COSBI LAB Model has been used to simulate gemcitabine mechanism of action. We show that simulated results reproduce the main dynamics observed in vitro


Gemcitabine is a nucleoside analog used in oncology to block DNA replication in tumor cells. The modeled metabolic network is shown belowe: gemcitabine (2’-2’-difluorodeoxycytidine, dFdC) is transported into the cell and then it is subjected to multiple phosphorylations leading to its active diphosphate (dFdCDP) and triphosphate (dFdCTP) metabolites. dFdCDP inhibits ribonucleotide reductase (RR) depleting the pool of deoxycytidine triphosphate (dCTP), which is the natural substrate for DNA synthesis. dFdCTP is incorporated into DNA competing with dCTP and causing chain termination. Gemcitabine is also deaminated to 2’,2’-difluoro-2’ –deoxyuridine (dFdU) which also competes for DNA incorporation.

gemcitabine image

COSBI LAB MODEL TABULAR INTERFACE
All information describing the model is arranged in panels: components, dynamics, space, and parameters. In this example, a simplified version of the metabolic network of gemcitabine is modeled.

1. COMPONENTS DEFINITION
The dFdC component has three phosphorylation sites, each one interacting with the appropriate kinase (dCK, NMPK, and NDPK respectively).


2. DYNAMICS
Biotransformations and interplay between components are expressed in a narrative language. In this example dCK enzyme is responsible for the first phosphorylation of dFdC. The kinetic parameter r_dFdC_dCK is associated to this reaction, its value will be set in the parameters tab. This kind of dynamics can occur only in the Cytoplasm compartment.


3. PARAMETERS
Parameter r_dFdC_dCK has to be instantiated, the default kinetic law is Mass-Action, but Michaelis-Menten, Hill, and User Defined are also allowed. In this case, we choose the Mass-Action law. Rates as well as other parameters can be expressed in different units of measure (both in terms of concentration or units). By changing values to these parameters, the user can easily perform multiple experiments without modifying the structure of the model.

Main image Component-Site Definition image 3-4bimol-par image

4. SIMULATION RESULTS PLOT
Once the model is complete it can be simulated. In this picture we show how the in silico model reproduces the concentration time courses observed by Veltkamp et al [2] in their in vitro experiments. Accumulation of main metabolites has been plotted, solid lines represent simulated results while dashed lines experimental data.


5. SENSITIVITY ANALYSIS
Inhibition mechanisms play a key-role in gemcitabine metabolic network and an exhaustive study of these interactions can lead to important conclusions on drug’s efficacy. COSBI LAB Model provides a parameter scan tool by which we performed a deep sensitivity analysis on the inhibitory effects that dCTP has on dCK enzyme. Inhibition mechanisms can be modeled in different ways, in this case, we considered an explicit inhibitory binding between dCTP and dCK. The picture to the left depicts the dependency of dFdCTP accumulation (expressed as the area under the curve, AUC) with respect to the rates of binding and unbinding.

Plot image Accumul image

REFERENCES

P. Lecca, O. Kahramanogullari, D. Morpurgo, C. Priami, R. Soo. Modelling the tumor shrinkage pharmacodynamics with BlenX, 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011

P. Lecca, O. Kahramanogullari, D. Morpurgo, C. Priami, R. Soo. Modelling and estimating dynamics of tumor shrinkage with BlenX and Kinfer, UKSim 2001 - 13th International Conference on Modelling and Simulation., 2011

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