The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects which contributed with a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions) which include both topology and kinetic rates of the chemical reactions is an NP-hard problem. In this paper we propose a hybrid architecture which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical systems. Simulations and analysis of two real models show promising results for the proposed method.