Thrombin has a vital role in regulating blood coagulation mechanism and its related disorders. Anti-thrombin agents/inhibitors interact mainly at the active site or the exosites I/II of thrombin, leading some structural and conformational changes to form the thrombin-inhibitor complex. Study of such conformational modifications helps to illustrate dynamic molecular interactions between them. Hirudin, a serine protease inhibitor’s N- terminal binds effectively to the active site and its C- terminal to exosite-I of thrombin. Here, we elucidate the insights of thrombinhirudin complex interaction by molecular dynamics (MD) simulation study. The 3-dimensional crystal complex of thrombin-hirudin was neutralized and kept in water cube for 1000 picoseconds (ps) at specific equilibrium. At every frame the movement, interaction and stability of the complex is studied and visualized. Results were analyzed based on change in energy of the system and parameters such as Root Mean Square Deviation (RMSD= 0.45 Å fluctuation), radius of gyration (18.04 Å) and hydrodynamic radius (19.06 Å) etc. It was seen that thrombin-hirudin complex interaction was stable throughout the experiment, similar as in the natural environment. It depicts the stability of drug (hirudin)- target (thrombin) complex and this study would provide valuable insights for thrombin inhibitor design in future.
