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Toolbox: Elimination Kinetics Model for Earthworms
Elimination Kinetics Model for Earthworms
Potential use:
The model estimates the elimination kinetics of organic chemicals in earthworms explicitly accounting for their metabolic potential.
Novelty and background:
Elimination kinetic data for 28 structurally similar organic chemicals in earthworms (Eisenia fetida) were extracted from the literature. Dataset includes lindane, 12 polycyclic aromatic hydrocarbons (PAH), two N- and S-heterocyclic polyaromatic chemicals (PAC), two PAC-quinones, seven polychlorinated biphenyls and five cyclic organochlorinated chemicals. Additional set of data for elimination of 15 PAHs in earthworms was generated within the framework of the NoMiracle project.  The mathematical formalism of the model is based on the probabilistic approach for simulation of metabolism combined with the assumption for first order kinetics.  The simulator of metabolism in earthworms was built hypothesizing that the principal transformations used by different organisms are similar and the main difference consists in their rates or enzymes that control the metabolism of xenobiotics.  The elimination kinetic data were used to determine organism specific model parameters.  Predictions are accompanied with an estimate whether that target chemical belongs to the applicability domain of the model.
Description of tool:
The tool is ready for use.  It is part of models implemented on the platform CATALOGIC for environmental models developed by LMC. The only required input information is molecular structure (SMILES, InChi, or other codes for 2D structure). Model output consists of first level predicted metabolites, variation of body concentration of chemicals in time and an estimate of the applicability domain.
Current state:
ready to use
  1. Dimitrov, S, Dimitrova, N, Spurgeon, D J, Hankard, P K, Van Gestel, C A M, Mekenyan, O (2007) Modeling elimination of polycyclic aromatic compounds in soil organisms. Poster presented at the 17th Annual Meeting of SETAC Europe, May 20-24, Porto, Portugal.
  2. Dimitrov S, (2008) Prediction Methods for Bioaccumulation and Single Processes: In Silico and In Vitro Systems, SETAC PELLSTON WORKSHOP, Pensacola Beach, Florida, January 27 – February 1.
  3. Dimitrova N, Dimitrov S,Georgieva D, Van Gestel C A M, Hankard P, Spurgeon D, Li H, Mekenyan O (submitted) Elimination kinetic model for organic chemicals in earthworms, (Sci Total Environ) (Cumulative Risk Special Issue)
Responsible scientists:
Prof. Ovanes Mekenyan, Ph. D., D. Sci.
Department of Physical Chemistry
Laboratory of Mathematical Chemistry, Head
Bourgas "Prof. As. Zlatarov" University "Yakimov" St. #1 8010 Bourgas Bulgaria
phone: ++359 56 880230 (also personal fax)
++359 56 858343
fax: ++359 56 880249
LMC website:
Related to deliverable:
D.2.3.12 and D.3.3.4A
Elimination Kinetics Model Earthworm.doc