Quantitative structure-activity relationship steric effects

The fundamental assumption of SAR and QSAR (Structure-Activity Relationships and Quantitative Structure-Activity Relationships) is that the activity of a compound is related to its structural and/or physicochemical properties. In a classic article Corwin Hansch formulated Eq. (15) as a linear frcc-cncrgy related model for the biological activity (e.g.. toxicity) of a group of congeneric chemicals [37, in which the inverse of C, the concentration effect of the toxicant, is related to a hy-drophobidty term, FI, an electronic term, a (the Hammett substituent constant). Stcric terms can be added to this equation (typically Taft s steric parameter, E,). 

For years, we have been studying QSAR (quantitative structure-activity relationship) analyses of pesticides and other bioactive compounds. In many examples, we have found a decisive role of the steric effect in determining the activity variation. In this chapter, applications of various steric constants such as E E°, Vw and STERIMOL parameters to QSAR studies mostly from our own laboratory are reviewed. 

Quantitative structure-activity relationships represent an attempt to correlate activities with structural descriptors of compounds. These physicochemical descriptors, which include hydrophobicity, topology, electronic properties, and steric effects, are determined empirically or, more recently, by computational methods. The success of a QSAR method depends on two factors the training dataset obtained by testing a group of chemicals and the descriptors obtained from some easily measurable or calculable property of the chemicals. 

Quantitative structure-activity relationship (QSAR) (Hansch and Klein, 1986 Hansch and Leo, 1995) represents an attempt to correlate structural descriptors of compounds with activities. The physicochemical descriptors include numerical parameters to account for electronic properties, steric effect, topology, and hydrophobicity of analogous compounds. In its simplest form, the biochemical activities are correlated to the numerical substituent descriptors of analogous compounds tested by a linear equation such as... 

The electronic properties of amino acid side chains are summarized in Table 3, and they represent a wide spectrum of measures. The NMR data are derived experimentally (37). The dipole (38), C mull, inductive, field, and resonance effects were derived from QM calculations (15). The VHSE5 (39) and Z3 (25) scales were developed for use in quantitative structure-activity relationship analysis of the biologic activity of natural and synthetic peptides. Both were derived from principal components analysis of assorted physico-chemical properties, which included NMR chemical shift data, electron-ion interaction potentials, charges, and isoelectric points. Therefore, these scales are composites rather than primary measures of electronic effects. The validity of these measures is indicated by their lack of overlap with hydrophobicity and steric parameters and by their ability to predict biologic activity of synthetic peptide analogs (25, 39). Finally, coefficients of electrostatic screening by amino acid side chains (ylocal and Ynon-local) were derived from an empirical data set (40), and they represent a composite of electronic effects. 

Fujita, T. (1978). Steric Effects in Quantitative Structure-Activity Relationships. Pure [Pg.568]

Kim, K.H. (1992b). 3D Quantitative Structure-Activity Relationships Investigation of Steric Effects with Descriptors Directly from 3D Structures Using a Comparative Molecular Field Analysis (CoMFA) Approach. QuantStruct.-Act.Relat., 11,453-460. 

Kim, KH. (1992) 3D quantitative structure-activity relationships investigation of steric effects with descriptors directly from 3D structures using a comparative molecular field analysis (CoMFA) approach. Quant. Struct. -Act. Rdat., 11, 453-460. 

A quantitative structure-activity relationship for the negative inotropic activity of a small series of 1,4-dihydro-pyridines has been developed (47.). For 2,6-dimethyl-3,5-dicarbo-methoxy-4-(substituted phenyl)-1,4-dihydropyridines the effect of the phenyl substituent is determined primarily by steric effects. Thus, for ortho-substituted derivatives,... 

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. 

The use of computer techniques in the correlation of biological activity with substrate physical-chemical properties has received much attention in the area of medicinal chemistry. The use of these techniques, denoted Quantitative Structure Activity Relationships (QSAR), were developed mostly by Hansch and his coworkers eind have been reviewed by Tute te), Purcell et. al. (9) and Dunn (10). These techniques were utilized by Greenberg (1 l) ln the correlation of odor threshold and suprathreshold data with Log P, the log (n-octanol/water partition coefficient). In the same study it was reported that steric and polar effects as measured by the Taft Steric and Polar Constants poorly correlated with odor intensity data. 

The study of structure-reactivity relationships by the organic chemist Hammett showed that there is often a quantitative relationship between the two-dimensional structure of organic molecules and their chemical reactivity. Specifically, he correlated the changes in chemical properties of a molecule that result from a small change in its chemical structure that is, the quantitative linear relationship between electron density at a certain part of a molecule and its tendency to undergo reactions of various types at that site. For example, there is a linear relationship between the effea of remote substituents on the equilibrium constant for the ionization of an acid with the effect of these substituents on the rate or equilibrium constant for many other types of chemical reaction. The relative value of Hammett substituent constants describes the similarity of molecules in terms of electronic properties. Taft expanded the method to include the steric hindrance of access of reagents to the reaction site by nearby substituents, a quantitation of three-dimensional similarity. In addition, Charton, Verloop, Austel, and others extended and refined these ideas. Finally, Hansch and Fujita showed that biological activity frequently is also quantitatively correlated with the hydrophobic character of the substituents. They coined the term QSAR, Quantitative Structure-Activity Relationships, for this type of analysis. 

Additionally, QSAR (quantitative structure-activity relationship) is used in the optimization process (Seydel et al., 1979 Draber et al., 1992). QSAR represents an attempt to correlate structural or property descriptors of compounds with biological activities. The physicochemical descriptors include parameters to account for hydro-phobicity, topology, electronic properties and steric effects. The method is also used to get informations how to decouple undesired toxic effect from desired biological activity. 

The alternatives to mathematical descriptors derived from molecular graphs or molecular geometry are the traditional QSAR (quantitative structure-activity relationship) descriptors and quantum chemically computed parameters. The former include the partition coefficient for oil/water (often octanol/water) (log P), the Hammet sigma value (electronic parameter that measures the electron withdrawal from and the electron release to the aromatic ring by a substituent, the Taft s parameters for the electronic effects of substituents in aliphatic compounds (a ), and a steric parameter for the proximity of substituents on reaction sites (Es)- Also selected molecular properties, such as molar refractivity (MR), polarizability (a), molecular weight (MW), and density (d), have been used. 

Fujita, T. and Iwamura, H. (1983). Applications of Various Steric Constants to Quantitative Analysis of Structure-Activity Relationships. In Steric Effects in Drug Design (Topics in Current Chemistry, Vol. 114) (Charton, M. and Motoc, I., eds.), Springer-Verlag, Berlin (Germany), pp. 119-157. 

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