A series of novel indole derivatives was synthesized as inhibitors of fructose-1,6-bisphosphatase (FBPase).Extensive structure-activity relationships were conducted and led to a potent FBPase inhibitor 3.9 with an IC50 of 0.99 μM.The binding mode of this series of indoles was predicted using CDOCKER algorithm.The results of this research will shed light on the further design and optimization of novel small molecules as FBPase inhibitors.