Biomedical subjects

Ralf-Uwe Ebert

Publications and source records attributed to Ralf-Uwe Ebert.

6 recordsLinked to original sources

PubMed2006

Prediction of the sorption of organic compounds into soil organic matter from molecular structure.

A new model to estimate the soil-water partition coefficient of non-ionic organic compounds normalized to soil organic carbon, Koc, from the two-dimensional molecular structure is presented. Literature data of log Koc for 571 organic chemicals were fitted to 29 parameters with a squared correlation coefficient r2 of 0.852 and a standard error of 0.469 log units. The application domain includes the atom types C, H, N, O, P, S, F, Cl, and Br in various important compound classes. The multilinear model contains the variables molecular weight, bond connectivity, molecular E-state, an indicator for nonpolar and weakly polar compounds, and 24 fragment corrections representing polar groups. The prediction capability is evaluated through an initial two-step development using an 80%:20% split of the data into training and prediction, cross-validation, permutation, and application to three external data sets. The discussion includes separate analyses for subsets of H-bond donors and acceptors as well as for nonpolar and weakly polar compounds. Comparison with existing models including linear solvation energy relationships illustrates the superiority of the new model.

Absorption↗

PubMed2006

Acute to chronic ratios in aquatic toxicity--variation across trophic levels and relationship with chemical structure.

For fish, daphnids, and algae, acute to chronic ratios (ACRs) have been determined from experimental data regarding new and existing chemicals. Only test results in accord with the European Union Technical Guidance Document (TGD) and validated by authorities were considered. Whereas the median ACRs of 10.5 (fish), 7.0 (daphnids), and 5.4 (algae) are well below the ACR safety factor of 100 as implied by the TGD, individual ACRs vary considerably and go up to 4400. The results suggest that a safety factor of 100 is not protective for all chemicals and trophic levels. Neither a correlation between ACR and baseline toxicity as modeled through the logarithmic octanol-water partition coefficient nor an ACR correlation across trophic levels exists. Narcosis is associated with a preference for a low ACR; nevertheless, low ACRs are frequently obtained for nonnarcotics. Analysis of chemical structures led to the derivation of structural alerts to identify compounds with a significantly increased potential for a high ACR, which may prove to be useful in setting test priorities. At present, however, life-cycle tests are the only way to conservatively predict long-term toxicity.

Animals↗

PubMed2005

Prediction of the temperature dependency of Henry's law constant from chemical structure.

A new model to estimate the temperature dependency of Henry's law constant in water for organic compounds from the two-dimensional structure is presented. Air/water partition enthalpies of 456 chemicals were fitted to 46 substructural parameters with a squared correlation coefficient r2 of 0.81 and a standard error of 7.1 kJ/mol. The compound set covers various organic compound classes with the atom types C, H, N, O, F, Cl, Br, I, and S. Application of the model together with experimental data for 25 degrees C to a set of 462 compounds with 2119 experimental Henry's law constants at temperatures below 20 degrees C yields a predictive squared correlation coefficient q2 of 0.99 and a standard error of 0.21 logarithmic units. The prediction capability is further evaluated using cross validation and permutation.

Algorithms↗

PubMed2005

Structural alerts--a new classification model to discriminate excess toxicity from narcotic effect levels of organic compounds in the acute daphnid assay.

Quantitative and qualitative structure-activity relationships (QSARs) have a great potential to support the risk assessment of chemicals, provided there are tools available that allow evaluation of the suitability of QSARs for the compounds of interest. In this context, a pragmatic approach is to discriminate excess toxicity from narcotic effect levels, because the latter can be estimated from QSARs and thus have a low priority for experimental testing. To develop a respective scheme for the acute daphnid toxicity as one of the primary ecotoxicological endpoints, 1067 acute toxicity data entries for 380 chemicals involving the daphnid species Daphnia magna were taken from the on-line literature, and quality checks such as water solubility were employed to eliminate apparently odd data entries. For 36 known narcotics with LC50 values referring to D. magna, a reference baseline QSAR is derived. Compounds with LC50 values above a certain threshold defined relative to their predicted baseline toxicity are classified as exerting excess toxicity. Three simple discrimination schemes are presented that enable the identification of excess toxicity from structural alerts based on the presence or absence of certain heteroatoms and their chemical functionality. Moreover, a two-step classification approach is introduced that enables a prioritization of organic compounds with respect to their need for experimental testing. The discussion includes reaction mechanisms that may explain the association of structural alerts with excess toxicity, a comparison with predictions derived from mode of action-based classification schemes, and a statistical analysis of the discrimination performance in terms of detailed contingency table statistics.

Animal Testing Alternatives↗

PubMed2003

Stepwise discrimination between four modes of toxic action of phenols in the Tetrahymena pyriformis assay.

For a set of 220 phenols with literature data on their toxicity and associated mode of action (MOA) toward the ciliate Tetrahymena pyriformis, a stepwise classification scheme was developed that allows the identification of four MOAs from molecular hydrophobicity and AM1-based quantum chemical descriptors, employing linear discriminant analysis or binary logistic regression. Taking the AM1 lowest unoccupied molecular orbital energy as the only parameter, an initial separation of polar narcotics and proelectrophiles from oxidative uncouplers and soft electrophiles is correct to 97%, and for the subsequent discrimination between polar narcotics and proelectrophiles as well as between oxidative uncouplers and soft electrophiles, 99 and 98% correct classifications are achieved using three and two molecular descriptors, respectively. The results are discussed in terms of detailed contingency table statistics and with respect to relationships between molecular descriptors and mechanisms of toxicity. Statistical model evaluation includes simulated external validation employing complementary subset models.

Animals↗

PubMedDate not supplied

Model selection based on structural similarity-method description and application to water solubility prediction.

A method is introduced that allows one to select, for a given property and compound, among several prediction methods the presumably best-performing scheme based on prediction errors evaluated for structurally similar compounds. The latter are selected through analysis of atom-centered fragments (ACFs) in accord with a k nearest neighbor procedure in the two-dimensional structural space. The approach is illustrated with seven estimation methods for the water solubility of organic compounds and a reference set of 1876 compounds with validated experimental values. The discussion includes a comparison with the similarity-based error correction as an alternative approach to improve the performance of prediction methods and an extension that enables an ad hoc specification of the application domain.

Journal Article↗