3.1 Active site analysis
Active site analysis of SARS-CoV-2 spike glycoprotein (S2), viral nuclease (NSP15 endoribonuclease) and protease (Main Protease 3CLpro) as conducted by DoG Site Scorer indicated that there are various active pockets within the studied viral virulence factors with druggability ranging from 0.12 to 0.86 (Table 1 ).
It was found that pockets P_11 (Drug score: 0.847), P_1 (Drug score:0.860) and P_0 (Drug score: 0.805) were energetically favourable for performing further molecular docking studies with the viral receptors being spike glycoprotein, NSP15 endoribonuclease and Main Protease 3CLpro, respectively. While conducting the active site analysis, the DoG Site Scorer tool analysed the heavy atom coordinates on the surface of the 3D structure of the respective viral receptors. Depending on these atomic coordinates, a hypothetical grid was spanned by outruling the chances of any spatial overlap of the grid with the heavy atoms. Furthermore, the tool engages in applying a Gaussian filter to the defined grids, so as to identify spherical pockets of binding. Druggability score (0-1) of the selected spherical pockets are deduced on the basis of their surface area, volume, enclosure and hydrophobicity. As a general rule, higher druggability score is indicative of a more druggable pocket (Volkamer et al., 2012). The most druggable pockets of SARS-CoV-2 spike glycoprotein, NSP15 endoribonuclease and main protease 3CLpro have been elucidated inFig. 2 .