The poor availability of many drug candidates to reach the target is the main reason for falling in the drug discovery pathway. In this regard, the development of drug delivery systems overcoming that problem is a helpful tool for enriching the drug universe. Herein, we propose a drug delivery system based in supramolecular structures formed by self-assembly of cell-penetrating lipo-peptides. Three lipopeptides constructs have been synthesized by linking the Nucleolar Targeting Peptide (NrTP6) with one, two or four Dodecanoic fatty acid (FA) chains. Critical Micellar Concentration (CMC) of lipopeptides was determined in water and phosphate buffer (PB) by pyrene fluorescence, and the effect of pH on the CMCs was also studied. Size and morphology of lipopeptides assemblies were characterized by Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM). Drug encapsulation and percentage of entrapment efficiency (%EE) results show that as the number of FA increases, the %EE was higher. Cellular uptake of the lipopeptides and lipopeptides-drug conjugates nanostructures have been studied. The lipo-peptides nanostructures have been shown not to be cytotoxic. However, when the number of lipidic chains increases some toxicity is observed.