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Document Figure 24 Protease 3D structural models: HIV protease-inhibitor complex and drug design http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_602.html [4/9/2004 1:29:47 AM] Page 602
Document Page 603 hydroxymethyl substituent within various types of nonhydrolyzable surrogates of the scissile amide bond (e.g., Ψ[CH(OH)], Ψ[CH(OH)CH 2], and Ψ[CH(OH) CH 2N]; see above). Nevertheless, there exist examples of highly potent inhibitors of renin e.g., the Ψ[CH 2NH]-modified 41 [47] and macrocylic peptide 99 [155] and HIV protease e.g., the pyrone-based series 108–111 [165–168] respectively) that do not possess a tetrahedral CH(OH) moiety per se. Serinyl Proteases The serinyl proteases include trypsin, chymotrypsin-A, elastase, thrombin, kallikrein, cathepsins-A, G, and R, Factor VII, Factors IXa-XIIa, and tissue plasminogen activator. High-resolution x-ray crystallographic structures of this protease family have been determined for thrombin (for a review see [175]; also refer to Table II [176–182]), Factor Xa [183], trypsin [184], kallikrein-A [185], and elastase [186–190]. As illustrated in Figure 25, a substrate-based inhibitor of thrombin having a boronic acid, B(OH) 2, substitution for the scissile amide was determine by x-ray crystallography to form a covalent bond to the active site Ser-195 residue [176]. The N-terminal Ac-D-Phe-Pro moiety of this inhibitor binds in a β-sheet type extended conformation that involves hydrogen-bonding contacts to the enzyme and well-defined hydrophobic and aromatic-aromatic (edge-to-face) stacking interactions. The inhibitor Arg side chain binds in an extended conformation and the guanidino moiety forms bidentate hydrogenbonding interactions with an Asp189 residue at the base of the S 1 “specificity” pocket as well as additional hydrogen-bonds to the enzyme, one of which is mediated through a structural water. Relative to the substrate-based peptidomimetic inhibitors of thrombin having C-terminal electrophilic groups (e.g., aldehyde, ketone, and boronic acid), the discovery and structure-based design of nonpeptide inhibitors not having P 1 electrophilic functionalization has also been extremely successful as represented by 52 [70], 60 [71], and 113 [182]. As shown in Figure 25, the design of a highly potent and selective amidinopiperidine-based thrombin inhibitor 113 was derived from analysis of the x-ray crystallographic structures of thrombin complexed with inhibitors 52 and 60. The latter two compounds showed different trajectories of their P 1 side chains (i.e., guanidinoalkyl and amidinophenyl, respectively) into the S 1 pocket to account for the observed opposite chirality preferences at the Cα-position of the P 1 amino acid residues. Also, the C-terminal cycloalkyl moieties of both 52 and 60 were observed to bind to the socalled inhibitor “P-pocket” (i.e., the P 2 substrate pocket), thus explaining that these compounds were not binding in a substrate-like conformation such as the peptidomimetic inhibitors Ac-D-Phe-Pro-boroArg- OH as described above. Thus, the design of the novel amidinopiperidine-based inhibitor 113 illustrates a “transposition” of the P-pocket binding group to an N-substituted Gly-β-Asp scaffold. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_603.html [4/9/2004 1:30:10 AM]
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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 Analysis of various HIV-1
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Document Table 3 HIV-1 RT Amino Aci
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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 Figure 1 Retroviral lifecy
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Document Figure 2 In vivo reactions
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Document Page 92 The role of the N-
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Document Figure 6 Molscript stereo
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Document Page 96 region in the HIV-
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Document Page 101 crystallized unde
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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 65. Gallay P, Swingler S,
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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 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 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 205 enzyme and of phe
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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 Subsequent studies have sh
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Page 739 and 740: Document Figure 22 Protease 3D stru
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Page 745 and 746: Document Page 605 For other serinyl
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Page 755 and 756: Document (Ser/Thr) peptide 2.9 Å 2
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Page 765 and 766: Document Acknowledgments Page 620 I
Page 767 and 768: Document 18. Sawyer TK. In: Peptide
Page 769 and 770: Document Page 622 Fukuroda T, Fukam
Page 771 and 772: Document Page 623 53. Bird J, Harpe
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Page 775 and 776: Document MA, Welch KM, Hallak H, Ta
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Page 783 and 784: Document Page 629 ML, Clare M, Decr
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Page 787 and 788: Document Page 631 197. Musil D, Zuc
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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 overview, 103-104, 108-109
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Document antagonistic activity, 416
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Document Kininogen, 119 high molecu
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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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