Research Article
Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat’s Claw) against the Main Protease 3CLpro of SARS-CoV-2 by Molecular Modeling
Figure 5
Complete analysis of the 250 ns trajectory of 3CLpro of SARS-CoV-2 bound with speciophylline. Monomer A is shown in orange and monomer B in blue. (a), (e), and (f) shows, from left to right, RMSD, all-to-all RMSD, PCA, and cluster counting (cutoff 1.5 Å). (b) shows the relative position of speciophylline molecules versus the center of mass of the S1 cavity along the simulation (black dashed line indicates the distance of the N3 inhibitor as reference). In (c), size of the ribbon is proportional to the flexibility of the protein backbone and the size on the ligand center is proportional to the amount of structural deviation of the ligand during the 250 ns. (d) reproduces the binding site S1 with the most important residues involved in the interactions.
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