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Iron oxide nanoparticles (IONPs) have proven to be of therapeutic potential against cancer. The feature of the surface coating can affect important properties of IONPs; it is therefore critical for further understanding how these materials react to physiological conditions, which is still needed to fully exploit the potential of IONPs for their theranostic applications. In this study, we explored the therapeutic potential of rutin and nisin conjugated IONPs as anticancer agents. One important hallmark of many cancers is the overexpression of the endoplasmic reticulum-resident chaperone, GRP78, and its translocation to many cellular compartments, including the cell membrane. We explored the potential binding affinity of rutin and nisin against the substrate-binding domain β (SBDβ) of GRP78. The results show promising results for both nisin and rutin, with more enhanced binding capability of the former due to its extended structure (peptide in nature), forming more non-bonded interactions with the GRP78 surface. Our findings pave the way for the use of these coating agents against the cell-exposed chaperone, GRP78, to alleviate its chemoresistance characteristics in cancer.