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Document Page 277 the S4 pocket formed by the aromatic residues Trp 215, Tyr 99, and Phe 174 (Figure 7). It was proposed that this collection of aryl residues forms the basis for a cation-π interaction that has recently been well documented in other cases [66]. Interestingly, this cation-π site is absent in thrombin's equivalent “aryl binding site” where the corresponding residues are Trp 215, Leu 99, and Ile 174—residues that cannot provide the π-electrons necessary for stabilization of the cation in the inhibitor. The apparent preference for FXa inhibitors to have cations in the P3,P4 position may be directly related to the ability of the Factor Xa S4 site to stabilize these cations via a cation-π interaction. Factor Xa appears to be unique among the coagulation factors in providing this electron-rich S4 pocket (Table 4). The initial discovery of bisamidine structures as potential Factor Xa inhibitors was actually made much earlier with the finding that compounds such as 4 showed an almost 300-fold preference for Factor Xa over thrombin with a K i of 13 nM (FXa) [67], As with the DX-9065 analogs and compounds 2 and 3, the Factor Xa potency was relatively insensitive to the positioning of the amidino groups (4,4' versus 3,3') while replacing the 7-membered cycloalkyl ring with the 5 or 6 membered ring analogs reduced potency by about 10 fold. Model building compound 4 and docking into Factor Xa [69], again using the x-ray benzamidine:thrombin complex [65] as a template, shows that the second aryl amidino group can be positioned into the S4 aromatic pocket of Factor Xa in a conformation closely related to the mode of binding proposed for DX9065a (Figure 8) [64]. In an effort to compare the relative efficacy of thrombin versus Factor Xa inhibitors, Markwardt et al. [67] synthesized a set of amidinoaryl compounds with moderate potency as Factor Xa inhibitors (5). Table 4 S4 Residues in Selected Serine Proteases Residue Position a Factor Xa Thrombin Factor VIIa Trypsin 99 Tyr Leu Thr Leu 174 Phe Ile Pro Gly 215 Trp Trp Trp Trp aChymotrypsin numbering system. Sequence alignments by comparison of x-ray structures (sequence for Factor VIIa). http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_277.html (1 of 2) [4/5/2004 5:13:15 PM]
Document Page 278 The n=3 chain length was optimal while the nature of the tosyl group on the α- nitrogen was relatively nonspecific, with tosylGly and Nα-β-naphthylsulfonyl- Gly being of similar potency. While the phenyl group on the amide nitrogen was best, other groups were also tolerated. Although the authors did not speculate on how these compounds were bound to Factor Xa, it is reasonable to suggest that the amidino phenyl group fits in the S1 pocket similar to the orientation determined by x-ray crystallography for benzamidine in the benzamidine:thrombin x-ray crystal structure. If the aryl amidino group of 5 is matched to that of benzamidine after alignment of the catalytic triad backbone atoms (N,Cα,C) for thrombin and Factor Xa, a proposed fit of 5 to Factor Xa can be made (Figure 9) [69]. This mode of binding is consistent with the structure activity relationships observed but does not suggest the reasons for the observed small preference for Factor Xa over thrombin. Figure 8 Molecular modeling fit of compound 4 in the Factor Xa active site [69]. The carbonyl of the cycloheptanone makes a hydrogen bond (3.12 Å) to N-Gly 216 . http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_278.html (1 of 2) [4/5/2004 5:13:20 PM]
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Document Page 108 mulate during tre
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Document cubation of phosphotyrosin
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Document 6 Structural Implications
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Document Table 1 Approval Indicatio
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Document A. The Canyon Page 491 The
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document [Human immunodeficiency vi
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Document RT inhibitor, 41, 56 Nonpe
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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