Liposomes and niosomes can be considered excellent drug delivery systems due to their ability to load all compounds, whether hydrophobic or hydrophilic. In addition, they can reduce the toxicity of the loaded drug without reducing its effectiveness. Synechocystis sp. is a unicellular, freshwater cyanobacteria strain that contains many bioactive compounds that qualify its use in industrial, pharmaceutical, and many other fields. This study investigated the potential of nano-liposomes (L) and nano-niosomes (N) for delivering Synechocystis sp. extract against cancer cell lines. Four different types of nanoparticles were prepared using a dry powder formulation and ethanol extract of Synechocystis sp. in both nanovesicles (N1 and N2, respectively) and liposomes (L1 and L2, respectively). Analysis of the formed vesicles using zeta analysis, SEM morphological analysis, and visual examination confirmed their stability and efficiency. L1 and L2 in this investigation had effective diameters of 419 and 847 nm, respectively, with PDI values of 0.24 and 0.27. Furthermore, the zeta potentials were found to range from −31.6 mV to −43.7 mV. Regarding N1 and N2, their effective diameters were 541 nm and 1051 nm, respectively, with PDI values of 0.31 and 0.35, and zeta potentials reported from −31.6 mV to −22.2 mV, respectively. Metabolic profiling tentatively identified 22 metabolites (1–22) from the ethanolic extract. Its effect against representative human cancers was studied in vitro, specifically against colon (Caco2), ovarian (OVCAR4), and breast (MCF7) cancer cell lines. The results showed the potential activities of the prepared N1, N2, L1, and L2 against the three cell lines, where L1 had cytotoxicity IC50 values of 19.56, 33.52, and 9.24 µg/mL compared to 26.27, 56.23, and 19.61 µg/mL for L2 against Caco2, OVCAR4, and MCF7, respectively. On the other hand, N1 exhibited IC50 values of 9.09, 11.42, and 2.38 µg/mL, while N2 showed values of 15.57, 18.17, and 35.31 µg/mL against Caco2, OVCAR4, and MCF7, respectively. Meanwhile, the formulations showed little effect on normal cell lines (FHC, OCE1, and MCF10a). All of the compounds were evaluated in silico against the epidermal growth factor receptor tyrosine kinase (EGFR). The molecular docking results showed that compound 21 (1-hexadecanoyl-2-(9Z-hexadecenoyl)-3-(6′-sulfo-alpha-D-quinovosyl)-sn-glycerol), followed by compounds 6 (Sulfoquinovosyl monoacylgycerol), 7 (3-Hydroxymyristic acid), 8 (Glycolipid PF2), 12 (Palmitoleic acid), and 19 (Glyceryl monostearate), showed the highest binding affinities. These compounds formed good hydrogen bond interactions with the key amino acid Lys721 as the co-crystallized ligand. These results suggest that nano-liposomes and nano-niosomes loaded with Synechocystis sp. extract hold promise for future cancer treatment development. Further research should focus on clinical trials, stability assessments, and pharmacological profiles to translate this approach into effective anticancer drugs.
