Structural Basis for Inhibition Promiscuity of Dual Specific Thrombin and Factor Xa Blood Coagulation Inhibitors

Abstract

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.

Structural binding evidence of the trypanocidal drugs Berenil® and Pentacarinate® active principles to a serine protease model

“…In ␤-tryp/dmz-B, the electron density around Gln192 side chain is continuous and well defined, suggesting the occurrence of a single conformation. This latter Gln192 side chain conformation (␤-tryp/dmz-B) is particularly different from those observed in ␤-tryp/pnt and ␤-tryp/dmz-A, as well as in a number of previously reported ␤-trypsin/ligand complex structures (PDB IDs: 1BJU and 1BJV [1], 1MTS, 1MTU, 1MTV and 1MTW [19], 1QB1, 1QB6 and 1QBN [12], 1C2F, 1C1T and 1C1Q [11], 1PPH [20], 1F0U [21], 1OYQ [22], 1K1I, 1K1J, 1K1M, 1K1N and 1K1P [13], 2ZDK, 2ZDL, 2ZDM and 2ZDN and 2ZFS; 1Y3U, 1Y3V and 1Y3W [23]). However, Katz et al [15] described an almost identical conformation for this amino acid residue in the crystallographic structure of bovine ␤-trypsin in complex with the ligand 124 (2-(2-hydroxy-phenyl)-1H-indole-5-carboxamidine) (PDB ID 1GI6 [15], rmsd of 0.36 Å for all Gln192 side chain atoms).…”

“…Additionally, isothermal titration calorimetry (ITC) assays performed on the binding of pentamidine to the enzyme allowed a complete thermodynamic description of the interaction. In the light of previously described thermodynamic data [2,5] and crystallographic structures of trypsin in complex with benzamidine-based compounds (PDB IDs: 1BJU and 1BJV [1]; 1MTS, 1MTU, 1MTV and 1MTW [19]; 1GI4, 1GI5 and 1GI6 [15]; 1QB1, 1QB6 and 1QBN [12]; 1C2F, 1C1T and 1C1Q [11]; 1PPH [20]; 1F0U [21]; 1OYQ [22]; 1K1I, 1K1J, 1K1M, 1K1N and 1K1P [13] and 1Y3U, 1Y3V and 1Y3W [23]), a comparative analysis with related complexes is presented in order to establish direct correlations between bindings mode and binding affinity in benzamidine-based platforms.…”

Effect of Phenprocoumon on Monitoring of Lepirudin, Argatroban, Melagatran and Unfractionated Heparin with the PiCT Method

“…An eventual inhibition promiscuity for FII and FX described for some inhibitors [21] should also be taken into consideration as a possible reason. Feedback mechanisms between FII, FVII, FIX and FX could also play a role in generating the differences between the effects of oral anticoagulation on the actions of each direct thrombin inhibitor [22].…”

Visions & Reflections Factor Xa - a promising target for drug development

“…The complex pathogenesis of thromboembolic processes which involves both plasmatic and cellular reactions requires a careful analysis of the usefulness of a combination of FXa inhibitors with other drugs showing different mechanisms and sites of action in order to enhance the therapeutic effect. Simultaneous direct inhibition of thrombin and FXa by synthetic proteinase inhibitors might represent a novel approach to develop antithrombotics with improved pharmacological properties [40]. Although the efficacy/safety profile of FXa inhibitors may be better than that for heparin or antithrombin agents, these agents may also cause undesired side effects such as bleeding complications.…”