Cancer remains one of the leading causes of death worldwide. Introduction of natural compounds with anticancer properties can be an effective step in the prevention and treatment of cancer. Antimicrobial peptides (AMPs) are short peptides whose anticancer activities have been proved previously. In the present study, Enterocin-P (EntP) as a bacteriocin of E. faecium was expressed in HEK expression system by pcDNA3.1 + vector. The recombinant peptide was purified from culture medium using Ni2+ affinity chromatography with an average yield of 0.6 mg/ml. The cytotoxic activity of the recombinant peptide was determined toward some cancer cell lines including: SW1353, HUH7, Huh-7.5, C26, B16F0 and NIH3T3 as a normal cell line. Our results showed that EntP peptide had selective cytotoxicity activity only against C26 ( IC50: 0.32 mg/ml) and SW1353 ( IC50: 1.36 mg/ml) as cancer cell and did not show cytotoxic properties against normal cell. In the second phase of our study, to better understand the mechanisms of EntP peptide, we have tried to predict the possible interaction of this peptide to predominantly negative charge molecules in the cell membrane of cancer cells. Our in-silico analysis revealed that EntP peptide has strong tendency to chondroitin sulfate (− 189 ± 6.24 kJ/mol) and heparan sulfate (− 115 ± 5.12 kJ/mol) as two well-known anionic molecules on surface cancer cells.

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