Fragmental methods in the analysis of biological activities of diverse compound sets.

The current mini-review explains how fragmental methods (FMs) can be used in the analysis and prediction of physicochemical properties and biological activities. The considered properties include log P, solubility, pK(a), intestinal permeability, P-gp substrate specificity and toxicity. The focus will be a description of a "mechanistic" approach, which implies a gradual reduction of alternative explanations for any property or activity. This means a flexible construction of fragmental parameters using large amounts of experimental data. Since biological activities involve multiple (unknown) target macromolecules with multiple binding modes, a stepwise classification (C-SAR) analysis is most useful. It involves the following procedures: (i). construction of physicochemical profiles using parameters that can be reliably predicted, (ii). identification of reactive functional groups and the largest active skeletons, (iii). generalization of these groups and skeletons in terms of "site-specific physicochemical profiling". This entails a dynamic construction of 2D pharmacophores that can be converted into 3D models.

Hydrophobicity of beta-lactam antibiotics. Explanation and prediction of their behaviour in various partitioning solvent systems and reversed-phase chromatography.

beta-Lactam antibiotics tend to undergo self-association in hydrophilic organic solvents, which leads to a strong dependence of their experimentally observable log P values on the partitioning conditions. As a result, most of the earlier obtained log P values for beta-lactam antibiotics cannot be applied as a common hydrophobicity measure, but they proved to be linearly related to each other and to a large body of reversed-phase chromatographic data. The retention of cephalosporins on reversed-phase liquid chromatographic columns is complicated by silanophilic interactions. However, under elution conditions that eliminate these silanophilic interactions, good correlations with log P data are observed, and a unified hydrophobicity scale for 90 penicillin and cephalosporin compounds could be evaluated. The Hansch and Leo additive scheme was shown to be valid for the calculation of hydrophobicities for penicillin and cephalosporin C-6(7) substituents, but it failed when applied to the prediction of cephalosporin C-3-substituent hydrophobicities. The hydrophobic increments for the sixteen most common cephalosporin C-3-substituents were empirically evaluated from literature data, and a simple equation was derived for an overall beta-lactam antibiotic hydrophobicity calculation. The proposed scale is valid for predicting the partitioning of most beta-lactam antibiotics in both hydrophilic and lipophilic organic-water systems, although it should be used with caution when applied to antibiotics containing additionally charged side-chains.

Increased nucleophile reactivity of amino acid beta-naphthylamides in alpha-chymotrypsin-catalyzed peptide synthesis.

Alpha-chymotrypsin-catalyzed acyl transfer from Boc-L-MetONp, Ac-L-TyrOEt, Bz-L-TyrOMe, Mal-L-PheOMe to the C-protected amino acids (L-AlaNH2, L-LeuNH2, L-ArgOMe and beta-naphthylamides of L-Arg, L-Leu, L-Ala and L-Glu) has been studied. Modification of the carboxylic groups with beta-naphthylamide was shown to increase the reactivity of nucleophiles in these reactions by a factor of more than 100 in comparison with amides and esters of the same amino acids. This effect can be accounted for by the effective formation of the nucleophile-acylenzyme complex due to hydrophobic interactions of the beta-naphthylamide moiety with the corresponding subsite of alpha-chymotrypsin. The reaction kinetics follows the scheme involving hydrolysis of the nucleophile-acylenzyme intermediate. The contribution of this pathway depends on the structures of both the acyl-group donor and the added nucleophile. The competitive inhibition by amino acid beta-naphthylamides is also observed. The results obtained show that modification of the COOH-group of added nucleophiles by beta-naphthylamide strongly affects the reactivity of these compounds in the alpha-chymotrypsin-catalyzed peptide synthesis.