Molecular descriptors, used structure-activity

Basak, S.C., Grunwald, G.D. and Niemi, G.J. (1997a). Use of Graph-Theoretic and Geometrical Molecular Descriptors in Structure-Activity Relationships. In From Chemical Topology to Three-Dimensional Geometry (Balaban, A.T., ed.). Plenum Press, New York (NY), pp. 73-116. 

Use of Graph-Theoretic and Geometrical Molecular Descriptors in Structure-Activity Relationships... 

The idea of using atom pairs as molecular features in structure-activity studies vas first proposed by Carhart et al. (84). AP descriptors are defined by their atom types and topological distance bins. An AP is a substructure defined by two atom types and the shortest path separation (or graph distance) between the atoms. The graph distance is defined as the smallest number of atoms along the path connecting two atoms in a molecular structure. The general form of an atom-pair descriptor is as follows ... 

Figure 10 Theoretical (a) and practical (b) representation of QSARs. Panel b describes a QSAR for the methanotrophic oxidation (activity of methane monooxygenase) of 6>r /i6>(Ci2)-substituted biphenyls. The structural backbone was biphenyl, and the substituents considered included all halogens, methyl-, methoxy-, hydroxyl-, nitro-, and amino-moieties (Lindner et al, 2003). The molecular descriptors used in (b) are (charge on the ortho-csubon), (Taft s steric parameter), and log ow...

Since data-set-dependent biases may cloud the analysis, additional sources of information, e.g., pharmacophore models, 3-D structural data for related targets, scientific and patent literature, can and should be used in a comparative manner. Whether or not meaningful alignments can be established, 2-D descriptors and alignment independent methods such as ALMOND should be used to enhance our understanding of the molecular basis for structure-activity relationships. 

Quantum-chemical molecular descriptors have been actively used in the quantitative structure-activity relationship studies of biological activities [1,2,72]. In the following, examples of QSARs involving quantum-chemical descriptors and applied on the enzymatic reactivity, pharmacological activity, and toxicity of compounds are discussed. 

Quantitative structure-activity relationships QSAR. The QSAR approach pioneered by Hansch and co-workers relates biological data of congeneric structures to physical properties such as hydrophobicity, electronic, and steric effects using linear regression techniques to estimate the relative importance of each of those effects contributing to the biological effect. The molecular descriptors used can be 1-D or 3-D (3D-QSAR). A statistically sound QSAR regression equation can be used for lead optimization. 

All the techniques described above can be used to calculate molecular structures and energies. Which other properties are important for chemoinformatics Most applications have used semi-empirical theory to calculate properties or descriptors, but ab-initio and DFT are equally applicable. In the following, we describe some typical properties and descriptors that have been used in quantitative structure-activity (QSAR) and structure-property (QSPR) relationships. 

A challenging task in material science as well as in pharmaceutical research is to custom tailor a compound s properties. George S. Hammond stated that the most fundamental and lasting objective of synthesis is not production of new compounds, but production of properties (Norris Award Lecture, 1968). The molecular structure of an organic or inorganic compound determines its properties. Nevertheless, methods for the direct prediction of a compound s properties based on its molecular structure are usually not available (Figure 8-1). Therefore, the establishment of Quantitative Structure-Property Relationships (QSPRs) and Quantitative Structure-Activity Relationships (QSARs) uses an indirect approach in order to tackle this problem. In the first step, numerical descriptors encoding information about the molecular structure are calculated for a set of compounds. Secondly, statistical and artificial neural network models are used to predict the property or activity of interest based on these descriptors or a suitable subset. 

Besides the aforementioned descriptors, grid-based methods are frequently used in the field of QSAR quantitative structure-activity relationships) [50]. A molecule is placed in a box and for an orthogonal grid of points the interaction energy values between this molecule and another small molecule, such as water, are calculated. The grid map thus obtained characterizes the molecular shape, charge distribution, and hydrophobicity. 

An alternative viewpoint for structure-activity investigations is to utilize quantitative models as probes into the mechanism of action of the set of compounds being studied. In this case it is most useful if the molecular descriptors are explicitly meaningful in terms of chemical reactivity or physiological behavior, e.g., distribution of the compound in an organism (see Table II). In a previous symposium, (18), we described our application of this approach toward the development of a quantitative structure-potency expression, equation 1,... 

Bagchi, M. C., Mills, D., Basak, S. C. Quantitative structure-activity relationship (QSAR) studies of quinolone antibacterials against M. fortuitum and M. smegmatis using theoretical molecular descriptors. 

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