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Document Figure 5 Schematic representation of the principal intermolecular interactions of a fibrinogen peptide A mimetic within the active site of thrombin. Page 252 Obst et al. [13], departing from the peptide template, designed and synthesized novel nonpeptide inhibitors of thrombin. They began with a cyclic template having attachment sites for three side chains that would be complementary to the S1, S2, and S3 sites in thrombin. Important to the design was a rigid template that would avoid hydrophobic collapse of the side chains and loss of conformational degrees of freedom upon complex formation with thrombin. Using computational approaches (Insight II/Discover/CVFF force field), possible templates were modeled within the active site of thrombin. These studies resulted in the synthesis of thirteen analogs that shared a common template. The most active molecule (K i = 90 nM, 8-fold selective versus trypsin) was studied further by x-ray crystallography (Figure 6). The positively charged benzamidine binds into the S1 pocket of thrombin forming a bidentate hydrogen bond with Asp189. The proximal carbonyl of the rigid template acts as a hydrogen-bond acceptor for the amide NH of Gly216. The methylene dioxybenzyl group at P3 interacts with thrombin in two ways. An edge-to-face interaction was observed with Trp215, and an oxygen of the methylenedioxy group acts as an acceptor for a hydrogen bond with the OH hydrogen of Tyr60A. Recent communications from Bristol-Myers Squibb [14,15] describe peptidomimetic inhibitors (Figure 7) that were designed to bind thrombin with an N- to C-polypeptide chain sense opposite that of the substrate and form interactions similar to those made by the first three residues of hirudin (lle1, Thr2, Tyr3). In the x-ray crystal structure of BMS-183507 (K i = 17.2 nM) with thrombin [15], the N terminus is facing the catalytic site while the methyl ester is http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_252.html (1 of 2) [4/5/2004 5:10:35 PM]
Document Figure 6 Schematic representation of the principal intermolecular interactions of a nonpeptide bicyclic inhibitor within the active site of thrombin. exposed to solvent. No specific interactions were observed with the catalytic triad. A bound water molecule hydrogen bonded to the Ser195 hydroxyl. Page 253 The complex is stabilized by a network of hydrogen bonds as well as hydrophobic interactions. The Phe1-O and the Phe3-NH form hydrogen bonds with Gly216, and the Phe1-NH hydrogen bonds to the backbone carbonyl of Ser214. The Phe1 phenyl group occupies the S2 site, while Phe3 interacts within the S3 site. The retro-inhibitors contain a 4-guanidinobutanoyl group that extends into the S1 specificity site. Rather than forming two hydrogen bonds between the guanidine and Asp189 in a manner similar to PPACK, BMS-183507 forms only one, with the second hydrogen bond being directed to the carbonyl oxygen of Gly219. Binding affinity, as evidenced by loss of more than two orders of magnitude in affinity on addition of one or two methylene groups, was sensitive to chain length at this position. The allo-Thr hydroxyl oxygen accepts a hydrogen bond from the backbone NH of Gly219. This additional interaction accounts, at least in part, for the increase in affinity when compared to the inhibitor with Leu in this position. Comparison of the crystal structures of thrombin complexed with BMS-183507 and with hirudin reveals that the hirudin residue, Thr2, and the allo-Thr of BMS-183507 interact differently with thrombin. The hirudin Thr2 binds at S2, http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_253.html (1 of 2) [4/5/2004 5:10:38 PM]
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Document Analysis of various HIV-1
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Document Page 54 Table 2) [12,54].
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Document Page 72 16. Goldman ME, Nu
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Document dine) and didanosine (dide
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Document 163. Lacey SF, Larder BA.
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Document Page 108 mulate during tre
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Document when metals are bound. Fin
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Document Page 141 receptor with int
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Document Page 166 As predicated, th
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Document References 1. Parks RE Jr.
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Document 17. Ealick SE, Rule SA, Ca
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Document 6 Structural Implications
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Document 17 Structure and Functiona
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Document Table 1 Approval Indicatio
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Document II. Type IFNs A great deal
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Document Page 441 sequence of the m
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Document Page 443 that allowed for
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Document Figure 5 Velcro-key model
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Document Page 476 nM, respectively.
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Document VI. Conclusion Page 480 It
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Document Page 488 against most of t
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Document A. The Canyon Page 491 The
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Document Figure 5 Some compounds wh
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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 [Protease targets] serinyl
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