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Document Page 178 studies show that there is not sufficient room in the S1'-S3' cleft to accommodate the native coiled triple collagen bundle. The active site consists of a series of subsites on either side of the catalytic zinc. These subsites are numbered starting at the catalytic zinc and preceding from N to C as S1', S2', etc., corresponding to the residues (P1', P2', etc.) of the substrate that is bound (Figure 2). Likewise the subsites are numbered S1, S2, etc. outward from the other side of the catalytic zinc. While the interaction of the substrate (and the inhibitor) with the catalytic zinc is the most important interaction, the remainder of the substrate (inhibitor) also forms hydrogen bonds with residues from the top strand of the β sheet and the loop region posterior to the Met-turn. These interactions with the substrate in the binding pockets of the MMPs are the prime targets for engineering specific MMP inhibitors. An in-depth understanding of the differences of the properties of these pockets in the different MMPs and the interactions of specific residues within these pockets is essential for structure-based design of inhibitors. IV. Main-Chain Substrate Interactions Most of the hydrogen bonds between the substrate and the MMP occur with the top strand of the β sheet. The P3 residue does not make any direct hydrogen bonds with the MMP. The P2 residue makes two hydrogen bonds with residue 184, which is a conserved alanine residue in all the aligned MMP sequences. Residue 183 is a conserved histidine, which is bound to the structural zinc, further stabilizing the conformation of the top strand. The carbonyl oxygen of P1 is liganded to the catalytic zinc. The lefthand side of the substrate is thus held in place by only two hydrogen bonds with the enzyme and one interaction with the catalytic zinc. Although the P3 residue does not make any hydrogenbond contributions to substrate binding, it is essential for catalytic activity [43]. The right-hand side of the substrate is held much tighter. The P1' residue's carbonyl oxygen makes a hydrogen bond with the amide nitrogen of residue 181, which is a conserved leucine residue. The amide nitrogen of the P1' residue is hydrogen bonded to the conserved alanine-182 carbonyl oxygen. The P2' substrate residue is held in place by hydrogen bonds to proline 238 and tyrosine 240, two more conserved residues. The amide nitrogen of P3' makes a hydrogen bond with the carbonyl oxygen of residue 179, the only nonconserved residue, making a main-chain interaction with the substrate. The use of conserved residues to maintain the main-chain interactions along the substrate backbone makes differentiation of the MMPs through these interactions difficult. Instead, differences in the regions where the side chains of the substrate interact can be used to drive the discovery of specific MMP inhibitors. The hydrogen-bonding pattern also indicates that right-hand side (P'- http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_178.html [4/5/2004 5:03:38 PM]
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Structure-based Drug Design 14 Stru
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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 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 dine (3TC), and 2',3'-dide
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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 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 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 122. Marshall WS, Beaton G
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Document dine) and didanosine (dide
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Document 149. Craig JC, Duncan IB,
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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 -62° for HIV-1 integrase,
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Document Figure 8 Molscript stereo
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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 44. Cushman M, Sherman P.
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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 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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Page 175 and 176: Document Figure 9 Composition of te
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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
Page 205 and 206: Document References 1. Parks RE Jr.
Page 207 and 208: Document 17. Ealick SE, Rule SA, Ca
Page 209 and 210: Document 6 Structural Implications
Page 211 and 212: Document Figure 1 A ribbon model of
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Page 221 and 222: Document Page 182 (SAR) model. The
Page 223 and 224: Document IX. S2' Interactions Page
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Page 233 and 234: Document 7 Structure—Function Rel
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Page 251 and 252: Document Page 205 enzyme and of phe
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Document Page 218 The catalytic loo
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Document Cyclotheonamide A (CtA), a
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Document balance its pro- and antic
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Document Table 2 Naturally Occurrin
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Document Table 3 Active Site Sequen
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Document Page 276 In both cases the
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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 Figure 1 Available drugs f
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Document Table 1 Trypanosomal Targe
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Document Figure 2 Glycolysis in blo
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Document Table 1 Known Three-Dimens
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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 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 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 Page 476 nM, respectively.
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Document 21. Both GW, Sleigh MJ, Co
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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 Figure 4 A ribbon diagram
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Document Figure 5 Some compounds wh
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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 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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