Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors

Structure. 2001 Jan 10;9(1):29-37. doi: 10.1016/s0969-2126(00)00551-7.


Background: A major current focus of pharmaceutical research is the development of selective inhibitors of the blood coagulation enzymes thrombin or factor Xa to be used as orally bioavailable anticoagulant drugs in thromboembolic disorders and in the prevention of venous and arterial thrombosis. Simultaneous direct inhibition of thrombin and factor Xa by synthetic proteinase inhibitors as a novel approach to antithrombotic therapy could result in potent anticoagulants with improved pharmacological properties.

Results: The binding mode of such dual specific inhibitors of thrombin and factor Xa was determined for the first time by comparative crystallography using human alpha-thrombin, human des-Gla (1--44) factor Xa and bovine trypsin as the ligand receptors. The benzamidine-based inhibitors utilize two different conformations for the interaction with thrombin and factor Xa/trypsin, which are evoked by the steric requirements of the topologically different S2 subsites of the enzymes. Compared to the unliganded forms of the proteinases, ligand binding induces conformational adjustments of thrombin and factor Xa active site residues indicative of a pronounced induced fit mechanism.

Conclusion: The structural data reveal the molecular basis for a desired unselective inhibition of the two key components of the blood coagulation cascade. The 4-(1-methyl-benzimidazole-2-yl)-methylamino-benzamidine moieties of the inhibitors are able to fill both the small solvent accessible as well as the larger hydrophobic S2 pockets of factor Xa and thrombin, respectively. Distal fragments of the inhibitors are identified which fit into both the cation hole/aromatic box of factor Xa and the hydrophobic aryl binding site of thrombin. Thus, binding constants in the medium-to-low nanomolar range are obtained against both enzymes.

MeSH terms

  • Animals
  • Blood Coagulation / drug effects*
  • Blood Coagulation Factor Inhibitors / pharmacology*
  • Cattle
  • Crystallography, X-Ray
  • Factor Xa / chemistry*
  • Factor Xa Inhibitors*
  • Humans
  • Ligands
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Thrombin / antagonists & inhibitors*
  • Thrombin / chemistry*
  • Thrombin / metabolism*
  • Thrombosis / prevention & control
  • Trypsin / metabolism


  • Blood Coagulation Factor Inhibitors
  • Factor Xa Inhibitors
  • Ligands
  • Trypsin
  • Thrombin
  • Factor Xa