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.