Elucidating the Structural Destabilization of HYAL1 in Mucopolysaccharidosis IX Through Computational Predictions and Molecular Dynamics

ABSTRACT Mucopolysaccharidosis type IX (MPS9) is one of the rarest lysosomal storage disorders, caused by deficiencies in hyaluronoglucosaminidase‐1, the enzyme responsible for degrading hyaluronan (HA). To elucidate the molecular basis of MPS9, we systematically analyzed HYAL1 variants using a comprehensive computational workflow. The Hyaluronidase‐1 sequence and structure were retrieved from protein databases, and 52 missense variants from ClinVar and HGMD were evaluated for pathogenicity, biophysical effects, evolutionary conservation, and structural stability using PredictSNP, Align‐GVGD, ConSurf, and iStable. Integrative screening identified two variants, C333S and C363S, as the most deleterious based on pathogenicity (8 SNPs), biophysical scores (6 SNPs), conservation (5 SNPs), and stability predictions (2 SNPs). Structural alterations were modeled using PyMOL and Swiss‐PDB Viewer, followed by 200 ns molecular dynamics simulations in GROMACS. The mutants exhibited pronounced backbone deviations in RMSD and RMSF profiles, reduced compactness, altered solvent exposure, and weakened hydrogen bonding networks, confirming structural destabilization. Overall, this study provides detailed structural and dynamic insights into HYAL1 dysfunction, highlighting C333S and C363S as key pathogenic variants that may contribute to hyaluronidase deficiency in MPS9 and support future therapeutic exploration.