Light-Activated Metal-dependent Protein Degradation (LAMP-D): A Heterobifunctional Ruthenium(II) Photosensitizer Targeting New Delhi Metallo-β-lactamase 1

The growth of antimicrobial resistance (AMR) is a significant global health threat, yet despite this alarming trend, antibiotic drug discovery has significantly slowed. Most compounds entering the clinic represent already discovered classes of compounds, to which bacteria have already established resistance mechanisms. We urgently need novel therapeutic modalities to address these resistances. Targeted protein degradation, typified by the highly successful proteolysis-targeting chimeras (PROTACs) is a promising approach that has already been successfully employed in oncology. Recently, the development of bacterial PROTACs (BacPROTACs) has shown that this modality can also be adapted to bacteria. A significant hurdle faced by these methods, however, is the complexity inherent in recruiting the host cell’s proteolytic processes. We herein describe an approach where the proteolysis is performed directly by a light-activated ruthenium complex, termed LAMP-D (Light-Activated Metal-dependent Protein Degradation), thus circumventing the need for ligase recruitment. Additionally, this method allows precise spatiotemporal control of protein degradation and may be adapted to degrade other proteins of interest. In a proof-of-concept study, New Delhi metallo-β-lactamase 1 (NDM-1) was chosen as a target protein for LAMP-D inhibition and degradation. NDM-1 is employed by Gram-negative bacteria to hydrolyse and inactivate β-lactam antibiotics and is considered one of the most clinically relevant β-lactamase targets due to its global prevalence. In in vitro assays, the complex Ru1 demonstrated a greater than 100-fold improvement in NDM-1 inhibition on exposure to light (450 nm, 20 J cm-2). Detailed analysis by SDS-PAGE, intact mass spectrometry and trypsin digest mass spectrometry show that Ru1 induces highly specific degradation of the protein adjacent to the active site. Ru1 was shown to inhibit NDM-1 in Escherichia coli expressing NDM-1 and demonstrated excellent rescue of antibiotic activity upon co-treatment with meropenem, exhibiting a 53-fold improvement in meropenem MIC with light irradiation (450 nm, 60 J cm-2). Furthermore, the complex was found to be highly selective, exhibiting no toxicity toward mammalian cells. Given the versatility, specificity, and controllability of LAMP-D, we believe that this degradation strategy will find broad application in combating antibiotic resistance and beyond.