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Abstract
The chameleonic behavior of cyclosporin A (CsA) was investigated through conformational ensembles employing multicanonical molecular dynamics simulations that could sample the cis and trans isomers of N-methylated amino acids; these assessments were conducted in explicit water, dimethyl sulfoxide, acetonitrile, methanol, chloroform, cyclohexane (CHX), and n-hexane (HEX) using AMBER ff03, AMBER10:EHT, AMBER12:EHT, and AMBER14:EHT force fields. The conformational details were discussed employing the free-energy landscapes (FELs) at T = 300 K; it was observed that the experimentally determined structures of CsA were only a part of the conformational space. Comparing the ROESY measurements in CHX-d12 and HEX-d14, the major conformations in those apolar solvents were essentially the same as that in CDCl3 except for the observation of some sidechain rotamers. The effects of the metal ions on the conformations, including the cis/trans isomerization, were also investigated. Based on the analysis of FELs, it was concluded that the AMBER ff03 force field best described the experimentally derived conformations, indicating that CsA intrinsically formed membrane-permeable conformations and that the metal ions might be the key to the cis/trans isomerization of N-methylated amino acids before binding a partner protein.
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Affiliation(s)
- Satoshi Ono
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Matthew R Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chieko Okumura
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Okimasa Okada
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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2
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Abstract
Cyclosporins are natural or synthetic undecapeptides with a wide range of actual and potential pharmaceutical applications. Several members of the cyclosporin compound family have remarkably high passive membrane permeabilities that are not well-described by simple structural metrics. Here we review experimental studies of cyclosporin structure and permeability, including cyclosporin-metal complexes. We also discuss models for the conformation-dependent permeability of cyclosporins and similar compounds. Finally, we identify current knowledge gaps in the literature and provide recommendations regarding future avenues of exploration.
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Affiliation(s)
- Karen M Corbett
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Leigh Ford
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Dallas B Warren
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - David K Chalmers
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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3
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Nguyen QNN, Schwochert J, Tantillo DJ, Lokey RS. Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach. Phys Chem Chem Phys 2018; 20:14003-14012. [DOI: 10.1039/c8cp01616j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), a new approach for determining solution structures.
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4
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Kahlert V, Prell E, Ohlenschläger O, Melesina J, Schumann M, Lücke C, Fischer G, Malešević M. Synthesis and biochemical evaluation of two novel N-hydroxyalkylated cyclosporin A analogs. Org Biomol Chem 2018; 16:4338-4349. [DOI: 10.1039/c8ob00980e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
N-Hydroxyalkylation of cyclosporine A residues Val5 and d-Ala8 significantly influenced their conformation behavior and pharmacological properties.
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Affiliation(s)
- Viktoria Kahlert
- Max Planck Research Unit for Enzymology of Protein Folding
- 06120 Halle/Saale
- Germany
| | - Erik Prell
- Max Planck Research Unit for Enzymology of Protein Folding
- 06120 Halle/Saale
- Germany
- Max-Planck Institute for Biophysical Chemistry
- Göttingen
| | | | - Jelena Melesina
- Martin-Luther-University Halle-Wittenberg
- Institute of Pharmacy
- Medicinal Chemistry department
- 06120 Halle
- Germany
| | - Michael Schumann
- Max Planck Research Unit for Enzymology of Protein Folding
- 06120 Halle/Saale
- Germany
- Martin-Luther-University Halle-Wittenberg
- Institute of Biochemistry and Biotechnology
| | - Christian Lücke
- Max Planck Research Unit for Enzymology of Protein Folding
- 06120 Halle/Saale
- Germany
| | - Gunter Fischer
- Max Planck Research Unit for Enzymology of Protein Folding
- 06120 Halle/Saale
- Germany
- Max-Planck Institute for Biophysical Chemistry
- Göttingen
| | - Miroslav Malešević
- Max Planck Research Unit for Enzymology of Protein Folding
- 06120 Halle/Saale
- Germany
- Martin-Luther-University Halle-Wittenberg
- Institute of Biochemistry and Biotechnology
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5
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Lin W, Erdmann F, Quintero A, Fischer G, Zhang Y. Thioxylated cyclosporin A for studying protein-drug interactions. Bioorg Med Chem Lett 2016; 26:5754-5756. [PMID: 27815116 DOI: 10.1016/j.bmcl.2016.10.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 12/20/2022]
Abstract
Single atom substitution of cyclosporin A (CsA) through thioxylation has been used to study the structure-activity relationship of the immunosuppressive complex, involving the CsA receptor protein cyclophilin 18 (Cyp18) and the immunological target protein phosphatase calcineurin (CaN), illustrating the contributions of peptide backbone in protein-drug interaction. Moreover, the subtle difference between thioxylation positions in CsA has led to a remarkable change in the quenching effect on Cyp18 intrinsic fluorescence. Using the thioxylated compound Cs7 as an isosteric derivative of CsA in competition assay, the experiment has led to the determination of koff value in solution. Whereas the conformational heterogeneity of CsA has been found to be associated with its two-phase binding kinetics to Cyp18, the dissociation rate of CsA from complex is independent from the initial ligand structure.
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Affiliation(s)
- Weilin Lin
- B CUBE Center for Molecular Bioengineering, Technical University Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Frank Erdmann
- Institute for Pharmacy, Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Andres Quintero
- B CUBE Center for Molecular Bioengineering, Technical University Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Gunter Fischer
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, BO Halle (Saale) Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Yixin Zhang
- B CUBE Center for Molecular Bioengineering, Technical University Dresden, Arnoldstr. 18, 01307 Dresden, Germany.
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