Discovery of two aminoglycoside antibiotics as inhibitors targeting the menin–mixed lineage leukaemia interface

[Display omitted] Menin functions as an oncogenic cofactor of mixed lineage leukaemia (MLL) fusion proteins in leukaemogenesis. The menin–MLL interface is a potential therapeutic target in acute leukaemia cases. In this study, approximately 900 clinical compounds were evaluated and ranked using pharmacophore-based virtual screening, the top 29 hits were further evaluated by biochemical analysis to discover the inhibitors that target the menin–MLL interface. Two aminoglycoside antibiotics, neomycin and tobramycin, were identified as menin–MLL inhibitors with binding affinities of 18.8 and 59.9μM, respectively. The results of thermal shift assay validated the direct interactions between the two antibiotics and menin. The results of isothermal titration calorimetry showed that the equilibrium dissociation constant between menin and neomycin was approximately 15.6μM. We also predicted the binding modes of inhibitors at the menin–MLL interface through molecular docking analysis. The results indicated that neomycin and tobramycin competitively occupy the binding site of MLL. This study has shed light on the development of powerful probes and new therapies for MLL-mediated leukaemogenesis.