A series of 6H-thiopyran-2,3-dicarboxylate derivatives 4a-d were synthesized and evaluated for their cytotoxic effect against HCT-15 colon and MCF-7 breast cancer cell lines using Sulforhodamine B (SRB) assay. The results showed that these compounds could exhibit a good cytotoxicity to both cell lines. In addition, these compounds were found to exhibit significant DNA-binding affinity. Ultraviolet-visible light (UV-Vis) spectroscopy was conducted to determine the ability of the ligand under analysis. The effect of ligand complexation on DNA structure led to overall affinity constants of K(4a)=3.5×10(4) M(-1), K(4b)=6.4×10(4) M(-1), K(4c)=3.2×10(4) M(-1), and K(4d)=2.4×10(4) M(-1). Our findings could provide new evidence showing the relationship between the chemical structure and biological activity and may be useful for the discovery of new anti-cancer drugs.