EPAC and PKA-Activation(Cilostamide)

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Binding Reaction

$\text{inactiveEPAC} + \text{Cilostamide} \rightleftharpoons \text{activeEPAC} + \text{Cilostamide}$

$\text{inactivePKA} + \text{Cilostamide} \rightleftharpoons \text{activePKA} + \text{Cilostamide}$

Kinetic equation

$v_{\text{EPAC-Activation}} = \frac{k_{cat} \cdot [\text{Cilostamide}] \cdot [\text{inactiveEPAC}] \cdot (1-\frac{[\text{activeEPAC}]}{[\text{inactiveEPAC}] \cdot K_{eq}})}{Km_{\text{inactiveEPAC}} \cdot (1 + \frac{[\text{inactiveEPAC}]}{Km_{\text{inactiveEPAC}}} + \frac{[\text{activeEPAC}]}{Km_{\text{activeEPAC}}})}$

$v_{\text{PKA-Activation}} = \frac{k_{cat} \cdot [\text{Cilostamide}] \cdot [\text{inactivePKA}] \cdot (1-\frac{[\text{activePKA}]}{[\text{inactivePKA}] \cdot K_{eq}})}{Km_{\text{inactivePKA}} \cdot (1 + \frac{[\text{inactivePKA}]}{Km_{\text{inactivePKA}}} + \frac{[\text{activePKA}]}{Km_{\text{activePKA}}})}$

final Parameter

Km_inactiveEPAC = 9699.87 M = 9.69987 * 10⁹ μM
Km_inactivePKA = 3102.31 M = 3.10231 * 10⁹ μM
kcat_PKA = 1.6605 1/s
kcat_EPAC = 9.34508 1/s

Annotations

Cilostamide is an inhibitor of phosphodiesterase 3 (PDE3). The function of PDE3 is the hydrolysation of cAMP and cGMP to AMP and GMP, respectively. It is expressed in various tissues. So by inhibiting PDE3 the cAMP level increases, which leads to an activation of PKA and EPAC. The PDE3, however, is not included in the model and therefore the indirect activation process via PDE3 inhibition is modelled as a direct activation process. Due to this reduction, there are no parameters for this process measured. The parameters used by us are the parameters by Xu et al (2010) and no standard deviation is assumed, because it is a fictive reaction for which assuming an error does not make sense. The same Michaelis-Menten constant for substrate and product is used.
There is no incident about the equilibrium constant. However because Xu et al. (2010) has modelled this reaction as irreversible we can assume that the equilibrium is far on the product side and therefore the equilibrium constant is high. We used K_eq = 10⁹.

Km_P value and equilibrium constant

The K_m value for the product is assumed to be similar to but slightly higher than the the K_m value of the substrate because of the similarity of the both species. Therefore the K_m value of the substrate is multiplied by 1.05 to gain the one of the product.

For information about the equilibrium constant please see here.