Developing a high throughput assay for determining an accurate intracellular concentration of compounds within gram-negative bacteria

Antibiotic resistance is an ever-growing problem in today's society and is only going to worsen through a combination of both the inappropriate use of antibiotics and a lack of new discovery. The most problematic resistant organisms are the ESKAPE pathogens and more specifically those that are Gram-negative. There are on-going efforts to develop new antibacterials to combat antimicrobial resistance in these problematic pathogens through both phenotypic and target-based drug discovery. The key issue with phenotypic screening though is that resource exhaustion is becoming a real possibility. With the majority of chemical libraries having already been screened, there are fewer novel hits being identified through this approach. Conversely, with target-based screening, the key issue is translation of the biochemical screen activity to whole cell activity. However, due to not having control over resource exhaustion, the target-based approach has been more readily adopted in recent times. The reason cellular activity is an issue in target-based screens is that inhibitors of bacterial proteins are often discovered during biochemical screening, but they do not work in the whole bacteria due to insufficient compound exposure in the bacteria, likely a consequence of poor permeation and/or efflux. Currently there is not a good enough understanding of how to improve the bacterial cell envelope permeability of current and newly discovered inhibitory compounds. The main way to help develop this understanding is through screening compounds for intracellular penetration in ESKAPE pathogens and identifying features that contribute to improving intracellular exposure. There are assays that currently exist that can be utilized to help investigate this and some have proved to be useful in providing very loose guidance on changes that can potentially increase intracellular penetration. These currently available assays, despite proving useful, cannot be used at the capacity to support drug discovery programmes, due to either limited throughput or limited accuracy. In this study we firstly developed a new assay that has both the appropriate level of throughput and resolution, and then demonstrated how it can be utilized to not only assist drug discovery programmes but can also be used in large screens to help take the necessary steps in developing a better understanding around compound intracellular exposure in Gram-negative ESKAPE pathogens.