In this work we used unbiased coarse-grained (CG) MD simulations to investigate the selfassembly of a PEG-PLGA NP and the simultaneous solubilization of the anti-cancer peptide EEK. This exact formulation has been tested against triple negative breast cancer cells in vivo. From our simulation, we study the internal structure of the NP and correspondingly, the local environment of EEK within the NP. We provide a molecular-level understanding of PEG-PLGA nanoparticle cargo loading by finding specific polymer conformations that drive the solubilization of EEK.