The current study produced Quercetin nanoemulsions (QuNEs) for the purpose of improving Quercetin solubility in an aqueous polar condition and to analyze QuNE-protein formation (QuNE-human serum albumin (HSA) and QuNE-holo-transferrin (HTF)). QuNE was produced by utilizing an ultrasound-based emulsification method and was characterized by DLS, TEM, and SEM. Its interaction with HSA and HTF proteins was studied by analyzing the results of FRET and RLS spectroscopy, Stern-Volmer plotting, the Van\\\\\\\'t Hoff equation, CD spectroscopy, and molecular docking methods. Finally, QuNE\\\\\\\'s cytotoxic impact, cell death type induction, and antioxidant properties were evaluated by applying an MTT assay on a human hepatocyte cancer cell (HepG2), measuring Cas-3 gene expression, and conducting a DPPH antioxidant test, respectively. Compared to the non-entrapped Quercetin, Quercetin-entrapped nano-emulsions formed stable complexes with HSA and HTF by improving hydrophilic-hydrophobic interactions. The binding constant (BC), ΔH0, and ΔS0 indices for both the QuNE-HSA and QuNE-HTF complexes were measured at (4.92 × 105 and 11.99 × 104 M−1), (170.96 and −131.19 KJ.mol−1), and (−464.86 and 342.83J.mol−1K−1), respectively. QuNE lowered the HepG2 viability by up-regulating Cas-3 gene expression and thus inducing apoptosis. Moreover, a notable antioxidant impact on the QuNE was detected. Due to its ability in delivering Quercetin to HSA and HTF proteins and stabilizing their protein complexes, QuNE can be used as a suitable primary transporting agent whose formation of stable bio-accessible QuNE-HSA and –HTF protein complexes creates a safe and natural secondary delivery system, which has potential to be used as an efficient anticancer compound.

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