Employing Metadynamics to Predict the Membrane Partitioning of Carboxy-2H-Azirine Natural Products

Natural products have diverse chemical structures and biological activities which often serve as sources of new therapeutic agents. Those containing a carboxy-2H-azirine moiety are an exciting target for investigation due in part to the broad-spectrum antimicrobial activity these compounds have and the significant chemical space for novel therapeutic development offered by this unique scaffold. The carboxy-2H-azirine moiety, including those appended to well-characterized chemical scaffolds, is understudied, which creates a challenge for understanding potential modes of inhibition. In particular, some known natural product carboxy-2H-azirines have long hydrophobic tails, which might lead to amphipathicity and implicate them in membrane associated processes. Metadynamics is an effective method for calculating the free energy changes associated with membrane embedding processes. In this study, we examined a small set of carboxy-2H-azirine natural products, including analogs with long alkyl chains, geometric isomers, and one comprising the simple carboxy-2H-azirine core. We compared the physiochemical properties of these compounds to those of established membrane embedders with similar chemical scaffolds. This was intended to isolate the physiochemical properties of the carboxy-2H-azirine group and understand molecular influences of this moiety on membrane partitioning. To accomplish this, we developed a force field for the 2H-azirine functional group and performed metadynamics simulations of the partitioning into a model membrane (75 % POPE, 25 % POPG) from aqueous solution. We determine that the carboxy-2H-azirine functional group is likely hydrophilic, imbuing the long chain analogs with amphipathicity similar to the known membrane binding molecules to which they were compared. For the long chain analogs, the carboxy-2H-azirine headgroup stays within 1 nm of the phosphate layer, while the carboxy-2H-azirines lacking the long alkyl chain partitions completely into aqueous solution.