Pharmacophore thrombin

Among the many other non-oxicam-type substances discovered are a sultam pro-drug for potential P3-lactam thrombin inhibitors <1998BML3683>. Furthermore, an anti-methicillin-resistant Staphylococcus aureus (anti-MRSA) pharmacophore based on the 1,2-thiazine structure has also been recently disclosed <1999BML673>. Workers at Bristol-Meyers Squibb have synthesized and evaluated sultam hydroxamates as MMP-2 inhibitors <2004JME2981>. Hydroxamate 38 displayed the best selectivity for MMP-2 over the other proteins in this superfamily of peptidases (Figure 27). As noted in Section 8.07.3.1, an X-ray crystal structure of 38 bound to the protein MMP-13 protein has been solved. 

The multiple potential pharmacophores for targets, such as protein active sites, are defined using complementary site points to exposed features accessible in the site. These site points (see section 2.3) create a hypothetical molecule that interacts with all pharmacophoric regions of the site. Figure 2 illustrates site points that were used for the thrombin site in selectivity studies for three serine protease inhibitors (see section 4.3). The potential pharmacophores are calculated for this molecule just as for any... 

An example of the method has been published [ 14] that compares studies on three closely related serine proteases thrombin, factor Xa and trypsin. 4-point multiple potential pharmacophore keys were generated from site-points positioned in the active sites using the results of GRID analyses. These are illustrated in figure 10, together with the number of overlapping... 

Figure 10. The numbers of potential 4-point pharmacophores calculated on the basis of complementary site-points placed in the active sites of thrombin, factor Xa, and trypsin, and number of overlapping pharmacophores (pair-wise and for all 3 serine protease sites).

The results shown in figure 12 indicate that the use of just 4-point potential pharmacophores can give correct indications as to relative selectivity for ligands for this set of related enzymes. The thrombin and factor Xa inhibitors exhibit greater similarity with the complementary 4-point potential pharmacophore keys of the thrombin and factor Xa active sites, respectively, than with the potential pharmacophore keys generated... 

Figure 15. 3- and 4-point multiple pharmacophore overlaps for the thrombin ligand MQPA and the serine protease active-site derived pharmacophores the left-side arrow indicates the incorrect indication of factor Xa selectivity from the 3-point figures, and the right-side arrow the observed activity and the increased resolution of selectivity using the 4-point relative pharmacophores. 

The thrombin-inhibitor example demonstrates a path from the bioactive 3-D struc-tnre of a peptide to small molecules. However, unambiguous structural information on the bioactive ligand conformation needed for snch a transformation is only available in a limited nnmber of cases. In most cases, additional complementary information has to be nsed to deduce the bioactive conformation of a bonnd ligand, and thns a pharmacophore model for virtual screening or design. 

The work described by Deadman et al. [100] considered a subset of the above set of thrombin inhibitors. A training set of 16 homologous nonpeptide inhibitors whose conformations had been generated in continuum solvent (MacroModel) and clustered into conformational families (XCluster) was regressed against this pharmacophore so as to obtain a 3D-QSAR mode. 

The structure-based pharmacophore was built using the crystallographic coordinates of argatroban complexed with thrombin [101] and the functional group definitions contained within the CATALYST software to predict the effects on the K[ values of structural modification of a set of homologous 4-aminopyridine (4-AP) thrombin inhibitors. 

Pharmacophore fingerprints generated from complementary site points can be used to direct combinatorial library design and to investigate selectivity. An example of the pharmacophore fingerprinting method for selectivity studies has been validated (37a,b) in studies of three closely related serine proteases thrombin, Factor Xa, and trypsin. Site points were... 

Greenidge PA, Weiser J. A comparison of methods for pharmacophore generation with the catalyst software and their use for 3D-QSAR application to a set of 4-aminopyridine thrombin inhibitors. Min Rev Med Chem 2001 1 79-87. 

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