Cancer is a disease of the age and is a public name for a large group of diseases that can infect many parts of the body. One of the most deadly types is Hepatocellular carcinoma (HCC) which destroy one of the life-threatening organ (liver). The problem is cells of cancer tend to grow fast, chemo drugs can solve this problem by killing fast-growing cells and eliminating cancer. So, chemists are interested in the synthesis of new chemotherapeutic drugs. We synthesized new chemical compounds which are expected to be like chemotherapeutic drugs. The [Pd(AEthP)Cl)] Cl .2H2O was prepared in the nano and bulk size by the interaction between Pd(II) ion and 1-(2-aminoethyl) piperazine (AEthP) ligand. The particles were formed within 10-30 nm with square planar geometry. The separated drug was characterized by different analysis tools like; elemental analysis, Fourier transform infrared (FTIR), electronic spectra, magnetic measurement and molar conductance techniques. The nano-size was confirmed by using the scanning electron microscope (SEM) technique. The optimized geometrical parameters were calculated. The formation constants of binary and ternary complexes were calculated, these complexes were formed due to the interaction between the synthesized drug with some selected bio-molecules. The most predominant species in the physiological range (pH of blood) between the synthesized drug with the selected bio-molecules were determined by plotting the speciation diagrams. It was found that the hepatocellular cytotoxic activity of the suggested drug within the bulk size was inactive, but its cytotoxic activity was observed (IC50 equals 20 µg/mL) by decreasing its size to the nano-scale. The same observation was noticed in the case of antibacterial activity. The docking active site interactions were evaluated using the selected proteins, Cyclin-dependent kinases (CDKs) (anticancer activity) and protein crystal structure of GlcN-O-P synthase (antimicrobial activity). It was observed that the aqua-form [Pd(AEthP)OH2)]2+ of the synthesized drug had powerful antioxidant and anti-inflammation activity in comparison to both its chloro-form [Pd(AEthP)Cl)]+ and the standard common drugs.