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Identification of a novel PHGDH covalent inhibitor by chemical proteomics and phenotypic profiling
- Source :
- Acta Pharmaceutica Sinica B, Vol 12, Iss 1, Pp 246-261 (2022), Acta Pharmaceutica Sinica. B
- Publication Year :
- 2022
- Publisher :
- Elsevier, 2022.
-
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.<br />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
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 22113835
- Volume :
- 12
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Acta Pharmaceutica Sinica B
- Accession number :
- edsair.doi.dedup.....3543b6d3266f2b136393cdedb4c3da23