Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine

Saba Ismail; Sajjad Ahmad; Syed Sikander Azam

The MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . TLR3 available under PDB id of 1ZIW was retrieved and used as a receptor molecule. TLR3 also named as CD283 is a transmembrane protein belongs to the family of pattern recognition receptor [61] . It detects viral infection-associated dsRNA and evoke the activation of interferon regulatory transcription factor (IRF3) and (Nuclear Factor kappa-lightchain-enhancer) NF-kB [62] . Unlike other TLRs, TLR3 uses TIR-domain-containing adapterinducing interferon-β (TRIF) as a primary adapter [63] . IRF3 eventually induces the development of type I interferons leading to the activation of innate immune system and eventually to long lasting adaptive immunity [64] . The TLR3 receptor and MEPVC were used in a blind docking approach through an online PATCHDOCK server interface [65] . The interacting molecules were docked according to the shape complementarity principle. The clustering RMSD is allowed to default 4.0 Å. The output docked solutions were immediately refined with Fast Interaction Refinement in Molecular Docking (FireDock) server [66] which provides an efficient framework for refining PATCHDOCK complexes. The refined complexes were examined and one with lowest global energy was considered as top ranked. The opted complex was subjected to in-depth MEPVC conformation with respect to the TLR3 using UCSF Chimera 1.13.1 [67] .