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Document Figure 13 Cyclotheonamide modeled into Factor Xa utilizing the x-ray structure of cyclotheonamide:trypsin [73] and cyclotheonamide:thrombin [74] as templates [69]. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_284.html [4/5/2004 5:13:51 PM] Page 284
Document Page 285 number of x-ray structures of complexes. Appropriate site-specific and random mutagenesis, particularly of the P3-P4' residues of a prototypic Kunitz inhibitor, bovine pancreatic trypsin inhibitor (BPTI), has been shown to result in potent and selective Factor Xa inhibitors [75,76]. A potent inhibitor of trypsin, kallikrein, and plasmin, BPTI does not inhibit Factor Xa. It binds to serine proteases such as trypsin in an extended substrate mode from residue 13 (P3) through 17 (P'2) [47]. A second loop from BPTI also extends into the active site bringing residues 34, 39, and 46 into contact with the protease-active site. In terms of spatial proximity of residues three clusters can be defined: cluster 1 (13,39); cluster 2 (11,17,19,34); and cluster 3 (16,18,20,46). While residue 39 is approximately in the same region of space as residue 13 (9.4 Å CB-CB) the CA rarrow.gif CB vectors are directed in different directions and substitution at 39 would not be expected to have a cooperative effect with residue 13. Residue 34 on the other hand is in a key position. It is centrally located between residues 11,17, and 19 with CB-CB distances of 5.6, 5.7, and 6.5 Å respectively, and its CA rarrow.gif CB vector converges with the corresponding vectors from these residues to a common point in space. This residue is therefore expected to have a substantial cooperative effect with the other residues of cluster 2. Finally residue 46 is close to residue 20 (CB—CB of 6.5 Å) although the CA rarrow.gif CB vectors are approximately parallel and cooperative effects are expected to be minimal. The BPTI residues 11,12,13,15–20, 34,39, and 46 were therefore the focus of the site-directed and random mutagenesis studies. Residue 14 is Cys in BPTI and was not modified in the mutants since it is required for structural reasons. A. Site Specific Mutagenesis As a starting point for the design of BPTI-<strong>based</strong> Factor Xa inhibitors, the second domain of TFPI (TFPI- II) was used as a template [75,76]. Table 5 shows the results of site-directed mutagenesis of BPTI. Mutant 50cl is a direct analog of TFPI-II with the exception of the Lys at position 46. The finding that 4c2 and 4c10 are essentially equivalent in potency (K i 2.8 versus 1.8 nM) and are identical Table 5 Site-Directed BPTI Mutants with Factor Xa Inhibition K i(nM) 12 13 14 15 16 17 18 19 20 34 39 46 r-TFPI-II 90 Gly Ile Cys Arg Gly Tyr Ile Thr Arg Lys Leu Glu 50cl 205 Gly Ile Cys Arg Ala Tyr Ile Thr Arg Lys Leu Lys 4c2 2.8 Gly Ile Cys Arg Ala Tyr Ile Thr Arg Val Leu Glu 4c10 1.8 Gly Ile Cys Arg Ala Tyr Ile Thr Arg Val Leu Lys 57c1 1.6 Gly Ile Cys Arg Ala Tyr Ile Ile Arg Val Leu Lys http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_285.html (1 of 2) [4/5/2004 5:13:54 PM]
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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 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 67 Biochemical data s
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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 reverse transcriptase inhi
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Document 106. Cirino NM, Cameron CE
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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 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 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 39. Mavunkel BJ, Lu Z, Kyl
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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 Page 182 (SAR) model. The
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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 Page 205 enzyme and of phe
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Document protein kinase core is ess
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Page 311 and 312: Document Cyclotheonamide A (CtA), a
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Page 363 and 364: Document 12 Polypeptide Modulators
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Document 65. João HC, Williams RJP
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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 All effects of the IL-1 fa
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Document Figure 13 The identified p
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Document 39. Saurat JH, Schfferli J
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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 4 Stereo view of IF
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Document Figure 5 Velcro-key model
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Document Figure 6 Proposed receptor
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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 Page 464 could not again b
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Document B. Protein Structure Page
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Document Page 471 molecules in the
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Document hydroxy, and 6 Neu5Ac2en -
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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 45. Varghese JN, Laver WG,
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Document 80. Suzuki Y, Sato K, Kiso
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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 Figure 7 HRV14 VP1 hydroph
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Document C. Structure-Activity Rela
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Document Page 555 N-acylpyrrolidine
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Document 30. O'Shea EK, Rutkowski R
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Document 22 Peptidomimetic and Nonp
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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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 son AH, Drummond AH, Huxle
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Document 274. (a) Kavanaugh WM, Wil
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Document inhibitor binding, 323, 33
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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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