Thrombin binding mode

Bohm described combinatorial docking [272] implemented in LUDI [216] for reductive amination in search for thrombin inhibitors. The binding mode of the most active one with a Ki value of 95 nM was even confirmed by X-ray structure analysis [234] (see Figure 4.5e). 

Figure 3.8. Schematic drawing of the active sites of thrombin, trypsin, and factor Xa. The crystallographic binding mode of the inhibitor NAPAP is shown to indicate the important subpockets SI, P, and D. Amino acids important for inhibitor binding and those differing between the enzymes are indicated (thrombin blue trypsin red factor Xa green common residues black).

Figure 1.14 Binding mode of tricyclic thrombin inhibitor 27d on the basis of X-ray crystallographic analysis of its protein complex.

The binding mode of three previously known inhibitors MD805 3 and NAPAP 4 (Fig. 4) as revealed in the X-ray structure of their complexes with thrombin [2,3] has some unexpected... 

Figure 3. Cartoon of the binding mode of fibrinogen 2 in thrombin with the arginine side chain in the recognition pocket, the valine side chain in the P-pocket and the leucine and phenylalanine side chains in the D-pocket.

Figure 5. Schematic representation of the experimentally determined binding mode of NAPAP 3 to thrombin.

The corresponding R=CH3 compound 10 from 3-Dimensional Pharmaceuticals has a Ki for thrombin of 11 nM and shows the same binding mode [40, 43]. 

It might have been expected that the chlorine would interact favorably with the alanine 190 side chain in thrombin and less well with the serine 190 -OH, giving selectivity for thrombin, but the inhibition constants reveal just the opposite. Trypsin is favored by AAG = 3 kcal moU, although the conserved water is indeed removed from both enzymes and the general binding mode is the same. 

In Section 7.7, the binding modes revealed by some crystal structures of thrombin-inhibitor complexes were discussed. Inhibitor studies on thrombin have been... 

It is now possible to produce a high-resolution structure of a thrombin-inhibitor complex in a day or so, which is quicker and easier than chiral separation. Where selectivity against related enzymes is an issue, which it certainly is for fhrombin, it has been repeatedly found that this can only be understood, and fhus improved, if the binding modes to these other enzymes can also be determined. This is particularly true where diastereomers are involved. 

X-ray analysis of thrombin complexed by recombinant hirudin showed that this inhibitor binds to two distinct sites of the protease - that is, the amino-terminal tet-rapeptide to the active site, and the C-ter-minal tail (hirudin residues 53-65) to the fibrinogen recognition site (FRE) [32, 93]. This heterobivalent binding mode explains the extremely high affinity and selectivity of hirudin, with a Ki of 21 fM [94]. De-... 

Figure 5 Proposed binding mode of compound 1 in complex with thrombin (A) and matriptase (B) as obtained from docking with DOCK. (See color plate at end of chapter.)...

Chirgadze, N.Y., Sail, D.J., Briggs, S.L., Clawson, D.K., Zhang, M., et al. (2000) The crystal structures of human a-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives a binding mode for a stmeturaUy novel class of inhibitors. Protein Sci. 9 29-36. 

Mathews 11, Padmanabhan K P, Ganesh V, et al. (1994). Crystallographic structures of thrombin complexed with thrombin receptor peptides Existence of expected and novel binding modes. Biochem. 33 3266-3279. 

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