Fig. 12
From: In vitro enzymatic and cell culture assays for SARS-CoV-2 main protease interaction with ambenonium
A comparative Root Mean Square Deviation (RMSD) analysis over time for the apo form, the dimer, and the monomer of the main protease and ambenonium. The x-axis represents time in picoseconds (ps), while the y-axis denotes RMSD in Angstroms, which quantifies structural deviation from the initial conformation. Blue line (apo form: dimer) represents the RMSD of the dimer in its unbound state, exhibiting relatively stable fluctuations around 4–5 Å and 100 ps. Orange line (combined: dimer + ambenonium) depicts the RMSD of the dimer complexed with ambenonium, showing a slightly higher deviation than the Apo Form, particularly after 200 ps, suggesting ligand-induced structural variations. Green line (combined: monomer + ambenonium) represents the monomer complexed with ambenonium. Initially, it shows the lowest RMSD values, indicating structural stability. However, around 800 ps, a sharp increase suggests significant conformational changes.
