Identification of natural compounds targeting the KRAS G12D mutation in pancreatic cancer through integrated in silico and in vitro approaches.

KRAS G12D mutations are among the most prevalent drivers of pancreatic ductal adenocarcinoma (PDAC) and remain challenging therapeutic targets due to their structural features and high GTP affinity. In this study, we identified potential natural inhibitors of KRAS G12D through structure-based virtual screening, using MRTX1133 as a reference. Lead compounds, including mangiferin and hesperetin 7-O-glucoside, were selected based on docking scores and hydrogen-bond interactions with the 12th residue of KRAS. Density functional theory (DFT) analyses revealed favorable electronic properties, with defined nucleophilic and electrophilic regions enhancing receptor-ligand interactions. Molecular dynamics simulations (100 ns) demonstrated that mangiferin and hesperetin 7-O-glucoside formed stable complexes, maintaining low RMSD, compact radius of gyration, and stable 12th residue interactions. Principal component analysis and Gibbs free energy landscape further confirmed their conformational stability, while MM/PBSA calculations suggest strong binding affinities (- 37.04 kcal/mol for mangiferin and - 21.15 kcal/mol for hesperetin 7-O-glucoside). In vitro analysis in PANC-1 cells carrying the KRAS G12D mutation confirmed dose-dependent cytotoxicity, reactive oxygen species accumulation, and apoptosis induction, validating the anticancer potential of the compounds. These results highlight the therapeutic potential of mangiferin and hesperetin 7-O-glucoside as KRAS G12D inhibitors in PDAC and support their further exploration in preclinical models for efficacy and combinatorial strategies.