David W. Gray

Multidrug efflux pumps are major drivers of antibiotic resistance, yet progress in understanding and inhibiting these transporters has been limited by a lack of selective chemical probes and inhibitor-bound structures. Here we report IMP-2380, a potent and selective chemical probe targeting the clinically important Staphylococcus aureus efflux pump NorA. A phenotypic high-throughput screen monitoring suppression of the ciprofloxacin-induced SOS DNA damage response identified a chemical series that selectively inhibits NorA and was optimized to yield IMP-2380. The probe restores ciprofloxacin susceptibility in methicillin-resistant S . aureus , delivering low-nanomolar potentiation in vitro and robust efficacy in an in vivo infection model. Cryo-electron microscopy at 2.52-Å resolution revealed the structure of NorA bound to a small-molecule inhibitor. IMP-2380 binds an ‘outward-open’ transporter conformation, occluding the cytosolic substrate-binding cavity and preventing antibiotic efflux. IMP-2380 provides a high-quality probe for dissecting multidrug efflux and establishes a structural framework for restoring antibiotic efficacy through efflux pump inhibition.

Different biochemical assays yield different rates of false positives than others either due to the nature of the enzyme, the technology associated with the assay, or properties of the compounds being screened. Ensuring that the right counter-screens are in place to identify false positives without wasting time and resources on them is of great importance. Herein we describe the results of a high throughput screen (HTS) against non-structural protein 3 (nsp3) protease PL ^Pro , which resulted exclusively in false-positive hits. By triaging hit compounds through purification of metal chelating resin, we identified contamination by either copper or palladium as the most likely source of false positives from the library screening campaign. We then performed a systematic assessment of the vulnerability of nsp3 protease screening to metal contamination and evaluated common additives to combat the inhibitory effects of different metal salts. We further conducted a thorough survey of the literature reports of nsp3 HTS campaigns with a focus on the presence of additives and what metal susceptibility was likely, given the results of our work. We conclude that the majority of reported nsp3 screens are susceptible to copper contamination with a smaller proportion also potentially susceptible to palladium contamination.

Antibiotic resistance is among the greatest threats of the modern era. Multidrug efflux pumps expel antibiotics from bacterial cells and present a particular challenge by conferring resistance to a broad range of antibiotic classes; however, there is currently a lack of potent and selective inhibitors. Here, we report the discovery of IMP-2380 , a drug-like chemical probe for the multidrug efflux pump NorA that delivers low-nanomolar potentiation of ciprofloxacin activity in vitro and activity in an in vivo S. aureus infection model. A phenotypic high-throughput screen for inhibitors of the ciprofloxacin-activated SOS DNA repair pathway in methicillin-resistant Staphylococcus aureus (MRSA) identified hit compounds targeting NorA, and subsequent optimization established IMP-2380 as the most potent NorA inhibitor discovered to date. The structure of NorA bound to IMP-2380 was solved by cryo-electron microscopy at 2.52 Å resolution, revealing that the small molecule locks the pump in the ‘outward-open’ conformation. This closes the inner face and prevents antibiotics binding from the cytosol, providing an explanation for the exceptional potency of IMP-2380 and structure-activity relationship across the series. IMP-2380 represents an in vivo active NorA inhibitor, functioning via a structurally defined outward-open binding mode, and will enable future exploration of NorA as a druggable target to combat antibiotic resistance.

Background Senescence identification is rendered challenging due to a lack of universally available biomarkers. This represents a bottleneck in efforts to develop pro-senescence therapeutics – agents designed to induce the arrest of cellular proliferation associated with a senescence response in cancer cells for therapeutic gain. This is particularly true in contexts such as basal-like breast cancer (BLBC), which often express high levels of widely reported senescence hallmarks, which has led to the designation of these subtypes as senescence marker positive (Sen-Mark+). Unfortunately, these are often cancers with the most limited treatment options, where novel pro-senescence compounds would be of potential clinical utility. Results To address these challenges, we have developed SAMP-Score, a machine learning classification tool for identifying senescence induction in Sen-Mark+ cancers. This technique builds upon our previous observation that senescent cells develop distinct senescence-associated morphological profiles (SAMPs), which can be assessed readily in traditionally challenging contexts for senescence identification, including high-throughput screens. Conclusions Through application of SAMP-Score, we have identified QM5928, a novel pro-senescence compound, that is able to induce senescence in a variety of Sen-Mark+ cancers and has potential utility as a tool molecule to explore the mechanisms and pathways through which senescence induction occurs in these cells.

The maturation of the RNA cap involving guanosine N-7 methylation, catalyzsed by the HsRNMT (RNA guanine-7 methyltransferase (HsRNMT)-RAM (RNA guanine-N7 methyltransferase activating subunit (RAM) complex, is currently under investigation as a novel strategy to combat PIK3CA -mutant breast cancer. However, the development of effective drugs is hindered by a limited understanding of the enzyme’s mechanism and a lack of small molecule inhibitors. Following the elucidation of the HsRNMT-RAM molecular mechanism, we report the biophysical characterizsation of two small molecule hits. Biophysics, biochemistry and structural biology confirm that both compounds bind competitively with cap and bind effectively to HsRNMT-RAM in the presence of the co-product SAH, with a binding affinity (KD) of approximately 1 μM. This stabilisation of the enzyme-–product complex results in uncompetitive inhibition. Finally, we describe the properties of the cap pocket and provided suggestions for further development of the tool compounds.

The maturation of the RNA cap involving guanosine N-7 methylation, catalyzed by the HsRNMT (RNA guanine-7 methyltransferase)-RAM (RNA guanine-N7 methyltransferase activating subunit) complex, is currently under investigation as a novel strategy to combat PIK3CA mutant breast cancer. However, the development of effective drugs is hindered by a limited understanding of the enzyme’s mechanism and a lack of small molecule inhibitors. Following the elucidation of the Hs RNMT-RAM molecular mechanism, we report the biophysical characterization of two small molecule hits. Biophysics, biochemistry and structural biology confirm that both compounds bind competitively with cap and bind effectively to Hs RNMT-RAM in the presence of the co-product SAM, with a binding affinity (K _D ) of approximately 1 μM. This stabilisation of the enzyme-product complex results in uncompetitive inhibition. Finally, we describe the properties of the cap pocket and provided suggestions for further development of the tool compounds.