Mapping binding landscape of allosteric inhibitor G6PDi-1 on human G6PD

Abstract

Targeting the oxidative pentose phosphate pathway by inhibiting glucose-6-phosphate dehydrogenase (G6PD), is a promising anticancer strategy, yet clinically useful inhibitors remain unavailable. A key limitation is the lack of molecular insight into how allosteric and non-competitive inhibitors perturb enzymatic activity, limiting rational optimization. Here, we investigated the mechanism of G6PDi-1, a potent, reversible, non-competitive G6PD inhibitor, by combining biochemical assays with molecular dynamics simulations, Markov state model and MM/PBSA binding energy calculations. Experimentally, G6PDi-1 reduced active dimer formation in hepatoblastoma HepG2 cells and increased the inactive monomer fraction, linking inhibition to disrupted oligomerization. Computationally, we identified multiple sites on the enzyme surface, with preferential binding at dimer interface that sterically blocks oligomerization. Importantly, additional distal sites showed enhanced inter-residue correlations, suggesting secondary allosteric effects that shift G6PD toward monomeric states less competent for oligomerization. These findings provide a molecular basis for structure-based development of improved strategies for G6PD inhibition suited for cancer therapy.