Computational characterization of GRP78 binding sites on mitochondrial GPX4: implications for targeting ferroptosis in triple-negative breast cancer

Abstract

Abstract About 20% of breast cancer cases are triple-negative breast cancer (TNBC), a highly aggressive subtype with limited therapeutic options. Emerging evidence suggests that ferroptosis — a form of regulated cell death — and stress-response pathways play critical roles in TNBC progression. We investigated the interaction between glucose-regulated protein 78 (GRP78), a central stress-response chaperone, and mitochondrial glutathione peroxidase 4 (mGPX4), a key regulator of ferroptosis resistance. Using a combined computational approach — including protein–protein docking, molecular dynamics (MD) simulations, and MM/GBSA free-energy calculations — we identified stable complexes between GRP78’s SBDβ domain and several regions of mGPX4. Docking with PRODIGY revealed binding affinities ranging from − 7.7 ± 0.5 to − 10.5 ± 0.6 kcal/mol, surpassing that of Pep42 (–6.9 ± 0.1 kcal/mol), with region III (the mitochondrial import sequence) showing the strongest binding (–10.5 ± 0.6 kcal/mol). HADDOCK scoring further highlighted region II as particularly favorable (–72.0 ± 5.4). After 100 ns of MD, MM/GBSA analysis estimated binding free energies from − 45.20 to − 86.39 kcal/mol, with the region-II complex exhibiting the highest affinity (–86.4 kcal/mol), driven predominantly by electrostatic and van der Waals interactions. This interaction could serve as a promising therapeutic target to undermine cancer cell survival by sensitizing TNBC cells to ferroptosis-inducing strategies.