Добавил:
Sekretar
kiopkiopkiop18@yandex.ru
t.me/Prokururor I Вовсе не секретарь, но почту проверяю
Опубликованный материал нарушает ваши авторские права? Сообщите нам.
Вуз:
Предмет:
Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5345_Библиотеки_им_академика_М_И_Перельмана.pdf

The “ETA” Indices in QSAR/QSPR/QSTR Research
branchedness, polarity, electronegative, electron-richness and hydrogen bonding property and also consider
contribution of active hydrogen atoms. So, the ETA indices consider more than just graph theoretical
aspects, employing detailed information on the atoms, bonds and the connectivity therein. Technically it
will be difficult to assume any single descriptor to encode universal chemical features. Different aspects
of chemical information are expressed in modeling different endpoints. In other words, endpoint like
aqueous solubility or partition coefficient can be explained by molecular size, branchedness or hydrogen
bonding aspects while electronic features and polarity information of a molecule may be of importance
while developing predictive models against molar refractivity. The ETA formalism attempts to provide
a platform of different chemical attributes so as to enable the designer with broader choice of predictor
variables within a single category (Roy & Das, 2011b; Roy & Ghosh, 2010). The ETA parameters are
also appended with dynamic chemical foundation suitable for deriving mechanistic basis. Moreover, all
the studies performed till date using the ETA indices infer that they contain sufficient diagnostic potential
for the development of predictive quantitative models for various classes of chemicals namely aliphatic
compounds, aromatic compounds, agrochemicals, drugs and pharmaceuticals, ionic liquids etc. encompassing industrial, laboratory and house hold usage. Like every successful innovation walks through
the development of new ideas and concepts, the ETA indices have followed a path of novel chemical
exploration and we shall look forward to more nourishment of enriched chemical information in future.
REFERENCES
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
Balaban, A. T. (1982). Highly discriminating distance based topological index. Chemical Physics Let-
ters, 89(5), 399–404. doi:10.1016/0009-2614(82)80009-2
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
Cayley, A. (1875). On the analytical forms called trees. American Journal of Mathematics, 4(1), 266–268.
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
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
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
Cros, A. F. A. (1863, January 9). Action de l’alcohol amylique sur l’organisme. Faculty of Medicine,
University of Strasbourg.
76
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use

The “ETA” Indices in QSAR/QSPR/QSTR Research
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
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
Dalton, J. (1808). New system of chemical philosophy. London: Chembridge Press.
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.
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
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
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
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
Dragon Version 6 TALETE srl, Italy. (2010). Retrieved April 30, 2014, http://www.talete.mi.it/products/
dragon_description.htm
Euler, L. (1736). Solutio problematis ad geometriam situs pertinentis. Commentarii Academiae Scien-
tiarum Imperialis Petropolitanae, 8, 128–140.
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
Fischer, N. W. (1974). Kekulé and organic classification. Ambix, 21(1), 29–52. doi:10.1179/
amb.1974.21.1.29
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
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
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
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
77

The “ETA” Indices in QSAR/QSPR/QSTR Research
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
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
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
Hammett, L. P. (1935). Some relations between reaction rates and equilibrium constants. Chemical
Reviews, 17(1), 125–136. doi:10.1021/cr60056a010
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
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
Higgins, W. A. (1789). Comparative view of the phlogistic and antiphlogistic theories. London: J. Murray.
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
Kier, L. B., & Hall, L. H. (1986). Molecular connectivity in structure-activity analysis. Chichester, UK:
Research Studies Press–John Wiley & Sons Ltd.
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
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
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
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.
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
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
Overton, C. E. (1901). Studien uber die narkose’: Zugleich ein beitrag zur allgemeinen pharmakologie.
Jena, Germany: Verlag von Gustav Fischer.
78
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use

The “ETA” Indices in QSAR/QSPR/QSTR Research
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.
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.
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
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.
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
Pauling, L. (1939). The nature of the chemical bond. Ithaca, NY: Cornell University Press.
Platt, J. R. (1947). Influence of neighbor bonds on additive bond properties in paraffins. Journal de
Chimie Physique, 15, 419–420.
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
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
Randić, M. (1975). On characterization of molecular branching. Journal of the American Chemical
Society, 97(23), 6609–6615. doi:10.1021/ja00856a001
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
Richardson, B. J. (1869). Physiological research on alcohols. The Medical Times and Gazzette, 2, 703–706.
Richet, C. (1893). On the relationship between the toxicity and the physical properties of substances.
Comptes Rendus Société Biologie, 5, 775–776.
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
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
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
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
79

The “ETA” Indices in QSAR/QSPR/QSTR Research
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.
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
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
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.
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
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
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
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
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
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
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
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
80
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use

The “ETA” Indices in QSAR/QSPR/QSTR Research
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
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. Che-
mosphere, 77(7), 999–1009. doi:10.1016/j.chemosphere.2009.07.072 PMID:19709717
Roy, K., & Ghosh, G. (2009c). QSTR with extended topochemical atom (ETA) Indices. 13. Modeling
+
channel blocking activity of diverse functional drugs using different chemometric tools.
Molecular Simulation, 35(15), 1256–1268. doi:10.1080/08927020903015379
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
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
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
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
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.
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.
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
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.
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.
Roy, K., & Saha, A. (2005). QSPR with TAU indices: Molar refractivity of diverse functional acyclic
compounds. Indian Journal of Chemistry, 44B, 1693–1707.
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
81

The “ETA” Indices in QSAR/QSPR/QSTR Research
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
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
Roy, K., Sanyal, I., & Roy, P. P. (2006b). QSPR of the bioconcentration factors of non-ionic organic
Research, 17(6), 563–582. doi:10.1080/10629360601033499 PMID:17162387
Sanderson, R. T. (1952). Electronegativity I. Orbital electronegativity of neutral atoms. Journal of
Chemical Education, 29, 540–546.
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
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
Seidell, A. (1912). A new bromine method for the determination of thymol, salicylates, and similar
compounds. Am. Chem. J., 47, 508–526.
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
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 THEO-
CHEM, 342, 173–179. doi:10.1016/0166-1280(95)90111-6
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
Sylvester, J. J. (1878). Chemistry and algebra. Nature, 17(432), 284–284. doi:10.1038/017284a0
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
Todeschini, R., & Consonni, V. (2000). Handbook of molecular descriptors. Weinheim, Germany:
Wiley-VCH. doi:10.1002/9783527613106
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
Traube, J. (1904). Theorie der osmose and narkose. Archiv für die gesamte Physiologie des Menschen
und der Tiere, 105(11−12), 541−558.
82
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use

The “ETA” Indices in QSAR/QSPR/QSTR Research
Verloop, A. (1987). The STERIMOL approach to drug design. New York: Marcel Dekker.
Wiener, H. (1947). Structural determination of paraffin boiling points. Journal of the American Chemi-
cal Society, 69(1), 17–20. doi:10.1021/ja01193a005 PMID:20291038
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. Communica-
tions on Pure and Applied Mathematics, 13(1), 1–14. doi:10.1002/cpa.3160130102
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
KEY TERMS AND DEFINITIONS
2D-Descriptor: A method where the considered chemical information corresponds to two-dimensional
geometry of the molecule.
Chemical Graphs: A method of presenting chemical structures using a “hydrogen-suppressed”
molecular skeleton where ‘atoms’ are denoted by ‘vertices’ and ‘bonds’ are represented by ‘edges’.
Descriptor: A numerical quantity for the depiction of molecular structure using a suitable algorithm.
Used as predictor variables in QSAR modeling analysis.
Extended Topochemical Atom (ETA) Indices: Indices where the topological information has been
enriched using suitable electronic, heteroatom count & type, hydrogen-bonding and other essential
chemical attributes. These are used as descriptors in QSAR modeling.
Hydrogen-Suppressed: A graph theoretical method of representing chemical structures where the
hydrogen atoms attached to carbon and other atoms are not shown. Also termed as hydrogen-depleted.
QSAR Analysis: A method of developing mathematical correlation between a response and descriptors, i.e., predictor variables for a series of chemical data.
Topology: A method assessing chemical structures using distance and connectivity information
considering hydrogen-suppressed molecular graph. The distance corresponds to minimum path between
vertices.
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
83

84
Chapter 3
Evolution of Multivariate
Image Analysis in QSAR:
The Case for a Neglected Disease
Matheus P. Freitas
Federal University of Lavras, Brazil
Mariene H. Duarte
Federal University of Lavras, Brazil
ABSTRACT
Multivariate Image Analysis applied in Quantitative Structure-Activity Relationship (MIA-QSAR) is
a simple method to achieve, at least in a variety of examples, QSAR models with predictive abilities
comparable to those of sophisticated tridimensional methodologies. MIA-QSAR is based on the correlation between properties (e.g. biological activities) and chemical descriptors, which are pixels of
images representing chemical structures in a congeneric series of molecules. The MIA-QSAR approach
has been improved since its creation, in 2005, both in terms of data analysis and development of more
descriptive information. This chapter reports the MIA-QSAR method, including its augmented version,
named aug-MIA-QSAR because of the introduction of new dimensions to better encode atomic properties.
In addition, the application to a case study illustrates the main practical differences between traditional
and augmented MIA-QSAR. The use of a neglected disease as example represents a challenge in QSAR,
which is particularly focused on diseases with higher economical appearance.
INTRODUCTION
Quantitative structure-activity relationship (QSAR) methods have shown to be powerful tools to comprehend the action mechanisms and structural profiles required to improve a drug performance, as well as
to estimate the bioactivity of a non-existing, proposed drug candidate. QSAR approaches are genuinely
structure-based methods, in which biological properties are reflected by structural changes in molecules,
despite the receptor information included in the modern multidimensional QSAR techniques. However,
traditional QSAR, which is based on descriptors easily accessible or calculated, such as logP, connectiv-
DOI: 10.4018/978-1-4666-8136-1.ch003
Copyright © 2015, IGI Global. Copying or distributing in print or electronic forms without written permission of IGI Global is prohibited.
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use

Evolution of Multivariate Image Analysis in QSAR
ity indices and a variety of other parameters derived from the 2D structure of a molecule, is not inferior
to methods based on the three-dimensional molecular structure, at least in many practical cases (Brown
& Martin, 1997; Estrada, Molina, & Perdomo-López, 2001).
Multivariate image analysis applied in QSAR (MIA-QSAR) appeared to correlate drawings of molecular structures with the corresponding biological activities (Freitas, Brown, & Martins, 2005); therefore,
it is essentially a 2D QSAR technique, since descriptors are obtained from the projection of a molecule
in the plane. The structural changes in a congeneric series of drug-like compounds explain the variance
in the bioactivities block; in MIA-QSAR, structural changes correspond to different coordinates of the
pixels composing the molecular drawings. Because the substitution pattern along with the congeneric
series of compounds is captured in the calibration step, usually performed using partial least squares
(PLS) regression, prediction of the bioactivities of similar compounds are often feasible. However, much
chemical information is lost when a given substituent is represented as letters in the drawings, although
other molecular properties, such as steric effects (e.g. for large side chains) and shape (e.g. the hexagonal
benzene ring), are appropriately encoded. For instance, the MIA-QSAR model is capable of recognizing that a bromine substituent bonded to a given aromatic carbon causes an effect on the bioactivity of
a molecular scaffold, but its description as “Br” in the drawing does not have chemical meaning. Thus,
an augmented version for the MIA-QSAR method (aug-MIA-QSAR) was developed by introducing
“dimensions” to better encode atomic sizes (using spheres with sizes proportional to the van der Waals
radii) and different types of atoms (using spheres with different colors) in a molecule (Nunes & Freitas,
2013). Because aug-MIA-QSAR has been recently implemented, there are many challenges to improve
its predictive ability, as well as its chemical interpretation; research directions include testing regression
and variable selection methods for the aug-MIA descriptors, and also searching for ways to indicate how
different atomic sizes and colors impact the trends in bioactivity in a series of drug-like compounds.
QSAR methods have been used in numerous studies in order to find a correlation between
chemical structures and biological activities related to profitable diseases, such as obesity, sexual
dysfunction and hypertension. Nevertheless, little attention has been devoted to neglected diseases,
which mostly affect poor people from the third world, being forgotten by the big pharmaceutical
companies (Ramalho, Freitas, & da Cunha, 2012). This chapter describes the development of a
variety of QSAR methods during decades, focusing on the MIA-based approaches, which is demonstrated here to a set of thiosemicarbazones as anti-Trypanosoma cruzi agents (Garkani-Nejad &
Ahmadi-Roudi, 2010). The efficacy of the current chemotherapy against T. cruzi is quite variable in
different regions of high endemicity, because the high biological, biochemical and genetic diversity
of T. cruzy strains (Zingales et al., 2009). Thus, the development of drugs based upon the structural
optimization of existing compounds, such as the Nifuroxazide, is advantageous, considering time
and efforts consumption.
Background
QSAR methods are based on the possibility of the bioactivity (or any other property) in being a function
of the molecular structure, that is bioactivity = f(structure), in which the structure is represented by mo-
lecular parameters called descriptors. This aims at planning new substances with improved therapeutic
profile. Therefore, this research field is expected to be of general interest, because the use of QSAR
methods avoids exhaustive exploratory syntheses, since these methods enable designing molecules with
well-defined properties, reducing time and costs during the drug development.
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
85
Соседние файлы в папке Библиотека им академика М.И. Перельмана
