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Document Page 275 be utilized to model known Factor Xa inhibitors using the x-ray coordinates of native Factor Xa. Preliminary modeling of the several inhibitors described below into the Factor Xa active site was accomplished by the author [69] by first superimposing the backbone atoms (N, Ca, C) of the catalytic triads (His 57, Asp 102, Ser 195 in the benzamidine:thrombin and PPACK:thrombin x-ray structures on the corresponding residues in Factor Xa. This allowed an excellent fit of the P1 basic groups, arylbenzamidine in the case of benzamidine and arginine for PPACK, into the S1 pocket of Factor Xa. These groups were then used as templates for positioning the appropriate P1 basic groups of the various synthetic inhibitors [69]. Holding these docked P1 groups fixed, the remaining rotatable bonds were manipulated to allow a reasonable and complementary fit of the inhibitor atoms to the solvent accessible surface of the Factor Xa active site. In those cases where it was possible, hydrogen bonds, particularly to Gly 216, were formed. To fit extended peptide sequences such as that for antistasin and the antistasinderived peptides described below, the backbone atoms of the residues around the cleavage site (e.g., P4–P4') were positioned using the corresponding BPTI backbone atoms as a template. This was done after first aligning the trypsin catalytic triad backbone in the BPTI:trypsin x-ray complex (vida infra) to Factor Xa. Where the side chains of the bound peptide segments differed from BPTI, their orientation was either modeled for maximum complementarity to the Factor Xa molecular surface or set by an algorithmic approach [78]. In some cases the structures obtained were energy minimized initially by steepest descent followed by conjugate gradient minimization. Recently, compounds based on a bisamidine motif (e.g., DX-9065a) have been reported as potent and selective Factor Xa inhibitors (1, DX-9065a) [60–63]. The position of the amidino group makes little difference to the Factor Xa potency of these compounds but, interestingly, has a dramatic effect on the selectivity towards thrombin [62]. It was also observed that one carboxylic acid isomer (CX-9065a) was 7 times more potent on Factor Xa than the other. A second set of analogs shows a similar SAR [60]. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_275.html [4/5/2004 5:13:08 PM]
Document Page 276 In both cases the acids are much more selective for Factor Xa over thrombin. An initial modeling study using a homology-built Factor Xa structure proposed a fit of DX9065a to Factor Xa in which the amidinoary1 group occupies the S1 pocket and the acetimidoyl group is directed out of the S4 pocket [60]. Lin et al. [64] have provided a more systematic study of possible fits of compound 2 and DX9065a using the recently available Factor Xa coordinates [4]. After aligning the His 57, Ser 195, and Asp 102 backbone atoms for Factor Xa and thrombin (in the benzamidine:thrombin x-ray structure [65]) the arylamidino group of 2 was superimposed on the benzamidine template and a systematic conformational search was performed on the rotatable bonds of inhibitor 2. Energetics and complementarity to the Factor Xa surface determined a saved set, about 300 low-energy conformations, for further study. The final result was an optimized structure in which the acetimino group of 2 fits into Figure 7 Molecular modeling fit of compound 2 with the arylamidino group positioned in the S1 pocket and the acetimino group in the S4 cation-π site [69]. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_276.html (1 of 2) [4/5/2004 5:13:12 PM]
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Document Table 1 Approval Indicatio
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document fragment-based programs, 5
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Document [Human immunodeficiency vi
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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