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Retinoic acid syndrome (RAS), 382 Retinoid X receptors (RXRs), 376 Retrosynthetic analysis, 67 Reversible phosphorylation, 339 Rheumatoid arthritis (RA), 315, 403

Rhizopus arrhizus, 251 Rho GTPases, 50 RmtA, 347 RmtB, 347 RmtC, 347 RNAPII, 341

Rodent cerebrocortical cultures (RCCs), 323

Root mean square (RMS) deviation, 285 Rotamer libraries, 26 RP algorithm, 69 RP approach, 70 RSVM, 311 Rubicon, 11 Ru-BINAP catalysts, 265 complexes, 265 RyR-associated proteins, 187

Saccharomyces cerevisiae, 247 SANDOCK, 219 SC58635, 116 Scaffold(s), 5, 29 synthetic 284, 285 terephthalamide 296 Scopoletin, 39 SCORE, 27 Scoring, 25 Scoring algorithms, 26 Scoring function(s) (SF), 9, 53, 73, 101, 109

first-principles-derived, 9 knowledge-based, 27, 74, 102 regression-based, 102 Scoring methods, 26 Screening, 3, 5, 64

structure-based 12, 17 SDF-1a/CXCR4 interactions, 492 Secnidazole, 245

Second extracellular loop (ECL2), 304 Selective GABA reuptake inhibitor (SGRI), 272

Semisynthetic drugs, 243 Septic-shock-like syndrome, 177 Sequential-growing approach, 110 Serial analysis of gene expression (SAGE), 484

Serotonin receptor, 46 Serotonin 5-HT1A receptor, 47 Serotonin 5-HT4 receptor, 47

Severe acute respiratory syndrome (SARS), 53

coronavirus, 53

3C-like proteinase, 53 SH2 region, 45 Shape scores, 102

Sharpless asymmetric dihydroxylation, 138

Side population cells, 482

Sigmoid function, 115

Signal conduction, 345

Silica matrix delivery approach, 356

Simmons-Smith cyclopropanation, 265

Simulated annealing, 9

Simulation methods, 26

Single-isomer drug, 240

Site-directed mutagenesis, 169, 304

SMAC, 425

Smac bind, 37

Small heterodimer partner (SHP), 473 Small molecule, 82 Small-molecule database, 28, 38 SmithKline Beecham results, 223 SmithKline Beecham's compound, 218 SMoG, 74 Smonoester, 251

Smooth muscle myosin light chain kinase

(smMLCK), 290 Snake venom phosphodiesterase, 173 Sol-gel materials, 356 Sol-gel synthesis parameters, 356 Somatic stem cells, 480 Sources of chiral drugs, 243 Spacer domains, 141, 142 modification, 14 synthesis of, 136 Sphere exclusion, 76 SPHGEN, 8

Spontaneous resolution, 256 SPROUT, 94 SPSS10.0, 43 STA-21, 46 p-p stacking, 283 Stat3, 45

dimerization, 46 dimerization, 46 DNA binding activity, 46 Stat3-dependent luciferase activity, 46 Stat3 signaling, blockade of, 45 Stem cell factor (SCF), 492 Stemness genes, 481

Stereoelectronic properties, 93 Stereoisomers, 231 potency of, 236 Stereoselective, 233

Stereoselective syntheses of (R)-terbutaline, 250

Steric considerations, 282 Stochastic search, 26

Stromal cell-derived factor (SDF)-la, 304, 308

Structural search, 91 Structure-activity analysis, 177

of natural bryostatins, 150 Structure-activity relation (SAR), 58, 64, 221, 421

Structure-activity relationship(s), 14, 134, 188

of cADPR, 195 Structure-based design, 5, 90 Substituted cysteine accessibility method

(SCAM), 452 Substructure analysis, 64 Substructure constraints, 82 Sulfoxidation, 268 Sumoylation of PML, 377 Superimposition of minimized conformations, 199 Surface area (SA) term, 10 Surface plasmon resonance (SPR), 119

assay, 287 Survivin, 424 SYBYL6.9, 47 SYBYL software, 42, 46 Symmetric synthesis, 262 Synphilin-1/SIAH complex, 339 Synthetic chemokine analogues, 317 Synthetic molecules, 292 Synthetically and modularly modified (SMM) chemokines, 317, 318, 320-323, 325 Systemic search, 26

Tabu search, 26 TACE, 43

Tachykinin NK1 receptor, 46, 47 Tachykinin receptors, 285 TAFII250, 339 Tail-vein injection, 470 Tanimoto coefficient, 65, 66 Tannin cytoprotection, 179

Tannins, 174, 181

in vivo effects of 178 Target-dependent methods, 64, 78 TBHP, 262

TBP-associated complex, 339 T-cell (T)-tropic strains, 303 Tej mutants, 169 Teleocidin B-4, 132 (R)-Terbutaline, 250 Terephthalamide derivatives, 296 Tetraethyl orthosilicate (TEOS), 357 Tetra-galloyl-glucose, 180 Tetramethyl orthosilicate (TMOS), 357 TFIIA, 340, 341 TFIIE, 340, 341 TGB, 272 TGT, 14

Thermal gravimetric analysis (TGA), 359 Thiazolindinedione (TZD), 468, 469 Thin-layer chromatography (TLC), 171 Third extracellular loop (ECL3), 304 Thymocyte aggregation, 156 Thyroid hormone receptor (TR), 376 Tilorone, 172

Time to progression (TTP), 417

TLC-based methods, 171

TNF-family cytokines Fas-ligand (FasL), 413

TNF-family ligands, 411

TNF-family receptors, 409, 412

Toll-like receptor-9 (TLR9), 418

TOPAS program, 94, 97

Topliss tree, 91

Topological state, 68

Torpedo californica AChE, 38

Torsional Search (TS), 12

TRADD, 412

Traditional drug discovery, 58 TRAIL, 413 Tramadol, 237

racemate of, 237 Transcriptome analyses, 482 Transferrin, 343

Transient receptor potential (TRP), 441 Transmembrane (TM) helices, 300 TreeDock, 36

Trichosporon sp. (TSL), 245 Trimipramine, 239 metabolites of, 239

Trisubstituted indanes, 285 Tromboxane A2, synthesis of, 269 Tubulin phosphorylation, 340 Tumor necrosis factor (TNF), 409, 412

cytokine family, 412 Tumor necrosis factor alpha (TNF-a), 130

Ubiquitin, 337

activating enzyme, 337 conjugating enzyme, 337 proteasome system, 337 protein ligase, 337 Ubiquitin-dependent proteolysis, 338 Ubiquitin-regulated proteolysis, 336 Ubiquitylation, 337, 338, 339 UBPs, 337, 338 UCHs, 337 UNITY, 51 UNITY4.4, 47 UNITY fingerprint, 65 UNSATP, 114 UVB irradiation, 179

V-10, 214, 215, 367 V-13661, 210 Verapamil, 237 Vinyl ether formation, 136 Vinyl sulfone-based peptides, 51 Viral capsid, 52

Viral macrophage inflammatory protein

(vMIP)-II, 308 Virtual filtering, 26 Virtual library, 5, 220 Virtual screening, 25, 45, 49, 64, 103, 109, 220

structure-based, 50 Vitamin D3 receptor (VDR), 376 Vlevofloxacin, 264 vMIP-II, 310, 311 VX-853, 214, 215

W191G cavity, 15

Waldenstrom macroglobulinemia, 401 WDI, 79

World drug index (WDI) database, 78

Xanthen-9-ones, 173

XIAP BIR3 domain, 37

X-linked inhibitor of apoptosis (XIAP), 37

X-ray crystallography, 6, 58, 295 X-SCORE, 46

Yamaguchi esterification, 135 protocol, 143

ZINC, 11

Zinc-ß-lactamase, 44 Zinc metalloenzymes, 44 Zn-dependent phosphotriesterase, 45 Zymosan, 177

Figure 1.2 Predicted complexes versus X-ray crystallographic structures that were subsequently determined. See text for full caption.

Figure 1.3 Docking predicted ligands from virtual screening against simple cavity sites. See text for full caption.

Figure 1.2 Predicted complexes versus X-ray crystallographic structures that were subsequently determined. See text for full caption.

Figure 1.3 Docking predicted ligands from virtual screening against simple cavity sites. See text for full caption.

l293

k315

A3ie J

Figure 1.4 Predicted versus experimental structures from virtual screening. See text for full caption.

Figure 2.3 Structural model of MSK-039 docked at the EGFR kinase active site (only selected residues are shown). Dashed lines represent hydrogen bonds between ligand and active site residues.

Glu85

Cys87

Glu85

Cys87

Lys38

Glu91

Lys38

Glu91

Figure 2.4 Structural model of a representative hit docked at the Chk-1 kinase active site (only selected residues are shown). Dashed lines represent hydrogen bonds between ligand and active site residues.

Aventis, US930720

Pfizer, EP19900418

Aventis, US930720

Pfizer, EP19900418

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