Identification of Small Molecule Inhibitors of 3-Phosphoglycerate Dehydrogenase to Target Serine Biosynthesis in Cancers

Abstract

Cancer cells are known to reprogram their metabolism in order to promote growth and proliferation. The amino acid serine is utilized in a plethora of anabolic reactions and supports the synthesis of all three major macromolecular classes: proteins, lipids, and nucleic acids. Serine can either be synthesized de novo via the phosphoserine pathway or imported from the extracellular space via amino acid transporters. The gene encoding the enzyme 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the first committed step of the phosphoserine pathway, is focally amplified in human cancers suggesting that it is pro-tumorigenic. Cancer cell lines that harbor PHGDH amplifications, or over express PHGDH independently of amplification, are uniquely sensitive to genetic ablation of the pathway. In contrast, cancer cell lines that express little PHGDH, and instead rely on serine import, are resistant to genetic ablation of the pathway. Given these observations, we speculated that PHGDH might be a clinically interesting target in oncology and sought to develop small molecule inhibitors of PHGDH in order to provide tool compounds with which to study the biology of PHGDH and evaluate the efficacy of inhibiting serine synthesis in cancers. In order to identify inhibitors of PHGDH an in vitro enzymatic assay was developed and libraries of drug-like small molecules were screened. Hit compounds were validated in biochemical assays to determine potency and selectivity for PHGDH. Selected compounds were tested on cells for their ability to inhibit de novo serine synthesis and one lead, CBR-5884, was identified. CBR-5884 was selectively toxic to PHGDH amplified or overexpressing cancer cells but had no effect on cells that express little PHGDH. Mechanistically, CBR-5884 was found to be a non-competitive inhibitor that showed a time dependent onset of inhibition and disrupted the oligomerization state of PHGDH. These results provide a proof-of-concept for targeting PHGDH and suggest that inhibiting PHGDH in cancers addicted to serine synthesis is a potentially viable targeted therapy option.