The cytokine granulocyte colony-stimulating factor (GCSF) is of great clinical importance, with primary application to rapidly elevate the peripheral neutrophil levels of chemotherapy patients through accelerated granulopoiesis. However, these mature bloodstream neutrophils express the GCSF receptor (GCSFR), presenting a significant and specific clearance mechanism of circulating GCSF that increases with time. Here, we formulate a mathematical model that describes these cell-level GCSF/GCSFR dynamics and correlate the effect of these endocytic trafficking processes to ligand depletion in an in vitro culture. We further incorporate this cell-level model into an existing pharmacokinetic/pharmacodynamic (PK/PD) model, to gain insight into the effects that specific molecular and cellular parameters may have on overall PK/PD effects in vivo. Our cell-level model suggests that ligand depletion may be reduced in vitro by decreasing the endosomal affinity of endocytosed GCSF/GCSFR complexes, matching experimental findings. Additionally, our modified PK/PD model suggests that a GCSF analog with a modification that effectively eliminates renal clearance should have a significantly longer half-life in vivo and should therefore improve peripheral neutrophil counts. This is consistent with clinical studies on a polyethylene glycol chemical conjugate of GCSF termed SD/01. The model predicts that a GCSF analog that eliminates renal clearance and has reduced endosomal binding affinity may result in an even longer ligand half-life and increased neutrophil counts at a lower dose than either wild-type GCSF or SD/01. More generally, this type of hierarchical model provides a correlation between the molecular and pharmacological properties of a drug and may elucidate design goals for such protein therapeutics.Currently, the design and development of a therapeutic drug takes, on the average, 12 years and costs more than $800 million. Of this total cost, approximately one third is spent on drugs and experiments that fail. In addition, once a candidate drug makes it into clinical trials, the success rate is still less than 20%. One of the major problems in the development of a successful drug is the inability to correlate the effects of a molecular perturbation in the drug to the resulting effects in efficacy and half-life in vivo. This correlation can be particularly nonintuitive for protein therapeutics, such as hematopoietic cytokines, that act as agonists for cell-surface receptors.The pharmacodynamic properties of such agonists depend not only on receptor binding affinity but also on subsequent intracellular signaling cascades and endocytic trafficking of the cell-surface cytokine/receptor complexes. Endocytic trafficking often serves to attenuate the generated signals, resulting in ligand depletion and receptor down-regulation, which in turn reduces the pharmacodynamic potency of the drug over time. Furthermore, the pharmacokinetic profile of such a cytokine is often determined not only by nonspecific renal and hepatic cl...