title: Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States.
abstract: The membrane permeability of cyclic peptides and peptidomimetics, which are generally larger and more complex than typical drug molecules, is likely strongly influenced by the conformational behavior of these compounds in polar and apolar environments. The size and complexity of peptides often limit their bioavailability, but there are known examples of peptide natural products such as cyclosporin A (CsA) that can cross cell membranes by passive diffusion. CsA is an undecapeptide with seven methylated backbone amides. Its crystal structure shows a "closed" twisted β-pleated sheet conformation with four intramolecular hydrogen bonds that is also observed in NMR measurements of CsA in chloroform. When binding to its target cyclophilin, on the other hand, CsA adopts an "open" conformation without intramolecular hydrogen bonds. In this study, we attempted to sample the complete conformational space of CsA in chloroform and in water by molecular dynamics simulations in order to better understand its conformational behavior in these two environments and to rationalize the good membrane permeability of CsA observed experimentally. From 10 μs molecular dynamics simulations in each solvent, Markov state models were constructed to characterize the metastable conformational states. The model in chloroform is compared to nuclear Overhauser effect NMR spectroscopy data reported in this study and taken from the literature. The conformational landscapes in the two solvents show significant overlap but also clearly distinct features.
authors.affiliation: Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
authors.forename: Jagna
authors.initials: J
authors.lastname: Witek
authors.affiliation: Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin , Takustrasse 3, 14195 Berlin, Germany.
authors.forename: Bettina G
authors.initials: BG
authors.lastname: Keller
authors.affiliation: Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, 4002 Basel, Switzerland.
authors.forename: Markus
authors.initials: M
authors.lastname: Blatter
authors.affiliation: Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, 4002 Basel, Switzerland.
authors.forename: Axel
authors.initials: A
authors.lastname: Meissner
authors.affiliation: Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, 4002 Basel, Switzerland.
authors.forename: Trixie
authors.initials: T
authors.lastname: Wagner
authors.affiliation: Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
authors.forename: Sereina
authors.initials: S
authors.lastname: Riniker
mesh_terms: D002463:Cell Membrane Permeability; D016572:Cyclosporine / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D006871:Hydrophthalmos; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D016572:Cyclosporine