In silico identification of pathogenic RAPSN mutations and ligand interactions in congenital myasthenic syndromes

Congenital myasthenic syndromes (CMS) are rare but genetically diverse neuromuscular disorders caused by mutations of over 35 distinct genes. They are characterized by muscle weakness due to defective neuromuscular transmission. The RAPSN gene plays a crucial role in the assembly of acetylcholine receptors at the neuromuscular junction and is linked to approximately 15 percent of cases of congenital myasthenic syndrome (CMS). We employed a computational framework in this study to investigate the pathological effects of non-synonymous single-nucleotide polymorphisms (nsSNPs) in the RAPSN gene, utilizing specialized bioinformatics programs such as SIFT, PolyPhen, and MutPred2. Out of 38,888 nsSNPs, 104 were identified as harmful with14 mutations including C382F (rs773403514), G240R (rs773316367) and G240W (rs773316367) impacting the stability and structure of the protein. Homology modelling detailed the structure of protein validated by high RMSD scores and Ramachandran plot which highlight the deviations from native structure. Molecular docking studies predicted the interactions of ligands such as silibinin, silymarin, EGCG and apocynin with mutant protein. Among these, silibinin exhibited the most promising interaction for mitigating the effects of oxidative stress and inflammation characteristic of CMS. Silibinin demonstrated stable dynamic binding confirmed via 100 ns MD validation. Further, post-translational modification analysis predicated the critical alteration i.e. loss of methylation and phosphorylation site and clustering analysis showed mutations such as G240R and G240W are associated with risk of cancer. Our findings provide important insights into the molecular mechanisms underlying CMS and highlight the potential for developing tailored therapeutic strategies targeting the RAPSN pathway to improve clinical outcomes.