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Toxicity Prediction Directly from Chemical Structure

  • Predicts key toxicity parameters (Ames mutagenicity, rat acute dose LD50 following iv or po administration) and aqueous solubility directly from structure.
  • No in vitro physicochemical or toxicity data required.
  • Save money and time by allowing toxicity to be assessed virtually (no synthesis required).
  • Provides early stage filter for directing chemistry and prioritizing screening.
chemTox Input Requirements Chemical structure, e.g. SMILES, mol or sdf
chemTox Data Delivery Predicted toxicity measures: Ames mutagenicity, rat acute dose LD50 following iv or po administration
Predicted aqueous solubility

A virtual screening tool for predicting toxicity from chemical structure alone.


How does it work?

chemTox is implemented as a node for the KNIME analytics platform which executes a model of the workflow illustrated in Figure 1 below.

Figure 1
chemTox workflow.

KNIME can be downloaded easily and for free. Cyprotex then provide the bespoke toxicity modules (chemTox) for the KNIME platform.


The following properties are reported:

  1. Ames mutagenicity classification (mutagenic/non-mutagenic).
  2. Ames mutagenicity probability (probability of being a mutagen).
  3. Rat LD50 (mmol/kg) following acute administration by intravenous route.
  4. Rat LD50 (mmol/kg) following acute administration by oral route.
  5. Aqueous solubility (mol/l).

Output is a KNIME data table facilitating saving to a file or database, or using the predictions as inputs to subsequent workflow steps.

Model Development
  • Models are quantitative-structure property relationships (QSPR) that calculate the toxicity properties of interest in terms of a compound's structural descriptors.
  • Models have been trained using large, well-validated datasets.
  • Training was performed using up-to-date, rigorous statistical pattern recognition methods.
  • Repeated 10-fold cross-validation has been used to generate the most robust statistics for prediction performance.


Data from chemTox

Figure 2
Receiver operating characteristic (ROC) plots for classification of rat acute LD50 following oral administration. (a) LD50 < 5mg/kg (b). LD50 < 50mg/kg (c). LD50 < 300mg/kg.

LD50 < 5mg/kg
LD50 < 50mg/kg
LD50 < 300mg/kg
Area under the ROC curve 0.905
Sensitivity 0.85
Specificity 0.82
Table 1
Statistics for predicted Ames mutagenicity based on 4336 compounds (1935 non-mutagenic and 2401 mutagenic).

Model variants can be generated having different balance of sensitivity and specificity to suit different screening requirements.

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Please give details of the assays you are interested in. Where appropriate please specify one or more species (human, rat, mouse etc.), isoforms (CYP1A1,CYP1B1, etc) or other relevant details.