Reactions in the intracellular medium occur in a highly organized and heterogenous environment rendering invalid modeling approaches based on the law of mass action or its stochastic counter-part. This has led to the recent development of a variety of stochastic microscopic approaches based on lattice-gas automata or Brownian dynamics. The main disadvantage of these methods is that they are computationally intensive. We propose a mesoscopic method which permits the efficient simulation of reactions occurring in the complex geometries typical of intracellular environments. This approach is used to model the transport of a substrate through a pore in a semi-permeable membrane, in which its Michaelis-Menten enzyme is embedded. We find that the temporal evolution of the substrate is a sensitive function of the spatial heterogeneity of the environment. The spatial organization and heterogeneities of the intracellular medium seem to be playing an important role in the regulation of biochemical reactions.