Electronic CoMFA

A widely used 3-D QSAR method that makes use of PLS is comparative molecular field analysis (CoMFA), in which a probe atom is used to calculate the steric and electronic fields at numerous points in a 3D lattice within which the molecules have been aligned. Poso et al. [56] used the technique to model the binding of coumarins to cytochrome P450 2A5, with similar results to those obtained by Bravi and Wikel [55]. Shi et al. [57] used it to model the estrogen receptor binding of a large diverse set of compounds, and Cavalli et al. [58] used it to develop a pharmacophore for hERG potassium... 

More recently, with the significant increases in computer power even on desktop PCs, methods for directly matching 3-D features of molecules have become more prevalent. Features here generally refer to various types of molecular fields, some such as electron density ( steric ) and electrostatic-potential fields are derived from fundamental physics (30,31) while others such as lipophilic potential fields (32) are constructed in an ad hoc manner. Molecular fields are typically represented as continuous functions. Discrete fields have also been used (33) albeit somewhat less frequently except in the case of the many CoMFA-based studies (34). 

Moreover, a final 3D-QSAR model vahdation was done using a prospective study with an external test set. The 82 compounds from the data set were used in a lead optimization project. A CoMFA model gave an (cross validated) value of 0.698 for four relevant PLS components and a conventional of 0.938 were obtained for those 82 compounds. The steric descriptors contributed 54% to the total variance, whereas the electrostatic field explained 46%. The CoMSIA model led to an (cross vahdated) value of 0.660 for five PLS components and a conventional of 0.933. The contributions for steric, electrostatic, and hydrophobic fields were 25, 44, and 31%. As a result, it was proved that the basic S4-directed substituents should be replaced against more hydrophobic building blocks to improve pharmacokinetic properties. The structural and chemical interpretation of CoMFA and CoMSIA contour maps directly pointed to those regions in the Factor Xa binding site, where steric, electronic, or hydrophobic effects play a dominant role in ligand-receptor interactions. 

From the studies above, it was shown that the use of 3D-QSAR models led to the identification of binding site regions, where steric, electronic, or hydrophobic effects played a dominant role. Although cationic interactions in both SI and S4 subsites were favorable for in vitro affinity, they might be detrimental for oral bio availability. Thus, the CoMFA steric field contribution could be seen as a balance between pure steric plus hydrophobic effects. The contributions for steric, electrostatic and hydrophobic fields from the CoM-SIA studies were 25, 44, and 31%, respectively. 

On the basis of this equation Zou et al. have concluded that hydrophobic compounds with inductively electron-donating ortho substituents would be favorable for the activity [193]. In continuation of this, Zou and coworkers have carried out CoMFA-based 3D-QSAR analysis of these compounds together with 5-[l-aryl-l,4-dihydro-6-methylpyridazin-4-one-3-ylj-2-arylamino- 1,3,4-oxadiazoles [ 194]. Here also the antifungal activity of these compounds has been found to be well explained by their steric and electrostatic properties. In addition to this, it has confirmed the bioisosterism... 

Kim, K.H. (1992a). 3D Quantitative Structure-Activity Relationships Description of Electronic Effects Directly from 3D Structures Using a Grid Comparative Molecular Field Analysis (CoMFA) Approach. QuantStruct-ActRelat, 11,127-134. 

Poso, A., Tuppurainen, K. and Gynther, J. (1994). Modeling of Molecular Mutagenicity with Comparative Molecular Field Analysis (CoMFA) Structural and Electronic Properties of MX Compounds Related to TAIOO Mutagenicity. J.Mol.Struct. (Theochem), 110,255-260. 

Kim, KH. (1992) 3D quantitative structure-activity relationships description of electronic effects directly from 3D structures using a grid comparative molecular field analysis (CoMFA) approach. Quant. Struct. -Act. Rdat., 11, 127-134. 

In this chapter only QSAR methods which use physicochemical or structural features of molecules will be discussed, while in Chapter 25 3D-QSAR approaches will be presented. These so-called 3D-QSAR techniques, e.g. CoMFA, use the basic statistical principles, such as partial least squares (PLS), of QSAR methods, but in addition use the three-dimensional characteristics of a molecule specifically related to electronic, steric and lipophilic field effects. In these methods the molecular superposition believed relevant to binding to the target is crucial. 

The use of additional (or other) fields than the default steric and electronic fields of the original CoMFA method, together with PLS analysis or GOLPE, is quite common as a valuable extension of the CoMFA program, but it also constitutes an alternative to the relatively expensive commercial software. A combination of shape, lipophilic, steric, and electrostatic potentials in comparative analyses was termed comparative molecular potential analysis (CoMPA) [1014],... 

CoMFA and related 3D QSAR approaches have been applied to correlate various physicochemical properties. Equilibrium constants of the hydration of carbonyl groups could be explained by a combination of C=0 bond order, steric, and electrostatic fields [1005]. 3D QSAR studies that correlate a, inductive, and resonance parameters of benzoic acids [1015, 1016] as well as pKg values ofclonidine analogs [1017] show that a H " field precisely describes such electronic parameters, e.g. (Jm.p of benzoic acids (n = 49 rpir = 0.976 snr = 0.082 Spress = 0.093). Steric parameters of benzoic acids, like surface area and van der Waals volume can be described by a steric field alone, while values of acetic acid methyl esters need a combination of both steric and electrostatic fields (n = 21 rpix = 0.984 Sfit = 0.133 SpREss = 0.209) [1016]. 

CoMFA fields were also proposed and used to derive new steric and electronic parameters for classical QSAR studies [38, 1018]. 

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