In my wildest dreams I would never have predicted that, one day, PAMPA (parallel artificial membrane permeability assay) would be so meaningful in my lab’s research. I think it is a superb way to evaluate the capacity of complex structures to undergo conformational rearrangements that result if modulation of polar surface area (PSA). The reason these measurements are all the rage nowadays is that PAMPA data correlates with cellular permeability, which is paramount in chemical biology and drug discovery. Briefly, the idea is to set up an experiment that is sketched below. You can see a small apparatus that contains two compartments separated by a hydrophobic membrane. Once injected into the donor well, a compound will eventually equilibrate and, depending on its balance of properties, will be more or less membrane-permeable. The ratio of concentrations is eventually converted to a number on a log scale. The lower the number, the better is the chance that the molecule of interest would be capable of traversing hydrophobic cellular membranes. You might ask: why use this contraption in favor of the “real world”? After all, a myriad different cell lines are available, of which Caco-2 is most commonly used in drug discovery. The answer lies in the presence of transporters in all those cells. Transporter proteins work as chaperones, pumping molecules in and out of cells. As a result, if one relies on cellular assays, too many false negatives would be generated. Interesting molecules might then be discarded too early. This is why researchers have embraced PAMPA as the go-to tool that is not confounded by nature’s tricks of active transport.
Synthetic chemists love to think in terms of intricate three-dimensional arrangements of atoms in their molecules, so how can PAMPA data relate to structure? This is exactly why I used to look down on seemingly “low-tech” methods such as PAMPA, but I have changed my mind. We recently published a paper where we were able to show how our macrocycles exercise control over the formation of hydrogen bond networks. You can see a comparison between one of our molecules on the left and the corresponding homodetic control. The linker region is our patented trick to modulate PSA. Dr. Jen Hickey of Encycle Therapeutics deserves a ton of credit for bringing this study to fruition.