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. 2022 Nov 4;27(21):7572. doi: 10.3390/molecules27217572

Figure 2.

Figure 2

Docking pose orientation of best-bound OEU and OC molecules on the crystal structure of wild-type (wt) SARS-CoV-2 full-length model of the Spike protein in the open conformation state (one RBD-up), based on PDB: 6VSB and embedded in a realistic membrane environment of lipid bilayer mimicking the composition of the endoplasmic reticulum–Golgi intermediate compartment after molecular dynamics simulation [75]. All structural models were downloaded from the Amaro lab (https://amarolab.ucsd.edu/covid19.php (accessed on 13 June 2021)). Target trimeric wt S protein is illustrated as cartoon colored by chain in deep purple, deep teal, and orange for each of the 3 protomers (a, b, and c, respectively). The critical one RBD-up domain is also indicated inside a transparent sphere. OEU and OC are rendered in sphere mode and colored according to atom type in light-pink and yellow-orange C atoms, respectively. OC is stabilized at the interface between the NTD (part of the S1) AS1 of protomer a and the RBD domain (CS1) of protomer c (inlaid depiction in transparent sphere). OEU is stabilized at the interface between the C-terminal domain 1 (CT1) of protomer b and the HR1 and CH domains of protomer c, being at the apical position of both the fusion peptide (FP) and fusion peptide region (FPR) of protomer c, flanked by the central helix (CH). In the structure are also depicted the heptad repeat 2 (HR2, 1163–1210), the transmembrane domain (TM, 1214–1234), and the cytoplasmic tail (CT, 1235–1273) domains. Color code used for lipid tails (surface representation): POPC, POPE, POPI, POPS, and cholesterol in cyan. P atoms of the lipid heads and cholesterol’s O3 atoms are highlighted in red. N-linked glycans (NAG moieties) are omitted from the structure for clarity. Molecular docking simulations were performed individually. Hydrogen atoms are omitted from both molecules, and sugar molecules glycosylating the protein are hidden for clarity. Heteroatom color code: O—red. The final structure was ray-traced and illustrated with the aid of PyMol Molecular Graphics Systems.