Structure-Directed Optimization of Ebselen Derivatives as Potent NDM‑1 Inhibitors Reverses Meropenem Resistance

“Superbugs” harboring the New Delhi metallo-β-lactamase-1 (NDM-1) have disseminated globally, posing a severe threat to the clinical efficacy of β-lactam antibiotics. Developing NDM-1 inhibitors to restore the efficacy of β-lactam antibiotics against resistant bacteria is critically important. Using ebselen as a lead, we designed and synthesized 59 novel derivatives to develop potent NDM-1 inhibitors. Among them, compound 27k demonstrated the most potent NDM-1 inhibitory activity with an IC50 value of 1.12 μM. The combination of 27k and Mem reduced the minimum inhibitory concentration (MIC) of Mem by 4–16-fold in NDM-1-producing isolates. Importantly, the combination of 27k and Mem effectively suppressed the bacterial loads in mice. Mechanistically, 27k effectively inhibits the activity of NDM-1 by forming a Se–S covalent bond with the NDM-1 protein. Collectively, these findings confirm that compound 27k is an excellent NDM-1 covalent inhibitor, offering a promising lead compound for addressing bacterial resistance driven by NDM-1.