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Mácha H, Zápal J, Kuzma M, Luptáková D, Lemr K, Havlíček V. Exploring the Effects of Cyclosporin A to Isocyclosporin A Rearrangement on Ion Mobility Separation. Anal Chem 2024; 96:4163-4170. [PMID: 38430121 PMCID: PMC10938282 DOI: 10.1021/acs.analchem.3c05165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024]
Abstract
Cyclosporin A (CycA) is a peptide secondary metabolite derived from fungi that plays a crucial role in transplantation surgery. Cyclic traveling wave ion mobility mass spectrometry (IM-MS) revealed an N → O peptidyl shift in singly protonated CycA to isocyclosporin A (isoA), whereas no such isomerization was observed for doubly protonated and sodiated molecules. CycA and isoA were able to be separated by considering doubly protonated precursors using a specific ion fragment. In parallel, sodium ion stabilization facilitated the simultaneous separation and quantitation of singly charged cyclosporin isomers with the limit of detection and coefficient of determination of 1.3% and 0.9908 for CycA in isoA and 1.0% and 0.9830 for isoA in CycA, respectively. Finally, 1H-13C gHSQC NMR experiments permitted parallel recording of up to 11 cyclosporin conformers. The ratios were determined by integrating the volume of cross-peaks of the upfield resonating hydrogen in the diastereotopic methylene group of sarcosine-3.
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Affiliation(s)
- Hynek Mácha
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Jakub Zápal
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
| | - Marek Kuzma
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Dominika Luptáková
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
| | - Karel Lemr
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Vladimír Havlíček
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
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Zimnicka M, Kalenius E, Jurczak J, Danikiewicz W. Ion mobility mass spectrometry - an efficient tool for the analysis of conformational switch of macrocyclic receptors upon anion binding. Analyst 2021; 146:5337-5346. [PMID: 34323262 DOI: 10.1039/d1an00958c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactions between anions and synthetic macrocyclic receptors belong to the extensively explored area of research due to the particularly important functions of anions in biological and environmental sciences. Structures of anion-macrocycle complexes are closely related to their function, highlighting the importance of structural analysis of the complexes. Here, we discuss the application of ion mobility mass spectrometry (IM-MS) and theoretical calculations to the structural analysis of tetralactam macrocycles (M) with varying flexibility and structural properties, and their complexes with anions [M + X]-. Collision cross section (CCS) values obtained from both direct drift tube (DT) and indirect using traveling-wave (TW) IM-MS measurements supplemented by theoretical calculations were successfully used to describe the structural properties of various macrocycle-anion complexes, proving the suitability of the IM-MS approach for sensitive, selective, and fast detection of anion complexes and characterization of their structures and conformations.
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Affiliation(s)
- Magdalena Zimnicka
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Gray ALH, Steren CA, Haynes IW, Bermejo GA, Favretto F, Zweckstetter M, Do TD. Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis- Trans Isomerization and the Chameleonic Roles of Calcium. J Phys Chem B 2021; 125:1378-1391. [PMID: 33523658 DOI: 10.1021/acs.jpcb.0c11152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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 Ca2+, 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 CDCl3. To adopt these conformations, the macrocyclic ring has to twist and bend via cis-trans 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 CD3OD/H2O and 55% in CD3CN. However, upon interacting with Ca2+, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca2+ complex is open and has all-trans peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one cis peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the cis-MeLeu9-MeLeu10 peptide bond into a trans 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 Ca2+:CycA complex may play an essential role in the binding of CycA to CypA.
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Affiliation(s)
- Amber L H Gray
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Carlos A Steren
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Isaac W Haynes
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Guillermo A Bermejo
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Filippo Favretto
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany.,Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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Link BA, Sindt AJ, Shimizu LS, Do TD. Selective host-guest chemistry, self-assembly and conformational preferences of m-xylene macrocycles probed by ion-mobility spectrometry mass spectrometry. Phys Chem Chem Phys 2020; 22:9290-9300. [PMID: 32309846 DOI: 10.1039/c9cp06938k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We demonstrated ion-mobility spectrometry mass spectrometry (IMS-MS) as a powerful tool for interrogating and preserving selective chemistry including non-covalent and host-guest complexes of m-xylene macrocycles formed in solution. The technique readily revealed the unique favorability of a thiourea-containing macrocycle MXT to Zn2+ to form a dimer complex with the cation in an off-axis sandwich structure having the Zn-S bonds in a tetrahedral coordination environment. Replacing thiourea with urea generates MXU which formed high-order oligomerization with weak binding interactions to neutral DMSO guests detected at every oligomer size. The self-assembly pathway observed for this macrocycle is consistent with the crystalline assembly. Further transformation of urea into squaramide produces MXS, a rare receptor for probing sulfate in solution. Tight complexes were observed for both monomeric and dimeric of MXS in which HSO4- bound stronger than SO42- to the host. The position of HSO4- at the binding cavity is a 180° inversion of the reported crystallographic SO42-. The MXS dimer formed a prism-like shape with HSO4- exhibiting strong contacts with the 8 amine protons of two MXS macrocycles. By eliminating intermolecular interferences, we detected the low energy structures of MXS with collisional cross section (CCS) matching cis-trans and cis-cis squaramides-amines, both were not observed in crystallization trials. The experiments collectively unravel multiple facets of macrocycle chemistry including conformational flexibility, self-assembly and ligand binding; all in one analysis. Our findings illustrate an inexpensive and widely applicable approach to investigate weak but important interactions that define the shape and binding of macrocycles.
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Affiliation(s)
- Benjamin A Link
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA.
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