Fig. 10
Per-residue free energy decomposition analysis for the four peptide–Mpro complexes. (A) AGVAKAKAV, (B) VAKAKAV, (C) WWTWTPFHLLV, and (D) LTINWQKYFNT. Bar plots represent the contribution of each peptide residue (ΔG_bind, kcal·mol⁻¹) to the total binding free energy obtained by MM-PBSA decomposition. Negative values indicate stabilizing contributions, whereas positive values indicate destabilizing effects. On the right side, we can see the last frame of each molecular dynamics simulation (100ns). The corresponding structural panels show each peptide (sticks) bound to Mpro (gray ribbon), with residues contributing most to binding highlighted. The recurrent electrostatic interaction between K7 and E166 is observed in panels (A) and (B), while aromatic and polar contacts involving tryptophan residues, W4 and W5, and Mpro residues R188 and Q189 characterize the interactions in panels (C) and (D), respectively. Since N3 has non-canonical amino acids, its complex cannot be displayed in this analysis.
