Fig. 3.

Best molecular docking complexes of three phthalocyanine (A-C) and three hypericin (D-F) molecules within the inner cavity of the spike glycoprotein. A, D) Drugs are shown as spheres, coloured by atom type with carbon atoms represented in grey. The spike glycoprotein is shown in blue cartoon representation with the HR1 regions highlighted in red. Molecular surface of the protein is shown in transparency. Residues 703-717 and 1070-1138 of the monomer A have been hidden. These images have been generated using the PyMOL 2.1.0 program (The PyMOL Molecular Graphics System, 2020). B, E) 3D representation of the main hydrophobic contacts established by the drugs within the pocket. Drugs and surrounding residues are represented in stick model and coloured by atom type, following the colour scheme described in the previous image. The pictures have been produced using the UCSF Chimera 1.13.1 program (Pettersen et al., 2004). C, F) 2D schematic view of the interactions established by the first docked molecule within the inner cavity of the spike glycoprotein. Hydrogen bonds are shown as green dashed lines between the interacting partners, represented as brown sticks. Hydrophobic interactions are shown as radial half-circles. Drugs bonds and carbon atoms are represented as blue sticks and black filled circles, respectively. Labels indicate residue names in one-letter code, residue numbers and the spike monomer to which each residue belongs. Pictures have been created using the LigPlot+ 1.4 software (Laskowski and Swindells, 2011). PHT: phthalocyanine, HYP: hypericin.