QTAIM in Drug Discovery and Protein Modeling

The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design

Volumn , Issue , 2007, Pages 471-498

  Sukumar, Nagamani ^a   Breneman, Curt M ^b  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b Research Rensselaer Polytechnic Institute   (United States)

Author keywords

Application to biological sciences; Application to drug design; Atom typing scheme; Atoms in molecules; Descriptor generation; Electron density; QSAR and drug discovery; QTAIM in drug discovery; QTAIM in protein modeling; Quantum Theorie; TAE reconstruction; Transferable atom equivalent (TAE) library

Indexed keywords

EID: 84889987668     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527610709.ch18     Document Type: Chapter

References (133)

1. C. Hansch and A. Leo, Exploring QSAR: Fundamentals and Applications in Chemistry and Biology, ed. S.R. Heller. 1995: American Chemical Society. 1-557.
2. C. Hansch and A. Leo, Exploring QSAR. 1995: American Chemical Society.
3. C.M. Breneman and M. Rhem, J. Comp. Chem., 1997. 18(2): p. 182-197.
4. R. Todeschini and V. Consonni, Handbook of Molecular Descriptors. Methods and Principles in Medicinal Chemistry, ed. R. Mannhold, H. Kubinyi, and H. Timmerman. Vol. 11. 2000: Wiley-VCH.
5. R.S. Pearlman and K.M. Smith, Novel Software Tools for Chemical Diversity, in 3D QSAR and Drug Design: Recent Advances, H. Kubinyi, Y. Martin, and G. Folkers, Editors. 1997, Kluwer Academic Publishers: Dordrecht, Netherlands.
6. R.S. Pearlman, Novel Software Tools for Addressing Chemical Diversity http://www.netsci.org/Science/Combichem/feature08.html
7. R.S. Pearlman and K.M. Smith, Perspectives in Drug Discovery Design, 1998. 9-11: p. 339-353.
8. V. Consonni, R. Todeschini, and M. Pavan, J. Chem. Inf. Comput. Sci., 2002. 42: p. 682-692.
9. V. Consonni, R. Todeschini, M. Pavan, and P. Gramatica, J. Chem. Inf. Comput. Sci., 2002. 42: p. 693-705.
10. J.H. Schuur, P. Selzer, and J. Gasteiger, J. Chem. Inf. Comput. Sci., 1996. 36: p. 334-344.
11. P. Labute, J. Mol. Graph. Model., 2000. 18: p. 464-477.
12. T. Clark, J. Molec. Graph. Model., 2004. 22: p. 519-525.
13. B. Ehresmann, B. Martin, A.H.C. Horn, and T. Clark, J. Mol. Model., 2003. 9: p. 342-347.
14. B. Ehresmann, M.J.D. Groot, A. Alex, and T. Clark, J. Chem. Inf. Comput. Sci., 2004. 44(2): p. 658-668.
15. P. Hohenberg and W. Kohn, Phys. Rev., 1964. 136: p. B864-B871.
16. R.F.W. Bader, S.G. Anderson, and A.J. Duke, J. Amer. Chem. Soc., 1979. 101(6): p. 1389-1395.
17. R.F.W. Bader, J. Chem. Phys., 1980. 73(6): p. 2871-2883.
18. R.F.W. Bader, Atoms in Molecules: A Quantum Theory. 1990, Oxford: Oxford Press.
19. R.F.W. Bader, Chem. Rev., 1991. 91(5): p. 893-928.
20. R.F.W. Bader, J. Phys. Chem. A, 1998. 102(37): p. 7314-7323.
21. I. Riess and W. Münch, Theor. Chim. Acta, 1981. 58: p. 295-300.
22. P.G. Mezey, Mol. Phys., 1999. 96(2): p. 169-178.
23. P.G. Mezey, J. Math. Chem., 2002. 30(3): p. 299-303.
24. W. Kohn and A. Yaniv, Proc. Natl. Acad. Sci. USA, 1978. 75(11): p. 5270-5272.
25. W. Kohn, Phys. Rev. Lett., 1996. 76(17): p. 3168-3171.
26. E. Prodan and W. Kohn, Nearsightedness of Electronic Matter. 2005: http://arxiv.org/abs/cond-mat/0503124
27. R.F.W. Bader and P. Becker, Chem. Phys. Lett., 1988. 148(5): p. 452-458.
28. W. Yang, Phys. Rev. Lett., 1991. 66: p. 1438.
29. W. Yang and T.-S. Lee, J. Chem. Phys., 1995. 103: p. 5674.
30. C.F. Matta, J. Phys. Chem. A, 2001. 105(49): p. 11088-11101.
31. P.D. Walker and P.G. Mezey, J. Amer. Chem. Soc., 1994. 116: p. 12022-12032.
32. P.D. Walker, G.A. Arteca, and P.G. Mezey, J. Comp. Chem., 1991. 12(2): p. 220-230.
33. N.S. Zefirov and V.A. Palyulin, J. Chem. Inf. Comput. Sci., 2002. 42: p. 1112-1122.
34. J.S. Murray and P. Politzer, Theor. Comput. Chem., 1998. 5: p. 198-202.
35. C.M. Breneman and M. Martinov, The Use of Electrostatic Potential Fields in QSAR and QSPR, in Molecular Electrostatic Potential: Concept and Applications, J.S. Murray and K. Sen, Editors. 1996, Elsevier: Amsterdam. p. 143-179.
36. J.S. Murray, N. Sukumar, S. Ranganathan, and P. Politzer, Int. J. Quantum Chem., 1990. 38: p. 611-629.
37. P. Politzer and D.G. Truhlar, Chemical Applications of Atomic and Molecular Electrostatic Potential. 1981, New York: Plenum Press.
38. P. Politzer, N. Sukumar, K. Jayasuriya, and S. Ranganathan, J. Amer. Chem. Soc., 1988. 110: p. 3425-3430.
39. R.G. Parr and W. Yang, J. Amer. Chem. Soc., 1984. 106: p. 4049-4050.
40. R.G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules. 1989, New York: Oxford University Press.
41. K. Fukui, T. Yonezawa, and C. Nagata, J. Chem. Phys., 1957. 27(6): p. 1247.
42. K. Fukui, Theory of Orientation and Stereoselection. 1975, Berlin: Springer.
43. M.J. Embrechts, J. Robert Kewley, and C. Breneman. Computationally Intelligent Data Mining for the Automated Design and Discovery of Novel Pharmaceuticals, in Smart Engineering Systems: Neural Networks, Fuzzy Logic, Evolutionary Programming, Data Mining and Rough Sets. 1998. St. Louis, MO: ASME Press.
44. M.J. Embrechts, F. Arciniegas, M. Ozdemir, and M. Momma. Scientific Data Mining with StripMiner, in Proceedings, 2001 SMCia Mountain Workshop on Soft Computing in Industrial Applications. Blacksburg, Virginia: IEEE Press.
45. R. Kewley, M.J. Embrechts, and C.M. Breneman, Neural Network Analysis for Data Strip Mining Problems, in Intelligent Engineering Systems through Artificial Neural Networks, C. Dagli, Editor. 1998, ASME Press. p. 391-396.
46. K. Bennett and C. Campbell, SIGKDD Explorations, 2000. 2(2): p. 1-13.
47. K. Bennett, A. Demiriz, and M. Embrechts. Semi-Supervised Clustering Using Genetic Algorithms, in Artificial Neural Networks in Engineering (ANNIE'99). 1999.
48. M.J. Embrechts, F.A. Arciniegas, M. Ozdemir, C.M. Breneman, K.P. Bennett, and L. Lockwood. Bagging Neural Network Sensitivity Analysis for Feature Reduction in QSAR Problems, in 2001 INNS-IEEE International Joint Conference on Neural Networks. 2001. Washington D.C: IEEE Press.
49. R.F.W. Bader, Phys. Rev. B, 1994. 49(19): p. 13348-13356.
50. R.F.W. Bader and P.M. Beddall, J. Chem. Phys., 1972. 56(7): p. 3320-3329.
51. R.F.W. Bader, P.M. Beddall, and J. Peslak, Jr., J. Chem. Phys., 1973. 58(2): p. 557-566.
52. R.F.W. Bader and P.M. Beddall, J. Amer. Chem. Soc., 1973. 95(2): p. 305-315.
53. R.F.W. Bader and R.R. Messer, Can. J. Chem., 1974. 52(12): p. 2268-2282.
54. R.F.W. Bader, Acc. Chem. Res., 1975. 8(1): p. 34-40.
55. R.F.W. Bader, Acc. Chem. Res., 1985. 18(1): p. 9-15.
56. R.F.W. Bader, M.T. Carroll, J.R. Cheeseman, and C. Chang, J. Amer. Chem. Soc., 1987. 109(26): p. 7968-7979.
57. R.F.W. Bader, A. Larouche, C. Gatti, M.T. Carroll, P.J. Macdougall, and K.B. Wiberg, J. Chem. Phys., 1987. 87(2): p. 1142-1152.
58. R.F.W. Bader, J. Chem. Phys., 1989. 91(11): p. 6989-7001.
59. R.F.W. Bader and C. Chang, J. Phys. Chem., 1989. 93(13): p. 5095-5107.
60. R.F.W. Bader and D.A. Legare, Can. J. Chem., 1992. 70(2): p. 657-676.
61. R.F.W. Bader and T.A. Keith, J. Chem. Phys., 1993. 99(5): p. 3683-3693.
62. R.F.W. Bader, P.L.A. Popelier, and T.A. Keith, Angew Chem. Int. Ed. Engl, 1994. 33: p. 620-631.
63. R.F.W. Bader, Phys. Rev. B: Condens. Matter, 1994. 49(19): p. 13348-13356.
64. P.L.A. Popelier, L. Joubert, and D.S. Kosov, J. Phys. Chem. A, 2001. 105(35): p. 8254-8261.
65. C.E. Whitehead, C.M. Breneman, N. Sukumar, and M.D. Ryan, J. Comp. Chem., 2003. 24: p. 512-529.
66. C. Whitehead, Modeling Intermolecular Interaction using the Transferable Atom Equivalent Method. Ph.D. Thesis, Rensselaer Polytechnic Institute: Troy, NY, 1999.
67. C.M. Breneman and K.B. Wiberg, J. Comp. Chem., 1990. 11(3): p. 361-373.
68. C.M. Breneman and L.W. Weber, Transferable Atom Equivalents. Assembling Accurate Electrostatic Potential Fields for Large Molecules from Ab-Initio and PROAIMS Results on Model Systems, in The Application of Charge Density Research to Chemistry and Drug Design, G.A. Jeffrey and J.F. Piniella, Editors. 1991, Plenum Press.
69. C.M. Breneman and T. Thompson, Modeling the Hydrogen Bond with Transferable Atom Equivalents, in Modeling the Hydrogen Bond, D. Smith, Editor. 1993, ACS Symposium Series: Washington, D.C. p. 152-174.
70. C.M. Breneman, T.R. Thompson, M. Rhem, and M. Dung, Computers & Chemistry, 1995. 19(3): p. 161.
71. L.H. Hall and L.B. Keir, J. Chem. Inf. Comput. Sci., 1995. 35: p. 1039.
72. D.E. Clark, J. Pharm. Sci., 1999. 88(8): p. 815-821.
73. N. Sukumar and C. Breneman, RECON. 2001-2006: http:// www.drugmining.com.
74. M.J. Frisch, G.W., et al. Gaussian 98. 1998, Gaussian, Inc.: Pittsburgh.
75. R.F.W. Bader, AIMPAC: http://www.chemistry.mcmaster.ca/aimpac.
76. B.M. Deb, R. Singh, and N. Sukumar, J. Molec. Struct. (Theochem), 1992. 259: p. 121-139.
77. N. Sukumar, C.M. Breneman, and W.P. Katt. Virtual high-throughput screening of large datasets using TAE/ RECON descriptors, in 221st National Meeting ACS. 2001. San Diego: American Chemical Society.
78. M. Randic, J. Amer. Chem. Soc., 1975. 97: p. 6609-6615.
79. C.M. Breneman, C.M. Sundling, N. Sukumar, L. Shen, W.P. Katt, and M.J. Embrechts, J. Comput. aided Mol. Design, 2003. 17: p. 231-240.
80. R.J. Zauhar and W.J. Welsh, Application of the "shape signatures" approach to ligand-and receptor-based drug design, in ACS National Meeting. 2000. Washington, D.C.: American Chemical Society.
81. K. Nagarajan, R.J. Zauhar, and W.J. Welsh, J. Chem. Inf. Comput. Sci., 2005. 45: p. 49-57.
82. L.H. Hall and L.B. Kier, Bull. Environ. Contam. Toxicol., 1984. 32: p. 354.
83. L.H. Hall, Computational Aspects of Molecular Connectivity and its Role in Structure-Activity Modeling, in Computational Chemical Graph Theory, D.H. Rouvray, Editor. 1989, Nova.
84. L.H. Hall and L.B. Kier, eds. The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling. Reviews in computational chemistry II, ed. K.B. Lipkowitz and D.B. Boyd. Vol. 1991. 1991, VCH Publishers. 367-422.
85. L.B. Kier, W.J. Murray, M. Randic, and L.H. Hall, J. Pharm. Sci., 1975. 64: p. 1971-1974.
86. L.B. Kier and L.H. Hall, Molecular Connectivity in Chemistry and Drug Research. 1976, New York: Academic Press.
87. L.B. Kier and L.H. Hall, Eur. J. Med. Chem., 1977. 12: p. 307.
88. L.B. Kier and L.H. Hall, J. Pharm. Sci., 1981. 70: p. 583.
89. L.B. Kier and L.H. Hall, Molecular Connectivity in Structure-Activity Analysis. 1986, New York: John Wiley.
90. M. Randic, J. Mol. Graph. Model., 2001. 20(1): p. 19-35.
91. M. Randic, J. Chem. Inf. Comput. Sci., 2004. 44: p. 373-377.
92. P. Politzer, J.S. Murray, and Z. Peralta-Inga, Int. J. Quantum Chem., 2001. 85(6): p. 676-684.
93. R.F.W. Bader, P.J. Macdougall, and C.D.H. Lau, J. Amer. Chem. Soc., 1984. 106(6): p. 1594-605.
94. C.M. Breneman, unpublished.
95. R.F.W. Bader and P.J. Macdougall, J. Amer. Chem. Soc., 1985. 107(24): p. 6788-6795.
96. P. Sjoberg, J.S. Murray, T. Brinck, and P. Politzer, Can. J. Chem., 1990. 68(8): p. 1440-1443.
97. C.M. Sundling, N. Sukumar, H. Zhang, M.J. Embrechts, and C.M. Breneman, Wavelets in Chemistry and Cheminformatics, in Reviews in Computational Chemistry, K.B. Lipkowitz, T.R. Cundari, and V.J. Gillet, Editors. 2006, John Wiley. p. 295-330.
98. C.M. Breneman, N. Sukumar, K.P. Bennett, M.J. Embrechts, M. Sundling, and L. Lockwood. Wavelet Representations of Molecular Electronic Properties: Applications in ADME, QSPR and QSAR, in ACS QSAR in Cells symposium. 2000. Washington, D.C.: American Chemical Society.
99. M. Wagener, J. Sadowski, and J. Gasteiger, J. Amer. Chem. Soc., 1995. 117(29): p. 7769-7775.
100. C.M.L. Sundling and C.M. Breneman. PEST vs. CoMFA: A comparative study of two 3D-QSAR technologies, in 229th National Meeting, ACS. 2005. San Diego: American Chemical Society.
101. R. Carbo, J. Arnau, and L. Leyda, Int. J. Quantum Chem., 1980. 17: p. 1185-1189.
102. R. Carbo and B. Calabuig, J. Mol. Struct. (THEOCHEM), 1992. 254: p. 517-531.
103. R. Carbo, B. Calabuig, L. Vera, and E. Besalu, Adv. Quantum Chem., 1994. 25: p. 253-313.
104. R. Carbo, E. Besalu, L. Amat, and X. Fradera, J. Math. Chem., 1995. 18: p. 237-246.
105. R. Carbo, Molecular Similarity and Reactivity: From Quantum Chemical to Phenomenological Approaches. 1995, Amsterdam: Kluwer Academic.
106. R. Carbo-Dorca and P.G. Mezey, Advances in Molecular Similarity. Vol. 1, 2. 1996, 1998, Greenwich, CT: JAI Press.
107. R. Carbo-Dorca, D. Robert, L. Amat, X. Girones, and E. Besalu, Molecular Quantum Similarity in QSAR and Drug Design. 2000, Berlin: Springer.
108. L. Amat, R. Carbo-Dorca, and R. Ponec, J. Comp. Chem., 1998. 19: p. 1575-1583.
109. R. Ponec, L. Amat, and R. Carbo-Dorca, J. Comput.-Aided Mol. Des., 1999. 13: p. 259-279.
110. R. Ponec, L. Amat, and R. Carbo-Dorca, J. Phys. Org. Chem., 1999. 12: p. 447-454.
111. P.L.A. Popelier, U.A. Chaudry, and P.J. Smith, Perkin Trans., 2002. II: p. 1231-1237.
112. P.L.A. Popelier, J. Phys. Chem., 1999. 103: p. 2883-2890.
113. S.E. O'brien and P.L.A. Popelier, Can. J. Chem., 1999. 77: p. 28-36.
114. S.E. O'brien and P.L.A. Popelier, J. Chem. Inf. Comput. Sci., 2001. 41: p. 764-775.
115. S.E. O'brien and P.L.A. Popelier, Perkin Trans., 2002. II: p. 478-483.
116. Y.C. Martin, J.L. Kofron, and L.M. Traphagen, J. Med. Chem., 2002. 45: p. 4350-4358.
117. N. Nikolova and J. Jaworska, QSAR Comb. Sci., 2003. 22: p. 1006-1026.
118. L. Leherte, N. Meurice, and D.P. Vercauteren, J. Chem. Inf. Comput. Sci., 2000. 40: p. 816-832.
119. X. Girones, A. Gallegos, and R. Carbo-Dorca, J. Chem. Inf. Comput. Sci., 2000. 40: p. 1400-1407.
120. X. Girones and R. Ponec, J. Chem. Inf. Model., 2006. 46(3): p. 1388-1393.
121. N. Sukumar, C.M. Breneman, S.A. Cramer, K.P. Bennett, C.M. Sundling, Q. Luo, and D. Zhuang. Intelligent Data Mining for Modeling and Prediction of Protein-Ligand, Protein-Surface and Protein-DNA Interactions, in Pacifichem 2005: International Congress of Pacific-Basin Societies. 2005. Honolulu, Hawaii: American Chemical Society.
122. S. Oloff, S. Zhang, N. Sukumar, C. Breneman, and A. Tropsha, J. Chem. Inf. Model., 2006. 46(2): p. 844-851.
123. M.J. Embrechts, MetaPLS (Analyze), Version 3.0. 2001, Rensselaer Polytechnic Institute: Troy, NY.
124. D.V. Eldred, C.L. Weikel, P.C. Jurs, and K.L.E. Kaiser, Chemical Research in Toxicology, 1999. 12(7): p. 670-678.
125. C. Nantasenamat, T. Naenna, C.I.N. Ayudhya, and V. Prachasittikul, J. Comput.-Aided Mol. Des., 2005. 19: p. 509-524.
126. Q. Luo, Design, Development and Utilization of Novel Molecular Descriptors and Machine Learning Methods. Ph.D. Thesis, Rensselaer Polytechnic Institute: Troy, NY, 2006.
127. J. Bicerano, Prediction of Polymer Properties. Plastics Engineering Series, ed. D.E. Hudgin. Vol. 27. 1996, New York: Marcel Dekker, Inc.
128. C.B. Mazza, N. Sukumar, C.M. Breneman, and S.M. Cramer, Anal. Chem., 2001. 73: p. 5457-5461.
129. M. Song, C.M. Breneman, J. Bi, N. Sukumar, K.P. Bennett, S. Cramer, and N. Tugcu, J. Chem. Inf. Comput. Sci., 2002. 42: p. 1347-1357.
130. N. Tugcu, M.H. Song, C.M. Breneman, N. Sukumar, K.P. Bennett, and S.M. Cramer, Anal. Chem., 2003. 75: p. 3563-3572.
131. C.M. Breneman, C.M. Sundling, N. Sukumar, K.P. Bennett, M.J. Embrechts, and S.M. Cramer. Beyond PEST descriptors: Binding site and ligand shape/property fingerprints, in 231st American Chemical Society National Meeting. 2006. Atlanta, GA: American Chemical Society.
132. C.M. Breneman and N. Sukumar, New Developments in Molecular Modeling, in Yearbook of Science & Technology. 2004, McGraw-Hill: New York. p. 208-211.
133. C.M. Breneman, K.P. Bennett, M. Embrechts, S. Cramer, M. Song, J. Bi, and N. Sukumar, Descriptor Generation, Selection and Model Building in Quantitative Structure-Property Analysis, in Experimental Design for Combinatorial and High Throughput Materials Development, J.N. Cawse, Editor. 2002, John Wiley: New York.