This article documents simulations using an agent-based modelling approach to analyse the system dynamics of the beta-lactamase-dependent therapeutic activation pro-drug delivery system, a novel approach for achieving selective release of anti-microbial drugs for treating antibiotic-resistant bacteria. It is thought that this strategy could be a promising approach for treating beta-lactamase over-expressing strains of bacteria that are resistant to traditional beta-lactam antibiotics such as penicillin. Test simulations were carried out to investigate the prodrug system from a theoretical standpoint and assess the effects of key parameters such as half-life, diffusion rate and reaction kinetics on the system behaviour. It is important to obtain a thorough understanding of the complex interplay between the various components involved in the pro-drug delivery system to be able to interpret results from laboratory testing, and ultimately, from the clinical setting. The agent-based model described here represents an important stepping stone in connecting the theoretical and practical understanding of the system as a whole.