Structural Consequences of PRNP Mutations: An Integrated Docking and Molecular Dynamics Approach to Prion Protein Dysfunction

Background and Objective: Prion protein (PrP), encoded by the PRNP gene, is a membrane-associated glycoprotein whose structural integrity is essential for maintaining normal cellular function. Pathogenic mutations in PRNP can destabilize the native α-helical conformation of PrP and promote its conversion into a β-sheet-rich misfolded isoform associated with prion diseases. This study aimed to identify deleterious nsSNPs in the PRNP gene and assess their impact on prion protein stability and structural integrity. Additionally, potential anti-prion compounds were screened to assess their binding affinity and interaction profiles with both wild-type and mutant PrP, along with an analysis of mutation-induced conformational dynamics. Materials and Methods: A total of 43 nsSNPs were prioritized through integrated computational analyses, among which 11 variants were consistently predicted as highly deleterious. The Cys214Tyr and Arg148Cys emerged as the most impactful mutations, showing significant effects on protein stability. Structural modeling revealed a predominantly α-helical C-terminal domain, while binding site prediction identified key pockets overlapping with functionally important and previously reported regions of PrP. Results: Molecular docking results demonstrated strong binding affinities of selected compounds, including Flunarizine, Astemizole, Tacrolimus, Amphotericin B, and rifampicin, within these critical regions. These ligands interacted with essential residues such as ARG136, MET134, GLN212, GLU207, ARG208, VAL161, and MET213, indicating their potential role in stabilizing the PrP structure. Molecular dynamics simulations further showed that Arg148Cys and Cys214Tyr mutations significantly destabilize the protein, as evidenced by increased RMSD fluctuations, reduced compactness, and altered energetic profiles. Overall, the findings highlight key structural determinants of PrP stability and suggest that selected compounds may stabilize the prion protein by targeting functionally relevant sites. Conclusion: However, these results are based on computational approaches and require experimental validation. Future studies involving in vitro and in vivo experiments, extended molecular simulations, and lead optimization are necessary to confirm therapeutic potential and further clarify mechanisms underlying prion protein misfolding and neurodegeneration.