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Document Page 282 using BPTI residues 11–19 as a template [69]. The modeled dR-ATS 32-38:FXa complex is shown in Figure 11. Interestingly, these peptides do not inhibit trypsin even at 1000-fold higher concentrations than their FXa inhibitory concentrations. Antistasin, on the other hand, inhibits trypsin with a K i of 10 nM. Preliminary reports have appeared describing a pentapeptide that is a potent (K i=3 nM) and selective inhibitor of Factor Xa (SEL2711) [70,71]. Two possible modes of binding can be envisioned for this compound with either the methylpyridinium group occupying the S1 site in a “substratelike mode” or the p-amidinophenyl group in the S1 pocket, which would require a reversed binding reminiscent of the hirudin-thrombin interaction [59]. Figure 12 shows the case for the amidinophenyl group in the Factor Xa S1 pocket [69]. In this mode of binding the methylpyridinium group easily fits the S4-aryl binding site and is well positioned for a π-cation interaction. Of interest from a drug-design viewpoint is the finding that cyclotheonamide, a compound isolated from a marine sponge and originally reported as a thrombin inhibitor, has been found to also inhibit Factor Xa with a K i of 50 nM [72]. Cyclotheonamide possesses a novel α-ketoamide transition state functionality and x-ray structures of cyclotheonamide with trypsin [73] and thrombin [74] provide templates for modeling this inhibitor into Factor Xa [69]. In the resulting fit (Figure 13) cyclotheonamide does not project functionality into the S4-cation-π site and would not be expected to show Factor Xa selectivity. VII. Defining the Requirements for Factor Xa Inhibition <strong>by</strong> Mutagenesis of BPTI It has been known for some time that many examples of naturally occurring Kunitz inhibitors exist, both isolated and as domains in larger proteins, which inhibit a variety of serine proteases [47]. This strongly suggests that this molecular framework is compatible with inhibition of this general class. The contact region between these inhibitors and their protease targets is known from a http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_282.html (1 of 2) [4/5/2004 5:13:38 PM]
Document Figure 12 Modeled fit of SEL2711 in Factor Xa with the arylamidino group positioned in the S1 pocket and the methylpyridinium group in the cation-π S4 site. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_283.html [4/5/2004 5:13:43 PM] Page 283
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Structure-based Drug Design 14 Stru
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Document 2 Structural Studies of HI
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Document dine (3TC), and 2',3'-dide
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Document Figure Continued Page 45 r
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Document monophosphate analogs whic
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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 56 It is also attract
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Document Table 3 HIV-1 RT Amino Aci
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Document ever, once an NNRTI is bou
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Document Page 69 determining the me
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Document Chris Tantillo. The work i
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Document Page 72 16. Goldman ME, Nu
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Document 30. Coffin JM. HIV populat
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Document 45. Majumadar C, Abbotts J
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Document reverse transcriptase inhi
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Document 106. Cirino NM, Cameron CE
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Document 122. Marshall WS, Beaton G
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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 106 on the same ring
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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 cubation of phosphotyrosin
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Document 4 Bradykinin Receptor Anta
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Document Page 121 Nearly all cells
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Document Page 123 were poorly satis
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Document Page 125 binding site on t
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Document Page 127 The des-Arg 9 for
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Document Page 129 tolerated by the
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Document receptor, it has not yet b
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Document Page 133 This initial stag
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Document Page 135 might be jointly
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Document Page 137 observed for the
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Document Figure 6 Rat and human B2
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Document Page 141 receptor with int
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Document Figure 9 Composition of te
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Document B. Pharmacology Figure 1 T
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Document We determined the structur
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Document Figure 3 Previously known
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Document large solvent channels and
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Document IV. Drug Design Progressio
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Document position eight from formin
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Document Table 1 Inhibition Data fo
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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 Figure 1 A ribbon model of
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Document Page 176 0.43 Å) as the c
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Document Page 178 studies show that
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Document Important for the validity
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Document Figure 4 Amino acids impor
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Document III. Results and Discussio
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Document Page 202 269, and valine-2
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Document Figure 6 Structure of α h
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Document Page 205 enzyme and of phe
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Page 363 and 364: Document 12 Polypeptide Modulators
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Document 17. Szelke M. Chemistry of
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Document 16 Progress in the Design
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Document Table 1 Known Three-Dimens
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Document Page 398 with growth hormo
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Document All effects of the IL-1 fa
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Document 17 Structure and Functiona
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Document Table 1 Approval Indicatio
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Document Page 438 proteins. One pot
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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 451 with the cytoplas
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Document Page 462 strains of influe
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Document B. Protein Structure Page
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Document Page 471 molecules in the
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Document Figure 8 Stereo image of t
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Document Page 476 nM, respectively.
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Document VI. Conclusion Page 480 It
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Document 21. Both GW, Sleigh MJ, Co
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Document 64. Ward CW, Elleman TC, A
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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 Subsequent studies have sh
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Document Page 495 of the RNA and pr
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Document Figure 4 A ribbon diagram
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Document Figure 5 Some compounds wh
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Document Acknowledgments Page 620 I
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Document Med Biol 1991; 306:9-21; (
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Document Page 629 ML, Clare M, Decr
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Document Page 631 197. Musil D, Zuc
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Document site, 52, 55, 61 triad, 24
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Document factors, 247 Combination t
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Document Cyclotheonamide A (CtA), 2
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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 overview, 103-104, 108-109
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Document [Inhibitors] 2-((3,4-dihyd
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Document antagonistic activity, 416
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Document [Interleukin-1] homology w
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Document Kininogen, 119 high molecu
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Document Matrix-metalloproteinase (
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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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