Identification of benzo[b]thiophene-1,1-dioxide derivatives as novel PHGDH covalent inhibitors

[Display omitted] •The benzo[b]thiophene-1,1-dioxide derivative B12 was identified as a novel covalent inhibitor of PHGDH.•B12 has potential PHGDH inhibitory activity and anti-proliferative activities against PHGDH overexpression cancer cell lines.•B12 was shown to inhibit de novo serine synthesis in MDA-MB-468 cells.•Mass spectrometry-based peptide profiling and mutagenesis experiment indicated that B12 was covalently bound to Cys421 of PHGDH. The increased de novo serine biosynthesis confers many advantages for tumorigenesis and metastasis. Phosphoglycerate dehydrogenase (PHGDH), a rate-limiting enzyme in serine biogenesis, exhibits hyperactivity across multiple tumors and emerges as a promising target for cancer treatment. Through screening our in-house compound library, we identified compound Stattic as a potent PHGDH inhibitor (IC50 = 1.98 ± 0.66 µM). Subsequent exploration in structural activity relationships led to the discovery of compound B12 that demonstrated the increased enzymatic inhibitory activity (IC50 = 0.29 ± 0.02 μM). Furthermore, B12 exhibited robust inhibitory effects on the proliferation of MDA-MB-468, NCI-H1975, HT1080 and PC9 cells that overexpress PHGDH. Additionally, using a [U-13C6]-glucose tracing assay, B12 was found to reduce the production of glucose-derived serine in MDA-MB-468 cells. Finally, mass spectrometry-based peptide profiling, mutagenesis experiment and molecular docking study collectively suggested that B12 formed a covalent bond with Cys421 of PHGDH.