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Document Page 179 side) inhibitors will bind with greater affinity. Indeed, most of the structures of MMPs were determined with right-hand side inhibitors, and most of the pharmaceuticals currently in development are also righthand side binders. A closer look at the binding pockets themselves also demonstrates the reasons for the preference of researchers for the right-hand side. V. Substrate-Binding Pockets The nonprimed or left-hand side of the cleft consists of a large shallow depression. The S1 pocket consists of a shallow ridge that complements the glycine residue of the collagen strands. Most of the interactions with the glycine residue are brought about due to its interaction with the catalytic zinc. Asparagine 180 approaches the P1 residue in HFC. Crystallographic evidence indicates an interaction of the thiophene ring of batimastat via electrostatic interactions of the p orbitals and the catalytic zinc and the possibility of a water-mediated hydrogen bond to the carbonyl O of residue 184 [35]. Larger substituents can be accommodated in regions adjacent to the P1 pocket, possibly in the large pocket above the S1 site (see Figure 2). Increased potency was noted for several compounds with cyclic imido P1 substituents that could bind here [2]. The S2 pocket is a large shallow depression offering no real binding cavities. One side of the pocket is made up from the conserved histidine at position 228 and the main chain from residue 227. The bottom of the pocket is formed by histidine 222. Both of these histidines are liganded to the catalytic zinc. The other side consists mostly of the residue 186 side chain with some hydrogen-bonding contacts possible from the tip of the glutamine side chain in the case of HFC and HNC. The S3 pocket offers a shallow cavity to bind the conserved proline. The proline residue of the substrate would lie between the side chains of His 183, Phe 185, and Ser172 [36]. Residues 183 and 185 are conserved among the MMPs with the minor exception of a tyrosine replacing phenylalanine 164 in stromelysin. Residue 172 shows some variability among the MMPs existing as a serine in HNC and HFC and a tyrosine in the remainder of the aligned MMPs. The primed or right-hand side of the active site exists as a narrow canyon with a large well at the beginning. The S1' pocket is a narrow, deep cavity providing an ideal binding site for inhibitor design. The S1' pocket is the most significant feature of the surface, extending as a tunnel completely through the enzyme in the case of neutrophil collagenase and stromelysin. This feature makes the S1' pocket an ideal candidate for use in designing an inhibitor with specificity for HNC, HFC, or HFS. The volumes of the S1' pockets vary greatly. Matrilysin has the smallest S1' pocket at 111 Å 3. The fibroblast collagenase pocket is not much larger at http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_179.html [4/5/2004 5:03:39 PM]
Document Figure 5 (a) A cut away view of the S1' pocket of HFC showing the termination of the pocket by Arg214. Matrilysin also has a truncated pocket. (b) A cut away view of the S1' pocket of HNC showing the clear path through to the other side of the enzyme. The gelatinases are also likely to have large extended S1' pockets. 123 Å 3. The pocket of the neutrophil collagenase that travels through the enzyme has a volume of 305 Å 3. Figure 5 demonstrates the differences in the relative sizes of the S1' pockets of HFC and HNC. Stromelysin has a pocket that should be of similar size as that of neutrophil collagenase [21]. The gelatinases and collagenase-3, based on sequence alignment, should also posses long tunnel-like S1' pockets. Page 180 The residues that line the S1' pocket are mostly hydrophobic residues (see Figure 3) and show a remarkable overall similarity. The specificity of a number of inhibitors of MMPs can be linked to differences in the S1' pockets. The S1' pocket of HFC is terminated by arginine 214, while matrilysin has a tyrosine residue that accomplishes the same thing. The remainder of the aligned MMPs have leucine residues at that position. In addition the conformation of the leucine residue is swung back, forming the tunnel. There are three additional residues that are significant in their differences within the S1' pocket: residues 239 and a two-residue insert, relative to HFC, after residue 242. These residues http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_180.html (1 of 2) [4/5/2004 5:03:48 PM]
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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 Page 56 It is also attract
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Document Table 3 HIV-1 RT Amino Aci
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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 dine) and didanosine (dide
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Document Page 108 mulate during tre
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Document 4 Bradykinin Receptor Anta
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Page 205 and 206: Document References 1. Parks RE Jr.
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Page 209 and 210: Document 6 Structural Implications
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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 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 Page 476 nM, respectively.
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Document Page 488 against most of t
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Document Page 495 of the RNA and pr
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Document D ddI, 152 tumour necrosis
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Document [Human immunodeficiency vi
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Document [Protease targets] serinyl
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