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Background: Cancer is a major cause of mortality and morbidity and given the limitations of many current cancer drugs, there is great need to discover and develop novel treatments. An alternative to the conventional drug discovery path is to exploit new classes of natural compounds such as cyclotides. This peptide family is characterized by linked C- and N-termini and a structural fold called the cyclic cystine knot (CCK). The CCK fold is responsible for the exceptional enzymatic, chemical and thermal stability of cyclotides. Methods: In the present study, an alternative to traditional cancer treatments, involving new nanomaterials and nanocarriers allowing efficient cyclotide delivery, is proposed. Using the polymers Eudragit® L 100-55 and RS 30 D, the cyclotides kalata B2 and parigidin-br1 (PBR1) were nanocapsulated, and nanoparticles 91 nm and 188 nm in diameter, respectively, were produced. Results: An encapsulation rate of up to 95% was observed. In vitro bioassays showed that the nanostructured cyclotides were partially able to control the development of the colorectal adenocarcinoma cell line CACO2 and the breast cancer cell line MCF-7. Conclusion: Data reported herein indicate that nanoformulated cyclotides exhibit antitumor activity and sustained drug release. Thus, the system using Eudragit® nanocapsules seems to be efficient for cyclotide encapsulation and probably could be used to target specific tumors in future studies.