The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19

Bishajit Sarkar; Md. Asad Ullah; Fatema Tuz Johora; Masuma Afrin Taniya; Yusha Araf

In protein-protein docking, the constructed SARS-CoV-2 vaccines were analyzed by docking against some MHC alleles as well as the toll like receptors (TLRs). During viral infections, the MHC complex recognize the viral particles as potent antigens. Since the different portions of the MHC molecules are encoded by different MHC alleles, the constructed vaccines should have very good binding affinity towards these segments of the MHC complex [150] . [152] . The coronavirus is an RNA virus [153] . For this reason, the vaccine constructs of Wuhan novel coronavirus were docked against TLR-8 (PDB ID: 3W3M). The protein-protein docking study was conducted using different online docking tools to improve the prediction accuracy of the docking study. At first, the docking was performed by ClusPro 2.0 (https://cluspro.bu.edu/login.php). The server ranks the docked complexes based on their center scores and lowest energy scores [154] - [156] . The binding affinity (ΔG in kcal mol -1 ) of the docked complexes were later analyzed by PRODIGY tool of HADDOCK webserver (https://haddock.science.uu.nl/). The lower binding energy of the server represents the higher binding affinity and vice versa [157] - [159] . Next, the docking was again carried out by PatchDock (https://bioinfo3d.cs.tau.ac.il/PatchDock/php.php) server and later refined and re-scored by FireDock server (http://bioinfo3d.cs.tau.ac.il/FireDock/php.php). The The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.05.935072 doi: bioRxiv preprint Surface Area (MM-GBSA) study was also calculated by the HawkDock server which works on specific algorithm that depicts that, the lower score and lower energy represent the better scores [160] - [163] . From the docking experiment, one best vaccine was selected based on the docking score. The docked structures were visualized by PyMol tool [164] .