2.7. Molecular docking and dynamics simulation of vaccine-TLRs complex

Human TLR-3 (PDB id 1ZIW), human TLR-4 (PDB id: 4G8A), mice TLR3 (3CIG) and mice TLR4 (PDB id 2Z64) were retrieved from the protein database (PDB) and prepared for docking analysis. Protein-protein docking was performed through the ClusPro 2.0 server. Based on the lowest energy score, efficiently docked complexes were selected and downloaded. Interactions between vaccine and TLR complexes were evaluated.

The docked Toll-like Receptor TLRs (human TLR3, 4 and mice TLR3, 4) and constructed multi-epitope vaccine complex MD simulations were computed using the YASARA dynamics suite [¹⁹]. The YASARA dynamics suite was also used to estimate conformational change and all possible interactions. AMBER 14 [²⁰] was considered for all MD simulations at constant temperature (298 K) using the NVT ensemble. The 0.9% concentration of NaCl salt was used to neutralize the system where water molecules (0.998 g/cm³ density) were added. The cell size was 20 Å larger than the complex in all cases. A cuboid cell box and periodic boundary conditions were employed for execution of the simulation. A cut-off radius of 8.0 Å was used for the particle-mesh Ewald (PME) method [²¹] for long-range electrostatic interaction calculations. For each system, the total simulation time for each case was 100 ns MD simulations with 100 ps time interval.