Unraveling the Interplay of D-2-HG in Glioblastoma Tumorigenesis via Integrated Machine Learning and Molecular Docking Analysis

Background: Glioblastoma (GBM) is an exceptionally aggressive type of brain tumor with a poor prognosis, underscoring the urgent need to identify new molecular targets for therapeutic development. The objective of this research is to clarify the molecular interactions affected by the oncometabolite D-2-hydroxyglutarate (D-2-HG) within the framework of GBM. Methods: Differential expression analysis of multi-omics data identified potential target genes linked to GBM pathogenesis. To enhance our understanding of the binding interactions between D-2-HG and the identified target proteins, we utilized an integrated methodology encompassing various machine learning algorithms, network pharmacology techniques, and molecular docking. Results: A sum of 135 genes was recognized as possible targets through which D-2-HG exerts its effects in GBM. The ensuing analysis, utilizing machine learning techniques, identified six crucial genes [eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1), fatty acid binding protein 3 (FABP3), potassium voltage-gated channel subfamily Q member 2 (KCNQ2), epithelial cell adhesion molecule (EPCAM), sphingosine-1-phosphate receptor 5 (S1PR5), and metabotropic glutamate receptor 3 (GRM3)] as key regulators. Among these, FABP3, KCNQ2, EPCAM, S1PR5, and GRM3 were significantly downregulated, whereas EIF4EBP1 was markedly upregulated (p < 0.05). Molecular docking simulations indicated a strong binding affinity of D-2-HG towards the target proteins. Conclusions: Our study suggests that D-2-HG plays a significant role in the pathogenesis of GBM by modulating specific genes and signaling pathways. Utilizing machine learning techniques, we identified six essential regulatory genes, and further molecular docking simulations revealed a strong affinity of D-2-HG for these critical targets. Collectively, these results establish a substantial basis for future investigations into the mechanistic role of D-2-HG in GBM oncogenesis.