Stability of ligand(s)-TMPRSS2 complexes and
Intermolecular interactions
Molecular dynamics is crucial to consider for the understanding of the
biological function of proteins. Here we performed 100 ns MD simulations
for the three ligand-TMPRSS2 complexes to explore the stability and the
binding affinity of the three drug molecules towards the TMPRSS2.Figure 4 & 5 displays the variation of RMSD and RMSF values of
the three complexes during the MD simulations. The RMSD values of the
three drug molecules casmostat, nafamstat, and leupeptin are remains
within 2 Å (Figure 4 (A-C), whereas the RMSD of protein in the
camostat-protein and nafamostat-protein complexes are found high on
compare with leupeptin bound protein complex (2.4 Å). Figure 5
(A-C) shows the variations of RMSF of amino acids TMPRSS2 of three
complexes; among these, a strong fluctuation is found in the region of
residue number 60 of camostat –TMPRSS2 complex and no such incidence is
noticed in the RMSF map of other two complexes. The superimposed form of
the three ligand-protein complexes (Figure 6) obtained from the
docking and MD simulations is showing the conformational difference of
ligands and TMPRSS2 protein in the respective complex; specifically,
this allows to visualize that how the conformation and the orientation
of the ligands and proteins are altered during the MD simulation.
Overall, the fluctuation of the leupeptin molecule is found to be very
less and it is normal. Furthermore, surprisingly, the superimposed form
of docked and MD complexes of leupeptin (Figure 6) is showing
not much deviation as the other two complexes deviates considerably;
this confirms that leupeptin is very stable while binds with TMPRSS2
protein.
The intermolecular interactions between the ligand and the active site
amino acids of TMPRSS2 of three complexes obtained from the MD
simulations are shown in (Figure 7 (A-C)). On compare these
interactions with the interactions found in the docked ligand-TMPRSS2
complexes (Figure 2), shows that, during the MD simulation some
interactions became strong and few new interactions also formed(Figure 7). Further, when we examine the interactions present
in the camostat-TMPRSS2 complex, the terminal NH2 group
of camostat molecule forms interactions with one of the key amino acids
Asp180 at the distances 1.6 and 1.7 Å and these interactions are also
very stable during the MD simulation. Whereas in the nafamostat-TMPRSS2
complex, we observed a similar trend, in which the molecule forms
interactions with Asp180 at the distances 2.0 and 1.9 Å; in addition
that it also forms an interaction with His41, the contact distance is
2.3 Å. And these two molecules also form several interactions with the
nearby amino acids present in the active site. In the leupeptin-TMPRSS2
complex, as found in the docked complex, the MD simulation also
reproduced the hydrogen bonding interactions between leupeptin and the
key amino acids Asp180, His41 and Ser186 at the distances, 1.8, 1.8 and
1.7 Å. These important interactions were highly stable throughout the
100 ns MD simulations and this can be well understood from theFigures 8(A-C), 9(A-C) & Figure 2S. The characterization of
interactions between the drug molecules and TMPRSS2, reveals that the
leupeptin molecule is highly stable and forms the expected interactions
with the key amino acids Asp180, His41, and Ser186 of catalytic site and
are found very strong. Whereas the other two drug molecules camostat and
nafamostat are lacking the interactions with His41 and Ser186 amino
acids. The binding energy for the three complexes were calculated using
MM-GBSA method. The calculated values of the binding energy of camostat,
nafamostat, and leupeptin molecules with TMPRESS2 are -42.77, -52.86,
and -55.25 kcal/mol. Among these molecules, relatively, leupeptin has a
high binding affinity with the TMPRSS2 serine protease. Overall
leupeptin exhibits high stability and forms very strong interactions
with the key amino acids than the other two drug molecules.