Simple SummaryPivotal factors that contribute to tumorigenesis were subjected to analysis by molecular modeling. In particular, the FAM72A-UNG2 protein–protein interaction was modeled to predict a potential solution for the treatment of cancer. We screened chemical libraries to identify withaferin B as a lead molecule capable of interfering with the FAM72A-UNG2 interaction, thus opening new therapeutic avenues for cancer.Family with sequence similarity 72 A (FAM72A) is a pivotal mitosis-promoting factor that is highly expressed in various types of cancer. FAM72A interacts with the uracil-DNA glycosylase UNG2 to prevent mutagenesis by eliminating uracil from DNA molecules through cleaving the N-glycosylic bond and initiating the base excision repair pathway, thus maintaining genome integrity. In the present study, we determined a specific FAM72A-UNG2 heterodimer protein interaction using molecular docking and dynamics. In addition, through in silico screening, we identified withaferin B as a molecule that can specifically prevent the FAM72A-UNG2 interaction by blocking its cell signaling pathways. Our results provide an excellent basis for possible therapeutic approaches in the clinical treatment of cancer.