1. Identification of a novel PHGDH covalent inhibitor by chemical proteomics and phenotypic profiling
- Author
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Jian-Guang Luo, Tianyu Zhu, Chen Chen, Yi Zhang, Hao Zhang, Dong-Rong Zhu, Xiao-Qin Liu, Ling-Yi Kong, Chao Han, and Sifang Wu
- Subjects
PHGDH, phosphoglycerate dehydrogenase ,PSAT, phosphoserine aminotransferase ,Allosteric regulation ,CuAAC, copper-catalyzed alkyne–azide cycloaddition ,Regulatory site ,ABPP, affinity-based protein profiling ,RM1-950 ,Proteomics ,RMSD, root mean square deviation ,Serine ,CETSA, cellular thermal shift assay ,03 medical and health sciences ,3-PHP, 3-phosphohydroxypyruvate ,ROS, reactive oxygen species ,0302 clinical medicine ,DARTS, drug affinity responsive target stability ,TCEP, tris(2-carboxyethyl) phosphine ,GSH, glutathione ,TBTA, tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine ,Phosphoglycerate dehydrogenase ,General Pharmacology, Toxicology and Pharmaceutics ,Covalent inhibitor ,Withanolides ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Chemical proteomics ,NADPH, nicotinamide adenine dinucleotide phosphate ,Serine synthesis pathway ,MD, molecular dynamics ,Small molecule ,3-PG, 3-phosphoglycerate ,Colon cancer ,RMSF, root mean square fluctuations ,Enzyme ,chemistry ,Biochemistry ,Oxidative stress ,SBD, substrate-binding domain ,030220 oncology & carcinogenesis ,Original Article ,BLI, biolayer interferometry assay ,Therapeutics. Pharmacology ,SSP, serine synthesis pathway ,Withangulatin A ,Cysteine - Abstract
The first rate-limiting enzyme of the serine synthesis pathway (SSP), phosphoglycerate dehydrogenase (PHGDH), is hyperactive in multiple tumors, which leads to the activation of SSP and promotes tumorigenesis. However, only a few inhibitors of PHGDH have been discovered to date, especially the covalent inhibitors of PHGDH. Here, we identified withangulatin A (WA), a natural small molecule, as a novel covalent inhibitor of PHGDH. Affinity-based protein profiling identified that WA could directly bind to PHGDH and inactivate the enzyme activity of PHGDH. Biolayer interferometry and LC–MS/MS analysis further demonstrated the selective covalent binding of WA to the cysteine 295 residue (Cys295) of PHGDH. With the covalent modification of Cys295, WA blocked the substrate-binding domain (SBD) of PHGDH and exerted an allosteric effect to induce PHGDH inactivation. Further studies revealed that with the inhibition of PHGDH mediated by WA, the glutathione synthesis was decreased and intracellular levels of reactive oxygen species (ROS) were elevated, leading to the inhibition of tumor proliferation. This study indicates WA as a novel PHGDH covalent inhibitor, which identifies Cys295 as a novel allosteric regulatory site of PHGDH and holds great potential in developing anti-tumor agents for targeting PHGDH., Graphical abstract WA is a novel covalent-allosteric inhibitor of phosphoglycerate dehydrogenase (PHGDH), and inhibits the serine synthesis pathway and proliferation of colon cancer cells with overexpression of PHGDH.Image 1
- Published
- 2022