Fig. 7: In silico docking of Mpro with D-Phe-Pro-Arg tripeptide. | Communications Biology

Fig. 7: In silico docking of Mpro with D-Phe-Pro-Arg tripeptide.

From: The main protease (Mpro) from SARS-CoV-2 triggers plasma clotting in vitro by activating coagulation factors VII and FXII

Fig. 7: In silico docking of Mpro with D-Phe-Pro-Arg tripeptide.

A Close-up view of D-Phe-Pro-Arg peptide (shown in stick) (i.e., the peptidyl moiety of PPACK D-Phe-Pro-Arg- CH2Cl) docked into Mpro active site (shown as van der Waals surface, light gray). Ligand atoms are color coded: nitrogen in blue, oxygen in red, carbon in dark gray. Relevant amino acid side-chains in Mpro are indicated. The Arg guanidyl-group is electrostatically coupled to Glu166 in the S1 site, whereas D-Phe points toward His41 in the active site (AS), whereas Pro interacts with Thr25 and Thr26 in the S1′ sub-site. HPEPDOCK software was used in docking simulations (see “Methods”). B Surface electrostatic potential of Mpro in the dimeric form. Calculations were carried out using the APBS software on the crystallographic structure of Mpro in the dimeric form (6y2e.pdb). The surface is colored according to the electrostatic potential (blue, positive; red, negative), as indicated, and expressed as kJ/(mol·q).

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