How accurate are continuum solvation models for drug-like molecules?

Journal of Computer-Aided Molecular Design

Volumn 23, Issue 7, 2009, Pages 395-409

  Kongsted, Jacob ^a   Söderhjelm, Pär ^b   Ryde, Ulf ^b  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b CHEMICAL CENTER   (Sweden)

Author keywords

Continuum methods; FDPB; Free energy of hydration; Generalised Born; Langevin dipoles; PCM; Solvation energy

Indexed keywords

BINDING ENERGY; FREE ENERGY; HYDRATION; POISSON EQUATION; SOLVATION;

BINDING CONSTANT; CONTINUUM METHOD; FDPB; FREE ENERGY OF HYDRATION; GENERALIZED BORN; LANGEVIN; LANGEVIN DIPOLE; SMALL ORGANIC MOLECULES; SOLVATION ENERGY; UNCERTAINTY;

MOLECULES;

11 AMIDINOBENZYLBENZYL INDOLE CARBOXAMIDE INHIBITOR; AVIDIN; BIOTIN DERIVATIVE; BLOOD CLOTTING FACTOR 10A INHIBITOR; BUTANE; CAFFEINE; CANNABIDIOL; EFAVIRENZ; ETHOXYRESORUFIN; GALECTIN 3; OMEPRAZOLE; PACLITAXEL; PARACETAMOL; PHENOLPHTHALEIN; PHENYLBUTAZONE; PROGESTERONE; QUERCETIN; SKATOLE; THALIDOMIDE; TIABENDAZOLE; TOLUENE; UNCLASSIFIED DRUG; WARFARIN; WATER;

ARTICLE; CALCULATION; CALIBRATION; CHEMICAL REACTION; CONTROLLED STUDY; GENERALIZED BORN METHOD; GEOMETRY; HYDRATION; INTERMETHOD COMPARISON; LANGEVIN DIPOLE METHOD; POISSON BOLTZMANN; POLARIZED CONTINUUM METHOD; PREDICTION; PRIORITY JOURNAL; SOLVATION;

EID: 84962366080     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-009-9271-6     Document Type: Article

References (98)

1. Cramer CJ, Truhlar DG (1999) Chem Rev 99:2161-2200
2. Orozco M, Luque FJ (2000) Chem Rev 100:4187-4225
3. Simonson T (2001) Curr Opin Struct Biol 11:243-252
4. Feig M, Brooks CL (2004) Curr Opin Struct Biol 14:217-224
5. Born M (1920) Zeitsch Physi 1:45
6. Onsager LJ (1936) Am Chem Soc 58:1486
7. Miertus S, Scrocco E, Tomasi J (1981) Chem Phys 55:117
8. Tomasi J, Persico M (1994) Chem Rev 94:2027-2094
9. Tomasi J, Mennucci B, Cammi R (2005) Chem Rev 105:2999-3093
10. Barone V, Cossi M (1998) J Phys Chem A 102:1995
11. Tomasi J, Mennucci B, Cances E (1999) J Mol Struct (Theochem) 464:211
12. Chipman DM (2000) J Chem Phys 112:5558
13. Klamt A, Schüürmann G (1993) J Chem Soc Perkin Trans 2:799
14. Vreven T, Mennucci B, da Silva MO, Morokuma K, Tomasi J (2001) J Chem Phys 115:62-72
15. Fedorov DG, Kitaura K, Li H, Jensen JH, Gordon MS (2006) J Comput Chem 27:976-985
16. Warwicker J, Watson HC (1982) J Mol Biol 157:671
17. Gilson MK, Honig B (1988) Prot Struct Funct Genet 3:32-52
18. Sharp KA, Honig B (1990) Annu Rev Biophys Biophys Chem 19:310
19. Sharp KA, Honig B (1995) Curr Opin Struct Biol 5:323
20. Sitkoff D, Sharp KA, Honig B (1994) J Phys Chem 98:1978-1988
21. Simonsson T, Brünger AT (1994) J Phys Chem 98:4683
22. Baker NA (2004) Methods Enzymol 383:94
23. Chen Y, Noodleman L, Case DA, Bashford D (1994) J Phys Chem 98:11875
24. Baldridge K, Fine R, Hager A (1994) J Comput Chem 15:1217
25. Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Ringnalda M, Goddard WA, Honig B (1994) J Am Chem Soc 116:11875
26. Gorgonea V, Merz KM (1999) J Phys Chem A 103:5171-5188
27. Schnieders MJ, Baker NA, Ren P, Ponder JW (2007) J Chem Phys 126:124114
28. Hoitjink GJ, de Boer E, Van der Meij PH, Weijland EP (1956) Recl Trav Pays-Bas 75:487
29. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) J Am Chem Soc 112:6127
30. Onufriev A, Bashford D, Case DA (2000) J Phys Chem B 104:3712-3720
31. Bashford D, Case DA (2000) Annu Rev Phys Chem 51:129-152
32. Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CI (2004) J Comput Chem 25:265-284
33. Schnieders MJ, Ponder JW (2007) J Chem Theory Comput 2007(3):2083-2097
34. Hawkins GD, Cramer CJ, Truhlar DG (1995) Chem Phys Lett 1995(246):122-129
35. Kelly CP, Cramer CJ, Truhlar DG (2005) J Chem Theory Comput 1:1133-1152
36. Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG (2007) J Chem Theory Comput 3:2011-2033
37. Warshel A (1979) J Phys Chem 83:1640
38. Florián J, Warshel A (1997) J Phys Chem B 101:5583
39. Florián J, Warshel A (1999) J Phys Chem B 103:10282-10288
40. Hermida-Ramón JM, Karlström G, Lindh R (2002) J Phys Chem B 106:7115-7120
41. Langevin P (1905) Annales de Chemie Physique 8:70
42. Sandberg L, Casemyr R, Edholm O (2002) J Phys Chem 106:7889-7897
43. Hermann RB (1972) J Phys Chem 76:2754-2759
44. Cossi M, Tomasi J, Cammi R (1995) Int Quantum Chem Quant Chem Symp 29:695
45. Floris FM, Tomasi JJ (1989) Comput Chem 10:616
46. Cossi M, Mennucci B, Cammi RJ (1996) Comput Chem 17:57
47. Rizzo RC, Aynechi T, Case DA, Kuntz ID (2006) J Chem Theory Comput 2:128-139
48. Tan C, Tan Y-H, Luo R (2007) J Phys Chem B 111:12263-12274
49. Maple JR, Cao Y, Damm W, Halgren TA, Kaminski GA, Zhang LY, Friesner RA (2005) J Chem Theory Comput 1:694-715
50. Wagoner JA, Baker NA (2006) Proc Natl Acad Sci USA 103:8331-8336
51. Gallicchio E, Zhang LY, Levy RM (2002) J Comp Chem 23:517-529
52. Gallicchio E, Levy RM (2004) J Comp Chem 25:479-499
53. Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ (1996) J Phys Chem 100:16098
54. Barone V, Cossi M, Tomasi J (1997) J Chem Phys 107:3210-3221
55. Tan C, Yang L, Luo R (2006) J Phys Chem B 110:18686-18687
56. Klamt A, Mennucci B, Tomasi J, Barone V, Curutchet C, Orozco M, Luque FJ (2009) Acc Chem Res, in press. doi: 10.1021/ar800187p
57. Shirts MR, Pitera JW, Swope WC, Pande VS (2003) J Chem Phys 119:5740-5761
58. Li J, Zhu T, Hawkins GD, Winge P, Liotard DA, Cramer CJ, Truhlar DG (1999) Theor Chim Acta 103:9-63
59. Thompson JD, Cramer CJ, Truhlar DG (2004) 108:6532-6542
60. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Acc Chem Res 33(12):889-897
61. Vorobjev YN, Hermans J (1999) Biophys Chem 78:195-205
62. Wolfenden R, Andersson L, Cullis PM, Southgate CCB (1981) Biochemistry 20:849-855
63. Kelly CP, Cramer CJ, Truhlar DG (2006) J Phys Chem B 110:16066-16081
64. Alagona G, Ghio C, Nagy PI (2004) Int J Quant Chem 99:161-178
65. Takano Y, Houk KN (2005) J Chem Theory Comput 1:70-77
66. Kuhn B, Kollman PA (2000) J Med Chem 43:3786-3791
67. Weis A, Katebzadeh K, Söderhjelm P, Nilsson I, Ryde U (2006) J Med Chem 49:6596-6606
68. Kongsted J; Ryde U (2009) J Comput Aided Mol Des 23:63-71
69. Matter H, Defossa E, Heinelt U, Blohm P-M, Schneider D, Müller A, Herok S, Schreuder H, Liesum A, Brachvogel V, Lönze P, Walser A, Al-Obeidi F, Wildgoose P (2002) J Med Chem 45:2749-2769
70. Sörme P, Arnoux P, Kahl-Knutsson B, Leffler H, Rini JM, Nilsson UJ (2005) J Am Chem Soc 127:1737-1743
71. Mobley DL, Chodera JD, Dill KA (2008) J Phys Chem B 112:938-946
72. Pugliese L, Coda A, Malcovati M, Bolognesi M (1993) J Mol Biol 231:698-710
73. Perola E, Charifson PS (2004) J Med Chem 47:2499-2510
74. PC Spartan (2001) Pro 1.0.6, Wavefunction, Inc. 18401 Von Karman Avenue, Irvine, CA 92612
75. Hariharan PC, Pople JA (1973) Theor Chim Acta 28:213
76. Mennucci B, Tomasi JJ (1997) Chem Phys 106:5151
77. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98 (Revision A.9). Gaussian Inc, Pittsburgh
78. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, Revision D.01. Gaussian Inc, Wallingford
79. Perdew JP, Burke K, Ernzerhof M (1997) Phys Rev Lett 78:1396
80. Besler BH, Merz KM, Kollman PA (1990) Atomic Charges Derived from semiempirical Methods. J Comput Chem 11:431-439
81. Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9. University of California, San Francisco
82. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1975) J Am Chem Soc 117:5179-5197
83. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T (2003) J Comput Chem 24:1999-2012
84. Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) J Phys Chem 97:10269-10280
85. Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL (2004) J Comput Chem 25:265-284
86. Rocchia W, Alexov E, Honig B (2001) J Phys Chem B 105:6507-6514
87. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Proc Natl Acad Sci USA 98:10037-10041
88. Hawkins GD, Cramer CJ, Truhlar DG (1996) J Phys Chem 100:19824-19839
89. Tsui V, Case DA (2001) Biopol 56:275-291
90. Onufriev A, Bashford D, Case DA (2004) Proteins 55:383-394
91. Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A (2007) J Chem Theory Comput 3:156-169
92. Bondi A (1964) J Phys Chem 68:441-451
93. Ghosh A, Rapp CS, Friesner RA (1998) J Phys Chem B 102:10983
94. Curutchet C, Orozco M, Luque FJ, Mennucci B, Tomasi J (2006) J Comput Chem 27:1769-1780
95. Gohlke H, Klebe G (2002) Angew Chem Int Ed 41:2644-2676
96. Raha K, Merz KM (2005) J Med Chem 48:4558-4575
97. Gohlke H, Case DA (2004) J Comput Chem 28:238-250
98. Jensen JH, Li H, Robertson AD, Molina PA (2002) J Phys Chem B 106:3486-3496