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Singh K, Tripathi RP. An Overview on Glyco-Macrocycles: Potential New Lead and their Future in Medicinal Chemistry. Curr Med Chem 2020; 27:3386-3410. [PMID: 30827227 DOI: 10.2174/0929867326666190227232721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
Macrocycles cover a small segment of molecules with a vast range of biological activity in the chemotherapeutic world. Primarily, the natural sources derived from macrocyclic drug candidates with a wide range of biological activities are known. Further evolutions of the medicinal chemistry towards macrocycle-based chemotherapeutics involve the functionalization of the natural product by hemisynthesis. More recently, macrocycles based on carbohydrates have evolved a considerable interest among the medicinal chemists worldwide. Carbohydrates provide an ideal scaffold to generate chiral macrocycles with well-defined pharmacophores in a decorated fashion to achieve the desired biological activity. We have given an overview on carbohydrate-derived macrocycle involving their synthesis in drug design and discovery and potential role in medicinal chemistry.
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Affiliation(s)
- Kartikey Singh
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Rama Pati Tripathi
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India.,National Institute of Pharmaceutical Education and Research Raebareli, New Transit Campus, Bijnor Road, Sarojani Nagar Near CRPF Base Camp, Lucknow 226002, U.P., India
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2
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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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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] [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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Tian GZ, Wang XL, Hu J, Wang XB, Guo XQ, Yin J. Recent progress of sugar amino acids: Synthetic strategies and applications as glycomimetics and peptidomimetics. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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5
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Oligomers and peptidomimetics consisting of methyl 3-amino-2,3-dideoxyhexopyranosiduronic acids. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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6
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Xie J, Bogliotti N. Synthesis and applications of carbohydrate-derived macrocyclic compounds. Chem Rev 2014; 114:7678-739. [PMID: 25007213 DOI: 10.1021/cr400035j] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Juan Xie
- PPSM, Institut d'Alembert, ENS Cachan, CNRS, UMR 8531 , 61 av. Président Wilson, F-94235 Cachan Cedex, France
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7
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Feher-Voelger A, Borges-González J, Carrillo R, Morales EQ, González-Platas J, Martín T. Synthesis and conformational analysis of cyclic homooligomers from pyranoid ε-sugar amino acids. Chemistry 2014; 20:4007-22. [PMID: 24616150 DOI: 10.1002/chem.201303841] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/16/2013] [Indexed: 12/12/2022]
Abstract
New pyranoid ε-sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution-phase coupling procedures, cyclic homooligomers containing pyranoid ε-sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X-ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U-shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five-membered hydrogen-bonded pseudocycles (C5) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.
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Affiliation(s)
- Andrés Feher-Voelger
- Instituto de Productos Naturales y Agrobiología-CSIC, Avda. Astrofísico Francisco Sánchez, 3, 38206-La Laguna, Tenerife (Spain), Fax: (+34) 922-260135
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8
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A compendium of cyclic sugar amino acids and their carbocyclic and heterocyclic nitrogen analogues. Amino Acids 2013; 45:613-89. [DOI: 10.1007/s00726-013-1521-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022]
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9
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Lv J, Yang D. A DFT/TDDFT study of hydrogen bonding interactions between resorufin anion and water molecules in the excited state. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Jiao ZG, Chang XW, Ding W, Liu GJ, Song KS, Zhu NY, Zhang DW, Yang D. β NO Turns and Helices Induced by β2-Aminoxy Peptides: Synthesis and Conformational Studies. Chem Asian J 2011; 6:1791-9. [DOI: 10.1002/asia.201000933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 11/07/2022]
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11
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Knijnenburg AD, Tuin AW, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, Otero JM, Llamas-Saiz AL, van Raaij MJ, van der Marel GA, Overkleeft HS, Overhand M. Exploring the Conformational and Biological Versatility of β-Turn-Modified Gramicidin S by Using Sugar Amino Acid Homologues that Vary in Ring Size. Chemistry 2011; 17:3995-4004. [DOI: 10.1002/chem.201002895] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Indexed: 11/11/2022]
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12
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Srinivas D, Vijayadas KN, Gonnade R, Phalgune UD, Rajamohanan PR, Sanjayan GJ. Concurrent display of both α- and β-turns in a model peptide. Org Biomol Chem 2011; 9:5762-5. [DOI: 10.1039/c1ob05553d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Schramm P, Sharma GVM, Hofmann HJ. Helix formation in β/δ-hybrid peptides: Correspondence between helices of different peptide foldamer classes. Biopolymers 2009; 94:279-91. [DOI: 10.1002/bip.21325] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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15
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Altamura M, Dragoni E, Infantino AS, Legnani L, Ludbrook SB, Menchi G, Toma L, Nativi C. Cyclic glycopeptidomimetics through a versatile sugar-based scaffold. Bioorg Med Chem Lett 2009; 19:3841-4. [DOI: 10.1016/j.bmcl.2009.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/31/2009] [Accepted: 04/03/2009] [Indexed: 11/25/2022]
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16
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Goren L, Pappo D, Goldberg I, Kashman Y. Acyclic and cyclic thioenamino peptides: solution- and solid-phase synthesis. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2008.12.072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Chandrasekhar S, Sudhakar A, Kiran MU, Babu BN, Jagadeesh B. β-Strand mimetics: formation of bend-strands in oligomers of enantiomeric β-amino acids. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.10.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Chandrasekhar S, Rao CL, Reddy MS, Sharma GD, Kiran MU, Naresh P, Chaitanya GK, Bhanuprakash K, Jagadeesh B. β-Sugar Aminoxy Peptides As Rigid Secondary Structural Scaffolds. J Org Chem 2008; 73:9443-6. [DOI: 10.1021/jo801810z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Srivari Chandrasekhar
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Chennamaneni Lohitha Rao
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Marepally Srinivasa Reddy
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Ganti Dattatreya Sharma
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Marelli Udaya Kiran
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Police Naresh
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Gunturu Krishna Chaitanya
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Kotamarthi Bhanuprakash
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
| | - Bharatam Jagadeesh
- Organic Division-I, Center for Nuclear Magnetic Resonance, and Inorganic Chemistry Division, Indian Institute of Chemical Technology, Hyderabad, India 500 007
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19
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Zhao GJ, Han KL. Effects of Hydrogen Bonding on Tuning Photochemistry: Concerted Hydrogen-Bond Strengthening and Weakening. Chemphyschem 2008; 9:1842-6. [DOI: 10.1002/cphc.200800371] [Citation(s) in RCA: 348] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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20
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Chandrasekhar S, Saritha B, Naresh P, Udayakiran M, Raji Reddy C, Jagadeesh B. Synthesis and Conformational Studies of a Hybrid Cyclic Peptide Based oncis-β-Furanoid Sugar Amino Acid (FSAA) and Ornithine. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Spitaleri A, Mari S, Curnis F, Traversari C, Longhi R, Bordignon C, Corti A, Rizzardi GP, Musco G. Structural basis for the interaction of isoDGR with the RGD-binding site of alphavbeta3 integrin. J Biol Chem 2008; 283:19757-68. [PMID: 18480047 DOI: 10.1074/jbc.m710273200] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asparagine deamidation at the NGR sequence in the 5th type I repeat of fibronectin (FN-I5) generates isoDGR, an alphavbeta3 integrin-binding motif regulating endothelial cell adhesion and proliferation. By NMR and molecular dynamics studies, we analyzed the structure of CisoDGRC (isoDGR-2C), a cyclic beta-peptide mimicking the FN-I5 site, and compared it with NGR, RGD, or DGR-containing cyclopeptides. Docking experiments show that isoDGR, exploiting an inverted orientation as compared with RGD, favorably interacts with the RGD-binding site of alphavbeta3, both recapitulating canonical RGD-alphavbeta3 contacts and establishing additional polar interactions. Conversely, NGR and DGR motifs lack the fundamental pharmacophoric requirements for high receptor affinity. Therefore, unlike NGR and DGR, isoDGR is a new natural recognition motif of the RGD-binding pocket of alphavbeta3. These findings contribute to explain the different functional properties of FN-I5 before and after deamidation, and provide support for the hypothesis that NGR --> isoDGR transition can work as a molecular timer for activating latent integrin-binding sites in proteins, thus regulating protein function.
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Affiliation(s)
- Andrea Spitaleri
- Dulbecco Telethon Institute Biomolecular NMR Laboratory c/o S. Raffaele Scientific Institute, 20132 Milan, Italy
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22
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Synthesis and conformational analysis of methyl 3-amino-2,3-dideoxyhexopyranosiduronic acids, new sugar amino acids, and their diglycotides. Carbohydr Res 2008; 343:1142-52. [DOI: 10.1016/j.carres.2008.02.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 02/19/2008] [Accepted: 02/19/2008] [Indexed: 11/19/2022]
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23
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Kendhale AM, Gonnade R, Rajamohanan PR, Hofmann HJ, Sanjayan GJ. Foldamers with unusual structural architecture from spirobi(indane) building blocks. Chem Commun (Camb) 2008:2541-3. [DOI: 10.1039/b800825f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Risseeuw MD, Overhand M, Fleet GW, Simone MI. A compendium of sugar amino acids (SAA): scaffolds, peptide- and glyco-mimetics. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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25
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Lastdrager B, Timmer MSM, van der Marel GA, Overkleeft HS, Overhand M. Transformation of Glucose into a Novel Carbasugar Amino Acid Dipeptide Isostere. J Carbohydr Chem 2007. [DOI: 10.1080/07328300701252623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Bas Lastdrager
- a Leiden Institute of Chemistry, Leiden University , Leiden, The Netherlands
| | - Mattie S. M. Timmer
- a Leiden Institute of Chemistry, Leiden University , Leiden, The Netherlands
| | | | | | - Mark Overhand
- a Leiden Institute of Chemistry, Leiden University , Leiden, The Netherlands
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26
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Danieli E, Trabocchi A, Menchi G, Guarna A. Synthesis and Conformational Analysis of Constrained β-Turn Mimetics Incorporating a Bicyclic Turn Inducer by Use of the Petasis Three-Component Reaction on Solid Phase. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600650] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Bughin C, Masson G, Zhu J. Rapid Synthesis of Cyclodepsipeptides Containing a Sugar Amino Acid or a Sugar Amino Alcohol by a Sequence of a Multicomponent Reaction and Acid-Mediated Macrocyclization. J Org Chem 2007; 72:1826-9. [PMID: 17253752 DOI: 10.1021/jo0621874] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclodepsipeptides incorporating a sugar amino acid (alcohol) have been synthesized. A three-component reaction of a sugar amino acid (SAA) derivative, an aldehyde, and a dipeptide isonitrile in refluxing methanol afforded the corresponding 5-aminooxazole which, after saponification, underwent a trifluoroacetic acid promoted macrocyclization to furnish the cyclic sugar amino acids.
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Affiliation(s)
- Carine Bughin
- Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France.
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28
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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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29
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ε-Amino acids based on bicyclic skeleton: bicyclo[3.3.0]octane-5-amino-1-carboxylic acids. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.07.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Blériot Y, Simone MI, Wormald MR, Dwek RA, Watkin DJ, Fleet GW. Sugar amino acids at the anomeric position of carbohydrates: synthesis of spirocyclic amino acids of 6-deoxy-l-lyxofuranose. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.tetasy.2006.07.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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31
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Fujimura F, Hirata T, Morita T, Kimura S, Horikawa Y, Sugiyama J. Columnar Assembly of Cyclic β-Amino Acid Functionalized with Pyranose Rings. Biomacromolecules 2006; 7:2394-400. [PMID: 16903687 DOI: 10.1021/bm060415y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel cyclic trimer and tetramer of protected beta-glycamino acids were synthesized and investigated on conformation and assembly formation. A characteristic point of these cyclic beta-glycamino acids is their better solubility than other cyclic beta-amino acids due to the pyranose rings. Thus, the assembling process of the cyclic molecules could be examined by CD or NMR spectroscopy. FT-IR and NMR measurements and geometry optimization revealed a highly symmetric and planar conformation for each cyclic beta-peptide with all-trans amide groups. The amide groups in the cyclic peptides took a vertical orientation against the cyclic skeleton to be suitably arranged for intermolecular hydrogen bonds, which should promote formation of molecular assembly in a columnar structure through molecular stacking. These cyclic beta-peptides were successfully crystallized to yield rod-shaped molecular assemblies in nanometer sizes. Evidence for the columnar structure in the crystals was obtained by electron diffraction analysis, which showed a layer spacing of ca. 4.8 A. Interestingly, the molecular assembly of the cyclic trimer showed a high aspect ratio, width less than 40 nm, and length more than 2 mum, suggesting stable molecular stacking in the column.
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Affiliation(s)
- Futoshi Fujimura
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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32
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Gómez RV, Kolender AA, Varela O. Synthesis of polyhydroxy amino acids based on d- and l-alanine from d-glycero-d-gulo-heptono-1,4-lactone. Carbohydr Res 2006; 341:1498-504. [PMID: 16618479 DOI: 10.1016/j.carres.2006.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 03/14/2006] [Accepted: 03/19/2006] [Indexed: 10/24/2022]
Abstract
2-Amino-2,3-dideoxy-D-manno-heptonic acid (7) has been synthesized from 2,5,6,7-tetra-O-acetyl-3-deoxy-D-gluco-heptono-1,4-lactone (1), which was readily prepared from D-glycero-D-gulo-heptono-1,4-lactone. O-Deacetylation of 1 followed by treatment with 13:1 (v/v) 2,2-dimethoxypropane/acetone in the presence of p-toluenesulfonic acid gave methyl 3-deoxy-4,5:6,7-di-O-isopropylidene-D-gluco-heptonate (3) as a crystalline product (80% yield). The free hydroxyl group (OH-2) of 3 was mesylated and substituted by azide to give the corresponding azide derivative 5. Hydrogenolysis and further hydrolysis of the ester function of 5 afforded alpha-amino acid 7 (43% overall yield from 1). Compound 7 is an analog of L-alanine having a polyhydroxy chain attached to C-3. The diastereoisomer of 7 at C-2, 2-amino-2,3-dideoxy-D-gluco-heptonic acid (12) was also prepared from 3, by a route that involved 2,3-dideoxy-2-iodo derivative 8 as a key intermediate.
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Affiliation(s)
- Romina V Gómez
- CIHIDECAR-CONICET, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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33
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Di Fabio G, Randazzo A, D'Onofrio J, Ausín C, Pedroso E, Grandas A, De Napoli L, Montesarchio D. Cyclic Phosphate-Linked Oligosaccharides: Synthesis and Conformational Behavior of Novel Cyclic Oligosaccharide Analogues. J Org Chem 2006; 71:3395-408. [PMID: 16626119 DOI: 10.1021/jo0600757] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CyPLOS (cyclic phosphate-linked oligosaccharides), that is, novel cyclic oligosaccharide surrogates, consisting of two, three, and four phenyl-beta-D-glucopyranoside units, 4,6-linked through stable phosphodiester bonds, were prepared by a straightforward and efficient solid-phase protocol. The assembly of the linear precursors was achieved by standard phosphoramidite chemistry on an automated DNA synthesizer, using a suitably protected 4-phosphoramidite derivative of D-glucose as the building block. For the crucial cyclization step a phosphotriester methodology was exploited, followed by a mild basic treatment releasing the desired cyclic molecules in solution in a highly pure form. The cyclic dimer and trimer were also independently prepared by classical solution synthesis, basically following the same approach. The solution structural preferences of the cyclic dimer and trimer, obtained by detailed NMR analysis, are also reported.
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Affiliation(s)
- Giovanni Di Fabio
- Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte S. Angelo, via Cynthia, 4, I-80126 Napoli, Italy
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Esho N, Desaulniers JP, Davies B, Chui HMP, Rao MS, Chow CS, Szafert S, Dembinski R. NMR conformational analysis of p-tolyl furanopyrimidine 2'-deoxyribonucleoside and crystal structure of its 3',5'-di-O-acetyl derivative. Bioorg Med Chem 2005; 13:1231-8. [PMID: 15670932 DOI: 10.1016/j.bmc.2004.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 11/08/2004] [Accepted: 11/08/2004] [Indexed: 11/16/2022]
Abstract
The conformation of a representative molecule of a new, potent class of antiviral-active modified nucleosides is determined. A bicyclic nucleoside, 3-(2'-deoxy-beta-D-ribofuranosyl)-6-(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one, shows C2'-endo and C3'-endo ribose conformations in solution (63:37, 37 degrees C; DMSO-d6), as determined by 1H NMR studies. The crystal structure of a 3',5'-di-O-acetyl-protected derivative (monoclinic, P21, a/b/c= 6.666(1)/12.225(1)/24.676(2) A, beta=90.24(1) degrees , Z=4) shows exclusively C2'-endo deoxyribose puckering. The base is found in the anti position both in solution and in crystalline form.
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Affiliation(s)
- Noor Esho
- Department of Chemistry and Center for Biomedical Research, Oakland University, 2200 N. Squirrel Rd, Rochester, MI 48309-4477, USA
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Simone MI, Soengas R, Newton CR, Watkin DJ, Fleet GW. Branched tetrahydrofuran α,α-disubstituted-δ-sugar amino acid scaffolds from branched sugar lactones: a new family of foldamers? Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.06.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ménand M, Blais JC, Hamon L, Valéry JM, Xie J. Synthesis of orthogonally protected cyclic homooligomers from sugar amino acids. J Org Chem 2005; 70:4423-30. [PMID: 15903321 DOI: 10.1021/jo0502899] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two new families of orthogonally protected cyclic homooligomers with two to four sugar units were synthesized from pyranoid sugar amino acids. Cyclic oligomers composed of amide-linked sugar amino acids (1-3) were prepared by cyclization of linear oligomers of the novel orthogonally protected pyranoid sugar amino acid 12 using a solution-phase coupling method. These orthogonally protected cyclic molecules can be selectively or fully deprotected, affording the macrocycles ready to further functionalization. The straightforward reduction of the amide bonds in the cyclic oligomers 1-3 gave the corresponding amine-linked macrocycles 4-6. This kind of amine-linked carbohydrate-based cyclic oligomer has never been reported before. These flexible molecular receptors could be studied as molecular hosts for molecular, cationic, and anionic recognition. Conformational analysis by molecular modeling (AM1) showed that all of the deprotected cyclic trimers and tetramers preferred a (4)C(1) chair conformation with oxygen atoms of the sugar ring located on the interior of the cavity and the secondary hydroxyl groups outward. In the amide-linked macrocycles, all of the amide bonds are in s-trans conformation. The estimated size of the internal cavity is about 4.5 A for the cyclic trimer and 6.9 A for the cyclic tetramer. The amine-linked macrocycles displayed similar conformational behavior with a slight decrease in internal cavity.
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Affiliation(s)
- Mickaël Ménand
- Synthèse, Structure et Fonction des Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, F-75005 Paris, France
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Sicherl F, Wittmann V. Orthogonally Protected Sugar Diamino Acids as Building Blocks for Linear and Branched Oligosaccharide Mimetics. Angew Chem Int Ed Engl 2005; 44:2096-9. [PMID: 15736239 DOI: 10.1002/anie.200462595] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Frank Sicherl
- Fachbereich Chemie, Universität Konstanz, Fach M 709, 78457 Konstanz, Germany
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38
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Sicherl F, Wittmann V. Orthogonal geschützte Zuckerdiaminosäuren als Bausteine für lineare und verzweigte Oligosaccharidmimetika. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Edwards AA, Fleet GWJ, Mayes BA, Hunter SJ, Tranter GE. Circular dichroism studies of carbopeptoid-cyclodextrins. Chirality 2005; 17 Suppl:S114-9. [PMID: 15779081 DOI: 10.1002/chir.20117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A series of sugar amino acids, based on open chain sugars, have been oligomerised and cyclised. The resulting cyclic carbopeptoids have been examined for desirable properties such as host-guest chemistry (as in cyclodextrins) or self-assembling properties (e.g., peptide nanotubes). Initial studies of these systems, by circular dichroism and X-ray crystallography, have given valuable insight into their stability and properties. One of the four cyclic species studied was found to interact with ion/molecular probes.
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Affiliation(s)
- Alison A Edwards
- Biological Chemistry, Division of Biomedical Sciences, Imperial College, London, United Kingdom
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40
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Johnson SW, Jenkinson (née Barker) SF, Angus D, Jones JH, Watkin DJ, Fleet GW. Pseudoenantiomeric oxetane δ-amino acid scaffolds derived from L-rhamnose and D-xylose: D/L-alanine-D-serine and glycine-L-serine dipeptide isosteres. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.08.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Chakraborty TK, Srinivasu P, Tapadar S, Mohan BK. Sugar amino acids and related molecules: Some recent developments. J CHEM SCI 2004. [DOI: 10.1007/bf02708268] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Grotenbreg GM, Timmer MSM, Llamas-Saiz AL, Verdoes M, van der Marel GA, van Raaij MJ, Overkleeft HS, Overhand M. An unusual reverse turn structure adopted by a furanoid sugar amino acid incorporated in gramicidin S. J Am Chem Soc 2004; 126:3444-6. [PMID: 15025470 DOI: 10.1021/ja0397254] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new reverse turn, replacing one of the native type II' beta-turns in the cyclic peptide antibiotic gramicidin S, induced by a furanoid sugar amino acid is revealed. The C3-hydroxyl function plays a pivotal role by acting as a H-bond acceptor, consequently flipping the amide bond between residues i and i + 1, as was established by NMR and X-ray crystallographic analysis.
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Affiliation(s)
- Gijsbert M Grotenbreg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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43
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Gregar TQ, Gervay-Hague J. Synthesis of oligomers derived from amide-linked neuraminic acid analogues. J Org Chem 2004; 69:1001-9. [PMID: 14961647 DOI: 10.1021/jo035312+] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-Fluoren-9-ylmethoxycarbonyl-protected sugar amino acids derived from alpha-O-methoxy- and 2,3-dehydroneuraminic acids have been prepared. Incorporation of these monomer units into solid-phase synthesis led to the efficient synthesis of two series of oligomers varying from one to eight units in length. The (1-->5)-linked amides of 2,3-dehydroneuraminic acid were further subjected to hydrogenation giving a third series of oligomers with a beta-hydrido substituent at the anomeric carbon.
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Affiliation(s)
- Travis Q Gregar
- Department of Chemistry, The University of Arizona, Tucson, Arizona 85721, USA
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44
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Abstract
The synthesis of 10 N-(fluoren-9-ylmethoxycarbonyl)glycopyranosylamine uronic acids that are amenable to solid-phase synthesis is described. The general synthetic strategy involves initial incorporation of the protected amine, followed by selective TEMPO oxidation of C-6 hydroxyl groups to give the corresponding Fmoc-protected sugar amino acids. Amine incorporation may be accomplished from aminolysis of the free sugar or from glycosyl azide reduction. The reactions can be carried out on multigram scale, providing access to unique monomer units for future incorporation into combinatorial library syntheses.
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Affiliation(s)
- Laiqiang Ying
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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45
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Huge (14-, 21-, 28-, 35-, 56- and 70-membered ring) macrocyclic lactams––a novel family of carbopeptoid-cyclodextrins. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2003.10.103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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