In drug-delivery systems containing nano-drug structures, targeting the tumorous tissue by anthraquinone molecules with high biological activity, and reaching and destroying tumors by their tumor-killing effect reveals remarkable results for the treatment of tumors. The various biological activities of anthraquinones and their derivatives depend on molecular conformation; hence, their intra-cell interaction mechanisms including deoxyribonucleic acid (DNA), ribonucleic acid (RNA), enzymes, and hormones. Computer-based drug design plays an important role in the design of drugs and the determination of goals for them. Molecular docking has been widely used in structure-based drug design. The effects of anthraquinone analogues in tumor cells as a result of their interaction with DNA strand has increased the number of studies done on them, and they have been shown to have a wide range of applications in chemistry, medicine, pharmacy, materials, and especially in the field of biomolecules.