Monoamine oxidase-b, 229–231
Monte Carlo sampling, 33
Monte Carlo simulations, 8, 39, 125, 272, 278
MOSAIC, 358–363
Mouse serum albumin, 123
Moxifloxacin, 309, 311, 326, 330
Multidrug resistant, 206, 307
Multiple myeloma, 253
Multi-target drug design, 32
Mur ligase, 315, 316
Muscarinic receptor, 30
Mutation, 2–4, 14, 16–18, 36, 55, 57, 64, 65,
179, 180, 188, 202, 275, 282, 314, 317,
322, 367
Mutational hotspots, 15, 16
Mutation scanning, 14, 16
Mycobacterial cyclopropane synthase, 314,
331
Mycobacterium tuberculosis, 75, 90, 119, 282,
307, 309
Mycolic acid, 40, 309, 311, 313–315, 325, 335
N
Natural compounds, 181
Natural products, 291, 316, 323
Network biology, 109, 110
Neurodegenerative, 228, 248, 251
Nilotinib, 16
Nitazoxanide, 332, 335
Non-covalent association, 8
Non-physical states, 8, 12
Normal mode analysis, 9, 152, 155
Nuclear Magnetic Resonance (NMR), 5, 110,
116, 144, 155, 238, 261, 262, 273, 286,
295, 323, 348, 349, 376, 379
Nucleoside analogues, 71, 74, 90, 94–96, 106
O
Occupancy, 118, 285
Optimization, 4, 16, 25, 26, 32, 35, 48, 115,
122, 144, 145, 150, 160, 204, 207, 208,
211, 223, 225, 232, 234, 241, 259, 260,
283, 285, 316, 323, 350, 358, 360–362
Orthosteric drugs, 61
Outliers, 120, 141, 142, 154
Oxazolidinone, 330, 333, 334
Oxidoreductase, 183, 315, 327, 330
P
Pan Assay Interference Compounds (PAINS),
160, 257
Partition functions, 7, 239
Pattern identification, 34, 35
Penicillin, 3, 129
Peptide deformylase, 318, 325
Peptidoglycan, 311, 313, 325
Pfdihydrofolatereductase, 179
Pharmacodynamic, 160, 221, 225, 240, 242,
311
Pharmacokinetics, 140, 203, 223, 324
Pharmacophore fingerprints, 39
Pharmacophore model, 25, 27–33, 35–41,
43–48, 213, 214, 287, 331
Phase, 4, 5, 8, 10, 29, 32, 34, 37, 38, 41–43,
146, 152, 154, 180, 198, 223, 226, 228,
230, 252, 257, 273, 275, 283, 286, 287,
320, 323, 333–335, 354, 383, 384, 395
Phase 1 clinical trials, 333
Phosphatidylinositol, 177, 182
Phosphorylation, 119, 120, 126, 130, 182, 249,
251, 318
Phylogenetic analysis, 119
Physico-chemical, 123, 145, 148, 275, 331
PimA, 315
PknB, 318, 325
PknG, 318, 325
Pks13, 314, 325
Point charge, 277, 283, 284
Poisson Boltzmann, 9, 152, 153, 222, 227, 283,
284
Poisson-Boltzmann equation, 9, 284
Polar surface area, 46, 148, 258
Polypharmacology, 46
Predictive models, 3
Principal component analysis, 124, 242
PROCHECK, 120, 121, 184
Prokaryotic, 119, 323
Protein data bank, 141, 180, 194, 263, 271,
274, 323, 375, 385
Protein design, 4, 64
Protein folding, 5, 180, 323, 324
Protein function, 2
Protein-ligand binding, 6, 7, 221
Protein-protein docking, 60, 61, 65, 277, 282
Protein-protein interactions, 25, 48, 55–57, 60,
65, 180, 240, 282, 295, 367
Proteolytic cleavage, 122, 140
Purine nucleoside phosphorylase, 113, 114,
129
Pyrazinamide, 309, 311, 321
Pyrimidine biosynthesis, 177, 184, 189, 190
Q
Quantum chemistry, 8, 280
Quinolone, 183, 184, 198, 331
Index
405
Monte Carlo sampling, 33
Monte Carlo simulations, 8, 39, 125, 272, 278
MOSAIC, 358–363
Mouse serum albumin, 123
Moxifloxacin, 309, 311, 326, 330
Multidrug resistant, 206, 307
Multiple myeloma, 253
Multi-target drug design, 32
Mur ligase, 315, 316
Muscarinic receptor, 30
Mutation, 2–4, 14, 16–18, 36, 55, 57, 64, 65,
179, 180, 188, 202, 275, 282, 314, 317,
322, 367
Mutational hotspots, 15, 16
Mutation scanning, 14, 16
Mycobacterial cyclopropane synthase, 314,
331
Mycobacterium tuberculosis, 75, 90, 119, 282,
307, 309
Mycolic acid, 40, 309, 311, 313–315, 325, 335
N
Natural compounds, 181
Natural products, 291, 316, 323
Network biology, 109, 110
Neurodegenerative, 228, 248, 251
Nilotinib, 16
Nitazoxanide, 332, 335
Non-covalent association, 8
Non-physical states, 8, 12
Normal mode analysis, 9, 152, 155
Nuclear Magnetic Resonance (NMR), 5, 110,
116, 144, 155, 238, 261, 262, 273, 286,
295, 323, 348, 349, 376, 379
Nucleoside analogues, 71, 74, 90, 94–96, 106
O
Occupancy, 118, 285
Optimization, 4, 16, 25, 26, 32, 35, 48, 115,
122, 144, 145, 150, 160, 204, 207, 208,
211, 223, 225, 232, 234, 241, 259, 260,
283, 285, 316, 323, 350, 358, 360–362
Orthosteric drugs, 61
Outliers, 120, 141, 142, 154
Oxazolidinone, 330, 333, 334
Oxidoreductase, 183, 315, 327, 330
P
Pan Assay Interference Compounds (PAINS),
160, 257
Partition functions, 7, 239
Pattern identification, 34, 35
Penicillin, 3, 129
Peptide deformylase, 318, 325
Peptidoglycan, 311, 313, 325
Pfdihydrofolatereductase, 179
Pharmacodynamic, 160, 221, 225, 240, 242,
311
Pharmacokinetics, 140, 203, 223, 324
Pharmacophore fingerprints, 39
Pharmacophore model, 25, 27–33, 35–41,
43–48, 213, 214, 287, 331
Phase, 4, 5, 8, 10, 29, 32, 34, 37, 38, 41–43,
146, 152, 154, 180, 198, 223, 226, 228,
230, 252, 257, 273, 275, 283, 286, 287,
320, 323, 333–335, 354, 383, 384, 395
Phase 1 clinical trials, 333
Phosphatidylinositol, 177, 182
Phosphorylation, 119, 120, 126, 130, 182, 249,
251, 318
Phylogenetic analysis, 119
Physico-chemical, 123, 145, 148, 275, 331
PimA, 315
PknB, 318, 325
PknG, 318, 325
Pks13, 314, 325
Point charge, 277, 283, 284
Poisson Boltzmann, 9, 152, 153, 222, 227, 283,
284
Poisson-Boltzmann equation, 9, 284
Polar surface area, 46, 148, 258
Polypharmacology, 46
Predictive models, 3
Principal component analysis, 124, 242
PROCHECK, 120, 121, 184
Prokaryotic, 119, 323
Protein data bank, 141, 180, 194, 263, 271,
274, 323, 375, 385
Protein design, 4, 64
Protein folding, 5, 180, 323, 324
Protein function, 2
Protein-ligand binding, 6, 7, 221
Protein-protein docking, 60, 61, 65, 277, 282
Protein-protein interactions, 25, 48, 55–57, 60,
65, 180, 240, 282, 295, 367
Proteolytic cleavage, 122, 140
Purine nucleoside phosphorylase, 113, 114,
129
Pyrazinamide, 309, 311, 321
Pyrimidine biosynthesis, 177, 184, 189, 190
Q
Quantum chemistry, 8, 280
Quinolone, 183, 184, 198, 331
Index
405