Modern drug development is marked by high failure rates in translation to the clinic. Further, many drugs that succeed in clinical trials work for only a fraction of patients. Systems pharmacology attempts to address these challenges by improving our understanding of the disease-therapy system, integrating detailed molecular interactions, cellular signaling, tissue architecture, and whole body physiology. I built cutting-edge, molecularly-detailed, multi-scale computational models to study the effects of immobilization of growth factors on signaling in angiogenesis, focusing in particular on the binding of vascular endothelial growth factor (VEGF) family members to the ECM. While most studies of VEGF signaling use only VEGF presented in solution, there is evidence that a large potion of VEGF may be ECM-bound in vivo, and relative expression of isoforms binding to ECM vs. found only in solution varies by tissue and changes in disease, motivating further study of this question. Starting at the in vitro level, we showed that differential signaling of VEGF-receptor 2 (VEGFR2) in response to soluble vs. immobilized VEGF can be explained by reduced internalization of ECM-VEGF-VEGFR2 complexes. Moving in vivo, we predicted differences in both growth factor distribution and receptor activation by VEGF family ligands, as a function of their ECM-binding properties. These predictions are consistent with observed vascular phenotypes in mice expressing single VEGF isoforms. Next, we explored how VEGF splicing changes in peripheral artery disease lead to impaired angiogenic responses to ischemia. Our model showed that the VEGF165b isoform, which does not bind to ECM or to the coreceptor NRP1, is a weak activator of VEGFR2 in vivo, and competes for binding to VEGF-receptor 1, but not VEGF-receptor 2. Finally, we used this model to screen potential therapeutic strategies designed to promote VEGF-mediated revascularization in ischemic disease and tissue engineering applications. Within a single system, we compared failed and promising biomaterial-based VEGF delivery systems, antibody-based therapeutics, and gene therapy strategies to identify key rules for design, optimization, and translation of these pro-angiogenic therapies
