The "ETA" indices in QSAR/QSPR/QSTR research

Quantitative Structure-Activity Relationships in Drug Design, Predictive Toxicology, and Risk Assessment

Volumn , Issue , 2015, Pages 48-83

  Roy, Kunal ^a,b   Das, Rudra Narayan ^a  

^a JADAVPUR UNIVERSITY   (India)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ANALYSIS;

BONDED INTERACTIONS; CHEMICAL INFORMATION; ELECTRONIC INFORMATION; EXPLICIT INFORMATION; MATHEMATICAL CORRELATION; MOLECULAR TOPOLOGIES; PREDICTOR VARIABLES; QUANTITATIVE STRUCTURE ACTIVITY;

COMPUTATIONAL CHEMISTRY;

EID: 84937817313     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-4666-8136-1.ch002     Document Type: Chapter

References (99)

1. Albert, A., Rubbo, S. D., & Goldacre, R. (1941). Correlation of basicity and antiseptic action in an acridine series. Nature, 147(3724), 332-333. doi:10.1038/147332a0
2. Balaban, A. T. (1982). Highly discriminating distance based topological index. Chemical Physics Letters, 89(5), 399-404. doi:10.1016/0009-2614(82)80009-2
3. Bell, P. H., & Roblin, R. O. Jr. (1942). Chemotherapy. VII. A theory of the relation of structure to activity of sulfanilamide-type compounds. Journal of the American Chemical Society, 64(12), 2905-2917. doi:10.1021/ja01264a055
4. Cayley, A. (1875). On the analytical forms called trees. American Journal of Mathematics, 4(1), 266-268.
5. Consonni, V., Todeschini, R., & Pavan, M. (2002). Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. Part 1. Theory of the novel 3D molecular descriptors. Journal of Chemical Information and Computer Sciences, 42(3), 682-692. doi:10.1021/ci015504a PMID:12086530
6. Coulson, C. A. (1939). The electronic structure of some polyenes and aromatic molecules. VII. Bonds of fractional order by the molecular orbital method. Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences, 16(938), 413-428. doi:10.1098/rspa.1939.0006
7. Cramer, R. D. III, Patterson, D. E., & Bunce, J. D. (1988). Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. Journal of the American Chemical Society, 110(18), 5959-5967. doi:10.1021/ja00226a005 PMID:22148765
8. Cros, A. F. A. (1863, January 9). Action de l'alcohol amylique sur l'organisme. Faculty of Medicine, University of Strasbourg.
9. Crosland, M. P. (1959). The use of diagrams as chemical 'equations' in the lecture notes of William Cullen and Joseph Black. Annals of Science, 15(2), 75-90. doi:10.1080/00033795900200088
10. Crum-Brown, A., & Fraser, T. R. (1868). On the connection between chemical constitution and physiological action. Part I. On the physiological action of the salts of the ammonium bases, derived from strychnine, brucia, thebaia, codeia, morphia, and nicotia. Journal of Anatomy and Physiology, 2(2), 224-242. PMID:17230757
11. Dalton, J. (1808). New system of chemical philosophy. London: Chembridge Press.
12. Das, R. N., & Roy, K. (2012). Development of classification and regression models for Vibrio fischeri toxicity of ionic liquids: Green solvents for the future. Toxicological Reviews, 1, 186-195.
13. Das, R. N., & Roy, K. (2013). QSPR with extended topochemical atom (ETA) indices. 4. Modeling aqueous solubility of drug like molecules and agrochemicals following OECD guidelines. Structural Chemistry, 24(1), 303-331. doi:10.1007/s11224-012-0080-5
14. Das, R. N., & Roy, K. (2014a). Predictive modeling studies for the ecotoxicity of ionic liquids towards the green algae Scenedesmus vacuolatus. Chemosphere, 104, 170-176. doi:10.1016/j.chemosphere. 2013.11.002 PMID:24296027
15. Das, R. N., & Roy, K. (2014b). Predictive in silico modeling of ionic liquids toward inhibition of the acetyl cholinesterase enzyme of electrophorus electricus: A predictive toxicology approach. Industrial & Engineering Chemistry Research, 53(2), 1020-1032. doi:10.1021/ie403636q
16. Das, R. N., Sanderson, H., Mwambo, A. E., & Roy, K. (2013). Preliminary studies on model development for rodent toxicity and its interspecies correlation with aquatic toxicities of pharmaceuticals. Bulletin of Environmental Contamination and Toxicology, 90(3), 375-381. doi:10.1007/s00128-012-0921-3 PMID:23238824
17. Dragon Version 6 TALETE srl, Italy. (2010). Retrieved April 30, 2014, http://www.talete.mi.it/products/dragon_description.htm
18. Euler, L. (1736). Solutio problematis ad geometriam situs pertinentis. Commentarii Academiae Scientiarum Imperialis Petropolitanae, 8, 128-140.
19. Ferguson, J. (1939). The use of chemical potentials as indices of toxicity. Proceedings of the Royal Society of London. Series B, Biological Sciences, 127(848), 387-403. doi:10.1098/rspb.1939.0030
20. Fischer, N. W. (1974). Kekulé and organic classification. Ambix, 21(1), 29-52. doi:10.1179/ amb.1974.21.1.29
21. Free, S. M., & Wilson, J. W. (1964). A mathematical contribution to structure-activity studies. Journal of Medicinal Chemistry, 7(4), 395-399. doi:10.1021/jm00334a001 PMID:14221113
22. Fujita, T., & Ban, T. (1971). Structure-activity relation. 3. Structure-activity study of phenethylamines as substrates of biosynthetic enzymes of sympathetic transmitters. Journal of Medicinal Chemistry, 14(2), 148-152. doi:10.1021/jm00284a016 PMID:5544401
23. Fukui, K., Yonezawa, Y., & Shingu, H. (1954). Theory of substitution in conjugated molecules. Bulletin of the Chemical Society of Japan, 27(7), 423-427. doi:10.1246/bcsj.27.423
24. Gálvez, J. (1998). On a topological interpretation of electronic and vibrational molecular energies. Journal of Molecular Structure THEOCHEM, 429, 255-264. doi:10.1016/S0166-1280(97)00366-7
25. Gordon, M., & Scantlebury, G. R. (1964). Non-random polycondensation: Statistical theory of the substitution effect. Transactions of the Faraday Society, 60, 604-621. doi:10.1039/tf9646000604
26. Gutman, I., & Trinajstić, N. (1972). Graph theory and molecular orbitals. Total π-electron energy of alternant hydrocarbons. Chemical Physics Letters, 17(4), 535-538. doi:10.1016/0009-2614(72)85099-1
27. Hammett, L. P. (1935). Some relations between reaction rates and equilibrium constants. Chemical Reviews, 17(1), 125-136. doi:10.1021/cr60056a010
28. Hansch, C., & Fujita, T. (1964). ρ-σ-π analysis: A method for the correlation of biological activity and chemical structure. Journal of the American Chemical Society, 86(8), 1616-1626. doi:10.1021/ja01062a035
29. Hansch, C., Maloney, P. P., Fujita, T., & Muir, R. M. (1962). Correlation of biological activity of phenoxyacetic acids with hammett substituent constants and partition coefficients. Nature, 194(4824), 178-180. doi:10.1038/194178b0
30. Higgins, W. A. (1789). Comparative view of the phlogistic and antiphlogistic theories. London: J. Murray.
31. Hosoya, H. (1971). Topological index: A newly proposed quantity characterizing the topological nature of structural isomers of saturated hydrocarbons. Bulletin of the Chemical Society of Japan, 44(9), 2332-2339. doi:10.1246/bcsj.44.2332
32. Kier, L. B., & Hall, L. H. (1986). Molecular connectivity in structure-activity analysis. Chichester, UK: Research Studies Press-John Wiley & Sons Ltd.
33. Kirchhoff, G. R. (1847). Über die auflösung der gleichungen, auf welche man bei der untersuchung der linearen verteilung galvanischer ströme geführt wird. Annales der Physik et Chimie, 72(12), 497-508. doi:10.1002/andp.18471481202
34. Kubinyi, H. (1976). Quantitative structure-activity relationships, 4. Nonlinear dependence of biological activity on hydrophobic character: A new model. Arzneimittel-Forschung. Drug Research, 26(11), 1991-1997. PMID:1037231
35. Lill, M. A. (2007). Multi-dimensional QSAR in drug discovery. Drug Discovery Today, 12(23-24), 1013-1017. doi:10.1016/j.drudis.2007.08.004 PMID:18061879
36. Meyer, H. (1899). Zur theorie der alkoholnarkose: 1. Welche eigenschaft der anästhetica bedingt ihre narkotische wirkung? ArchArchiv for Experimentelle Pathologie und Pharmakologie, 42, 109-118.
37. Moriguchi, I., Canada, Y., & Komatsu, K. (1976). van der Waals volume and the related parameters for hydrophobicity in structure-activity studies. Chemical & Pharmaceutical Bulletin, 24(8), 1799-1806. doi:10.1248/cpb.24.1799
38. Mulliken, R. S. (1955). Electronic population analysis on LCAO-MO molecular wave functions. I. The Journal of Chemical Physics, 23(10), 1833-1840. doi:10.1063/1.1740588
39. Overton, C. E. (1901). Studien uber die narkose': Zugleich ein beitrag zur allgemeinen pharmakologie. Jena, Germany: Verlag von Gustav Fischer.
40. Pal, D. K., Purkayastha, S. K., Sengupta, C., & De, A. U. (1992). Quantitative structure-property relationships with TAU indices: Part I-Research octane numbers of alkane fuel molecules. Indian Journal of Chemistry, 31B, 109-114.
41. Pal, D. K., Sengupta, C., & De, A. U. (1988). A new topochemical descriptor (TAU) in molecular connectivity concept: Part I - Aliphatic compounds. Indian Journal of Chemistry, 27B, 734-739.
42. Pal, D. K., Sengupta, C., & De, A. U. (1989). Introduction of a novel topochemical index and exploitation of group connectivity concept to achieve predictability in QSAR and RDD. Indian Journal of Chemistry, 28B, 261-267.
43. Pal, D. K., Sengupta, M., Sengupta, C., & De, A. U. (1990). QSAR with TAU (τ) indices: Part I - Polymethylene primary diamines as amebicidal agents. Indian Journal of Chemistry, 29B, 451-454.
44. Pal, P., Mitra, I., & Roy, K. (2014). QSPR modeling of odor threshold of aliphatic alcohols using extended topochemical atom (ETA) indices. Croatica Chemica Acta, 87(1), 29-37. doi:10.5562/cca2284
45. Pauling, L. (1939). The nature of the chemical bond. Ithaca, NY: Cornell University Press.
46. Platt, J. R. (1947). Influence of neighbor bonds on additive bond properties in paraffins. Journal de Chimie Physique, 15, 419-420.
47. Plavšić, D., Nikolić, S., Trinajstić, N., & Mihalić, Z. (1993). On the Harary index for the characterization of chemical graphs. Journal of Mathematical Chemistry, 12(1), 235-250. doi:10.1007/BF01164638
48. Pramanik, S., & Roy, K. (2014). Modeling bioconcentration factor (BCF) using mechanistically interpretable descriptors computed from open source tool "PaDEL-Descriptor". Environmental Science and Pollution Research International, 21(4), 2955-2965. doi:10.1007/s11356-013-2247-z PMID:24170502
49. Randić, M. (1975). On characterization of molecular branching. Journal of the American Chemical Society, 97(23), 6609-6615. doi:10.1021/ja00856a001
50. Ray, S., & Roy, K. (2013). Modeling adsorption of organic compounds on activated carbon using ETA indices. Chemical Engineering Science, 104, 427-438. doi:10.1016/j.ces.2013.09.018
51. Richardson, B. J. (1869). Physiological research on alcohols. The Medical Times and Gazzette, 2, 703-706.
52. Richet, C. (1893). On the relationship between the toxicity and the physical properties of substances. Comptes Rendus Société Biologie, 5, 775-776.
53. Rohrbaugh, R. H., & Jurs, P. C. (1987). Descriptions of molecular shape applied in studies of structure/ activity and structure/property relationships. Analytica Chimica Acta, 199, 99-109. doi:10.1016/S0003-2670(00)82801-9
54. Roy, K., & Das, R. N. (2010). QSTR with extended topochemical atom (ETA) indices. 14. QSAR modeling of toxicity of aromatic aldehydes to Tetrahymena pyriformis. Journal of Hazardous Materials, 183(1-3), 913-922. doi:10.1016/j.jhazmat.2010.07.116 PMID:20739120
55. Roy, K., & Das, R. N. (2011a). On some novel extended topochemical atom (ETA) parameters for effective encoding of chemical information and modeling of fundamental physicochemical properties. SAR and QSAR in Environmental Research, 22(5-6), 451-472. doi:10.1080/1062936X.2011.569900 PMID:21598192
56. Roy, K., & Das, R. N. (2011b). On extended topochemical atom (ETA) indices for QSPR studies. In E. A. Castro & A. K. Hagi (Eds.), Advanced methods and applications in chemoinformatics: Research progress and new applications (pp. 380-411). Hershey, PA: IGI Global.
57. Roy, K., & Das, R. N. (2012). QSTR with extended topochemical atom (ETA) indices. 15. Development of predictive models for toxicity of organic chemicals against fathead minnow using second generation ETA indices. SAR and QSAR in Environmental Research, 23(1-2), 125-140. doi:10.1080/106293 6X.2011.645872 PMID:22292780
58. Roy, K., & Das, R. N. (2013). QSTR with extended topochemical atom (ETA) indices. 16. Development of predictive classification and regression models for toxicity of ionic liquids towards Daphnia magna. Journal of Hazardous Materials, 254-255, 166-178. doi:10.1016/j.jhazmat.2013.03.023 PMID:23608063
59. Roy, K., & Ghosh, G. (2003). Introduction of extended topochemical atom (ETA) Indices in the valence electron mobile (VEM) environment as tools for QSAR/QSPR studies. Internet Electronic Journal of Molecular Design, 2(9), 599-620.
60. Roy, K., & Ghosh, G. (2004a). QSTR with extended topochemical atom indices. 2. Fish toxicity of substituted benzenes. Journal of Chemical Information and Computer Sciences, 44(2), 559-567. doi:10.1021/ ci0342066 PMID:15032536
61. Roy, K., & Ghosh, G. (2004b). QSTR with extended topochemical atom indices. 3. Toxicity of nitrobenzenes to Tetrahymena pyriformis. QSAR & Combinatorial Science, 23(2-3), 99-108. doi:10.1002/ qsar.200330864
62. Roy, K., & Ghosh, G. (2004c). QSTR with extended topochemical atom indices. 4. Modeling of the acute toxicity of phenylsulfonyl carboxylates to Vibrio fischeri using principal component factor analysis and principal component regression analysis. QSAR & Combinatorial Science, 23(7), 526-535. doi:10.1002/ qsar.200430891
63. Roy, K., & Ghosh, G. (2005). QSTR with extended topochemical atom indices. Part 5. Modeling of the acute toxicity of phenylsulfonyl carboxylates to Vibrio fischeri using genetic function approximation. Bioorganic & Medicinal Chemistry, 13(4), 1185-1194. doi:10.1016/j.bmc.2004.11.014 PMID:15670927
64. Roy, K., & Ghosh, G. (2006a). QSTR with extended topochemical atom (ETA) indices. VI. Acute toxicity of benzene derivatives to tadpoles (Rana japonica). Journal of Molecular Modeling, 12(3), 306-316. doi:10.1007/s00894-005-0033-7 PMID:16249936
65. Roy, K., & Ghosh, G. (2006b). QSTR with extended topochemical atom (ETA) indices. 8. QSAR for the inhibition of substituted phenols on germination rate of Cucumis sativus using chemometric tools. QSAR & Combinatorial Science, 25(10), 846-859. doi:10.1002/qsar.200510211
66. Roy, K., & Ghosh, G. (2007). QSTR with extended topochemical atom (ETA) indices. 9. Comparative QSAR for the toxicity of diverse functional organic compounds to Chlorella vulgaris using chemometric tools. Chemosphere, 70(1), 1-12. doi:10.1016/j.chemosphere.2007.07.037 PMID:17765287
67. Roy, K., & Ghosh, G. (2008). QSTR with extended topochemical atom indices. 10. Modeling of toxicity of organic chemicals to humans using different chemometric tools. Chemical Biology & Drug Design, 72(5), 383-394. doi:10.1111/j.1747-0285.2008.00712.x PMID:19012574
68. Roy, K., & Ghosh, G. (2009a). QSTR with extended topochemical atom (ETA) indices. 11. Comparative QSAR of acute NSAID cytotoxicity in rat hepatocytes using chemometric tools. Molecular Simulation, 35(8), 648-659. doi:10.1080/08927020902744664
69. Roy, K., & Ghosh, G. (2009b). QSTR with extended topochemical atom (ETA) indices. 12. QSAR for the toxicity of diverse aromatic compounds to Tetrahymena pyriformis using chemometric tools. Chemosphere, 77(7), 999-1009. doi:10.1016/j.chemosphere.2009.07.072 PMID:19709717
70. Roy, K., & Ghosh, G. (2009c). QSTR with extended topochemical atom (ETA) Indices. 13. Modeling of hERG K+ channel blocking activity of diverse functional drugs using different chemometric tools. Molecular Simulation, 35(15), 1256-1268. doi:10.1080/08927020903015379
71. Roy, K., & Ghosh, G. (2010). Exploring QSARs with extended topochemical atom (ETA) indices for modeling chemical and drug toxicity. Current Pharmaceutical Design, 16(24), 2625-2639. doi:10.2174/138161210792389270 PMID:20642426
72. Roy, K., & Kabir, H. (2012a). QSPR with extended topochemical atom (ETA) indices. Modeling of critical micelle concentration of non-ionic surfactants. Chemical Engineering Science, 73, 86-98. doi:10.1016/j.ces.2012.01.005
73. Roy, K., & Kabir, H. (2012b). QSPR with extended topochemical atom (ETA) indices. 3. Modeling of critical micelle concentration of cationic surfactants. Chemical Engineering Science, 81, 169-178. doi:10.1016/j.ces.2012.07.008
74. Roy, K., & Kabir, H. (2013). QSPR with extended topochemical atom (ETA) indices. Exploring effects of hydrophobicity, branching and electronic parameters on logCMC values of anionic surfactants. Chemical Engineering Science, 87, 141-151. doi:10.1016/j.ces.2012.10.002
75. Roy, K., Pal, D. K., De, A. U., & Sengupta, C. (1999). Comparative QSAR studies with molecular negentropy, molecular connectivity, STIMS and TAU indices: Part I - tadpole narcosis of diverse functional acyclic compounds. Indian Journal of Chemistry, 38B, 664-671.
76. Roy, K., Pal, D. K., De, A. U., & Sengupta, C. (2001). Comparative QSAR studies with molecular negentropy, molecular connectivity, STIMS and TAU indices: Part II- General anaesthetic activity of aliphatic hydrocarbons, halocarbons and ethers. Indian Journal of Chemistry, 40B, 129-135.
77. Roy, K., & Saha, A. (2003a). Comparative QSPR studies with molecular connectivity, molecular negentropy and TAU indices part I: Molecular thermochemical properties of diverse functional acyclic compounds. Journal of Molecular Modeling, 9(4), 259-270. doi:10.1007/s00894-003-0135-z PMID:12827454
78. Roy, K., & Saha, A. (2003b). Comparative QSPR studies with molecular connectivity, molecular negentropy and TAU indices. Part 2. Lipid-water partition coefficient of diverse functional acyclic compounds. Internet Electronic Journal of Molecular Design, 2, 288-305.
79. Roy, K., & Saha, A. (2003c). QSPR with TAU indices: Water solubility of diverse functional acyclic compounds. Internet Electronic Journal of Molecular Design, 2, 475-491.
80. Roy, K., & Saha, A. (2005). QSPR with TAU indices: Molar refractivity of diverse functional acyclic compounds. Indian Journal of Chemistry, 44B, 1693-1707.
81. Roy, K., & Sanyal, I. (2006). QSTR with extended topochemical atom indices. 7. QSAR of substituted benzenes to Saccharomyces cerevisiae. QSAR & Combinatorial Science, 25(4), 359-371. doi:10.1002/ qsar.200530172
82. Roy, K., Sanyal, I., & Ghosh, G. (2006a). QSPR of n-octanol/water partition coefficient of nonionic organic compounds using extended topochemical atom (ETA) indices. QSAR & Combinatorial Science, 26(5), 629-646. doi:10.1002/qsar.200610112
83. Roy, K., Sanyal, I., & Roy, P. P. (2006b). QSPR of the bioconcentration factors of non-ionic organic compounds in fish using extended topochemical atom (ETA) indices. SAR and QSAR in Environmental Research, 17(6), 563-582. doi:10.1080/10629360601033499 PMID:17162387
84. Sanderson, R. T. (1952). Electronegativity I. Orbital electronegativity of neutral atoms. Journal of Chemical Education, 29, 540-546.
85. Schultz, H. P. (1989). Topological organic chemistry. 1. Graph theory and topological indices of alkanes. Journal of Chemical Information and Computer Sciences, 29(3), 227-228. doi:10.1021/ci00063a012
86. Schuur, J., Selzer, P., & Gasteiger, J. (1996). The coding of the three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity. Journal of Chemical Information and Computer Sciences, 36(2), 334-344. doi:10.1021/ci950164c
87. Seidell, A. (1912). A new bromine method for the determination of thymol, salicylates, and similar compounds. Am. Chem. J, 47, 508-526.
88. Simon, Z. (1974). Specific interactions. Intermolecular forces, steric requirements, and molecular size. Angewandte Chemie International Edition in English, 13(11), 719-727. doi:10.1002/anie.197407191
89. Stankevich, I. V., Skovortsova, M. I., & Zefirov, N. S. (1995). On a quantum chemical interpretation of molecular connectivity indices for conjugated hydrocarbons. Journal of Molecular Structure THEOCHEM, 342, 173-179. doi:10.1016/0166-1280(95)90111-6
90. Stanton, D. T., & Jurs, P. C. (1990). Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies. Analytical Chemistry, 629(21), 2323-2329. doi:10.1021/ac00220a013
91. Sylvester, J. J. (1878). Chemistry and algebra. Nature, 17(432), 284-284. doi:10.1038/017284a0
92. Taft, R. W. Jr. (1952). Polar and steric substituent constants for aliphatic and o-benzoate groups from rates of esterification and hydrolysis of esters. Journal of the American Chemical Society, 74(12), 3120-3128. doi:10.1021/ja01132a049
93. Todeschini, R., & Consonni, V. (2000). Handbook of molecular descriptors. Weinheim, Germany: Wiley-VCH. doi:10.1002/9783527613106
94. Todeschini, R., Lasagni, M., & Marengo, E. (1994). New molecular descriptors for 2D- and 3Dstructures. Theory. Journal of Chemometrics, 8(4), 263-273. doi:10.1002/cem.1180080405
95. Traube, J. (1904). Theorie der osmose and narkose. Archiv für die gesamte Physiologie des Menschen und der Tiere, 105(11-12), 541-558.
96. Verloop, A. (1987). The STERIMOL approach to drug design. New York: Marcel Dekker.
97. Wiener, H. (1947). Structural determination of paraffin boiling points. Journal of the American Chemical Society, 69(1), 17-20. doi:10.1021/ja01193a005 PMID:20291038
98. Wigner, E. P. (1960). The unreasonable effectiveness of mathematics in the natural sciences. Richard courant lecture in mathematical sciences delivered at New York University, May 11, 1959. Communications on Pure and Applied Mathematics, 13(1), 1-14. doi:10.1002/cpa.3160130102
99. Yap, C. W. (2011). PaDEL-Descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry, 32(7), 1466-1474. doi:10.1002/jcc.21707 PMID:21425294