Molecular dynamics simulation and binding free energy
To understand the stability, intermolecular interactions, and the
binding energy of the three ligand-TMPRSS2 complexes, the molecular
dynamics (MD) simulation has been performed using the OPLS3e force
field [29] implemented in Desmond v5package[30]. Further, the system was built with
the pre-defined TIP4P water model and orthorhombic periodic boundary
conditions at the distances 10 Å. Then the counterions were used to
neutralize the charge of these complexes with the balancing
Na+/Cl− ions. Further, the
constructed system for each ligand-TMPRSS2 complex was energy minimized
by heating and equilibrium processes before the MD simulation. For the
minimization, the minimization and heating protocol was fixed based on
the steepest descent method, annealing temperature at 0-300 K, and 2000
steps with the time steps of 0.001 ps. Further, the system was
normalized in an equilibrium state at 1000 steps with a time step of
0.001 ps. Finally, the production step of the systems was continued up
to 100 ns with the time steps of 0.001 ps, 300 K, 1 ATM pressure, and
applied using the Nose-Hoover method with NPT
ensemble[31]. Intermolecular interactions and
conformation of each ligand-protein complex was analyzed from the final
results of MD simulation. Among the 1000 fractions, 10, 20, 30, 40, 50,
60, 70, 80, 90, and 100 ns fractions were used to determine the binding
free energy (MM/GBSA) of the ligand-TMPRSS2 complexes by Primeapplication incorporated to Schrodinger software
package[32].