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Jwad R, Weissberger D, Hunter L. Strategies for Fine-Tuning the Conformations of Cyclic Peptides. Chem Rev 2020; 120:9743-9789. [PMID: 32786420 DOI: 10.1021/acs.chemrev.0c00013] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.
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Affiliation(s)
- Rasha Jwad
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
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Slough DP, McHugh SM, Lin YS. Understanding and designing head-to-tail cyclic peptides. Biopolymers 2018; 109:e23113. [PMID: 29528114 PMCID: PMC6135719 DOI: 10.1002/bip.23113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/30/2023]
Abstract
Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.
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Affiliation(s)
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, United States
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Slough DP, McHugh SM, Cummings AE, Dai P, Pentelute BL, Kritzer JA, Lin YS. Designing Well-Structured Cyclic Pentapeptides Based on Sequence-Structure Relationships. J Phys Chem B 2018; 122:3908-3919. [PMID: 29589926 PMCID: PMC6071411 DOI: 10.1021/acs.jpcb.8b01747] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides are a promising class of molecules for unique applications. Unfortunately, cyclic peptide design is severely limited by the difficulty in predicting the conformations they will adopt in solution. In this work, we use explicit-solvent molecular dynamics simulations to design well-structured cyclic peptides by studying their sequence-structure relationships. Critical to our approach is an enhanced sampling method that exploits the essential transitional motions of cyclic peptides to efficiently sample their conformational space. We simulated a range of cyclic pentapeptides from all-glycine to a library of cyclo-(X1X2AAA) peptides to map their conformational space and determine cooperative effects of neighboring residues. By combining the results from all cyclo-(X1X2AAA) peptides, we developed a scoring function to predict the structural preferences for X1-X2 residues within cyclic pentapeptides. Using this scoring function, we designed a cyclic pentapeptide, cyclo-(GNSRV), predicted to be well structured in aqueous solution. Subsequent circular dichroism and NMR spectroscopy revealed that this cyclic pentapeptide is indeed well structured in water, with a nuclear Overhauser effect and J-coupling values consistent with the predicted structure.
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Affiliation(s)
- Diana P. Slough
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
| | - Sean M. McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
| | | | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
| | - Yu -Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
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Toniolo C, Crisma M, Formaggio F, Alemán C, Ramakrishnan C, Kalmankar N, Balaram P. Intramolecular backbone···backbone hydrogen bonds in polypeptide conformations. The other way around: ɛ-turn. Biopolymers 2017; 108. [DOI: 10.1002/bip.22911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/17/2016] [Accepted: 06/29/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Carlos Alemán
- Departament d'Enginyeria Quimica; ETSEIB, Universitat Politècnica de Catalunya; Barcelona 08028 Spain
| | | | - Neha Kalmankar
- National Centre for Biological Sciences (TIFR); GKVK Campus Bangalore 560065 India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
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Arnhold FS, Linden A, Heimgartner H. Synthesis of Aib- and Phe(2Me)-Containing Cyclopentapeptides. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201400323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Culf AS, Čuperlović-Culf M, Léger DA, Decken A. Small head-to-tail macrocyclic α-peptoids. Org Lett 2014; 16:2780-3. [PMID: 24797336 DOI: 10.1021/ol501102b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute , 35 Providence Street, Moncton, NB E1C 8X3, Canada
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Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control. J Mol Model 2012; 18:3181-97. [DOI: 10.1007/s00894-011-1326-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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Chatterjee J, Mierke D, Kessler H. N-methylated cyclic pentaalanine peptides as template structures. J Am Chem Soc 2007; 128:15164-72. [PMID: 17117868 DOI: 10.1021/ja063123d] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The N-methylation of cyclic peptides can be used to modify the activity and/or selectivity of biologically active peptides. As N-methylation introduces different flexibility and lipophilicity, it can also improve the bioavailability (the ADMET profile). To search for conformationally constrained cyclic peptides, a library of 30 different N-methylated peptides with the basic sequence cyclo(-D-Ala-L-Ala4-) was synthesized. Based on the NMR analysis, seven of these peptides exhibited single conformations (>98%). The structural features of these peptides were determined by a combination of NMR and distance geometry and then further refined by molecular dynamics simulations in an explicit DMSO solvent box. The structures provided from these efforts can now serve as templates for the rational design of cyclic pentapeptides with a distinct backbone conformation or for "spatial screening" to explore the bioactive conformation of medically important peptide systems.
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Affiliation(s)
- Jayanta Chatterjee
- Department Chemie, Lehrstuhl II für Organische Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
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Heimgartner H, Arnhold FS, Fritschi SP, Koch KN, Magirius JEF, Linden A. 1,3-Oxazol-5(4H)-ones as intermediates in the formation of macrolides, cyclodepsipeptides and cyclopeptides. J Heterocycl Chem 1999. [DOI: 10.1002/jhet.5570360614] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Weisshoff H, Präsang C, Henklein P, Frömmel C, Zschunke A, Mügge C. Mimicry of beta II'-turns of proteins in cyclic pentapeptides with one and without D-amino acids. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 259:776-88. [PMID: 10092864 DOI: 10.1046/j.1432-1327.1999.00097.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The solution structure of eight cyclic pentapeptides has been determined by two-dimensional 1H-NMR spectroscopy combined with spectra simulations and restrained molecular dynamic simulations. Six of the cyclic pentapeptides were derived from the C-terminal cholecystokinin fragment CCK-4 enlarged with Asp1 resulting in the sequence (Asp-Trp-Met-Asp-Phe), one L-amino acid after the other was substituted by its D-analog. In addition, two peptides, including an all-L-amino-acid-containing cyclic pentapeptide, cyclo(Asp-Phe-Lys-Ala-Thr) and cyclo(Asp-Phe-Lys-Ala-D-Thr) were investigated. All D-amino-acid-containing peptides show beta II'-turn conformations with the D-amino acid in the i + 1 position, excepting the D-aspartic-acid-containing peptides. These two peptides are characterized by the lack of beta-turns at pH values less than 4, suggesting that D-aspartic acid in the full-protonized state avoids the formation of beta-turns in these compounds. At pH values greater than 5, a conformational change into the beta II'-turn conformation was also observed for these peptides. Conformations without beta-turns are expected for cyclic all-L pentapeptides, but both cyclo(Asp-Phe-Lys-Ala-Thr) and the D-Thr analog cyclo(Asp-Phe-Lys-Ala-D-Thr) exhibit beta II'-turn conformations around Thr-Asp and D-Thr-Asp. Thus cyclic all-L pentapeptides and those with one D-amino acid are able to form similar structures preferably with a beta II'-turn. The beta-turn formation in cyclic pentapeptides containing a D-aspartic acid is dependent on the ionization state. The relevance of the work to the design of beta'-turn mimetics is discussed.
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Affiliation(s)
- H Weisshoff
- Institute of Chemistry, Humboldt University Berlin, Germany
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