Azacoccone E inhibits cancer cell growth by targeting 3-phosphoglycerate dehydrogenase

Serine plays critically important roles in tumorigenesis. Homo sapiens 3-phosphoglycerate dehydrogenase (PHGDH) catalyzes the first committed step for the synthesis of glucose-derived serine via the phosphoserine pathway and has been associated with a wide variety of cancers, including breast cancer, melanoma, colon cancer, glioma, nasopharyngeal carcinoma, cervical adenocarcinoma, etc. Azacoccone E, an aza-epicoccone derivative from the culture of Aspergillus flavipes, exhibited effective inhibitory activity against PHGDH in vitro. The microscale thermophoresis (MST) method and the cellular thermal shift assay (CETSA) confirmed that azacoccone E directly bound to PHGDH. And the cell-based experiments showed that this compound was selectively toxic to PHGDH-dependent cancer cells and could cause apoptosis. Further biochemical assays revealed that it was a noncompetitive inhibitor with respect to the substrate of 3-PG and exhibited a time-dependent inhibition. Furthermore, molecular docking demonstrated that azacoccone E coordinated in an allosteric site of PHGDH with low binding energy. Therefore, azacoccone E can be considered as a possible drug candidate targeting at PHGDH for treatment of cancers.