Molecular Dynamics Simulation of SIRT6 and COX-2

The molecular dynamics simulation was carried out for 10000 ps using the GROMACS 4.6.5 package^{80 (link)}. The topology parameters for SIRT6 (3K35) and COX-2 (6COX) were generated by Gromacs, whereas for thieno[3,2-c]pyran analogs and RONS, the ACPYE module of AmberTools16^{81 (link)} and the Automated Topology Builder server^{82 (link)} were used, respectively. Charges for RONS, were adopted from QM-based hybrid DFT. Prior to simulation, an energy minimization was performed to full system without constraints using steepest descent integrator for 2000 steps. The system was then equilibrated for 200 ps of NVT and NPT ensemble, applying the position restraints on protein, inhibitors, and counterions at 310.15 K with periodic boundary conditions. The temperature was kept constant by a Berendsen thermostat, while the pressure was maintained at 1 bar using a Parrinello-Rahman scheme. Electrostatic interactions were calculated using the particle mesh Ewald method and cut-off distances for the calculation of Coulomb and van der Waals interactions were 1.4 nm during the equilibration. Finally, the system was subjected to 10000 ps MD at a temperature of 310.15 K (V-rescale thermostat) and a pressure of 1 bar (Parrinello-Rahman barostat). A periodic boundary condition was imposed on the system and the motion equations were integrated by applying the leaf-frog algorithm with a time step of 2 fs.