Identification and Validation of B-Cell Epitopes on the VP1 Protein of Parvovirus B19 through Molecular Docking and Dynamics Simulation

This study aimed to identify B-cell epitope candidates using multiple epitope identification software and in silico analysis of the modeled B19 V protein against specific antibodies using molecular docking and dynamics simulation. Materials and Methods: Full-length amino acid sequences of the VP1 protein of B19 V were retrieved from NCBI. A consensus sequence was generated using CLC sequence viewer. Linear B cell epitopes were identified using Bepipred 2.0, ABCpred, and LBTope. The linear epitope was synthesized and validated against B19 V-specific antibodies. A 3D model of the B19 V VP1 consensus protein was generated using the ITASSER server. Discontinuous B cell epitopes were identified using Discotope 2.0 and Ellipro. Molecular docking and molecular dynamics simulation was performed to investigate the interaction between the modeled B19 V protein and specific anti-B19 V antibody. Results: The identified epitope was 100% conserved and similarly identified through ABCpred and LBTope. The HADDOCK score and MDS analysis, such as hydrogen bond interactions and MMPBSA analysis, revealed that the VP1 and mAb H chains formed a significantly stable complex. The MDS demonstrated that the VP1-mAb H chain complexes had lower RMSF values around 130 to 200 residues, a region responsible for the catalytic network for enzyme activity; as a result, the flexibility of the antibody-bound VP1 decreased when compared to Apo-VP1. Conclusion: A viable epitope identified through this process was synthesized and validated using ELISA, which highlighted the role of the epitope identification process in diagnostics. This study also sheds light on the complex interplay between VP1 and the mAb H chain and highlights key binding specificity and stability determinants.