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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.
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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.
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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
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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.
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