NM23-H2 protein is identified as a transcriptional factor of the important oncogene c-myc,that can bind specifically to defined DNA sequences to promote gene transcription.However,due to its role in tumoregenesis remains unclear and its hard to achieve a real transcription factors inhibitor,there is few report on using it as an anticancer drug target.Herein,we reveal the transcription regulatory effect of this protein on genome-wide genes that are related to tumor signaling and its great impact on human cervical tumor cells HeLa.Basing on these findings,we screen the NM23-H2 inhibitor from our natural products and derivatives library.According to this screen and further thorough studies data,an isaindigotone derivative,SYSU-ID-01,shows great activity on interacting and inhibiting NM23-H2.In vitro and cellular studies indicate that this compound is capable of dissociating the binding of NM23-H2 to c-myc promoter,inhibit c-myc transcription and translation,and exhibited great potential in suppressing HeLa cells growth similar to those obtained by knocking-down of NM23-H2.Further biophysical and computational analyses of the compound-protein interaction provide additional insight on the molecular mode of action of SYSU-ID-01,which is interfering the binding of NM23-H2 to specific DNA sequences that can fold to alternative structure,such like G-quadruplex.These findings illustrate the potential druggability of transcription factors and provide a new molecular basis for targeting the NM23-H2 with small molecules.