All Atom Molecular Dynamics Simulations of Ritonavir, Lopinavir and Inhibitor N3 at the Binding Pocket of SARS-CoV-2 Main Protease
Serdar Durdagi1,*, Busecan Aksoydan1,2, Berna Dogan1, Kader Sahin1, Aida Shahraki1,3
1 Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
2 Neuroscience Program, Graduate School of Health Sciences, Bahçeşehir University, Istanbul, Turkey
3 Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
Data includes all of the trajectories of classical all-atom molecular dynamics (MD) simulations of ritonavir lopinavir and inhibitor N3 at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program for ritonavir and lopinavir. Initial position of N3 was retrieved from PDB, 6LU7. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the ritonavir and lopinavir simulations. Corresponding production time for N3 was used as 100-ns.