The mathematical model of group of neurons and astrocytes in the ischemic stroke is discussed. The model includes the description of synaptic signal transmission between the neurons, calcium signaling in astrocytes, ionic currents between the cells and extracellular space and the diffusion through extracellular space. The new modeling approach, based on the creation of appropriate graph, is developed to describe the structure of the system. Using the model, we have analyze the influence of inhibitory synapses on system functioning. We also have shown how the use of medications supporting the activity of inhibitory synapses affects the system behavior in ischemic stroke.