Добавил:
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_5587_Библиотеки_им_академика_М_И_Перельмана.pdf
Скачиваний:
0
Добавлен:
31.08.2026
Размер:
34 Мб
Скачать
Evolution of Multivariate Image Analysis in QSAR
Bro, R. (1996). Multiway calibration: Multilinear PLS. Journal of Chemometrics, 10(1), 47–61. doi:10.1002/(SICI)1099-128X(199601)10:1<47::AID-CEM400>3.0.CO;2-C
Bro, R. (1997). PARAFAC: Tutorial and applications. Chemometrics and Intelligent Laboratory Systems, 38(2), 149–171. doi:10.1016/S0169-7439(97)00032-4
Brown, R. D., & Martin, Y. C. (1997). The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. Journal of Chemical Information and Computer Sciences, 37(1), 1–9. doi:10.1021/ci960373c
Chirico, N., & Gramatica, P. (2012). Real external predictivity of QSAR models. Part 2. New inter­comparable thresholds for different validation criteria and the need for scatter plot inspection. Journal of Chemical Information and Modeling, 52(8), 2044–2058. doi:10.1021/ci300084j PMID:22721530
Cormanich, R., Nunes, C. A., & Freitas, M. P. (2012). Chemical drawings correlate to biological proper­ties: MIA-QSAR. Quimica Nova, 35, 1157–1163. doi:10.1590/S0100-40422012000600017
Cormanich, R. A., Goodarzi, M., & Freitas, M. P. (2009). Improvement of multivariate image analy­sis applied to quantitative structure–activity relationship (QSAR) analysis by using wavelet-principal component analysis ranking variable selection and least-squares support vector machine regression: QSAR study of checkpoint kinase WEE1 inhibitors. Chemical Biology & Drug Design, 73(2), 244–252. doi:10.1111/j.1747-0285.2008.00764.x PMID:19207427
Cramer, R. D., 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
Crum-Brown, A., & Fraser, T. R. (1869). On the connection between chemical constitution and physi­ological action. Part 1: On the physiological action of the ammonium bases derived from Strychia, Brucia, Thebia, Codeia, Morphia, and Nicotia. Transactions of the Royal Society of Edinburgh, 25, 257–274.
Davis, L. (Ed.). (1991). Handbook of genetic algorithms. London: Van Nostrand-Reinhold.
Deeb, O., Alfalah, S., Freitas, M. P., da Cunha, E. F. F., & Ramalho, T. C. (2012). Exploring MIA-QSARs for farnesyltransferase inhibitory effect of antimalarial compounds refined by docking simulations. Journal of Biophysical Chemsitry, 3(01), 58–71. doi:10.4236/jbpc.2012.31008
Dennington, R. D., II, Keith, T. A., & Millam, J. M. (2008). GaussView 5.0. Wallingford.
Du, X., Guo, C., Hansell, E., Doyle, P. S., Caffrey, C. R., & Holler, T. P. etal. (2002). Synthesis and structure-activity relationship study of potent trypanocidal thio semicarbazone inhibitors of the trypano­somal cysteine protease cruzain. Journal of Medicinal Chemistry, 45(13), 2695–2707. doi:10.1021/ jm010459j PMID:12061873
Estrada, E., Molina, E., & Perdomo-López, I. (2001). Can 3D structural parameters be predicted from 2D (topological) molecular descriptors? Journal of Chemical Information and Computer Sciences, 41(4), 1015–1021. doi:10.1021/ci000170v PMID:11500118
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), 387–404. doi:10.1098/rspb.1939.0030
116
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
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
Freitas, M. P. (2006). MIA-QSAR modelling of anti-HIV-1 activities of some 2-amino-6-arylsulfonylben­zonitriles and their thio and sulfinyl congeners. Organic & Biomolecular Chemistry, 4(6), 1154–1159. doi:10.1039/b516396j PMID:16525561
Freitas, M. P., Brown, S. D., & Martins, J. A. (2005). MIA-QSAR: A simple 2D image-based approach for quantitative structure-activity relationship analysis. Journal of Molecular Structure, 738(1-3), 149–154.
Freitas, M. P., da Cunha, E. F. F., Ramalho, T. C., & Goodarzi, M. (2008). Multimode methods applied on MIA descriptors in QSAR. Current Computer-aided Drug Design, 4(4), 273–282. doi:10.2174/157340908786786038
Freitas, M. P., & Ramalho, T. C. (2013). Employing conformational analysis in the molecular modeling of agrochemicals: Insights on QSAR parameters of 2,4-D. Ciência & Agrotecnologia, 37(6), 485–494. doi:10.1590/S1413-70542013000600001
Freitas, M. P., & Rittner, R. (2008). MIA-QSAR as an alternative approach for modeling some antifun­gals. QSAR & Combinatorial Science, 27(5), 582–585. doi:10.1002/qsar.200710047
Garkani-Nejad, Z., & Ahmadi-Roudi, B. (2010). Modeling the antileishmanial activity screening of 5-nitro-2-heterocyclic benzylidene hydrazides using different chemometrics methods. European Journal of Medicinal Chemistry, 45(2), 719–726. doi:10.1016/j.ejmech.2009.11.019 PMID:19959260
2
Golbraikh, A., & Tropsha, A. (2002). Beware of q
! Journal of Molecular Graphics & Modelling, 20(4),
269–276. doi:10.1016/S1093-3263(01)00123-1 PMID:11858635
Goodarzi, M., da Cunha, E. F. F., Freitas, M. P., & Ramalho, T. C. (2010). QSAR and docking studies of novel antileishmanial diaryl sulfides and sulfonamides. European Journal of Medicinal Chemistry, 45(11), 4879–4889. doi:10.1016/j.ejmech.2010.07.060 PMID:20728249
Goodarzi, M., & Freitas, M. P. (2009). Prediction of electrophoretic enantioseparation of aromatic amino acids/esters through MIA-QSPR. Separation and Purification Technology, 68(3), 363–366. doi:10.1016/j. seppur.2009.06.005
Goodarzi, M., Freitas, M. P., & Ferreira, E. B. (2009). Influence of changes in 2-D chemical structure drawings and image formats on the prediction of biological properties using MIA-QSAR. QSAR & Combinatorial Science, 28(4), 458–464. doi:10.1002/qsar.200810146
Goodarzi, M., Freitas, M. P., & Jensen, R. (2009). Ant colony optimization as a feature selection method in the QSAR modeling of anti-HIV-1 activities of 3-(3,5-dimethylbenzyl)uracil derivatives using MLR, PLS and SVM regressions. Chemometrics and Intelligent Laboratory Systems, 98(2), 123–129. doi:10.1016/j.chemolab.2009.05.005
Goodarzi, M., Freitas, M. P., & Jensen, R. (2009). Feature selection and linear/nonlinear regression methods for the accurate prediction of glycogen synthase kinase-3β inhibitory activities. Journal of Chemical Information and Modeling, 49(4), 824–832. doi:10.1021/ci9000103 PMID:19338295
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
117
Evolution of Multivariate Image Analysis in QSAR
Guimarães, M. C., Silva, D. G., da Mota, E. G., da Cunha, E. F. F., & Freitas, M. P. (2014). Computer­assisted design of dual-target anti-HIV-1 compounds. Medicinal Chemistry Research, 23(3), 1548–1558. doi:10.1007/s00044-013-0765-3
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
Hopfinger, A. J., Wang, S., Tokarski, J. S., Jin, B., Albuquerque, M., Madhav, P. J., & Duraiswami, C. (1997). Construction of 3D-QSAR Models Using the 4D-QSAR Analysis Formalism. Journal of Me- dicinal Chemistry, 119, 10509–10524.
Jana, G. A., Delgado, E. J., & Medina, F. E. (2014). How important is the synclinal conformation of sulfonylureas to explain the inhibition of AHAS: A theoretical study. Journal of Chemical Information and Modeling, 54(3), 926–932. doi:10.1021/ci400721y PMID:24548139
Jensen, R. (2006). Studies in computational intelligence (A. Abraham, C. Grosan, & V. Ramos, Eds.). Heidelberg: Springer.
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 4–25. doi:10.1016/S0169-409X(96)00423-1 PMID:11259830
Lozano, N. B. H., Maltarollo, V. G., Weber, K. C., Honorio, K. M., Guido, R. V. C., Andricopulo, A. D., & da Silva, A. B. F. (2012). Molecular features for antitrypanosomal activity of thiosemicarba­zones revealed by OPS-PLS QSAR studies. Medicinal Chemistry (Shariqah, United Arab Emirates), 8, 1045–1056. PMID:22779790
Martin, Y. C. (2009). Let’s not forget tautomers. Journal of Computer-Aided Molecular Design, 23(10), 693–704. doi:10.1007/s10822-009-9303-2 PMID:19842045
Meyer, H. H. (1899). On the theory of alcohol narcosis: First communication. Which property determines its narcotic effect? Archives of Experimental Pathology and Pharmacology, 42, 109–118. doi:10.1007/ BF01834479
Mitra, I., Saha, A., & Roy, K. (2010). Exploring quantitative structure–activity relationship studies of antioxidant phenolic compounds obtained from traditional Chinese medicinal plants. Molecular Simula- tion, 36(13), 1067–1079. doi:10.1080/08927022.2010.503326
Nunes, C. A., & Freitas, M. P. (2013). Introducing new dimensions in MIA-QSAR: A case for che­mokine receptor inhibitors. European Journal of Medicinal Chemistry, 62, 297–300. doi:10.1016/j. ejmech.2013.01.005 PMID:23357311
Ojha, P. K., Mitra, I., Das, R. N., & Roy, K. (2011). Further exploring r QSPR models. Chemometrics and Intelligent Laboratory Systems, 107(1), 194–205. doi:10.1016/j. chemolab.2011.03.011
Overton, E. (1901). Studien Uber die Narkose. Jena, Germany: Fischer.
118
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
2
metrics for validation of
m
Evolution of Multivariate Image Analysis in QSAR
Pan, D., Tseng, Y., & Hopfinger, A. J. (2003). Quantitative structure-based design: Formalism and application of receptor-dependent RD-4D-QSAR analysis to a set of glucose analogue inhibitors of glycogen phosphorylase. Journal of Chemical Information and Computer Sciences, 43(5), 1591–1607. doi:10.1021/ci0340714 PMID:14502494
Polanski, J. (2009). Receptor dependent multidimensional QSAR for modeling drug-receptor interactions. Current Medicinal Chemistry, 16(25), 3243–3257. doi:10.2174/092986709788803286 PMID:19548875
Ramalho, T. C., Freitas, M. P., & da Cunha, E. F. F. (Eds.). (2012). Chemoinformatics: Directions toward
Richet, M. C. (1893). Sur le rapport entre la toxicité et les propriétés physiques des corps. Comptes Rendus des Seances de la Société de Biologie et de ses Filiales, 45, 775–776.
Roy, K., Chakraborty, P., Mitra, I., Ojha, P. K., Kar, S., & Das, R. N. (2013). Some case studies on
2
application of “r
” metrics for judging quality of quantitative structure–activity relationship predic-
m
tions: Emphasis on scaling of response data. Journal of Computational Chemistry, 34(12), 1071–1082. doi:10.1002/jcc.23231 PMID:23299630
Roy, K., Mitra, I., Kar, S., Ojha, P. K., Das, R. N., & Kabir, H. (2012). Comparative studies on some metrics for external validation of QSPR models. Journal of Chemical Information and Modeling, 52(2), 396–408. doi:10.1021/ci200520g PMID:22201416
Roy, P. P., Paul, S., Mitra, I., & Roy, K. (2009). On two novel parameters for validation of predictive QSAR models. Molecules (Basel, Switzerland), 14(5), 1660–1701. doi:10.3390/molecules14051660 PMID:19471190
Selassie, C. D. (2003). Burger’s medicinal chemistry and drug discovery (D. J. Abraham, Ed.). New York: John Wiley & Sons.
Silva, D. G., Freitas, M. P., da Cunha, E. F. F., Ramalho, T. C., & Nunes, C. A. (2012). Rational design of small modified peptides as ACE inhibitors. Medicinal Chemistry Communications, 3(10), 1290–1293. doi:10.1039/c2md20214j
Teófilo, R. F., Martins, J. P. A., & Ferreira, M. M. C. (2009). Sorting variables by using informative vectors as a strategy for feature selection in multivariate regression. Journal of Chemometrics, 23(1), 32–48. doi:10.1002/cem.1192
Vedani, A., & Dobler, M. (2002). 5D-QSAR: The key for simulating induced fit? Journal of Medicinal Chemistry, 45(11), 2139–2149. doi:10.1021/jm011005p PMID:12014952
Vedani, A., Dobler, M., & Lill, M. A. (2005). Combining protein modeling and 6D-QSAR. Simulating the binding of structurally diverse ligands to the estrogen receptor. Journal of Medicinal Chemistry, 48(11), 3700–3703. doi:10.1021/jm050185q PMID:15916421
Whitley, D. (1994). A genetic algorithm tutorial. Statistics and Computing, 4(2), 65–85. doi:10.1007/ BF00175354
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
119
Evolution of Multivariate Image Analysis in QSAR
Zingales, B., Andrade, S. G., Briones, M. R. S., Campbell, D. A., Chiari, E., & Fernandes, O. etal. (2009). A new consensus for Trypanosoma cruzi intraspecific nomenclature: Second revision meeting recommends TcI to TcVI. Memorias do Instituto Oswaldo Cruz, 104(7), 1051–1054. doi:10.1590/S0074- 02762009000700021 PMID:20027478
ADDITIONAL READING
Charton, M. (1999). Advances in Molecular Structure Research. Greenwich: JAI Press.
Damale, M. G., Harke, S. N., Khan, F. A. K., Shinde, D. B., & Sangshetti, J. N. (2014). Recent advances in multidimensional QSAR (4D-6D): A critical review. Mini Reviews in Medicinal Chemistry, 14(1), 35–55. doi:10.2174/13895575113136660104 PMID:24195665
Esbensen, K., & Geladi, P. (1989). Strategy of multivariate image analysis (MIA). Chemometrics and Intelligent Laboratory Systems, 7(1-2), 67–86. doi:10.1016/0169-7439(89)80112-1
Esbensen, K. H., Hjelmen, K. H., & Kvaal, K. (1996). The AMT approach in chemometrics - first forays. Journal of Chemometrics, 10(5-6), 569–590. doi:10.1002/(SICI)1099-128X(199609)10:5/6<569::AID- CEM466>3.0.CO;2-W
Ferreira, M. M. C. (2002). Multivariate QSAR. Journal of the Brazilian Chemical Society, 13(6), 742–753. doi:10.1590/S0103-50532002000600004
Freitas, M. P. (2007). Multivariate QSAR: From classical descriptors to new perspectives. Current Computer-aided Drug Design, 3(4), 235–239. doi:10.2174/157340907782799408
Freitas, M. P. (2009). MIA-QSTR study of different organic compounds to Pimephales promelas. Me- dicinal Chemistry Research, 18(8), 648–655. doi:10.1007/s00044-008-9156-6
Freitas, M. R., Matias, S. V. B. G., Macedo, R. L., Freitas, M. P., & Venturin, N. (2013). Augmented multivariate image analysis applied to quantitative structure−activity relationship modeling of the phytotoxicities of benzoxazinone herbicides and related compounds on problematic weeds. Journal of Agricultural and Food Chemistry, 61(36), 8499–8503. doi:10.1021/jf4024257 PMID:23947385
Geladi, P., & Esbensen, K. (1991). Regression on multivariate images: Principal component regression for modeling, prediction and visual diagnostic tools. Journal of Chemometrics, 5(2), 97–111. doi:10.1002/ cem.1180050206
Geladi, P., & Grahn, H. (1996). Multivariate Image Analysis. Chichester: Wiley.
Geladi, P., & Kowalski, B. R. (1986). Partial least-squares regression: A tutorial. Analytica Chimica Acta, 185, 1–17. doi:10.1016/0003-2670(86)80028-9
Geladi, P., Wold, S., & Esbensen, K. (1986). Image analysis and chemical information in images. Ana- lytica Chimica Acta, 191, 473–480. doi:10.1016/S0003-2670(00)86335-7
120
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
Goodarzi, M., & Freitas, M. P. (2008). Predicting boiling points of aliphatic alcohols through multi­variate image analysis applied to quantitative structure-property relationships. The Journal of Physical Chemistry A, 112(44), 11263–11265. doi:10.1021/jp8059085 PMID:18841953
13
Goodarzi, M., Freitas, M. P., & Ramalho, T. C. (2009). Prediction of
C chemical shifts in methoxy­flavonol derivatives using MIA-QSPR. Spectrochimica Acta. Part A: Molecular Spectroscopy, 74(2), 563–568. doi:10.1016/j.saa.2009.07.003 PMID:19648055
Guimarães, M. C., da Mota, E. G., Silva, D. G., & Freitas, M. P. (2014). aug-MIA-QSPR modelling of the toxicities of anilines and phenols to Vibrio fischeri and Pseudokirchneriella subcapitata. Chemometrics and Intelligent Laboratory Systems, 134, 53–57. doi:10.1016/j.chemolab.2014.03.005
Hansch, C., & Leo, A. (1979). Substituent constants for correlation analysis in Chemistry and Biology. New York: Wiley.
Hansch, C., Leo, A., & Hoekman, D. (1979). Exploring QSAR. Hydrophobic, electronic, and steric constants. Washington: American Chemical Society.
Livingstone, D. J., & Salt, D. W. (2005). Judging the significance of multiple linear regression models. Journal of Medicinal Chemistry, 48(3), 661–663. doi:10.1021/jm049111p PMID:15689150
Maya, J. D., Cassels, B. K., Iturriaga-Vásquez, P., Ferreira, J., Faúndez, M., & Galanti, N. etal. (2007). Mode of action of natural and synthetic drugs against Trypanosoma cruzi and their interaction with the mammalian host. Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiol- ogy, 146(4), 601–620. doi:10.1016/j.cbpa.2006.03.004 PMID:16626984
Shahlaei, M. (2013). Descriptor selection methods in quantitative structure-activity relationship stud­ies: A review study. Chemical Reviews, 113(10), 8093–8103. doi:10.1021/cr3004339 PMID:23822589
Silla, J. M., Nunes, C. A., Cormanich, R. A., Guerreiro, M. C., Ramalho, T. C., & Freitas, M. P. (2011). MIA-QSPR and effect of variable selection on the modeling of kinetic parameters related to activities of modified peptides against dengue type 2. Chemometrics and Intelligent Laboratory Systems, 108(2), 146–149. doi:10.1016/j.chemolab.2011.06.009
Todeschini, R., Consonni, V., Mannhold, R., Kubinyi, H., & Timmerman, H. (2008). Handbook of Molecular Descriptors. Weinheim: Wiley-VCH.
Tropsha, A. (2010). Best practices for QSAR model development, validation, and exploration. Molecular informatics, 29, 476-488.
Wold, H. (1966). Multivariate Analysis (K. R. Krishnaiah, Ed.). New York: Academic Press.
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
121
Evolution of Multivariate Image Analysis in QSAR
KEY TERMS AND DEFINITIONS
logP: The logarithm of the octanol/water partition coefficient. It measures the hydrobobicity of a
substance and was the milestone parameter used in QSAR.
MIA: Multivariate image analysis. First explored by Paul Geladi (University of Umea) in hyperspec-
tral remote sensing analysis and further used in chemical applications.
PCA: Principal component analysis, a multivariate method widely used for pattern recongnition. It is
mathematically defined as an orthogonal linear transformation that transforms the data to a new coordinate system such that the greatest variance by some projection of the data comes to lie on the first coordinate (called the first principal component), the second greatest variance on the second coordinate, and so on.
PLS: Partial least squares, a multivariate method widely used for linear regression. PLS is used to
find the fundamental relations between two matrices (X and Y), i.e. a latent variable approach to model­ing the covariance structures in these two spaces.
QSAR: Quantitative structure-activity relationship. QSAR regression models relate a set of “predic-
tor” variables (X) to the potency of the response variable (Y), while classification QSAR models relate the predictor variables to a categorical value of the response variable.
Trypanosomiasis: The name of several diseases invertebrates caused by parasitic protozoan trypano-
somes of the genus Trypanosoma. In the Latin America, the human form of trypanosomiasis is called Chagas disease and it is cause by the protozoan T. cruzi.
Validation: The main procedure in QSAR to attest its reliability and predictability. The most com-
mon validation methods include cross-validation and external validation.
122
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
Chapter 4
Quantitative Structure-Activity/
Property/Toxicity Relationships
through Conceptual Density
Functional Theory-Based
Reactivity Descriptors
123
Sudip Pan
Indian Institute of Technology Kharagpur, India
Ashutosh Gupta
Udai Pratap Autonomous College, India
ABSTRACT
Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very help­ful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.
1. INTRODUCTION
The properties of molecules mainly depend on the distribution of electron density within the individual molecules. It is, therefore, believed that molecules having similar structures will exhibit similar proper­ties. On this hypothesis, the idea of structure-activity relationship (SAR) exists (Nantasenamat et al.,
2009). Accordingly, it is assumed that molecules with similar structures exhibit comparable activities (properties), and, so on the basis of known properties of a set of molecules, prediction of the properties of unknown molecules having similar structures could be made, provided appropriate models are de-
Indian Institute of Technology Kharagpur, India
Venkatesan Subramanian
Central Leather Research Institute, India
Pratim K. Chattaraj
DOI: 10.4018/978-1-4666-8136-1.ch004
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
Quantitative Structure-Activity/Property/Toxicity Relationships
veloped. Models which are able to predict the properties of an unknown molecule on a qualitative basis are termed as Qualitative Structure-Activity Relationship models (Arning et al., 2008), and, the ones which can quantify such relationship are termed as Quantitative Structure-Activity Relationship (QSAR) models (Gramatica, 2007). Such QSAR models are very useful in the design of molecules which can serve as a better drug or in the manufacturing of materials which could serve as better substance in terms of utility, economy, durability and environmental effects in totality. The quest for such molecules begins with SAR studies. On the basis of activities of a set of molecules of similar structures or parameters, different SAR models are designed. Thereafter, those molecules which are found to have a potential to show a desired characteristic (property/activity) are filtered with the aid of such models, and, then the systematic efforts towards their syntheses begin. Thus, such an approach helps in the reduction of the cost effectively. Since a molecule can have different kinds of properties, a large number of QSAR models could be developed for the same set of molecules depending on their properties. Such properties could be physico-chemical properties, quantum-chemical properties or even toxicity properties. It clearly implies that not only the unknown toxicity parameter of a molecule of whose different parameters are yet to be assessed, could be determined, but its other set of properties could also be determined provided effective QSAR models are generated. When the attempt is to determine the toxicological effect of a molecule based on a model having correlation between structure and toxicity of already determined molecules, then such an approach is defined as Quantitative Structure-Toxicity Relationship (QSTR) model (Roy and Ghosh, 2004). Such models are very effective in the prediction of toxicity of molecules which have potential to act as a toxic substance. Thus, QSTR helps in building up of an effective regression model that helps in predicting the reactivity of an unknown molecule on the basis of behavior of an analogous set of chemically or structurally similar compounds.
QSTR models are proposed based on different parameters. Most often these parameters are defined in terms of descriptors. These descriptors could be based on different experimental and theoretical properties such as physico-chemical and quantum-chemical properties, respectively. One of the most popular and cheap methods in the field of quantum-chemical prediction of the properties of molecules is Density Functional Theory (DFT) (Parr & Yang, 1989). It predicts the properties of a molecule based on its molecular electron density. A closely related method describing the chemical properties such as electronegativity, ionization potential, hardness etc with the aid of DFT method is known as Conceptual Density Functional Theory method (CDFT) (Chattaraj, 2009; Chakraborty et al., 2010; Chattaraj & Giri, 2009; Geerlings et al., 2003). This method has been successfully and exhaustively employed in the generation of different descriptors, which have been able to produce QSAR and QSTR models of very high efficiency. Thus, CDFT has helped in the assessment of activity and toxicity of different molecules within the ambit of QSAR and QSTR respectively. It has been found that CDFT is quite cheaper in comparison to other expensive quantum-chemical methods such as ab initio methods. CDFT has been proven to develop effective and efficient QSTR models.
In this chapter, at first we have provided a general introduction highlighting the necessity of structure­activity/toxicity based regression models. Various QSAR/QSPR/QSTR based methods are outlined in section 2. Section 3 describes the conceptual density functional theory and the related global and local reactivity descriptors. Section 4 deals with the utility of electrophilicity index and net electrophilicity index and their local variants in predicting toxicity of various classes of molecules. Section 5 mentions about the importance of the group philicity towards modeling an effective QSAR. Section 6 highlights the effect of studied levels and / or basis sets in constructing QSAR/QSPR/QSTR models. Section 7 concludes the chapter by mentioning the effectiveness of various CDFT based descriptors in building QSAR/QSPR/QSTR models.
124
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
Quantitative Structure-Activity/Property/Toxicity Relationships
2. QUANTITATIVE STRUCTURE-ACTIVITY/ PROPERTY/TOXICITY RELATIONSHIPS
Quantitative Structure Activity Relationship (QSAR) acts as a function which connects structure of a molecule to different properties. Those properties which show medicinal applications are considered as an activity of a molecule, and, are thus studied within the purview of QSAR. In the present world of global recession, such a technique is able to save money and time. Much of the efforts are now directed towards development of models which predict accurately the properties of a molecule on the basis of their structures. Thus, QSAR models are able to predict biological activities and physico-chemical properties and rationalize the mechanism of action for different chemical reactions. Normally, in order to develop a QSAR, five to ten compounds are necessary for each descriptor as argued by Topliss and Costello (1972) and further mentioned by Schultz et al. (2003c). However, in order to develop robust QSAR, many more compounds are required. With the advent of sophisticated techniques, new software, and, hardware which works on novel algorithms, has made the task of generation of an accurate model within the purview of QSAR simplier. QSAR has its genesis in the pioneering work of Hansch and coworkers (1962, 1964) wherein they used linear multiple regression models to describe the biological property of the com­pounds, which were not synthesized till then. Different parameters such as hydrophobicity, electronic effects and steric properties were utilized to generate a relationship among them and the concentration of the molecule. Free and Wilson (1964) and Fujita et al. (1971) developed non-parameteric methods to define biological activity. Later Linear Solvation Free Energy Relationship (LSFER) was proposed which predicted the properties of a molecule on solute-solvent interactions (Kamlet et al., 1983; Taft et al., 1985). It consists of different solvatochromic descriptors such as cavity/bulk term, polarizability term, and H-bond terms which are used to derive a relationship between overall property of a molecule and different parameters. A good account of the role of QSAR in chemical toxicology was elaborated by Schultz et al. (2003a, 2003b). Other articles also highlight the development of the QSAR methodology and their role in the prediction of bio-toxicity (Gombar et al., 2006; Kar & Roy, 2010; Nantasenamat et al., 2009; Puzyn et al., 2010; Selassie et al., 2010). Hammett (1935, 1937) by employing correlation principles, in 1930s had efficiently shown the effect of structural changes on reaction mechanism of substituted benzoic acid derivatives. It led subsequently to the birth of well known linear free-energy relationship essentially by connecting Gibbs free energy of reaction and Gibbs free energy of activation which in a broader sense established a connection between thermodynamics and kinetics. The concept was further extended by Taft (1956) for aliphatic compounds. This paved the way of strong QSAR models as was evident from the further work carried out by Hansch and coworkers (1993, 1996) wherein they discussed the role of QSAR. The role of QSAR in the study of chemico-biological interactions (Blaney & Hansch, 1990; Debnath et al., 1994; Gao et al., 1999; Hansch et al., 1986, 1989, 1995, 1997, 1998, 2001; Hansen et al., 1995; Langridge & Klein, 1990; Lien et al., 1968;) and also for the drug design (Bajot, 2006; Garg et al., 1999; Hansch et al., 1973, 1995; Kubinyi, 1997; Maddalena, 1998; Norinder, 1998; Voskresensky & Levitsky, 2002; Yang & Huang, 2006;) was also established.
In order to generate an effective QSAR model, the first and foremost requirement is the collection of data and generation of database. This helps in defining training sets which generally consist of known data obtained from various sources. With the aid of such data, different kinds of descriptors are developed on the basis of molecular formula (1-D descriptor), the 2-dimensional structure (2-D descriptor), and the 3-dimensional conformation (3-D descriptor) of a molecule. Generally, molecular descriptors generated from some special types of atoms or fragments counting or based on bulk and physico-chemical proper-
EBSCOhost - printed on 2/14/2023 7:16 AM via . All use subject to https://www.ebsco.com/terms-of-use
125