Human and animal cells are very complex: very different chemical processes are going on at the same time, but they are separated from each other because the cells are divided in compartments. These compartments may also have a profound effect on the potential efficacy of therapeutics, because the drug needs to end up in the same compartment as the target it is aimed at.

Cell compartments make lead optimization unpredictable

Developing targets has been particularly troublesome in the treatment of bacteria that hide themselves within our cells to evade the immune system, because antibiotics also have to accumulate in the same compartment to be able to kill the bacteria. If this doesn’t match, this can lead to late-stage failure of the therapy, and this effect isn’t always visible in in vitro assays. All in all, cell compartments have led to the late-stage failure of many promising antibiotics and the surprising success of others. In short: it’s unpredictable.

Seeing the fate of intracellular bacteria

In order to facilitate the success of this pipeline, we have developed two imaging technologies that allows us to image the fate of intracellular pathogens in detail. This approach, called ‘correlative light-electron microscopy’ (CLEM), in combination with click chemistry, makes it possible to study and quantify antibiotic efficacy against intracellular pathogens. If we then combine CLEM with antibiotic treatment we can study how these antibiotics affect bacteria residing in different subcellular compartments. 

Localizing the therapy in the cell

We have also developed a technique to pinpoint the activity of target and/or therapeutic enzymes. Using this method, we were able to show that the therapeutic enzyme Cerezyme accumulated in the correct subcellular vesicles after enzyme replacement therapy. 

To conclude, this case study highlights the role that high-resolution and high-content imaging can play in the lead optimization process. Because if we can evaluate lead candidates in detail, any late-stage in vivo hurdles can be prevented.