Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery

Journal of Computational Chemistry

Volumn 31, Issue 8, 2010, Pages 1722-1732

  Puranen, J Santeri ^a   Vainio, Mikko J ^a,b   Johnson, Mark S ^a  

^a ÅBO AKADEMI UNIVERSITY   (Finland)

^b Visipoint Ltd   (Finland)

Author keywords

Conformation dependent; Electronegativity equalization; Molecular electrostatic potential; Partial charges; Polarizable

Indexed keywords

AB INITIO METHOD; COMPUTATIONAL COSTS; DRUG DISCOVERY; DRUG MOLECULES; ELECTRONEGATIVITY EQUALIZATION; ELECTROSTATIC POTENTIALS; FLEXIBLE MOLECULES; FREE OF CHARGE; GENERATION TOOLS; HIGH-THROUGHPUT; IN-SILICO; MOLECULAR ELECTROSTATIC POTENTIALS; NEW PARAMETERS; PARTIAL CHARGES; QUANTUM MECHANICAL METHOD; QUANTUM MECHANICS; SOFTWARE IMPLEMENTATION;

CHEMICAL BONDS; CONFORMATIONS; ELECTRONEGATIVITY; MOLECULAR INTERACTIONS; QUANTUM THEORY;

ELECTROSTATICS;

DRUG;

ARTICLE; CALIBRATION; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATION; DRUG DEVELOPMENT; HIGH THROUGHPUT SCREENING; REPRODUCIBILITY; STATIC ELECTRICITY;

CALIBRATION; COMPUTER SIMULATION; DRUG DISCOVERY; HIGH-THROUGHPUT SCREENING ASSAYS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PHARMACEUTICAL PREPARATIONS; REPRODUCIBILITY OF RESULTS; SOFTWARE; STATIC ELECTRICITY;

EID: 77952402385     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21460     Document Type: Article

References (57)

1. Politzer, P.; Murray, J. S. Theor Chem Acc 2002, 108, 134.
2. Cramer, C. J. Essentials of Computational Chemistry, 2nd ed. (reprint 2007); John Wiley: Chichester, England, 2004.
3. Toufar, H.; Baekelandt, B. G.; Janssens, G. O. A.; Mortier, W. J.; Schoonheydt, R. A. J. Phys Chem 1995, 99, 13876.
4. Mo, Y. R.; Gao, J. L.; Peyerimhoff, S. D. J Chem Phys 2000, 112, 5530.
5. Cho, A. E.; Guallar, V.; Berne, B. J.; Friesner, R. J Comput Chem 2005, 26, 915.
6. Rick, S. W.; Stuart, S. J. Rev Comput Chem 2002, 18, 89.
7. Mackerell, A. D. J. J Comput Chem 2004, 25, 1584.
8. Sanderson, R. Science 1951, 114, 670.
9. Mortier, W. J.; Ghosh, S. K.; Shankar, S. J Am. Chem Soc 1986, 108, 4315.
10. Rappe, A. K.; Goddard, W. A. J Phys Chem 1991, 95, 3358.
11. Yang, Z.-Z.; Wang, C.-S. J Phys Chem A 1997, 101, 6315.
12. Njo, S. L.; Fan, J.; van de Graaf, B. J Mol Catal A Chem 1998, 134, 79.
13. Bultinck, P.; Langenaeker, W.; Lahorte, P.; De Proft, F.; Geerlings, P.; Waroquier, M.; Tollenaere, J. P. J Phys Chem A 2002, 106, 7887.
14. Gilson, M. K.; Gilson, H. S.; Potter, M. J. J Chem Inf Comput Sci 2003, 43, 1982.
15. Chaves, J.; Barroso, J.; Bultinck, P.; Carbó-Dorca, R. J Chem Inf Model 2006, 46, 1657.
16. Shulga, D.; Oliferenko, A.; Pisarev, S.; Palyulin, V.; Zefirov, N. SAR QSAR Environ Res 2008, 19, 153.
17. Ouyang, Y.; Ye, F.; Liang, Y. Phys Chem Chem Phys 2009, 11, 6082.
18. Gasteiger, J.; Marsili, M. Tetrahedron Lett 1978, 34, 3181.
19. Gasteiger, J.; Marsili, M. Tetrahedron 1980, 36, 3219.
20. Bader, R. F. W. Chem Rev 1991, 91, 893.
21. Hirshfeld, F. Theor Chim Acta 1977, 44, 129.
22. Bultinck, P.; Van Alsenoy, C.; Ayers, P. W.; Carbó-Dorca, R. J Chem Phys 2007, 126, 144111.
23. Van Damme, S.; Bultinck, P.; Fias, S. J Chem Theor Comput 2009, 5, 334.
24. Bultinck, P.; Langenaeker, W.; Lahorte, P.; De Proft, F.; Geerlings, P.; Van Alsenoy, C.; Tollenaere, J. P. J Phys Chem A 2002, 106, 7895.
25. Bultinck, P.; Vanholme, R.; Popelier, P.; De Proft, F.; Geerlings, P. J Phys Chem A 2004, 108, 10359.
26. Singh, U. C.; Kollman, P. A. J Comput Chem 1984, 5, 129.
27. Breneman, C.; Wiberg, K. J Comput Chem 1990, 11, 361.
28. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J Phys Chem 1993, 97, 10269.
29. Franci, M. M.; Carey, C.; Chirlian, L. E. J Comput Chem 1996, 17, 367.
30. Sigfridsson, E.; Ryde, U. J Comput Chem 1998, 19, 377.
31. Franci, M. M.; Chirlian, L. E. Rev Comput Chem 2000, 14, 1.
32. Jirouǎková, Z.; Vařeková, R. S.; Vaněk, J.; Koča, J. J Comput Chem 2008, 30, 1174.
33. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J Am Chem Soc 1985, 107, 3902.
34. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. J Comput Chem 2000, 21, 132.
35. Jakalian, A.; Jack, D. B.; Bayly, C. I. J Comput Chem 2002, 23, 1623.
36. Halgren, T. A. J Comput Chem 1996, 17, 490.
37. Vainio, M.; Johnson, M. J Chem Inf Model 2007, 47, 2462.
38. Pearson, R. J Am Chem Soc 1963, 85, 3533.
39. Parr, R.; Pearson, R. J Am Chem Soc 1983, 105, 7512.
40. Geerlings, P.; Proft, F. D.; Langenaeker, W. Chem Rev 2003, 103, 1793.
41. Bultinck, P.; Carbó-Dorca, R. Chem Phys Lett 2002, 364, 357.
42. Smirnov, K. S.; van de Graaf, B. J Chem Soc Faraday Trans 1996, 92, 2469.
43. Vařeková, S. R.; Jirouǎková, Z.; Vaněk, J.; Suchomel, S.; Koča, J. Int J Mol Sci 2007, 8, 575.
44. Levenberg, K. Q Appl Math 1944, 2, 164.
45. Marquardt, D. SIAM J Appl Math 1963, 11, 431.
46. Berente, I.; Czinki, E.; Naray-Szabo, G. J Comput Chem 2007, 28, 1936.
47. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; 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, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision D.02. Gaussian, Inc., Wallingford, CT, 2004.
48. Tropsha, A.; Gramatica, P.; Gombar, V. K. QSAR Comb Sci 2003, 22, 69.
49. OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508.
50. The PubChem database. Available at: http://pubchem.ncbi.nlm.nih.gov/ Accessed on January 9, 2008.
51. Deb, K.; Pratap, A.; Agarwal, S.; Meyarivan, T. IEEE Trans Evolut Comput 2002, 6, 182.
52. Lipinski, C.; Lombardo, F.; Dominy, B.; Feeney, P. Adv Drug Deliv Rev 1997, 23, 3.
53. Wishart, D. S.; Knox, C.; Guo, A. C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. Nucl Acids Res 2008, 36, D901.
54. Weininger, D. J Chem Inf Comput Sci 1988, 28, 31.
55. Weininger, D.; Weininger, A.; Weininger, J. L. J Chem Inf Comput Sci 1989, 29, 97.
56. Computerchemie, M. N. G. Corma v3.2 - Generation of 3D coordinates. Computer program. Molecular Networks GmbH - Computerchemie.
57. Rocha, G. B.; Freire, R. O.; Simas, A. M.; Stewart, J. J. P. J Comput Chem 2006, 27, 1101.