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

Saba Ismail; Sajjad Ahmad; Syed Sikander Azam

Bioinformatic modelling driven molecular docking of the desingned MEPVC to one representative innate immune response receptor TLR3 was carried out in order to decode MEPVC potential of binding to the innate immune receptors. This was fundamental to understand as TLR3 is significant in recognition of virus associated molecular patterns and of activaiton of type I interferons and NF-kappa B. The docking assesment predicted top 20 complexes sorted mainlny on scoring functions along with interacting molecules area size, desolvation energy, and complexes actual rigid transformation. Following, the complexes were subjected to FireDock web server for refinement assay. This ease in discarding flexibility errors of the docking procedure and provide a deep refinement of the predictions thus limiting the chances of false positive docking calculations. According to the global energy, solution 8 was considered as a best complex with net global energy of -20.78 kJ/mol ( Table 2 ). This energy is the output of -16.88 kJ/mol attractive van der Waals (vdW), 3.81 kJ/mol repulsive vdW, 8.14 kJ/mol atomic contact energy (ACE), and -0.93 kJ/mol hydrogen bond energy. The docked conformation and chemical interacting residues of the MEPVC with TLR3 is shown in Fig.9 . Visual inspection of the complex leads to observation of deep binding of the MEPVC at the center of TLR3 and favor rigorously rigoursly hydrogen and weak van dar Waals interactions with various residues of TLR3. Within 3 Ã…, the MEPVC was noticed to formed interactions with His39,Val55,Asn57,Asp81,Phe84,Val103,Asn105,Gln107,His108,Thr126,Glu127,Ser132,Hi s129,Thr151,His156,Gln174,GLu175,Lys200,Lys201,Glu203,Asn229,Ser256,Asp280,Ser28 2,Tyr283,Tyr302,Phe304,Tyr307,Lys330,Tyr383,Tyr326,Asn328,His359,Asn361, and Glu363.