Index
549
Ensemble docking, 503, 507, 516, 519, 521
advantages of, 530
concept of, 504
driving force of, 528
MD-based, 531
MD-derived, 524
methodological improvements in, 531
molecular dynamis-based, 506
potential of, 530
strategies, 519
workflow of, 504
Enzymes, 1, 61, 62, 80, 95, 100, 217, 241
Epoxide ring opening, 296, 299, 317
Excited states, 2, 10, 13, 194, 309
F
Flexibility, 502–504, 509, 512, 520, 531
conformational, 139, 146, 187, 199, 243
in DNA, 81
molecular, 451
G
G-quartets, 184, 187, 189, 190, 192, 193, 195
H
Hybrid Quantum Mechanics Molecular
Mechanics See QM/MM method, 1
Hydrogen bonds, 24, 29, 30, 32, 35, 43, 118,
125, 139, 142, 522
intramolecular, in 2’
deoxyribonucleotide, 148–150
intramolecular, in 2′
deoxyribonucleotide, 146
I
In silico, 114, 125, 126, 199
approaches, 121, 122
docking, 119
modeling, 496
Intercalation, 13, 23, 24, 26, 31, 32, 35, 40,
41, 43, 44, 47, 198
K
Kernel Ridge Regression (KRR), 434, 438
Kidney stones, 232, 272, 285, 290
L
Ligand binding, 23, 24, 28, 36, 38, 40, 46,
196, 503, 521, 529
Light switch effect, 13–15
M
MD simulation, 122, 124, 246, 249, 264, 506,
510, 511, 514, 518, 519, 521, 522,
528–530
Mechanisms of actions
of viral DNA polymerase inhibitors, 122
Medicinal chemistry, 199, 209, 216, 435, 455
Metal complexes, 198, 273, 274, 279
Minor groove binding, 23, 32, 188
energy analysis of, 47
Mixtures,
equilibrium, 187
Molecular dynamics simulation, 27, 29, 34,
61, 81, 122, 123, 125, 197, 503, 528
principles of, 506, 507
Molecular modeling, 24, 117, 250, 452, 544
N
Nucleotides, 99–101, 104, 125, 138–140, 142,
151, 155, 156, 165, 167, 170
anionic, 160, 167, 169, 174
pyrimidine, 166
O
One-class support vector machines, 434, 445
P
Permeability, 462–465, 467, 495
Phase transition, 244–246
Phospholipid membrane, 222, 243, 265
Pol inhibitors, 96, 104, 105, 122, 126, 127
Polarization, 4, 11, 12, 14, 190
Polyphenol glycosides, 273
Proton affinity, 167
Q
QM/MM method, 2, 3, 7, 16, 197, 226
Quadruplex DNA, 183–187, 196
Quantitative structure-activity relationship
(QSAR)
modeling of, 435
Quantitative structure–activity relationship
(QSAR), 471
modeling of, 209, 474
Quantum chemistry calculations, 209
R
Rational design, 22, 27, 124–126
Reaction mechanism, 76, 77, 83, 302
Reactive halogen species, (RHS) 60
Reactive nitrogen oxide species (RNOS), 60
549
Ensemble docking, 503, 507, 516, 519, 521
advantages of, 530
concept of, 504
driving force of, 528
MD-based, 531
MD-derived, 524
methodological improvements in, 531
molecular dynamis-based, 506
potential of, 530
strategies, 519
workflow of, 504
Enzymes, 1, 61, 62, 80, 95, 100, 217, 241
Epoxide ring opening, 296, 299, 317
Excited states, 2, 10, 13, 194, 309
F
Flexibility, 502–504, 509, 512, 520, 531
conformational, 139, 146, 187, 199, 243
in DNA, 81
molecular, 451
G
G-quartets, 184, 187, 189, 190, 192, 193, 195
H
Hybrid Quantum Mechanics Molecular
Mechanics See QM/MM method, 1
Hydrogen bonds, 24, 29, 30, 32, 35, 43, 118,
125, 139, 142, 522
intramolecular, in 2’
deoxyribonucleotide, 148–150
intramolecular, in 2′
deoxyribonucleotide, 146
I
In silico, 114, 125, 126, 199
approaches, 121, 122
docking, 119
modeling, 496
Intercalation, 13, 23, 24, 26, 31, 32, 35, 40,
41, 43, 44, 47, 198
K
Kernel Ridge Regression (KRR), 434, 438
Kidney stones, 232, 272, 285, 290
L
Ligand binding, 23, 24, 28, 36, 38, 40, 46,
196, 503, 521, 529
Light switch effect, 13–15
M
MD simulation, 122, 124, 246, 249, 264, 506,
510, 511, 514, 518, 519, 521, 522,
528–530
Mechanisms of actions
of viral DNA polymerase inhibitors, 122
Medicinal chemistry, 199, 209, 216, 435, 455
Metal complexes, 198, 273, 274, 279
Minor groove binding, 23, 32, 188
energy analysis of, 47
Mixtures,
equilibrium, 187
Molecular dynamics simulation, 27, 29, 34,
61, 81, 122, 123, 125, 197, 503, 528
principles of, 506, 507
Molecular modeling, 24, 117, 250, 452, 544
N
Nucleotides, 99–101, 104, 125, 138–140, 142,
151, 155, 156, 165, 167, 170
anionic, 160, 167, 169, 174
pyrimidine, 166
O
One-class support vector machines, 434, 445
P
Permeability, 462–465, 467, 495
Phase transition, 244–246
Phospholipid membrane, 222, 243, 265
Pol inhibitors, 96, 104, 105, 122, 126, 127
Polarization, 4, 11, 12, 14, 190
Polyphenol glycosides, 273
Proton affinity, 167
Q
QM/MM method, 2, 3, 7, 16, 197, 226
Quadruplex DNA, 183–187, 196
Quantitative structure-activity relationship
(QSAR)
modeling of, 435
Quantitative structure–activity relationship
(QSAR), 471
modeling of, 209, 474
Quantum chemistry calculations, 209
R
Rational design, 22, 27, 124–126
Reaction mechanism, 76, 77, 83, 302
Reactive halogen species, (RHS) 60
Reactive nitrogen oxide species (RNOS), 60