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Document Page 542 crystal structures to determine binding sites of molecular fragments, i.e., discrete positions on the binding site surface suitable to form hydrogen bonds and/or to fill hydrophobic sites of the receptor. Alternatively, it uses simple rules or the output of the program GRID [9–12] to generate the interaction sites. Finally, the fragments fitted in the interaction sites are connected by linker groups. Other fragmentbased programs are GROUPBUILD [13]; GROW [14], HOOK [15], NEWLEAD [16], SPROUT [17], and TORSION [18]. These and other strategies for computer-aided structure-based ligand design have been reviewed by several contributors [13,19,20]. II. Docking Molecular Fragments A. Multiple Copy Simultaneous Search The present approach for ligand design is based on the combinatorial selection of molecular fragments optimally docked on the protein binding site to form a population of diverse candidate ligands. The multiple copy simultaneous search (MCSS) procedure combines the advantages of random distribution and simultaneous minimization of a set of replicas of a chemical fragment to obtain maps of energetically favorable positions and orientations (local energy minima) [21,22]. These maps, which contain all possible low-energy minima of a fragment-protein complex, are called functionality maps. A plethora of structural and thermodynamic data on inhibitor-enzyme complexes [23–26] suggest that the burial of nonpolar groups of the ligand in hydrophobic pockets of the protein is important for binding affinity and that intermolecular electrostatic interactions determine selectivity. For this reason, and because most of the known enzymes' binding sites have both hydrophilic and hydrophobic character, very diverse functional groups are used in MCSS. Representative examples include charged (e.g., acetate, benzamidine, methylammonium, methylguanidinium, pyrrolidine); polar (e.g., methanol, 2propanone, N-methylacetamide); aromatic (e.g., benzene, pyrrole, imidazole, phenol); and aliphatic (e.g., propane, isobutane, cyclopentane, cyclohexane) groups. Although most of these fragments are rigid, MCSS can also generate the functionality maps of flexible medium-size fragments, e.g., the amino acid side chains. Additional functional groups and more complex heterocyclic systems are currently being introduced to increase the diversity of the resulting ligands and to better characterize the specificity of the binding pockets (A. Caflisch and C. Ehrhardt, unpublished results). As shown by a flowchart in Figure 1, the method is fully automated, although certain critical parameters (e.g., number of replicas, radius of the sphere for random distribution, CHARMM parameters for the minimization) can be adjusted by the user to optimize it for specific applications. Several thousand replicas of a given group are randomly distributed inside a sphere http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_542.html [4/9/2004 12:51:09 AM]
Document Figure 1 Schematic representation of the MCSS procedure. Conditional statements are enclosed by diamonds. Page 543 whose radius is chosen large enough to cover the entire region of interest. This can be a known binding site or the entire protein, if one wants to explore alternative binding pockets. The initial random distribution also can be performed inside a parallelepiped if the region of interest is elongated in one or two directions. A minimal distance can be given as input to avoid bad contacts between functional group atoms and protein atoms for the initial distribution. Subsets of between 500 and 3000 randomly distributed replicas of the same group are simultaneously minimized in the force field of the protein. The http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_543.html (1 of 2) [4/9/2004 12:51:17 AM]
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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 Page 54 Table 2) [12,54].
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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 reverse transcriptase inhi
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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 6 Molscript stereo
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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 4 Bradykinin Receptor Anta
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Document large solvent channels and
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Document Table 1 Inhibition Data fo
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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 Important for the validity
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Document Figure 4 Amino acids impor
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Document 17 Structure and Functiona
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Document Table 1 Approval Indicatio
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Page 693 and 694: Document structure. 2. Ligand probe
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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 [Protease targets] serinyl
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