A Novel Antibacterial Adjuvant, SKQ1, Targeting NDM-1 to Overcome Meropenem-resistant Escherichia coli

The widespread dissemination of New Delhi metallo-β-lactamase-1 (NDM-1) has severely compromised the clinical efficacy of carbapenem antibiotics. SKQ1 was identified through surface plasmon resonance (SPR)-based screening. Broth microdilution checkerboard assays demonstrated strong synergy between SKQ1 and meropenem (FICI = 0.25–0.5). Enzyme kinetic analyses revealed that SKQ1 acts as a noncompetitive inhibitor of NDM-1 (IC₅₀ =34.99 ± 3.13 μg/mL). Molecular docking, molecular dynamics simulations, microscale thermophoresis (MST) and thermal stability assays collectively demonstrated the direct binding of SKQ1 to NDM-1, resulting in the inhibition of its hydrolytic activity. Further analyses revealed that SKQ1 exhibits potent membrane activity, disrupting membrane integrity, altering the membrane potential and inducing oxidative stress, which also underlies its strong synergy with colistin. Both in vitro and in vivo models confirmed its synergistic efficacy. SKQ1 reduced the effective doses of meropenem and colistin while attenuating lipopolysaccharide (LPS)-induced inflammation, thereby enhancing therapeutic efficacy against multidrug-resistant infections. Together, these findings demonstrate that SKQ1 overcomes resistance through a dual mechanism of enzyme inhibition and membrane disruption, offering a novel strategy for developing synergistic therapies against multidrug-resistant bacteria.