Abstract

Background Active oxidative phosphorylation is increasingly recognized as a defining metabolic feature of high-risk neuroblastoma (NB). NADH:ubiquinone oxidoreductase subunit S6 (NDUFS6), encoding an essential subunit of mitochondrial respiratory chain complex I, plays a critical role in sustaining oxidative phosphorylation. Nevertheless, its precise contribution to NB pathogenesis and progression remains largely undefined. Methods To characterize the expression landscape of NDUFS6, publicly available single-cell and bulk RNA sequencing datasets were analyzed, and the GSE49710 dataset was used to evaluate its prognostic significance. Immunohistochemical staining was performed to assess NDUFS6 expression across distinct clinical subgroups. Stable SK-N-BE(2) and SH-SY5Y cell lines with NDUFS6 overexpression or knockdown were generated to conduct functional assays, including Cell Counting Kit-8 (CCK-8) proliferation, colony formation and Transwell assays. Transcriptomic alterations induced by NDUFS6 modulation were profiled by RNA sequencing. In parallel, a structure-based virtual screening of the MedChemExpress (MCE) Bioactive Compound Library Plus was conducted to identify candidate small-molecule inhibitors of NDUFS6, with selected compounds evaluated for cytotoxicity in NB cells. Results NDUFS6 expression was significantly upregulated in high-risk NB (HR-NB) and was positively associated with disease progression and poor prognosis. Functional assays revealed that NDUFS6 knockdown suppressed proliferation, invasion, and migration of NB cells, whereas its overexpression promoted these malignant behaviors. Transcriptomic analysis revealed that high NDUFS6 expression activated pathways related to energy metabolism and adenosine triphosphate (ATP) synthesis, while concurrently suppressing neuronal differentiation and immune activation. Structure-based virtual screening identified several candidate inhibitors of NDUFS6, including guanosine 5’-triphosphate (disodium