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

Saba Ismail; Sajjad Ahmad; Syed Sikander Azam

The vital hydrogen bond interactions involved between TLR3 receptor and MEPVC shortlisted by VMD were subjected to a novel AFD analysis to elucidate 3D movements of MEPVC atoms with respect to a reference TLR3 residues atom in simulation time. To this objective, interactions mentioned in the RDF were used in AFD. Preliminary investigation suggested that only three interactions: TLR3-Asp52-MEPVC-Arg705, TLR3-Glu328-MEPVC-Tyr638, and TLR3-Glu323-MEPVC-Arg643 are mainly represented frequently and found in most of the simulation frames. The TLR3-Asp52-MEPVC-Arg705 is uncovered in 4997 frames, TLR3-Glu328-MEPVC-Tyr638 in 4988, and TLR3-Glu323-MEPVC-Arg643 in 4985 making these interactions ideal for interpreting density distribution of the interactions on XYZ planes and also appropriate for gaining ideas about conformational changes of the interacting atoms with respect to each other. As the local structure movements and rotations are responsible for functional shifts, their understanding in our system is important to be unveiled. For TLR3-Asp52-MEPVC-Arg705 (Fig.12) , the density distribution is not uniform, dispersed and behave flexibility in affinity on all three axis for the receptor atom. Parallel, the strength of interaction is also observed affected due to these minor structural movements of the MEPVC residue atom. Though, the mentioned interaction depicts MEPVC is still within the vicinity of the TLR3 reference residue and enjoys this interaction flexibility with the said MEPVC residue during simulation. TLR3-Glu328-MEPVC-Tyr638 interaction (Fig.13 ) has less distribution area and has much higher intensity illustrating strong affinity of the interacting atoms for each other. It also gives an idea of the lesser movements of the atoms with respect to each other, an indication of a correct system conformation. The distribution area TLR3-Glu323-MEPVC-Arg643 is much dispersed though high intensity of the interaction can be seen in close vicinity (Fig.14) .