Effective long-term treatment of Type 2 Diabetes Mellitus (T2DM) implies modification of the disease processes that cause this progressive disorder. This paper proposes a mechanism-based approach to disease progression modeling of T2DM that aims to provide the ability to describe and quantify the effects of treatment on the time-course of the progressive loss of beta-cell function and insulin-sensitivity underlying T2DM. It develops a population pharmacodynamic model that incorporates mechanism-based representations of the homeostatic feedback relationships between fasting levels of plasma glucose (FPG) and fasting serum insulin (FSI), and the physiological feed-forward relationship between FPG and glycosylated hemoglobin A1c (HbA1c). This model was developed on data from two parallel one-year studies comparing the effects of pioglitazone relative to metformin or sulfonylurea treatment in 2,408 treatment-naïve T2DM patients. It was found that the model provided accurate descriptions of the time-courses of FPG and HbA1c for different treatment arms. It allowed the identification of the long-term effects of different treatments on loss of beta-cell function and insulin-sensitivity, independently from their immediate anti-hyperglycemic effects modeled at their specific sites of action. Hence it avoided the confounding of these effects that is inherent in point estimates of beta-cell function and insulin-sensitivity such as the widely used HOMA-%B and HOMA-%S. It was also found that metformin therapy did not result in a reduction in FSI levels in conjunction with reduced FPG levels, as expected for an insulin-sensitizer, whereas pioglitazone therapy did. It is concluded that, although its current implementation leaves room for further improvement, the mechanism-based approach presented here constitutes a promising conceptual advance in the study of T2DM disease progression and disease modification.

The Visual Predictive Check (VPC) is a valuable and supportive instrument for evaluating model performance. However in its most commonly applied form, the method largely depends on a subjective comparison of the distribution of the simulated data with the observed data, without explicitly quantifying and relating the information in both. In recent adaptations to the VPC this drawback is taken into consideration by presenting the observed and predicted data as percentiles. In addition, in some of these adaptations the uncertainty in the predictions is represented visually. However, it is not assessed whether the expected random distribution of the observations around the predicted median trend is realised in relation to the number of observations. Moreover the influence of and the information residing in missing data at each time point is not taken into consideration. Therefore, in this investigation the VPC is extended with two methods to support a less subjective and thereby more adequate evaluation of model performance: (i) the Quantified Visual Predictive Check (QVPC) and (ii) the Bootstrap Visual Predictive Check (BVPC). The QVPC presents the distribution of the observations as a percentage, thus regardless the density of the data, above and below the predicted median at each time point, while also visualising the percentage of unavailable data. The BVPC weighs the predicted median against the 5th, 50th and 95th percentiles resulting from a bootstrap of the observed data median at each time point, while accounting for the number and the theoretical position of unavailable data. The proposed extensions to the VPC are illustrated by a pharmacokinetic simulation example and applied to a pharmacodynamic disease progression example.

Disease system analysis constitutes a scientific basis for the distinction between symptomatic versus protective drug effects in relation to specific disease processes as well as the identification of the exposure-response relationship during the time-course of disease.

nlmixr is a free and open‐source R package for fitting nonlinear pharmacokinetic (PK), pharmacodynamic (PD), joint PK‐PD, and quantitative systems pharmacology mixed‐effects models. Currently, nlmixr is capable of fitting both traditional compartmental PK models as well as more complex models implemented using ordinary differential equations. We believe that, over time, it will become a capable, credible alternative to commercial software tools, such as NONMEM, Monolix, and Phoenix NLME.

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