In silico analysis of missense SNPs in <i>APPL1</i> gene: implications on APPL1–AKT2 complex and its relation to MODY 14

Abstract

Maturity-Onset Diabetes of the Young type 14 (MODY14) is a rare monogenic diabetes linked to APPL1 variants that impair insulin signaling. This study evaluated how missense substitutions in the APPL1 PTB domain affect its interaction with the AKT2 catalytic domain, a key step in glucose regulation. Among 475 APPL1 missense SNPs, four conserved variants (R526C, H535R, S543W, G585R) were prioritized using predictive algorithms and conservation scoring. Protein-protein docking and 300-ns molecular dynamics simulations were performed. Structural stability and interaction dynamics were assessed through RMSD, RMSF, radius of gyration, hydrogen bonding, and center-of-mass distance, complemented by principal component analysis and Gibbs free energy landscapes. Docking identified the HADDOCK-derived model as the most reliable complex. Simulations showed that H535R, S543W, and G585R induced only mild deviations from the wild type, with limited effects on stability and flexibility. In contrast, R526C produced pronounced destabilization, including elevated backbone fluctuations, increased flexibility, reduced compactness, irregular hydrogen bonding, and greater inter-domain separation. PCA confirmed broader conformational sampling for R526C, and its free-energy landscape lacked the well-defined minima observed in the wild type and the other variants. R526C consistently emerged as the most destabilizing substitution, likely impairing AKT2 activation and glucose uptake, supporting its pathogenic role in MODY14. This integrative computational approach demonstrates the diagnostic value of structural modeling for prioritizing rare variants in monogenic diabetes. Importantly, disruption of the APPL1-AKT2 complex may compromise insulin-stimulated glucose uptake and represents a potential molecular target for therapeutic intervention.