Diverse coordination of dipicolinic acid to Pd(II) ion result antitumor complexes, their interaction with CT-DNA by spectroscopic experiments and computational methods

•DNA binding of three Pd(II) complexes were studied using different methods.•The metal complexes showed antitumor activity against MCF-7cancer cell line.•DFT calculations were performed for these Pd(II) complexes.•Docking simulation revealed all complexes have groove binding mode with DNA. Three metal complexes wherein picolinic acid (dipic) diversely coordinated to palladium with formula trans-[Pd(Hdipic)2].2H2O (I), K[Pd(dipic)Cl].H2O (II) and trans-Na2[Pd(dipic)2].2H2O (III) had been selected from literature and accordingly made them in our laboratory. Complex ions of these three compounds bear 0.00 (I), -1.00 (II), and -2.00 (III) charges. In this study, DFT calculations i.e., molecular geometry analysis, molecular electrostatic potential map and frontier molecular orbital analysis were performed for the Pd(II) complexes I, II and III. Preliminary cytotoxic activity of them along with carboplatin as standard, against cancer cell line MCF-7, showed the promising effect. Thus in-detail interaction of I, II, and III with calf thymus DNA was investigated through spectrophotometric, fluorometric, partition coefficient, viscometric measurement, gel electrophoresis, and docking assay for more analysis. All the data obtained from these above studies indicate that the complex with zero charge (I) shows better cytotoxic and DNA interaction affinity than the II and III having -1.00 and -2.00 charges which might be due to their repulsion by negative charges present on phosphate diester of the DNA backbone. [Display omitted]