Metabolomics-guided structure-based virtual screening prioritizes obtusifolin as a geroprotector in Caenorhabditis elegans

Microbial diets and their metabolites can influence host aging, yet identifying geroprotective compounds from complex culture matrices remains challenging. Here, a diet supplemented with the human gut-derived Enterococcus faecium SI194 extended the mean lifespan of Caenorhabditis elegans by 23.24%, improved aging-associated phenotypes, and enhanced SKN-1-responsive signaling. No lifespan extension was detected in skn-1(zu67) mutants, consistent with the involvement of SKN-1. To prioritize metabolites for independent phenotypic evaluation, we integrated untargeted metabolomics with structure-based virtual screening against glycogen synthase kinase-3 (GSK-3), a negative regulator of SKN-1. Among 71 structurally annotated features enriched in the OP50-SI194 liquid-culture preparation, the feature annotated as obtusifolin had the most favorable Vina docking score. A single 100-ns molecular dynamics trajectory supported the conformational persistence of the modeled GSK-3-Obt complex under the simulated conditions. Exogenous obtusifolin (Obt; 30μM) extended mean lifespan by 14.55%, reduced DCFH-DA-derived fluorescence and age-associated intestinal autofluorescence, and increased gst-4p::GFP fluorescence. These findings support the geroprotective effects of the SI194-supplemented diet and exogenous Obt as distinct interventions and illustrate the workflow's utility for candidate prioritization. Future studies should clarify Obt's contribution to SI194-associated lifespan extension and its relationship with SKN-1 and GSK-3.