Molecular modeling of Wuhan SARS-CoV-۲ RBD in complex with ferritin nanoparticle

Backgrounds: In regard to finding treatment strategies for managing the SARS-CoV-۲ outbreak,nanoparticle vaccines are currently the most effective vaccines against this virus. Ferritin-basedvaccines such as ferritin-RBD vaccines in SARS-CoV-۲ cause not only a stable antibodyresponse but also a long-term response. However, the atomistic structural mechanism of thiscomplex is not well understood. In this study, molecular modeling to build up the model of theSARS-CoV-۲ RBD-ferritin nanoparticle complex was used, for the first time, aiming to improvethe effectiveness of the current commercial vaccines.Materials and Methods: The protein structures obtained from protein data bank (PDB id: ۲fg۸and ۷lo۴. Molecular docking was performed using a haddock ۲.۴ server to dock ferritin andReceptor Binding Domain proteins together and biomolecular visualization of the complex wascarried out by PyMOL.Results: The complex structure of the RBD modeled (residues: ۳۳۳-۳۳۸, ۳۵۸-۳۶۵, ۳۸۵-۳۹۳, ۵۱۶-۵۳۲) with ferritin nanoparticle (residues: ۵۹۵-۶۱۳). Examination of the molecular dockingoutputs showed that among the energetic terms of the interactions, the driving force of thisattachment is electrostatics. The most probable binding pose is through a loop in the ferritin unitson the opposite side of the receptor binding motif site. The reliability of this model wasconfirmed by a very small RMSD value among previous docking results (۰.۳ Å).Conclusion: The SARS-CoV-۲ RBD - ferritin nanoparticle complex modeled and calculationsshowed that the electrostatic is the driving force of this interaction. This is the first atomisticmodel of ferritin-RBD nanoparticles reported.

کلیدواژه ها:

Nanoparticle ، Ferritin ، Molecular docking ، SARS-CoV-۲ RBD