Design, synthesis, biological evaluation and molecular docking studies of dabigatran analogs as potential thrombin inhibitors

A series of fluorinated dabigatran analogs were designed and synthesized. All the target compounds were characterized by 1H NMR, 13C NMR, and FT-ICR-MS. The thrombin inhibitory activities of the new synthesized compounds were also evaluated in vitro. The results show that compound 12a has the highest IC50 of thrombin inhibition (IC50 = 5.41 nM). Moreover, molecular docking simulation was carried out to elucidate the conformations of the compounds and key amino acid residues at the active site of thrombin protein. The results show there is an appropriate relationship between IC50 and the docking scores for compounds 12a–e. We suggest that the hydrogen bond interaction between Asp189, Gly219 of thrombin and the compounds appear to play major role in thrombin inhibition.