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Figure 4 | Veterinary Research

Figure 4

From: Tomatidine inhibits porcine epidemic diarrhea virus replication by targeting 3CL protease

Figure 4

In silico tomatidine targeted the active pocket of PEDV 3CL protease. A Docked conformations of tomatidine with PEDV nsp3 PLP2, nsp5 3CLpro, nsp12 RdRp, nsp13 NTP, nsp14 ExoN, nsp15 Nendo U, and nsp16 2′-o-methyltransferase. The compounds and proteins are represented as sticks and cartoons, respectively. The compounds are colored green. The proteins are colored according to their secondary structures (helix = blue, sheet = purple, loop = pink). The active sites of enzyme pockets are shown as a mesh. B The binding energy of the tomatidine–protein complex, calculated using Autodock, is listed. C Overall dynamic behaviors in the MD simulations. (i) RMSD of backbones of nsp5 (red) and nsp16 (blue); (ii) Distance between tomatidine and active pocket of nsp5 (red) and nsp16 (blue); (iii) Number of hydrogen bond interactions of tomatidine with nsp5 (red) and nsp16 (blue). D Docked conformations of tomatidine with PEDV 3CLpro or inactive 3CLpro. The compounds and proteins are represented as sticks and cartoons, respectively. The compounds are colored green. The proteins are colored according to their secondary structures (helix = blue, sheet = purple, loop = pink). The active sites of enzyme pockets are shown as a mesh. E The binding energy of the tomatidine–protein complex, calculated using Autodock, is listed.

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