Interpretation of scoring functions using 3D molecular fields. Mapping the diacyl-hydrazine-binding pocket of an insect ecdysone receptor.

A method is presented for the interpretation of receptor docking score values (rough measures of binding affinities) of ligands in terms of 3D molecular field interaction contributions. The FlexX and FlexX-Pharm methods were used to dock the structures of designed sets of ligands into the ligand-binding pocket of a selected receptor. In the next step the relationship was investigated between the FlexX and CScore scores and 3D molecular fields obtained for the docked conformations of the ligands, using the CoMFA (Comparative Molecular Field Analysis) and CoMSIA (Comparative Molecular Similarity Indices Analysis) methods. The approach yielded highly significant CoMFA and CoMSIA models demonstrating that a high portion of the variance in the docking score values of the ligands can be explained by steric, electrostatic, hydrophobic, and hydrogen bond donor and acceptor molecular field interaction contributions. The approach was exemplified by using the crystal structure of the ligand-binding domain of the ecdysone receptor (EcR) of the moth Heliotis virescens as well as virtual molecule libraries of analogues of known diacyl-hydrazine (DAH) type ecdysteroid agonists. By docking appropriately designed virtual compound libraries into the DAH binding pocket of EcR followed by CoMFA and CoMSIA of the docked conformations, hitherto unexplored regions of the receptor cavity could be mapped. By mapping the significant molecular field interaction contributions onto the model of the receptor-ligand complex, important receptor-ligand interactions could be highlighted that may help the design of novel highly scored receptor ligands. An advantage of the method is that no experimental biological activity data are required to exhaustively map the receptor-binding site.

Opposite effects of antimicrotubule agents on c-myc oncogene expression depending on the cell lines used.

We investigated the expression of c-myc in HT29-D4, HBL100 and Caco-2 cells treated with microtubule stabilising (paclitaxel) or depolymerising agents (vinblastine, nocodazole). After induction by epidermal growth factor (EGF), c-myc expression decreased in HT29-D4 cells treated with all the antimicrotubule agents. In HBL100 and Caco-2, when microtubules were stabilised with paclitaxel, c-myc expression also decreased. In contrast, its expression increased after treatment with depolymerising agents. In both cell lines, we also observed that depolymerising agents alone induced c-myc expression whilst paclitaxel had no effect. This mRNA induction was confirmed at the protein level. In HT29-D4, no variation of c-myc expression was observed. Then, we showed that the increase of mRNA level was due to activation of gene transcription. These results indicate that modulation of c-myc expression varied depending on the cell lines used and the type of antimicrotubule agents. This work provides a potential link between the microtubular network and c-myc gene expression.

Comparative three-dimensional quantitative structure-activity relationship study of safeners and herbicides.

The competitive antagonist hypothesis for safeners and herbicides was investigated by studying the 3D similarity between 28 safener and 20 herbicide molecules in their putative biologically active, low-energy conformations using comparative molecular field analysis (CoMFA). In addition, CoMFA provided information about the structural requirements for the interactions of safeners and herbicides with a proteinaceous component (SafBP) isolated from etiolated corn seedlings. Statistically significant CoMFA models have been developed for the united and separate safener and herbicide molecule sets using retrospective binding affinity data of the ligands measured at the SafBP receptor. The predictive power of the models was characterized by squared cross-validated correlation coefficients (q(2)) of 0.708, 0.564, and 0.4000 for the united safener plus herbicide set, the safener set, and the herbicide set, respectively. The CoMFA results support the competitive antagonist hypothesis between certain types of safeners and herbicides. The findings suggest that structural similarity between these two classes of agrochemicals is a useful guide in the design of new safeners.

Analysis of esterase zymograms of Fusarium sambucinum and related species.

Esterase zymograms were obtained following polyacrylamide slab gel electrophoresis of protein extracts Fusarium sambucinum and related species originating from different geographic locations and different matrices. The sites of esterase activity were recorded, and the Rfs were calculated. The data were used for the construction of phenograms by cluster analysis and nonlinear mapping by computerized classification techniques. The fifteen isolates of F. sambucinum, the eight isolates of F. torulosum and the six isolates of F. spec. nov. each had identical profiles, and are therefore electrophoretically distinct species. The isolates of F. sarcochroum, one of F. sambucinum sensu lato (BBA 64280) and fifteen isolates of F. sambucinum were electrophoretically indistinguishable from each other. We assume they are synonymous. The isolate of F. bacteridiodes, one of F. sambucinum sensu lato (BBA 64993) and eight isolates of F. torulosum had uniform EST patterns, therefore the two species are electrophoretically identical. We assume they are also synonymous. The remaining three isolates of F. sambucinum sensu lato are somewhat closely related to F. sambucinum isolates on the basis of our investigations.

Thin-layer chromatography of some methylated amino acids with aqueous salt solutions used as eluents.

The retention order of methylated lysine and arginine derivatives followed a reversed-phase separation pattern on various silicas with aqueous salt solutions used as eluents. Principal component analysis established that the origin of the silica exerts a dominant influence on their chromatographic performance, and the effect of impregnation and salt quality are of secondary importance. Good linear correlations were found between the lipophilicity-decreasing effect of monovalent cations and their ionic radii.

Principal component analysis for a better understanding of the herbicidal effectivity of some benzonitriles.

To gain more insight in mode of action of ten different 4-hydroxy-benzonitrile derivatives, their biological activities in eight bioassays, and their lipophilicity and adsorptivity determined by thin-layer chromatography in nine different systems were subjected to principal component analysis. Four background components explained about 90% of total variance. Only three of eight biological activities, the inhibition of the 2,6-dichlorophenol-indophenol reduction by spinach and wheat chloroplasts and the CO2 fixation of wheat seedlings had not any common background components with the physico-chemical parameters of the compounds. The nonlinear mapping of principal component loadings and variables showed, that the in vivo and in vitro biological activities differed considerably and depended on the object investigated. The effectivity of compounds is governed mainly by the number of substituents and by the presence of free hydroxy group.