Mechanism Reveals a Novel Site for Allosteric Inhibition of Carcinogenic Activity of Human 3-Phosphoglycerate Dehydrogenase

3-Phosphoglycerate Dehydrogenase (PHGDH) is primarily known for catalyzing the oxidation of 3-phosphoglycerate (3PG) to 3-phosphohydroxypyvurate (3PHP) by reducing NAD+ to NADH, an important step during L-serine biosynthesis in human cells, however, it also catalyzes the reduction of α-ketoglutarate (α-KG) into 2-Hydroxyglutarate (2-HG), a carcinogenic reaction, as a secondary function. Therefore, inhibiting the secondary function, i.e., α-KG2-HG conversion in PHGDH enzymes has therapeutic implications for cancer treatment. Herein, using a mechanism-based study, we propose a novel binding site, far away from the catalytic site, which can allosterically inhibit the carcinogen activity without affecting the catalytic residues. We used hybrid QM/MM calculations to find the reaction mechanism and the role of catalytic residues, thereafter, we performed extensive MD simulations of the inhibitor-bound enzyme-substrate complex to study the mechanism of allosteric conformational change induced by the inhibitor binding. Our study shows that the binding of the inhibitor at the novel hinge site induces an allosteric effect that blocks the interaction between two interfacial helices between the substrate and nucleotide-binding domain. This study could lead a new insight for developing effective allosteric inhibitors for the PHGDH enzyme.