (CD) and viscosity) and computational (molecular docking, molecular dynamics simulation and qm/mm) methods. The estimated binding constants for the DNA-complex and HSA-complex were about 104 M−1. Molecular docking studies revealed the binding of Ni(II) complex to the minor groove of DNA and warfarin binding site of protein by formation of hydrogen bond, π-cation and hydrophobic interactions. MD simulation studies revealed that complexation with NiL2 changed the structure of HSA when compared to free protein. Finally, the ONIOM results showed that the structural parameters of the compound changed along with binding to DNA and HSA, indicating the strong interaction between the compound and these biomacromolecules.