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chemPK™ V.2

Human PK Prediction Directly from Chemical Structure

  • Predicts key human oral and intravenous pharmacokinetic parameters directly from structure.
  • No in vitro ADME or physicochemical data requirements.
  • Save money and time by allowing pharmacokinetics to be characterized virtually (no synthesis required).
  • Provides early stage filter for directing chemistry and prioritizing screening.
  • Superior approach which uses PBPK model optimized from human clinical (in vivo) data.
A virtual screening tool for predicting human pharmacokinetics from chemical structure alone.


chemPK™ Input Requirements
  • Chemical structure, e.g., SMILES, mol or sdf.
  • Dosing regimen.
chemPK™ Data Delivery
  • Predicted pharmacokinetic parameters following oral and intravenous dosing regimens (for single and repeat doses).
  • Predicted time concentrations for plasma (or blood) and all tissues/organs with graphical representation.
  • Predicted time series hepatic metabolism, renal elimation and fecal elimination.

How does it work?

chemPK™ utilizes a KNIME workflow-based approach which executes the processes illustrated in Figure 1.

chemPK - PK prediction from chemical structure
Figure 1
chemPK™ workflow processes.

KNIME can be downloaded easily and for free. Cyprotex can then provide the bespoke KNIME nodes (chemPK™) for the workflow including Generate PK inputs, Run PK simulation and Calculate PK parameters nodes.

The Generate PK inputs node includes calculations of the following parameters:
  • 10 Tissue partition coefficients (Kp) trained on in vivo data
    • Adipose, brain, heart, gut wall, kidney, liver, lung, muscle and skin.
    • Tissue partition coefficient for the remaining tissues and organs that are not explicitly represented in the PBPK model.
  • Rate of renal clearance trained using in vivo plasma and urine profiles following intravenous (bolus and infusion), oral and subcutaneous dosing.
  • Rate of metabolism in the liver trained using intravenous in vivo profiles (bolus and infusion).
  • Rate of absorption from the gastrointestinal tract trained using oral in vivo profiles (rapid release).
The Run PK simulation node:
  • Executes the PBPK model with intravenous and oral dosing including a repeat dose option.
  • Requires the parameters generated by the Generate PK inputs node.
  • Output is in KNIME table (data frame) format that can be processed in any way required, e.g.:
    • Converted to XLS
    • Converted to CSV
    • Plotted using Python, R etc.
    • Written to a database using a connector
The Calculate PK parameters node reports the following predicted PK parameters:
  • CL, t1/2, MRT, V, Vss, AUC and fraction absorbed to the last timepoint.
  • Cmax, tmax and AUClast for all model tissues/organs.


Data from chemPK™

PK ParameterMFEaRank
Total clearance 2.54 0.51
Half-life (t1/2) 2.16 0.52
Mean time a molecule resides in the body (MRT) 2.26 0.47
Volume of distribution (V) 2.08 0.71
Volume of distribution at steady-state conditions (Vss) 2.03 0.69
Table 1
Intravenous PK parameters for an independent test set of 62 compounds.

a Mean fold error
PK ParameterMFEbRank
Highest drug concentration in plasma (Cmax) 3.30 0.72
Time at which the highest concentration occurs (tmax) 1.73 0.17
Area under the plasma drug concentration-time curve (AUClast) 3.46 0.71
Table 2
Oral PK parameters for an independent test set of 35 compoundsa.

a MW < 450 g/mol
b Mean fold error
In silico PK prediction
Figure 2
Plot of the predicted volume of distribution versus the observed volume of distribution for a test set of 62 compounds.

We are looking for partners with whom we can further develop the chemPK™ model. If you would like to be involved then please get in touch.

Contact for a demonstration.

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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.