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Document Page 124 predictable geometry. A series of peptides containing these types of constraints can be useful for extrapolating the steric and electronic environment of a given binding site. This structural information can be derived regardless of whether or not the constrained peptide binds to the target receptor. Since peptides can be prepared rapidly, it is typical to establish a structure-activity relationship using them and then at some later time transpose that information onto a nonpeptide lead molecule in an attempt to improve its potency. As part of an expansion upon the hypothesis that a C-terminal β turn was a structural prerequisite to highaffinity antagonist binding, a novel series of constrained decapeptides was prepared [22–24]. These peptides are of the sequence DArg 0-Arg 1-Pro 2-Hyp 3-Gly 4-Phe 5-Ser 6-DHype 7-Y 8-Arg 9, where Y is either tetrahydroisoquinoline-3-carboxylic acid (Tic), or octahydroindole-2-carboxylic acid (Oic). DHype denotes an organic ether of D-4-hydroxyproline in either the cis or trans geometric form. The C-terminal portion of a representative member of this class of peptides was shown—first by empirical calculation [22], then by NMR at 600 MHz—to adopt a β turn nearly unambiguously (figure 2) [25,26]. Moreover, it was shown by calculation that the turn was adopted regardless of the nature of the ether group (alkyl, aryl, etc.) or its geometry (cis or trans). Hence, a diverse series of these peptides was initially used as a tool to probe the steric and electrostatic topology of an antagonist Figure 2 Lowest 5 kcal mol -1 of the calculated overall potential energy surface for a model peptide of Ser-DHype(trans propyl)-Oic-Arg. The contour interval is 0.5 Kcalmol -1 and the highest (outermost) and lowest contour energy values are labeled. Superimposed on the contour plots are values for ψ i+1 and ψ i+2 from each of the thirty structures generated from the NMR data corresponding to the tetrapeptide Ser-DHype(trans propyl)-Oic-Arg. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_124.html (1 of 2) [4/5/2004 4:57:43 PM]
Document Page 125 binding site on the bradykinin B2 receptor in the guinea pig ileum. The cis ethers, in all cases, bound to the receptor with significantly lower affinity than did the trans. A more complete listing of the peptides used in the study is shown in Table 1. These results support the hypothesis that the domain of the receptor that binds these antagonist ligands is partly made up of a hydrophobic cavity about one side of the C-terminal turn. However, adjacent to the other side of the http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_125.html (1 of 2) [4/5/2004 4:58:44 PM]
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Document Page 33 sustained in many
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Document 8. Kaplan AH, Zack JA, Kni
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Document 22. Krausslich HG, Ingraha
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Document 60. Condra JH, Schleif WA,
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Document 74. Reddy RM, Varney MD, K
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Document 2 Structural Studies of HI
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Document Figure 1 (a) Chemical stru
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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 Figure 2 Ribbon diagrams o
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Document Figure 3 Overall structure
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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 61 now clear that the
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Document Page 63 most of the amino
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Document Page 65 cal properties of
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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 45. Majumadar C, Abbotts J
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Document reverse transcriptase inhi
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Document 75. Ring CS, Sun E, McKerr
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Document 89. Hughes SH, Arnold E, H
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Document 106. Cirino NM, Cameron CE
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Document 122. Marshall WS, Beaton G
Page 103 and 104: Document dine) and didanosine (dide
Page 105 and 106: Document 149. Craig JC, Duncan IB,
Page 107 and 108: Document 163. Lacey SF, Larder BA.
Page 109 and 110: Document Figure 1 Retroviral lifecy
Page 111 and 112: Document Figure 2 In vivo reactions
Page 113 and 114: Document Page 88 transfer (Figure 3
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Page 117 and 118: Document Page 92 The role of the N-
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Page 127 and 128: Document Page 101 crystallized unde
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Page 131 and 132: Document proposed mechanisms. For e
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Page 135 and 136: Document Page 108 mulate during tre
Page 137 and 138: Document when metals are bound. Fin
Page 139 and 140: Document cubation of phosphotyrosin
Page 141 and 142: Document 4. Vink C, Plasterk RHA. T
Page 143 and 144: Document Page 115 21. Kulkosky J, J
Page 145 and 146: Document 44. Cushman M, Sherman P.
Page 147 and 148: Document 65. Gallay P, Swingler S,
Page 149 and 150: Document 4 Bradykinin Receptor Anta
Page 151 and 152: Document Page 121 Nearly all cells
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Page 157 and 158: Document Page 127 The des-Arg 9 for
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Page 169 and 170: Document Figure 6 Rat and human B2
Page 171 and 172: Document Page 141 receptor with int
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Page 179 and 180: Document 16. Martorana PA, Kettenba
Page 181 and 182: Document 39. Mavunkel BJ, Lu Z, Kyl
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Page 185 and 186: Document B. Pharmacology Figure 1 T
Page 187 and 188: Document We determined the structur
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Page 195 and 196: Document large solvent channels and
Page 197 and 198: Document IV. Drug Design Progressio
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Page 201 and 202: Document Table 1 Inhibition Data fo
Page 203 and 204: 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 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 IX. S2' Interactions Page
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Document 7 Structure—Function Rel
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Document Figure 1 Reactions catalyz
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Document Figure 2 Structure of lico
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Document Figure 3 (Continued) Page
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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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Document Page 207 sure and the acti
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Document 13. Wilson RC, Krozowski Z
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Document 29. Baker ME. Genealogy of
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Document 46. Ribas dePoplana L, Fot
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Document Page 214 viruses. Specific
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Document Page 218 The catalytic loo
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Document Figure 3 (a) Ternary compl
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Document Figure 5 (a) Staurosporine
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Document protein kinase core is ess
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Document 10. Knighton DR, Zheng J-H
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Document 24. Madhusudan Xuong N-H,
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Document 9 Structural Studies of Al
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Document diverse ARIs have been sho
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Document Figure 3 C α trace of the
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Document Figure 4 Surface represent
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Document Figure 7 Stereo of zopolre
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Document This method was used to sc
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Document 10 Structure-Based Design
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Document Cyclotheonamide A (CtA), a
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Document Page 256 The discovery pro
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Document balance its pro- and antic
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Document 31. Kettner C, Shaw E. D-P
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Document Table 2 Naturally Occurrin
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Document Lys in the P1 position is
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Document Figure 11 dArg-ATS 32-38 m
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Document 12 Polypeptide Modulators
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Document Figure 2 Amino acid sequen
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Document 13 Rational Design of Reni
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Document Page 323 been suggested th
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Document C. Specificity Figure 4 Th
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Document Figure 5 The S 3 specifici
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Document IV. Rational Drug Design F
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Document 17. Szelke M. Chemistry of
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Document Figure 4 Amino acid sequen
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Document Figure 8 The catalytic mac
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Document Figure 10 Structures of so
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Document Page 359 easily reach the
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Document Table 1 Trypanosomal Targe
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Document Table 2 Three-Dimensional
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Document Figure 2 Glycolysis in blo
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Document Figure 12 Predicted bindin
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Document 65. João HC, Williams RJP
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Document 84. Verlinde CLMJ, Hol WGJ
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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 Figure 2 Structural alignm
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Document Page 405 strands constitut
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Document Figure 4 (a) Stereo diagra
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Document Figure 7 (a) Superposition
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Document Page 412 ture is unlike ot
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Document Figure 11 Functional resid
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Document Figure 13 The identified p
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Document B. Interleukin-1 Receptor
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Document Page 425 Antinflammatory D
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Document Page 427 These aromatic di
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Document 5. Dinarello CA. On the Bi
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Document 21. Seckinger P, Lowenthal
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Document 39. Saurat JH, Schfferli J
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Document 74. Bender PE, Lee JC., ed
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Document 102. Machin PJ, Osbond JM,
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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 Figure 3 (a) A MOLSCRIPT [
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Document B. Protein Structure Page
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Document Figure 5 (a) Stereo image
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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 Page 478 lished—was asso
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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 64. Ward CW, Elleman TC, A
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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 Figure 10 Possible hydroge
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Document Page 514 sis. Large number
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Document 21 Structure-Based Combina
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Document Page 545 protein binding s
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Document Figure 8 Minimized structu
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Document Page 555 N-acylpyrrolidine
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document 97; (e) Fujii I, Nakamura
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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 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 [Inhibitors] 2-((3,4-dihyd
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Document antagonistic activity, 416
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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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