JMJD5 Dioxygenase Inhibition Mechanism by 2-Hydroxyglutarate: A QM/MM Study

Abstract

Jumonji domain-containing protein 5 (JMJD5) is a FeII/2-oxoglutarate-dependent oxygenase implicated in cellular metabolism and cancer-related processes. Although the oncometabolite 2-hydroxyglutarate (2-HG) is known to inhibit JMJD5, the molecular origin of this inhibition remains unclear. Here, molecular dynamics simulations and QM/MM calculations were employed to investigate the inhibition mechanisms of L-2-HG and D-2-HG in JMJD5. The calculations show that dioxygen binding forms a quintet FeIII-superoxo species in both systems. However, unlike catalytically competent substrates in nonheme dioxygenases, 2-HG contributes negligible spin density to the Fe-dioxygen unit, leading to inefficient 2-HG-to-oxygen electron transfer during dioxygen activation. Reaction pathway calculations reveal prohibitively high barriers for oxidative decarboxylation, particularly for L-2-HG (83.4 kcal·mol–1) compared with D-2-HG (34.3 kcal·mol–1). The stereochemical difference originates primarily from distinct 2-HG binding orientations within the active site. Overall, the results demonstrate that inhibition of JMJD5 by 2-HG arises from insufficient electronic coupling with the Fe-dioxygen center together with unfavorable 2-HG positioning, thereby preventing formation of the catalytically competent FeIV-oxo intermediate. These findings provide mechanistic insight into JMJD5 inhibition and may help the future design of selective FeII/2-OG oxygenase inhibitors.