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Document Page 18 related 4-hydroxypyrans and 4-hydroxycoumarins, the cyclic urea-based DMP323 series, and AG1284. Design and Structure of AG1343 (Nelfinavir) Analysis of the crystal structure of saquinavir with HIV PR indicated that while the nonpeptidic components of the ligand, namely the decahydroisoquinoline and the t-butylamide moieties fill the S1' and S2' subsites nearly optimally, the N-terminal portion offered the possibility for remodeling, aimed at the elimination of the peptidic character. Also, the contribution of the quinoline to the binding affinity to HIV PR was difficult to rationalize. Since the removal of quinoline resulted in a nearly 1000-fold loss in binding constant, it was concluded that the stacking interactions of the P1 phenyl ring and the P3 aromatic moiety of quinoline are necessary for the conformational stability of Ro 31-8959. In an attempt to redesign the N-terminal part of the ligand, the nonpeptidic portions of the P1' and P2' were maintained but for reasons of synthetic accessibility, the decahydroisoquinoline moiety was replaced by an orthosubstituted benzylamide [35]. Crystallographic analysis of both compounds showed that saquinovir and the modified LY289612 bind essentially identically to the active site of HIV PR and their inhibition constants and antiviral activity were very similar (Table 4 and Table 3). In the first attempt to functionally substitute the P2 side chain of asparagine, the isophthalic-acidcontaining compound was modeled and the low-energy conformation of the aromatic ring, required for binding in the S2 subsite, was stabilized by a tertiary carboxamide in the P3 region of the inhibitor [36]. The analysis of the binding mode and interactions of the isophthalic ring in the S2 subsite indicated a lipophilic pocket deep on the border between the S2 and S1' subsites, which could be conveniently filled with a methyl group extending from the 2 position of the ring. The resulting compound II in Table 4 lost most of the peptidomimetic character of LY289612 but retained its inhibitory potency. In an independent line of design, the relationship between the P1 phenylalanine side chain and the P3 quinoline was investigated. In the crystal structure of saquinavir bound to the active site of HIV PR (Figure 4), the aromatic ring of the P1 phenylalanine makes several van der Waals contacts with residues forming the S1 subsite. Computer modeling indicated that an extension of the phenylalanine side chain to phenethyl (homophenylalanine) would lead to prohibitive close contacts of the phenyl ring with the aliphatic side chains of HIV PR. On the other hand, replacement of the γ-carbon of the homophenylalanine by sulphur, which has a more acute C-S-C bond angle, would direct the aromatic ring into the neighbouring S3 subsite without changing the desired lipophilic nature of the P1 side chain. The increased area of hydrophobic interactions in the S1 and S3 subsites by compounds with the Sphenylcysteine and http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_18.html [4/5/2004 4:44:45 PM]
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Page 11 and 12: Document TF—transframe, PR—prot
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Page 19 and 20: Document Page 15 Thiazoles are less
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Document ever, once an NNRTI is bou
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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 dine) and didanosine (dide
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Document Page 108 mulate during tre
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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 receptor, it has not yet b
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Document Figure 6 Rat and human B2
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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 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 6 Structural Implications
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Document Page 176 0.43 Å) as the c
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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 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 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 protein kinase core is ess
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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 B. Structures Figure 8 Seq
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Document This method was used to sc
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Document Cyclotheonamide A (CtA), a
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Document Table 2 Naturally Occurrin
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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 Page 297 whereas, calcium
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Document Figure 2 Amino acid sequen
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Document A. Chemical Modification P
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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 Table 1 Trypanosomal Targe
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Document Table 2 Three-Dimensional
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Document 5-Methoxytryptamine 19.0 9
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Document Figure 12 Predicted bindin
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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 Page 405 strands constitut
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Document Figure 4 (a) Stereo diagra
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Document Figure 6 (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 10 Schematic diagra
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Document Page 416 positions of the
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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 423 American Home Pro
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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 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 for directed subcellular t
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Document Figure 1 A schematic diagr
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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 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 A. The Canyon Page 491 The
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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 conformational transition
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Document Med Biol 1991; 306:9-21; (
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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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