Structural Flexibility of Cyclosporine A Is Mediated by Amide - Isomerization and the Chameleonic Roles of Calcium.

Falling outside of Lipinski's rule of five, macrocyclic drugs have accessed unique binding sites of their target receptors unreachable by traditional small molecules. Cyclosporin(e) A (CycA), an extensively studied macrocyclic natural product, is an immunosuppressant with undesirable side effects such as electrolytic imbalances. In this work, a comprehensive view on the conformational landscape of CycA, its interactions with Ca, and host-guest interactions with cyclophilin A (CypA) is reported through exhaustive analyses that combine ion-mobility spectrometry-mass spectrometry (IMS-MS), nuclear magnetic resonance (NMR) spectroscopy, distance-geometry modeling, and NMR-driven molecular dynamics. Our IMS-MS data show that CycA can adopt extremely compact conformations with significantly smaller collisional cross sections than the closed conformation observed in CDCl. To adopt these conformations, the macrocyclic ring has to twist and bend via - isomerization of backbone amides, and thus, we termed this family of structures the "bent" conformation. Furthermore, NMR measurements indicate that the closed conformation exists at 19% in CDOD/HO and 55% in CDCN. However, upon interacting with Ca, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca complex is open and has all- peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the -MeLeu9-MeLeu10 peptide bond into a bond. Last, we were able to capture the native binding of CycA and CypA to give forth evidence that IMS-MS is able to probe the solution-phase structures of the complexes and that the Ca:CycA complex may play an essential role in the binding of CycA to CypA.