1
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Curran TP, Marrone A, Davidson LM, Pokharel N, Frempong JF, Tolbatov I, Phillip ML, Gober CB, Yang H, Stewart J. Parallel arrangement of peptides appended to a rigid, bimetallic, constrained ring system. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Alessandro Marrone
- Dipartimento di Farmacia Università degli Studi “G. D'Annunzio” Chieti‐Pescara Chieti Italy
| | | | | | | | - Iogann Tolbatov
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB) Université de Bourgogne Franche‐Comté (UBFC) Dijon France
| | | | - Cosmic B. Gober
- Department of Chemistry Trinity College Hartford Connecticut USA
| | - Haoyu Yang
- Department of Chemistry Trinity College Hartford Connecticut USA
| | - Joanne Stewart
- Department of Chemistry Hope College Holland Michigan USA
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2
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Zhang J, Liu Z, Yin Z, Yang X, Ma Y, Szostak R, Szostak M. Preference of cis-Thioamide Structure in N-Thioacyl-N-methylanilines. Org Lett 2020; 22:9500-9505. [DOI: 10.1021/acs.orglett.0c03512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jin Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Zhulin Liu
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Zheng Yin
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Xiufang Yang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Yangmin Ma
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Roman Szostak
- Department of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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3
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Ricardo MG, Moya CG, Pérez CS, Porzel A, Wessjohann LA, Rivera DG. Improved Stability and Tunable Functionalization of Parallel β-Sheets via Multicomponent N-Alkylation of the Turn Moiety. Angew Chem Int Ed Engl 2020; 59:259-263. [PMID: 31797518 PMCID: PMC6973259 DOI: 10.1002/anie.201912095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Indexed: 01/13/2023]
Abstract
In contrast to the myriad of methods available to produce α-helices and antiparallel β-sheets in synthetic peptides, just a few are known for the construction of stable, non-cyclic parallel β-sheets. Herein, we report an efficient on-resin approach for the assembly of parallel β-sheet peptides in which the N-alkylated turn moiety enhances the stability and gives access to a variety of functionalizations without modifying the parallel strands. The key synthetic step of this strategy is the multicomponent construction of an N-alkylated turn using the Ugi reaction on varied isocyano-resins. This four-component process assembles the orthogonally protected turn fragment and incorporates handles serving for labeling/conjugation purposes or for reducing peptide aggregation. NMR and circular dichroism analyses confirm the better-structured and more stable parallel β-sheets in the N-alkylated peptides compared to the non-functionalized variants.
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Affiliation(s)
- Manuel G. Ricardo
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120Halle/SaaleGermany
- Faculty of ChemistryUniversity of Havana10400HavanaCuba
| | - Celia G. Moya
- Faculty of ChemistryUniversity of Havana10400HavanaCuba
| | | | - Andrea Porzel
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120Halle/SaaleGermany
| | - Ludger A. Wessjohann
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120Halle/SaaleGermany
| | - Daniel G. Rivera
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120Halle/SaaleGermany
- Faculty of ChemistryUniversity of Havana10400HavanaCuba
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4
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Ricardo MG, Moya CG, Pérez CS, Porzel A, Wessjohann LA, Rivera DG. Improved Stability and Tunable Functionalization of Parallel β‐Sheets via Multicomponent N‐Alkylation of the Turn Moiety. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Manuel G. Ricardo
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
- Faculty of Chemistry University of Havana 10400 Havana Cuba
| | - Celia G. Moya
- Faculty of Chemistry University of Havana 10400 Havana Cuba
| | | | - Andrea Porzel
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
| | - Daniel G. Rivera
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
- Faculty of Chemistry University of Havana 10400 Havana Cuba
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5
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Ramachandra SN, Srinivasulu C, Hosamani B, L S, Sureshbabu VV. A Simple, Mild and Straight forward Route for the Synthesis of α‐Ureidopeptidomimetics Using Cbz‐Protected Amino Acid Esters. ChemistrySelect 2018. [DOI: 10.1002/slct.201802892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sagar N. Ramachandra
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - C. Srinivasulu
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - Basavaprabhu Hosamani
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - Santhosh L
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - Vommina V. Sureshbabu
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
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6
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Zhai L, Wang S, Nara M, Takeuchi K, Shimada I, Otani Y, Ohwada T. Application of C-Terminal 7-Azabicyclo[2.2.1]heptane to Stabilize β-Strand-like Extended Conformation of a Neighboring α-Amino Acid. J Org Chem 2018; 83:13063-13079. [DOI: 10.1021/acs.joc.8b01756] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luhan Zhai
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Siyuan Wang
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Nara
- Department of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Ichikawa, Chiba 272-0827, Japan
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo 135-0064, Japan
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuko Otani
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiko Ohwada
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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7
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Danelius E, Andersson H, Jarvoll P, Lood K, Gräfenstein J, Erdélyi M. Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation. Biochemistry 2017; 56:3265-3272. [PMID: 28581720 PMCID: PMC5510091 DOI: 10.1021/acs.biochem.7b00429] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Halogen
bonding is a weak chemical force that has so far mostly
found applications in crystal engineering. Despite its potential for
use in drug discovery, as a new molecular tool in the direction of
molecular recognition events, it has rarely been assessed in biopolymers.
Motivated by this fact, we have developed a peptide model system that
permits the quantitative evaluation of weak forces in a biologically
relevant proteinlike environment and have applied it for the assessment
of a halogen bond formed between two amino acid side chains. The influence
of a single weak force is measured by detection of the extent to which
it modulates the conformation of a cooperatively folding system. We
have optimized the amino acid sequence of the model peptide on analogues
with a hydrogen bond-forming site as a model for the intramolecular
halogen bond to be studied, demonstrating the ability of the technique
to provide information about any type of weak secondary interaction.
A combined solution nuclear magnetic resonance spectroscopic and computational
investigation demonstrates that an interstrand halogen bond is capable
of conformational stabilization of a β-hairpin foldamer comparable
to an analogous hydrogen bond. This is the first report of incorporation
of a conformation-stabilizing halogen bond into a peptide/protein
system, and the first quantification of a chlorine-centered halogen
bond in a biologically relevant system in solution.
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Affiliation(s)
- Emma Danelius
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Hanna Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Patrik Jarvoll
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Kajsa Lood
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden.,Swedish NMR Centre , Medicinaregatan 5, SE-41390 Gothenburg, Sweden
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8
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Hu T, Connor AL, Miller DP, Wang X, Pei Q, Liu R, He L, Zheng C, Zurek E, Lu ZL, Gong B. Helical Folding of Meta-Connected Aromatic Oligoureas. Org Lett 2017; 19:2666-2669. [DOI: 10.1021/acs.orglett.7b01005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ting Hu
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Alan L. Connor
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Xiao Wang
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Qiang Pei
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Rui Liu
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Lan He
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
- National Institute for Food and Drug Control, Institute of Chemical Drug Control, TianTanXiLi 2, Beijing, 100050, China
| | - Chong Zheng
- Department
of Chemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Eva Zurek
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Zhong-lin Lu
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Bing Gong
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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9
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Mishra SK, Suryaprakash N. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations. Molecules 2017; 22:E423. [PMID: 28272370 PMCID: PMC6155419 DOI: 10.3390/molecules22030423] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/02/2017] [Indexed: 01/24/2023] Open
Abstract
The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| | - N Suryaprakash
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
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10
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Mishra SK, Suryaprakash N. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations. Phys Chem Chem Phys 2016; 17:15226-35. [PMID: 25993543 DOI: 10.1039/c5cp01505g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
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11
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Singh A, Kast J, Dirain MLS, Huang H, Haskell-Luevano C. Synthesis and Structure-Activity Relationships of Substituted Urea Derivatives on Mouse Melanocortin Receptors. ACS Chem Neurosci 2016; 7:196-205. [PMID: 26645732 DOI: 10.1021/acschemneuro.5b00273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The melanocortin system is involved in the regulation of several complex physiological functions. In particular, the melanocortin-3 and -4 receptors (MC3R/MC4R) have been demonstrated to regulate body weight, energy homeostasis, and feeding behavior. Synthetic and endogenous melanocortin agonists have been shown to be anorexigenic in rodent models. Herein, we report synthesis and structure-activity relationship (SAR) studies of 27 nonpeptide small molecule ligands based on an unsymmetrical substituted urea core. Three templates containing key residues from the lead compounds, showing diversity at three positions (R(1), R(2), R(3)), were designed and synthesized. The syntheses were optimized for efficient microwave-assisted chemistry that significantly reduced total syntheses time compared to a previously reported room temperature method. The pharmacological characterization of the compounds on the mouse melanocortin receptors identified compounds 1 and 12 with full agonist activity at the mMC4R, but no activity was observed at the mMC3R when tested up to 100 μM concentrations. The SAR identified compounds possessing aliphatic or saturated cyclic amines at the R(1) position, bulky aromatic groups at the R(2) position, and benzyl group at the R(3) position resulted in mMC4R selectivity over the mMC3R. The small molecule template and SAR knowledge from this series may be helpful in further design of MC3R/MC4R selective small molecule ligands.
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Affiliation(s)
- Anamika Singh
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Johannes Kast
- Department
of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Marvin L. S. Dirain
- Department
of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Huisuo Huang
- Department
of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Carrie Haskell-Luevano
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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12
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Li ZT. Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks. Beilstein J Org Chem 2015; 11:2057-71. [PMID: 26664626 PMCID: PMC4661011 DOI: 10.3762/bjoc.11.222] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/09/2015] [Indexed: 01/22/2023] Open
Abstract
This mini-review covers the growth, education, career, and research activities of the author. In particular, the developments of various folded, helical and extended secondary structures from aromatic backbones driven by different noncovalent forces (including hydrogen bonding, donor-acceptor, solvophobicity, and dimerization of conjugated radical cations) and solution-phase supramolecular organic frameworks driven by hydrophobically initiated aromatic stacking in the cavity of cucurbit[8]uril (CB[8]) are highlighted.
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Affiliation(s)
- Zhan-Ting Li
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
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13
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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14
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Venugopalan P, Kishore R. Antiparallel Self-Association of a γ,α-Hybrid Peptide: More Relevance of Weak Interactions. Chem Asian J 2015; 10:1753-60. [PMID: 25965414 DOI: 10.1002/asia.201500373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Indexed: 11/08/2022]
Abstract
To learn how a preorganized peptide-based molecular template, together with diverse weak non-covalent interactions, leads to an effective self-association, we investigated the conformational characteristics of a simple γ,α-hybrid model peptide, Boc-γ-Abz-Gly-OMe. The single-crystal X-ray diffraction analysis revealed the existence of a fully extended β-strand-like structure stabilized by two non-conventional C-H⋅⋅⋅O=C intramolecular H-bonds. The 2D (1) H NMR ROESY experiment led us to propose that the flat topology of the urethane-γ-Abz-amide moiety is predominantly preserved in a non-polar environment. The self-association of the energetically more favorable antiparallel β-strand-mimic in solid-state engenders an unusual 'flight of stairs' fabricated through face-to-face and edge-to-edge Ar⋅⋅⋅Ar interactions. In conjunction with FT-IR spectroscopic analysis in chloroform, we highlight that conformationally semi-rigid γ-Abz foldamer in appositely designed peptides may encourage unusual β-strand or β-sheet-like self-association and supramolecular organization stabilized via weak attractive forces.
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Affiliation(s)
- Paloth Venugopalan
- Department of Chemistry, Panjab University, Sector 14, Chandigarh-, 160 014, India
| | - Raghuvansh Kishore
- Protein Science & Engineering Division, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh-, 160 036, India.
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15
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Yang Y, Chen CF. Hydrogen Bonding-Mediated Self-assembly of Aromatic Supramolecular Duplexes. LECTURE NOTES IN CHEMISTRY 2015. [DOI: 10.1007/978-3-662-45756-6_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Mishra SK, Suryaprakash N. Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations. RSC Adv 2015. [DOI: 10.1039/c5ra19537c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - N. Suryaprakash
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
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17
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Robinson CW, Rye CS, Chessum NEA, Jones K. A model β-sheet interaction and thermodynamic analysis of β-strand mimetics. Org Biomol Chem 2015; 13:7402-7. [DOI: 10.1039/c5ob00886g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two novel β-strand mimetics are synthesized and their binding to a model peptide is studied in detail by 1H NMR.
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Affiliation(s)
- Colin W. Robinson
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Carl S. Rye
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Nicola E. A. Chessum
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
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18
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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19
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Nair RV, Baravkar SB, Ingole TS, Sanjayan GJ. Synthetic turn mimetics and hairpin nucleators: Quo Vadimus? Chem Commun (Camb) 2014; 50:13874-84. [PMID: 25051222 DOI: 10.1039/c4cc03114h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.
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Affiliation(s)
- Roshna V Nair
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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21
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Bellucci MC, Volonterio A. Synthesis ofN-Glycosyl Conjugates through a Multicomponent Domino Process. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301887] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Xin D, Holzenburg A, Burgess K. Small Molecule Probes That Perturb A Protein-protein Interface In Antithrombin. Chem Sci 2014; 5:4914-4921. [PMID: 25396040 DOI: 10.1039/c4sc01295j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Small molecule probes for perturbing protein-protein interactions (PPIs) in vitro can be useful if they cause the target proteins to undergo biomedically relevant changes to their tertiary and quaternary structures. Application of the Exploring Key Orientations (EKO) strategy (J. Am. Chem. Soc., 2013, 135, 167 - 173) to a piperidinone-piperidine chemotype 1 indicated specific derivatives were candidates to perturb a protein-protein interface in the α-antithrombin dimer; those particular derivatives of 1 were prepared and tested. In the event, most of them significantly accelerated oligomerization of monomeric α-antithrombin, which is metastable in its oligomeric state. This assertion is supported by data from gel electrophoresis (non-denaturing PAGE; throughout) and probe-induced loss of α-antithrombin's inhibitor activity in a reaction catalyzed by thrombin. Kinetics of α-antithrombin oligomerization induced by the target compounds were examined. It was found that probes with O-benzyl-protected serine side-chains are the most active catalysts in the series, and reasons for this, based on modeling experiments, are proposed. Overall, this study reveals one of the first examples of small molecules designed to act at a protein-protein interface relevant to oligomerization of a serpin (ie α-antithrombin). The relevance of this to formation of oligomeric serpin fibrils, associated with the disease states known as "serpinopathies", is discussed.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Andreas Holzenburg
- Microscopy and Imaging Center, Department of Biology, and Department of Biochemistry & Biophysics TAMU, College Station, TX 77843-2257
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
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23
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Abstract
Peptide self-assembly is a powerful method to create functional nanoscale materials such as optoelectronically relevant organic nanostructures. The enormous potential that may come from bringing π-conjugated electronic function into biological environments is poised to impact cell and tissue engineering, biosensors, and related biomedical applications. However, very little synthetic guidance is available with respect to uniting these two different materials sets in a generally applicable manner. In this Account, I describe my group's work to synthesize and assemble peptidic nanostructures built around organic electronic elements. The Account begins with a very brief background to the area of supramolecular electronics, followed by a description of areas where these nanomaterials could be useful in biology. I then discuss the synthetic approaches that we utilized to embed a variety of π-electron units directly within peptide backbones. A key supramolecular challenge with respect to subsequent self-assembly of these new molecules is balancing electrostatic contributions within the resulting nanomaterials, because the suitable geometries for stabilizing peptide assemblies may not necessarily correspond to those suitable for maximizing intermolecular π-electron interactions. Regardless of the respective magnitudes of these two major influences, the assembly paradigm is fairly robust. Variation of the π-electron units and the peptide sequences that make up the "peptide-π-peptide" triblock molecules consistently leads to fairly uniform tape-like nanostructures that maintain strong electronic coupling among the component π-electron units. We explored a diverse range of π-electron units spanning fluorescent oligo(phenylene vinylene)s, electron-accepting rylene diimides, and hole-transporting oligothiophenes. I then describe the characterization of the nanomaterials that form after molecular self-assembly in order to understand their internal structures, electronic interactions, and morphologies as existing within self-supporting hydrogel matrices. I also describe how a facile shearing process provided globally aligned macroscopic collections of one-dimensional electronic fibrils in hydrogel matrices. These general assembly processes influence intermolecular π-stacking among the embedded chromophores, and the assemblies themselves can facilitate the covalent cross-linking and polymerization (for example, of reactive diyne units). The latter offers an exciting possibility to create peptidic nanostructures comprised of single polymer chains. Finally, I discuss electronic properties as manifested in the interactions of transition dipoles within the nanomaterials and electrical properties resulting from field-effect gating. The ability to tune the observable electrical properties of the nanostructures externally will allow for their transition to in vitro or in vivo platforms as a powerful new approach to regulating biological interactions at the nanoscale.
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Affiliation(s)
- John D. Tovar
- Department of Chemistry, Department of Materials Science and Engineering, and Institute for NanoBioTechnology Johns Hopkins University 3400 North Charles Street (NCB 316), Baltimore, Maryland 21218, United States
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24
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Abstract
Interactions among β-sheets occur widely in protein quaternary structure, protein-protein interaction, and protein aggregation and are central in Alzheimer's and other amyloid-related diseases. This Perspective looks at the structural biology of these important yet under-appreciated interactions from a supramolecular chemist's point of view. Common themes in the supramolecular interactions of β-sheets are identified and richly illustrated though examples from proteins, amyloids, and chemical model systems. β-Sheets interact through edge-to-edge hydrogen bonding to form extended layers and through face-to-face hydrophobic or van der Waals interactions to form layered sandwich-like structures. Side chains from adjacent layers can fit together through simple hydrophobic contacts or can participate in complementary interdigitation or knob-hole interactions. The layers can be aligned, offset, or rotated. The right-handed twist of β-sheets provides additional opportunities for stabilization of edge-to-edge contacts and rotated layered structures.
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Affiliation(s)
- Pin-Nan Cheng
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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25
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Qaroush AK, Al-Hamayda AS, Khashman YK, Vagin SI, Troll C, Rieger B. Highly efficient isocyanate-free microwave-assisted synthesis of [6]-oligourea. Catal Sci Technol 2013. [DOI: 10.1039/c3cy00117b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Abstract
With an intelligent design of the monomers, considerable effort has so far focused on the creation of aromatic oligoamide foldamers which are able to mimic the secondary structures of biopolymers. Supersecondary structure is a growing set of known and classifiable protein folding patterns that provides an important organizational context to this complex endeavor. In this article, we highlight the design, chemical synthesis, and structural studies of artificial supersecondary structures based on aromatic oligoamide foldamers in recent years.
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Affiliation(s)
- Hai-Yu Hu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
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27
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Vijayadas KN, Nair RV, Gawade RL, Kotmale AS, Prabhakaran P, Gonnade RG, Puranik VG, Rajamohanan PR, Sanjayan GJ. Ester vs. amide on folding: a case study with a 2-residue synthetic peptide. Org Biomol Chem 2013; 11:8348-56. [DOI: 10.1039/c3ob41967c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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28
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Zhang DW, Zhao X, Hou JL, Li ZT. Aromatic Amide Foldamers: Structures, Properties, and Functions. Chem Rev 2012; 112:5271-316. [PMID: 22871167 DOI: 10.1021/cr300116k] [Citation(s) in RCA: 509] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dan-Wei Zhang
- Department of Chemistry, Fudan
University, 220 Handan Road, Shanghai 200433, China
| | - Xin Zhao
- Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai
200032, China
| | - Jun-Li Hou
- Department of Chemistry, Fudan
University, 220 Handan Road, Shanghai 200433, China
| | - Zhan-Ting Li
- Department of Chemistry, Fudan
University, 220 Handan Road, Shanghai 200433, China
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29
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Hassan HHAM, El-Banna SG, Elhusseiny AF, Mansour ESME. Antioxidant activity of new aramide nanoparticles containing redox-active N-phthaloyl valine moieties in the hepatic cytochrome P450 system in male rats. Molecules 2012; 17:8255-75. [PMID: 22781439 PMCID: PMC6268142 DOI: 10.3390/molecules17078255] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/07/2012] [Accepted: 06/12/2012] [Indexed: 12/25/2022] Open
Abstract
We report the synthesis of aramide nanoparticles containing a chiral N-phthaloyl valine moiety and their antioxidant activities on hepatic contents of cytochrome P₄₅₀, amidopyrene N-demethylase, aniline-4-hyroxylase and induced the hepatic content of cytochrome b5 and nicotinamide adenine dinucleotide phosphate (NADPH) cytochrome C-reductase. Polymers were obtained as well-separated spherical nanoparticles while highly aggregated particles via H-bonding organization of the aramide-containing pyridine led to a thin layer formation. The effects of the nanoparticles and CCl₄ on enzyme activities and thiobarbituric acid reactive substances (TBARS) levels of male rat liver were studied. Pretreatments of rats with the polyamides prior to the administration of CCl₄ decreased the hepatic content of the tested enzymes. Doses reduced the toxic effects exerted by (•CCl₃) upon the liver through inhibition of the cytochrome P₄₅₀ system. Inhibition of such metabolizing enzymes could reduce the carcinogenic effects of chemical carcinogens.
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Affiliation(s)
- Hammed H A M Hassan
- Department of Chemistry, Faculty of Science, Alexandria University, P. O. Box 2-Moharram Beck, Alexandria 21598, Egypt.
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30
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Wu CF, Zhao X, Lan WX, Cao C, Liu JT, Jiang XK, Li ZT. A 1,4-diphenyl-1,2,3-triazole-based β-turn mimic constructed by click chemistry. J Org Chem 2012; 77:4261-70. [PMID: 22489820 DOI: 10.1021/jo300063u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of 1,4-diphenyl-1,2,3-triazole-incorporated amide derivatives have been designed and prepared. X-ray crystallographic and (1D and 2D) (1)H NMR studies reveal that these compounds fold into stable U-shaped conformations driven by three-center intramolecular C-H···O hydrogen-bonding formed between the triazole C-5 H atom and the two ether O atoms. Such folded structures make this 1,4-diphenyl-1,2,3-triazole skeleton a good candidate to be used as β-turn mimic. To prove this, the formation of a β-hairpin structure induced by this β-turn motif has been further demonstrated.
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Affiliation(s)
- Chun-Fang Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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31
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Medda AK, Park CM, Jeon A, Kim H, Sohn JH, Lee HS. A Nonpeptidic Reverse-Turn Scaffold Stabilized by Urea-Based Dual Intramolecular Hydrogen Bonding. Org Lett 2011; 13:3486-9. [DOI: 10.1021/ol201247x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amiya K. Medda
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea, and Chungnam National University, Daejeon 305-764, Korea
| | - Chul Min Park
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea, and Chungnam National University, Daejeon 305-764, Korea
| | - Aram Jeon
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea, and Chungnam National University, Daejeon 305-764, Korea
| | - Hyunwoo Kim
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea, and Chungnam National University, Daejeon 305-764, Korea
| | - Jeong-Hun Sohn
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea, and Chungnam National University, Daejeon 305-764, Korea
| | - Hee-Seung Lee
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea, and Chungnam National University, Daejeon 305-764, Korea
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32
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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33
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Lozano JM, Lesmes LP, Carreño LF, Gallego GM, Patarroyo ME. Development of designed site-directed pseudopeptide-peptido-mimetic immunogens as novel minimal subunit-vaccine candidates for malaria. Molecules 2010; 15:8856-89. [PMID: 21135800 PMCID: PMC6259129 DOI: 10.3390/molecules15128856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 10/28/2010] [Indexed: 11/16/2022] Open
Abstract
Synthetic vaccines constitute the most promising tools for controlling and preventing infectious diseases. When synthetic immunogens are designed from the pathogen native sequences, these are normally poorly immunogenic and do not induce protection, as demonstrated in our research. After attempting many synthetic strategies for improving the immunogenicity properties of these sequences, the approach consisting of identifying high binding motifs present in those, and then performing specific changes on amino-acids belonging to such motifs, has proven to be a workable strategy. In addition, other strategies consisting of chemically introducing non-natural constraints to the backbone topology of the molecule and modifying the α-carbon asymmetry are becoming valuable tools to be considered in this pursuit. Non-natural structural constraints to the peptide backbone can be achieved by introducing peptide bond isosters such as reduced amides, partially retro or retro-inverso modifications or even including urea motifs. The second can be obtained by strategically replacing L-amino-acids with their enantiomeric forms for obtaining both structurally site-directed designed immunogens as potential vaccine candidates and their Ig structural molecular images, both having immuno-therapeutic effects for preventing and controlling malaria.
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MESH Headings
- Animals
- Haplorhini
- Humans
- Malaria Vaccines/chemical synthesis
- Malaria Vaccines/chemistry
- Malaria Vaccines/immunology
- Malaria Vaccines/pharmacology
- Malaria, Falciparum/immunology
- Malaria, Falciparum/prevention & control
- Mice
- Mice, Inbred BALB C
- Peptidomimetics/chemical synthesis
- Peptidomimetics/chemistry
- Peptidomimetics/immunology
- Peptidomimetics/pharmacology
- Vaccines, Subunit/chemical synthesis
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Vaccines, Subunit/pharmacology
- Vaccines, Synthetic/chemistry
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/pharmacology
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Affiliation(s)
- José Manuel Lozano
- Fundación Instituto de Inmunología de Colombia (FIDIC), Universidad del Rosario and Universidad Nacional de Colombia, Bogotá DC, Colombia.
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34
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Ranatunga S, Liyanage W, Del Valle JR. Synthesis and conformational analysis of bicyclic extended dipeptide surrogates. J Org Chem 2010; 75:5113-25. [PMID: 20593836 PMCID: PMC2914495 DOI: 10.1021/jo1008433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regio- and diastereoselective reactions of a homoproline enolate enable the synthesis of novel extended dipeptide surrogates. Bicyclic carbamate 9 and fused beta-lactam scaffold 11 were prepared from L-pyroglutamic acid via substrate-controlled electrophilic azidation. Synthesis of orthogonally protected hexahydropyrrolizine, hexahydropyrrolizinone, and hexahydropyrroloazepinone dipeptide surrogates relied on allylation of proline derivative 5, followed by Curtius rearrangement to introduce the N-terminal carbamate group. A total of six azabicycloalkane derivatives were evaluated for conformational mimicry of extended dipeptides by a combination of X-ray diffraction and molecular modeling. Analysis of putative backbone dihedral angles and N- to C-terminal dipeptide distances indicate that compounds (alpha'S)-14b and 21 approximate the conformation of dipeptides found in beta-sheets, while tripeptide mimic 28 is also highly extended in the solid state. Structural data suggest that ring size and relative stereochemistry have a profound effect on the ability of these scaffolds to act as beta-strand mimetics and should inform the design of related conformational probes.
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35
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Moriuchi T, Hirao T. Design of ferrocene-dipeptide bioorganometallic conjugates to induce chirality-organized structures. Acc Chem Res 2010; 43:1040-51. [PMID: 20377253 DOI: 10.1021/ar100022n] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The highly ordered molecular assemblies in proteins can have a variety of functions, as observed in enzymes, receptors, and the like. Synthetic scientists are constructing bioinspired systems by harnessing the self-assembling properties of short peptides. Secondary structures such as alpha-helices, beta-sheets, and beta-turns are important in protein folding, which is mostly directed and stabilized by hydrogen bonding and the hydrophobic interactions of side chains. The design of secondary structure mimics that are composed of short peptides has attracted much attention, both for gaining fundamental insight into the factors affecting protein folding and for developing pharmacologically useful compounds, artificial receptors, asymmetric catalysts, and new materials. Ferrocenes are an organometallic scaffold with a central reverse-turn unit based on the inter-ring spacing of about 3.3 A, which is a suitable distance for hydrogen bonding between attached peptide strands. The conjugation of organometallic compounds with biomolecules such as amino acids, peptides, and DNA should provide novel systems that reflect properties of both the ferrocene and the biologically derived moieties. In this Account, we focus on recent advances in the design of ferrocene-peptide bioconjugates, which help illustrate the peptidomimetic basis for protein folding and the means of constructing highly ordered molecular assemblies. Ferrocene-peptide bioconjugates are constructed to form chirality-organized structures in both solid and solution states. The ferrocene serves as a reliable organometallic scaffold for the construction of protein secondary structures via intramolecular hydrogen bonding: the attached dipeptide strands are constrained within the appropriate dimensions. The introduction of the chiral dipeptide chains into the ferrocene scaffold induces the conformational enantiomerization of the ferrocenyl moiety; the chirality-organized structure results from intramolecular hydrogen bonding. The configuration and sequence of the amino acids are instrumental in the process. Regulation of the directionality and specificity of hydrogen bonding is a key component in the design of various molecular assemblies. Ferrocene-peptide bioconjugates also have a strong tendency to self-assemble through the contributions of available hydrogen-bonding donors in the solid state. Some ferrocene-peptide bioconjugates bearing only one dipeptide chain exhibit a helically ordered molecular assembly through a network of intermolecular (rather than intramolecular) hydrogen bonds. The propensity to form the chiral helicity appears to be controlled by the chirality of the dipeptide chains. Organization of host molecules is a useful strategy for forming artificial receptors. The conformationally regulated ferrocene-peptide bioconjugate provides the chirality-organized binding site for size-selective and chiral recognition of dicarboxylic acids through multipoint hydrogen bonds. Metal ions serve a variety of purposes in proteins, including structural stabilization for biological function. The complexation of ferrocene-peptide bioconjugates with palladium(II) compounds not only stabilizes the chirality conformational regulation but also induces conformational regulation of the dipeptide chain through complexation and intramolecular chirality organization. Construction of the chirality-organized ferrocene-peptide bioconjugates is also achieved by metal-directed assembly. These varied examples amply demonstrate the value of ferrocene-peptide bioconjugates in asserting architectural control over highly ordered molecular assemblies.
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Affiliation(s)
- Toshiyuki Moriuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Toshikazu Hirao
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
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36
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Rabong C, Jordis U, Phopase JB. NXO Building Blocks for Backbone Modification of Peptides and Preparation of Pseudopeptides. J Org Chem 2010; 75:2492-500. [DOI: 10.1021/jo902518r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Jaywant B. Phopase
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
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37
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Fischer L, Guichard G. Folding and self-assembly of aromatic and aliphatic urea oligomers: Towards connecting structure and function. Org Biomol Chem 2010; 8:3101-17. [DOI: 10.1039/c001090a] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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38
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Frkanec L, Žinić M. Chiral bis(amino acid)- and bis(amino alcohol)-oxalamidegelators. Gelation properties, self-assembly motifs and chirality effects. Chem Commun (Camb) 2010; 46:522-37. [DOI: 10.1039/b920353m] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Grauer A, König B. Peptidomimetics – A Versatile Route to Biologically Active Compounds. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900599] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andreas Grauer
- Institute für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany, Fax: +49‐941‐943‐1717
| | - Burkhard König
- Institute für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany, Fax: +49‐941‐943‐1717
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40
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Ke D, Zhan C, Li X, Li AD, Yao J. The urea-dipeptides show stronger H-bonding propensity to nucleate β-sheetlike assembly than natural sequence. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.07.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Freire F, Gellman SH. Macrocyclic design strategies for small, stable parallel beta-sheet scaffolds. J Am Chem Soc 2009; 131:7970-2. [PMID: 19456161 DOI: 10.1021/ja902210f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pairs of short peptide strands can be induced to adopt an antiparallel beta-sheet secondary structure in aqueous solution via a macrocyclic constraint, as illustrated by many natural and designed peptides. We show that an analogous strategy is successful for creation of small units of parallel beta-sheet secondary structure in aqueous solution. Cyclization in this case requires nonpeptide segments for N-to-N and C-to-C interstrand linkage. Surprisingly, we find that only one of these segments needs to be preorganized.
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Affiliation(s)
- Felix Freire
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Sureshbabu VV, Naik SA, Hemantha HP, Narendra N, Das U, Guru Row TN. N-Urethane-Protected Amino Alkyl Isothiocyanates: Synthesis, Isolation, Characterization, and Application to the Synthesis of Thioureidopeptides. J Org Chem 2009; 74:5260-6. [DOI: 10.1021/jo900675s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vommina V. Sureshbabu
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - Shankar A. Naik
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - H. P. Hemantha
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - N. Narendra
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - Ushati Das
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Tayur N. Guru Row
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
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Dutt A, Dutta A, Kar S, Koley P, Drew MG, Pramanik A. Stabilization of two smallest possible diastereomeric β-hairpins in a water soluble tetrapeptide containing non-coded α-amino isobutyric acid (Aib) and m-amino benzoic acid. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.03.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Drexler C, Milne M, Morgan E, Jennings M, Kraatz HB. Synthesis and characterization of new ferrocene peptide conjugates. Dalton Trans 2009:4370-8. [DOI: 10.1039/b817670a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Narendra N, Chennakrishnareddy G, Sureshbabu VV. Application of carbodiimide mediated Lossen rearrangement for the synthesis of α-ureidopeptides and peptidyl ureas employing N-urethane α-amino/peptidyl hydroxamic acids. Org Biomol Chem 2009; 7:3520-6. [DOI: 10.1039/b905790k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fan X, Feng D, Wang X, Qu Y, Zhang X. A novel preparation of pyridineâurea hybrids and elucidation of their structures. HETEROATOM CHEMISTRY 2009. [DOI: 10.1002/hc.20560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hu HY, Xiang JF, Chen CF. Conformationally constrained aromatic oligoamide foldamers with supersecondary structure motifs. Org Biomol Chem 2009; 7:2534-9. [DOI: 10.1039/b903178b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kim UI, Suk JM, Naidu V, Jeong KS. Folding and Anion-Binding Properties of Fluorescent Oligoindole Foldamers. Chemistry 2008; 14:11406-14. [DOI: 10.1002/chem.200801713] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Naidu VR, Kim MC, Suk JM, Kim HJ, Lee M, Sim E, Jeong KS. Biased Helical Folding of Chiral Oligoindole Foldamers. Org Lett 2008; 10:5373-6. [DOI: 10.1021/ol8022243] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Min Cheol Kim
- Department of Chemistry, Yonsei University, Seoul-120-749 Korea
| | - Jae-min Suk
- Department of Chemistry, Yonsei University, Seoul-120-749 Korea
| | - Ho-Joong Kim
- Department of Chemistry, Yonsei University, Seoul-120-749 Korea
| | - Myongsoo Lee
- Department of Chemistry, Yonsei University, Seoul-120-749 Korea
| | - Eunji Sim
- Department of Chemistry, Yonsei University, Seoul-120-749 Korea
| | - Kyu-Sung Jeong
- Department of Chemistry, Yonsei University, Seoul-120-749 Korea
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