Within the past decade, Quantitative Systems Pharmacology (QSP) has emerged as a new field seeking to improve pharmaceutical research and development (R&D). It combines mathematical modelling of subcellular and whole body scale events with experimental data to provide insight into the mechanisms of action underlying drug efficacy, and to test predicted therapeutic strategies likely to achieve clinical validation. These models can also be used to predict causes of drug failure, identify new drug targets, and help improve clinical trial design and optimisation [1]. The growing investigation into the therapeutic indications for phytocannabinoids found in, and derived from, Cannabis sativa (cannabis) makes it an interesting case for a QSP approach. Despite the conclusive data on the therapeutic effects of cannabinoids upon diseases such as childhood epilepsy, there is a need to further explore their mechanisms of action and their therapeutic potential for other indications. To begin to address this, we are taking a QSP approach by modelling mechanisms of action possibly underlying the biological effects of these phytochemicals. Through proprietary data, we have identified the molecular targets that cannabidiol (CBD), a major compound of cannabis [2], significantly binds to and activates/inhibits. We have connected these targets to the biomarkers of two diseases of interest, Tuberous Sclerosis Complex (TSC) and Rett Syndrome (RTT), via relevant cell signalling pathways. Using Michaelis-Menten kinetics and the Law of Mass Action, we have created a mathematical model integrating the molecular interactions in the pathways with body scale information and clinical data. This model will be used to test the efficacy of CBD for both TSC and RTT, and predict the mechanisms through which it exerts its effect. To summarise, we discuss the advantages of integrating mathematical models into pharmaceutical R&D, and will demonstrate the utility of these models to gain insight into the therapeutic potential of a drug and the mechanisms by which it acts.