237
52. Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R (2002) Binding of d- and
l-captopril inhibitors to metallo-β-lactamase studied by polarizable molecular mechanics and
quantum mechanics. J Comput Chem 23(13):1281–1296. doi:10.1002/jcc.10111
53. Antony J, Piquemal J-P, Gresh N (2005) Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics.
Validation on model binding sites by quantum chemistry. J Comput Chem 26(11):1131–1147.
doi:10.1002/jcc.20245
54. Chen X, Gao F, Zhou Z-X, Yang W-Y, Guo L-T, Ji L-N (2010) Effect of ancillary ligands
on the topoisomerases II and transcription inhibition activity of polypyridyl ruthenium(II)
complexes. J Inorg Biochem 104(5):576–582. doi:10.1016/j.jinorgbio.2010.01.010
55. Casini A, Edafe F, Erlandsson M, Gonsalvi L, Ciancetta A, Re N, Ienco A, Messori L,
Peruzzini M, Dyson PJ (2010) Rationalization of the inhibition activity of structurally related organometallic compounds against the drug target cathepsin B by DFT. Dalton Trans
39(23):5556–5563. doi:10.1039/c003218b
56. Shokhen M, Khazanov N, Albeck A (2011) The mechanism of papain inhibition by peptidyl
aldehydes. Proteins 79(3):975–985. doi:10.1002/prot.22939
57. Greig NH, Sambamurti K, Yu Q, Brossi A, Bruinsma GB, Lahiri DK (2005) An overview of
phenserine tartrate, a novel acetylcholinesterase inhibitor for the treatment of Alzheimer’s
disease. Curr Alzheimer Res 2(3):281–290. doi:10.2174/1567205054367829
58. Lahiri DK, Farlow MR, Hintz N, Utsuki T, Greig NH (2000) Cholinesterase inhibitors, betaamyloid precursor protein and amyloid beta-peptides in Alzheimer’s disease. Acta Neurol
Scand 102(s176):60–67. doi:10.1034/j.1600-0404.2000.00309.x
59. Leader H, Wolfe AD, Chiang PK, Gordon RK (2002) Pyridophens: binary pyridostigmineaprophen prodrugs with differential inhibition of acetylcholinesterase, butyrylcholinesterase,
and muscarinic receptors. J Med Chem 45(4):902–910. doi:10.1021/jm010196t
60. Yu Q, Holloway HW, Flippen-Anderson JL, Hoffman B, Brossi A, Greig NH (2001) Methyl
analogues of the experimental Alzheimer drug phenserine: synthesis and structure/activity relationships for acetyl- and butyrylcholinesterase inhibitory action. J Med Chem 44(24):4062–
4071. doi:10.1021/jm010080x
61. Correa-Basurto J, Flores-Sandoval C, Marín-Cruz J, Rojo-Domínguez A, Espinoza-Fonseca
LM, Trujillo-Ferrara JG (2007) Docking and quantum mechanic studies on cholinesterases
and their inhibitors. Eur J Med Chem 42(1):10–19. doi:10.1016/j.ejmech.2006.08.015
62. Zhang Y, Kua J, McCammon JA (2002) Role of the catalytic triad and oxyanion hole in
acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc 124(35):10572–
10577. doi:10.1021/ja020243m
63. Nascimento ECM, Martins JBL, dos Santos ML, Gargano R (2008) Theoretical study of
classical acetylcholinesterase inhibitors. Chem Phys Lett 458(4–6):285–289. doi:10.1016/j.
cplett.2008.05.006
64. Khan MAS, Lo R, Bandyopadhyay TT, Ganguly BB (2011) Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: hydroxylamine anion is predicted to be a better antidote with DFT calculations. J Mol Graph Model 29(8):1039–1046.
doi:10.1016/j.jmgm.2011.04.009
65. Khan MAS, Ganguly B (2012) Assessing the reactivation efficacy of hydroxylamine anion towards VX-inhibited AChE: A computational study. J Mol Model 18(5):1801–1808.
doi:10.1007/s00894-011-1209-y
66. Shi Y-B, Fu L, Hasebe T, Ishizuya-Oka A (2007) Regulation of extracellular matrix remodeling and cell fate determination by matrix metalloproteinase stromelysin-3 during thyroid
hormone-dependent post-embryonic development. Pharmacol Therapeut 116(3):391–400.
doi:10.1016/j.pharmthera.2007.07.005
67. Smith MF, Ricke WA, Bakke LJ, Dow MPD, Smith GW (2002) Ovarian tissue remodeling:
role of matrix metalloproteinases and their inhibitors. Mol Cell Endocrinol 191(1):45–56.
doi:10.1016/S0303-7207(02)00054-0
7 Density Functional Theory Calculations of Enzyme–Inhibitor …
52. Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R (2002) Binding of d- and
l-captopril inhibitors to metallo-β-lactamase studied by polarizable molecular mechanics and
quantum mechanics. J Comput Chem 23(13):1281–1296. doi:10.1002/jcc.10111
53. Antony J, Piquemal J-P, Gresh N (2005) Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics.
Validation on model binding sites by quantum chemistry. J Comput Chem 26(11):1131–1147.
doi:10.1002/jcc.20245
54. Chen X, Gao F, Zhou Z-X, Yang W-Y, Guo L-T, Ji L-N (2010) Effect of ancillary ligands
on the topoisomerases II and transcription inhibition activity of polypyridyl ruthenium(II)
complexes. J Inorg Biochem 104(5):576–582. doi:10.1016/j.jinorgbio.2010.01.010
55. Casini A, Edafe F, Erlandsson M, Gonsalvi L, Ciancetta A, Re N, Ienco A, Messori L,
Peruzzini M, Dyson PJ (2010) Rationalization of the inhibition activity of structurally related organometallic compounds against the drug target cathepsin B by DFT. Dalton Trans
39(23):5556–5563. doi:10.1039/c003218b
56. Shokhen M, Khazanov N, Albeck A (2011) The mechanism of papain inhibition by peptidyl
aldehydes. Proteins 79(3):975–985. doi:10.1002/prot.22939
57. Greig NH, Sambamurti K, Yu Q, Brossi A, Bruinsma GB, Lahiri DK (2005) An overview of
phenserine tartrate, a novel acetylcholinesterase inhibitor for the treatment of Alzheimer’s
disease. Curr Alzheimer Res 2(3):281–290. doi:10.2174/1567205054367829
58. Lahiri DK, Farlow MR, Hintz N, Utsuki T, Greig NH (2000) Cholinesterase inhibitors, betaamyloid precursor protein and amyloid beta-peptides in Alzheimer’s disease. Acta Neurol
Scand 102(s176):60–67. doi:10.1034/j.1600-0404.2000.00309.x
59. Leader H, Wolfe AD, Chiang PK, Gordon RK (2002) Pyridophens: binary pyridostigmineaprophen prodrugs with differential inhibition of acetylcholinesterase, butyrylcholinesterase,
and muscarinic receptors. J Med Chem 45(4):902–910. doi:10.1021/jm010196t
60. Yu Q, Holloway HW, Flippen-Anderson JL, Hoffman B, Brossi A, Greig NH (2001) Methyl
analogues of the experimental Alzheimer drug phenserine: synthesis and structure/activity relationships for acetyl- and butyrylcholinesterase inhibitory action. J Med Chem 44(24):4062–
4071. doi:10.1021/jm010080x
61. Correa-Basurto J, Flores-Sandoval C, Marín-Cruz J, Rojo-Domínguez A, Espinoza-Fonseca
LM, Trujillo-Ferrara JG (2007) Docking and quantum mechanic studies on cholinesterases
and their inhibitors. Eur J Med Chem 42(1):10–19. doi:10.1016/j.ejmech.2006.08.015
62. Zhang Y, Kua J, McCammon JA (2002) Role of the catalytic triad and oxyanion hole in
acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc 124(35):10572–
10577. doi:10.1021/ja020243m
63. Nascimento ECM, Martins JBL, dos Santos ML, Gargano R (2008) Theoretical study of
classical acetylcholinesterase inhibitors. Chem Phys Lett 458(4–6):285–289. doi:10.1016/j.
cplett.2008.05.006
64. Khan MAS, Lo R, Bandyopadhyay TT, Ganguly BB (2011) Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: hydroxylamine anion is predicted to be a better antidote with DFT calculations. J Mol Graph Model 29(8):1039–1046.
doi:10.1016/j.jmgm.2011.04.009
65. Khan MAS, Ganguly B (2012) Assessing the reactivation efficacy of hydroxylamine anion towards VX-inhibited AChE: A computational study. J Mol Model 18(5):1801–1808.
doi:10.1007/s00894-011-1209-y
66. Shi Y-B, Fu L, Hasebe T, Ishizuya-Oka A (2007) Regulation of extracellular matrix remodeling and cell fate determination by matrix metalloproteinase stromelysin-3 during thyroid
hormone-dependent post-embryonic development. Pharmacol Therapeut 116(3):391–400.
doi:10.1016/j.pharmthera.2007.07.005
67. Smith MF, Ricke WA, Bakke LJ, Dow MPD, Smith GW (2002) Ovarian tissue remodeling:
role of matrix metalloproteinases and their inhibitors. Mol Cell Endocrinol 191(1):45–56.
doi:10.1016/S0303-7207(02)00054-0
7 Density Functional Theory Calculations of Enzyme–Inhibitor …