Kinase Regulation Through Metabolic Control Points Directs Glucose Fate

Glucose metabolism is organized through interconnected metabolic pathways whose enzymes determine whether glucose is utilized for energy production, storage, or biosynthesis. Although protein kinases modulate metabolic enzymes through phosphorylation, how kinase signaling collectively interfaces with the glucose metabolic network remains unclear. In addition, many reported kinase–substrate relationships are derived from prediction-based resources and lack experimental validation. Here, we systematically mapped kinase associations for 144 enzymes across six glucose metabolic pathways by integrating kinase–substrate databases, quantitative phosphoproteomics from 154 human studies, and protein–protein interaction networks. We developed a multi-layer prioritization framework combining kinase–substrate annotations, phosphoproteomic co-regulation, and interaction-supported evidence to rank kinase–enzyme associations and reconstruct a phosphoproteomic-supported kinase–metabolism network. Prioritization reduced a large initial association space to a refined set of candidate kinase–enzyme associations while retaining broad coverage across glucose metabolism. The resulting network revealed an uneven distribution of kinase associations across metabolic pathways and enzymes, with the highest kinase association density observed at metabolic control points, particularly enzymes integrating branch-point and flux-control functions. Pathway-level analysis further showed that glycogen metabolism exhibited the greatest kinase association density despite comprising relatively few enzymes, while futile-cycle pairs displayed distinct patterns of shared and reaction-specific kinase associations. Network analysis identified a small subset of highly connected kinase hubs together with bridge proteins linking the kinase and metabolic enzyme layers, providing a systems-level view of kinase association patterns across glucose metabolism. Together, these findings indicate that kinase associations are not uniformly distributed across glucose metabolism but preferentially concentrate at metabolic control points that govern pathway routing and glucose allocation. This study provides a systems-level framework for prioritizing candidate kinase–enzyme associations and a resource for investigating signaling–metabolism interactions in metabolic disease and cancer.