Those pyrimidine-based compounds were then optimized in the work by Dolsak et. al and were analyzed through the application of molecular docking and MD simulations, followed by proteinligand interaction analysis through the application of Dynophores . In the work of Sadeghkhani et al. pharmacophore models were developed and used for a virtual screening campaign with the hits of the screening undergoing molecular docking to obtain potential TLR8 agonists. MD simulations were performed to validate the molecular docking results and free energy calculations were performed on the protein-ligand complexes of the best hits . An important application of MD simulations in the study of TLR8 was also performed by Bzówka et. al., who applied MD simulations to obtain insights about the cleavage of the TLR8 Z-loop . However, there is a knowledge gap in the mechanism of TLR8 agonists and antagonists unbinding.