1
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Xiao X, Zhou M, Cong Z, Zou J, Liu R. Advance in the Polymerization Strategy for the Synthesis of β-Peptides and β-Peptoids. Chembiochem 2023; 24:e202200368. [PMID: 36226554 DOI: 10.1002/cbic.202200368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/20/2022] [Indexed: 02/04/2023]
Abstract
Peptide mimics, possessing excellent biocompatibility and protease stability, have attracted broad attention and research in the biomedical field. β-Peptides and β-peptoids, as two types of vital peptide mimics, have demonstrated great potential in the field of foldamers, antimicrobials and protein binding, etc. Currently, the main synthetic strategies for β-peptides and β-peptoids include solid-phase synthesis and polymerization. Among them, polymerization in one-pot can minimize the repeated separation and purification used in solid-phase synthesis, and has the advantages of high efficiency and low cost, and can synthesize β-peptides and β-peptoids with high molecular weight. This review summarizes the polymerization methods for β-peptides and β-peptoids. Moreover, future developments of the polymerization method for the synthesis of β-peptides and β-peptoids will be discussed.
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Affiliation(s)
- Ximian Xiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Min Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Zihao Cong
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Jingcheng Zou
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Runhui Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, China.,Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, 200237, Shanghai, China.,East China University of Science and Technology Shenzhen Research Institute, Shenzhen, China
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2
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Simon M, Milbeo P, Liu H, André C, Wenger E, Martinez J, Amblard M, Aubert E, Legrand B, Calmès M. 12/10‐Helix in Mixed β‐Peptides Alternating Bicyclic and Acyclic β‐Amino Acids: Probing the Relationship between Bicyclic Side Chain and Helix Stability. Chemistry 2018; 24:18795-18800. [DOI: 10.1002/chem.201804404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Matthieu Simon
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Pierre Milbeo
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Hongtao Liu
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Christophe André
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Emmanuel Wenger
- CRM2UMR 7063 CNRS Université de Lorraine Boulevard des Aiguilletes 54506 Vandoeuvre-lès-Nancy Cedex France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Emmanuel Aubert
- CRM2UMR 7063 CNRS Université de Lorraine Boulevard des Aiguilletes 54506 Vandoeuvre-lès-Nancy Cedex France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Monique Calmès
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
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3
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Eddinger GA, Gellman SH. Differential Effects of β 3 - versus β 2 -Amino Acid Residues on the Helicity and Recognition Properties of Bim BH3-Derived α/β-Peptides. Angew Chem Int Ed Engl 2018; 57:13829-13832. [PMID: 30161284 DOI: 10.1002/anie.201806909] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/13/2018] [Indexed: 01/07/2023]
Abstract
Oligomers containing α- and β-amino acid residues (α/β-peptides) have been shown to mimic the α-helical conformation of conventional peptides when the unnatural residues are derived from β3 -amino acids or cyclic β-amino acids, but the impact of incorporating β2 residues has received little attention. The effects of β2 residues on the conformation and recognition behavior of α/β-peptides that mimic an isolated α-helix were investigated. This effort has focused on 26-mers based on the Bim BH3 domain; a set of isomers with identical α/β backbones that differ only in the placement of certain side chains along the backbone (β3 vs. β2 substitution) was compared. Circular dichroism data suggest that β2 residues can be helix-destabilizing relative to β3 residues, although the size of this effect seems to depend on side chain identity. Binding data show that β3 →β2 substitution at sites that contact a partner protein, Bcl-xL , can influence affinity in a way that transcends effects on helicity.
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Affiliation(s)
- Geoffrey A Eddinger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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4
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Eddinger GA, Gellman SH. Differential Effects of β
3
‐ versus β
2
‐Amino Acid Residues on the Helicity and Recognition Properties of Bim BH3‐Derived α/β‐Peptides. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Geoffrey A. Eddinger
- Department of ChemistryUniversity of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Samuel H. Gellman
- Department of ChemistryUniversity of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
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5
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Xiao R, Dane EL, Zeng J, McKnight CJ, Grinstaff MW. Synthesis of Altrose Poly-amido-saccharides with β-N-(1→2)-d-amide Linkages: A Right-Handed Helical Conformation Engineered in at the Monomer Level. J Am Chem Soc 2017; 139:14217-14223. [DOI: 10.1021/jacs.7b07405] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ruiqing Xiao
- Department
of Chemistry and ‡Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Physiology and Biophysics and ∥Department of
Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Eric L. Dane
- Department
of Chemistry and ‡Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Physiology and Biophysics and ∥Department of
Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Jialiu Zeng
- Department
of Chemistry and ‡Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Physiology and Biophysics and ∥Department of
Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Christopher J. McKnight
- Department
of Chemistry and ‡Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Physiology and Biophysics and ∥Department of
Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Mark W. Grinstaff
- Department
of Chemistry and ‡Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Physiology and Biophysics and ∥Department of
Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, United States
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6
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Kiss L, Mándity IM, Fülöp F. Highly functionalized cyclic β-amino acid moieties as promising scaffolds in peptide research and drug design. Amino Acids 2017. [PMID: 28634827 DOI: 10.1007/s00726-017-2439-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptide-based drug research has received high attention in the field of medicinal chemistry over the past decade. For drug design, to improve proteolytic stability, it is desirable to include unnatural building blocks, such as conformationally restricted β-amino acid moieties, into the peptide sequence. Accordingly, the synthesis and incorporation of such conformationally rigid systems into novel type of peptides has gained large interest. Our research group has designed highly efficient methods for the construction of potential antimicrobial peptides. Moreover, a number of synthetic approaches have been developed for the synthesis of various pharmacologically interesting cyclic β-amino acid derivatives as monomers with multiple stereogenic centers.
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Affiliation(s)
- Loránd Kiss
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720, Szeged, Hungary.
| | - István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720, Szeged, Hungary
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720, Szeged, Hungary.,MTA-SZTE Stereochemistry Research Group, Hungarian Academy of Sciences, Eötvös u. 6, 6720, Szeged, Hungary
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7
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Malik A, Kumar MG, Bandyopadhyay A, Gopi HN. Helices with additional H-bonds: crystallographic conformations of α,γ-hybrid peptides helices composed of β-hydroxy γ-amino acids (statines). Biopolymers 2017; 108. [DOI: 10.1002/bip.22978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/05/2016] [Accepted: 08/25/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Ankita Malik
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Anupam Bandyopadhyay
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
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8
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Hao Y, An K, Zhang DW, Yang D. A Short Helix Formed by Cyclic β2,3-Aminoxy Peptides in Protic Solvents. Chem Asian J 2015; 10:2126-9. [DOI: 10.1002/asia.201500338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/25/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Hao
- Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Ke An
- Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Dan-Wei Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Dan Yang
- Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
- Department of Chemistry; Fudan University; Shanghai 200433 China
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9
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Wang Y, Frasconi M, Liu WG, Liu Z, Sarjeant AA, Nassar MS, Botros YY, Goddard WA, Stoddart JF. Folding of Oligoviologens Induced by Radical–Radical Interactions. J Am Chem Soc 2015; 137:876-85. [DOI: 10.1021/ja5111305] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuping Wang
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Marco Frasconi
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Wei-Guang Liu
- Materials
and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Zhichang Liu
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Amy A. Sarjeant
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Majed S. Nassar
- Joint
Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Youssry Y. Botros
- Joint
Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
- University
Research Office, Intel Corporation, Building RNB-6-61, 2200 Mission
College Boulevard, Santa Clara, California 95054, United States
| | - William A. Goddard
- Materials
and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - J. Fraser Stoddart
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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10
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Liu C, Ponder JW, Marshall GR. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence. Proteins 2014; 82:3043-61. [PMID: 25116421 PMCID: PMC4206583 DOI: 10.1002/prot.24665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/03/2014] [Indexed: 02/03/2023]
Abstract
Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.
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Affiliation(s)
- Chengyu Liu
- Department of Chemistry, Washington University, St. Louis, Missouri, 63130
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11
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Sharma GVM, Ravindranath H, Bhaskar A, Jeelani Basha S, Gurava Reddy PRG, Sirisha K, Sarma AVS, Hofmann HJ. Design and Study of Peptides Containing 1:1 Left- and Right-Handed Helical Patterns from Aminopyrancarboxylic Acids. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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13
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Zhao J, Shi J, Wang J. Amide-I characteristics of helical β-peptides by linear infrared measurement and computations. J Phys Chem B 2013; 118:94-106. [PMID: 24328259 DOI: 10.1021/jp4095936] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we have examined the amide-I characteristics of three β-peptide oligomers in typical helical conformations (two in 14-helix and one in 12/10-helix), solvated in water, methanol, and chloroform, respectively. Local-mode frequencies and their distributions were computed using a molecular-mechanics force field based frequency map that was constructed on the basis of molecular dynamics simulations. The local-mode frequencies were found to be determined primarily by peptide backbone and side chain, rather by solvent, suggesting their local structural sensitivities. Intermode vibrational couplings computed using a transition dipole scheme were found to be very sensitive to peptide conformation, with their signs and magnitudes varying periodically along the peptide chain. Linear infrared absorption spectra of the three peptides, simulated using a frequency-frequency time-correlation function method, were found to be in fair agreement with experimental results. Normalized potential energy distribution analysis indicated that the amide-I mode can delocalize over a few amide units. However, the IR band structure appears to be more sophisticated in helical β-peptides than in helical α-peptides.
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Affiliation(s)
- Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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14
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Haridas V, Sadanandan S, Gopalakrishna MVS, Bijesh MB, Verma RP, Chinthalapalli S, Shandilya A. Bispidine as a helix inducing scaffold: examples of helically folded linear peptides. Chem Commun (Camb) 2013; 49:10980-2. [DOI: 10.1039/c3cc45649h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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15
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Jadhav SV, Bandyopadhyay A, Gopi HN. Protein secondary structure mimetics: crystal conformations of α/γ4-hybrid peptide12-helices with proteinogenic side chains and their analogy with α- and β-peptide helices. Org Biomol Chem 2013; 11:509-14. [DOI: 10.1039/c2ob26805a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Lin SC, Ho RM, Chang CY, Hsu CS. Hierarchical Superstructures with Control of Helicity from the Self-Assembly of Chiral Bent-Core Molecules. Chemistry 2012; 18:9091-8. [DOI: 10.1002/chem.201200057] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Indexed: 11/11/2022]
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17
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Bandyopadhyay A, Gopi HN. Hybrid Peptides: Direct Transformation of α/α, β-Unsaturated γ-Hybrid Peptides to α/γ-Hybrid Peptide 12-Helices. Org Lett 2012; 14:2770-3. [DOI: 10.1021/ol300987d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
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18
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Bandyopadhyay A, Jadhav SV, Gopi HN. α/γ4-Hybrid peptide helices: synthesis, crystal conformations and analogy with the α-helix. Chem Commun (Camb) 2012; 48:7170-2. [DOI: 10.1039/c2cc32911e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Affiliation(s)
- Claudia Tomasini
- Dipartimento di Chimica “G. Ciamician” Alma Mater Studiorum Università di Bologna via Selmi 2, 40126 Bologna, Italy, Fax: +39‐051‐2099456
| | - Gaetano Angelici
- Department of Chemistry, University of Basel, St. Johanns‐Ring 19, 4056 Basel, Switzerland
| | - Nicola Castellucci
- Dipartimento di Chimica “G. Ciamician” Alma Mater Studiorum Università di Bologna via Selmi 2, 40126 Bologna, Italy, Fax: +39‐051‐2099456
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20
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Afarinkia K, Royappa M, Scowen IJ. Synthesis and Folding Properties of α-Hydroxy Phenylphosphinate Pseudopeptides. PHOSPHORUS SULFUR 2011. [DOI: 10.1080/10426507.2010.533723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Martin Royappa
- a Institute of Cancer Therapeutics , Bradford , United Kingdom
| | - Ian J. Scowen
- b Analytical Center , University of Bradford , Bradford , United Kingdom
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21
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Ho RM, Chiang YW, Lin SC, Chen CK. Helical architectures from self-assembly of chiral polymers and block copolymers. Prog Polym Sci 2011. [DOI: 10.1016/j.progpolymsci.2010.09.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic characterization of 12-helical secondary structure in β-peptides containing side chain groups. J Am Chem Soc 2011; 132:13879-85. [PMID: 20828159 DOI: 10.1021/ja1062532] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3(10)-helix). The β-peptide 12-helix is defined by i, i+3 C═O···H-N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a β(3)-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C═O···H-N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.
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Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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23
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Zhao J, Wang J. Amide vibrations and their conformational dependences in β-peptide. J Phys Chem B 2010; 114:16011-9. [PMID: 21070067 DOI: 10.1021/jp108324p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The characteristics of the amide-A and amide-I modes in a β-homoalanine dipeptide (β-HADP) have been examined as a function of backbone dihedral angles. The harmonic frequencies were obtained using the density functional theory. The anharmonic frequencies and diagonal anharmonicities were obtained by using the Morse potential. Local-mode frequencies and intermode couplings were obtained using the computed normal-mode frequencies and eigenvectors. It was found that the vibrational frequencies for the two types of amide modes are both conformational-dependent. The inter-amide-A and inter-amide-I couplings in the β-peptides were predicted to be generally weaker than those in the α-peptides. Structural bases of the amide-A and amide-I local modes in the β-peptides are discussed.
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Affiliation(s)
- Juan Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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24
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Structural Chemistry of Peptides Containing Backbone Expanded Amino Acid Residues: Conformational Features of β, γ, and Hybrid Peptides. Chem Rev 2010; 111:657-87. [DOI: 10.1021/cr100100x] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Prema. G. Vasudev
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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25
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Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic characterization of helical secondary structures in 2:1 and 1:2 alpha/beta-peptides. J Am Chem Soc 2010; 131:2917-24. [PMID: 19203269 DOI: 10.1021/ja808168y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligomers containing both alpha- and beta-amino acid residues ("alpha/beta-peptides") are intriguing as potential foldamers. A large set of alpha/beta-peptide backbones can be generated by combining alpha- and beta-amino acid residues in different patterns; however, most research to date has focused on the simplest pattern, 1:1 alpha:beta. We have begun to explore the range of variation that can be achieved with alpha-residue/beta-residue combinations by examining the folding behavior of oligomers that contain 2:1 and 1:2 alpha:beta patterns. The beta-residues in our systems have a five-membered-ring constraint (trans-2-aminocyclopentanecarboxylic acid (ACPC) residues), because these preorganized subunits strongly promote helical folding for 1:1 alpha:beta backbones and pure beta backbones. Previously we concluded that two helical conformations are available to 2:1 and 1:2 alpha/beta-peptides containing ACPC or analogously constrained beta-residues, one helix defined by i,i+3 CO...H-N backbone hydrogen bonds and the other defined by i,i+4 CO...H-N hydrogen bonds. These deductions were based on 2D NMR analysis of a 2:1 heptamer and a 1:2 hexamer in methanol. Crystallographic analysis of a pair of analogous nonpolar alpha/beta-peptides showed only the i,i+3 hydrogen-bonded helical conformations. We now report four new crystal structures of 2:1 alpha/beta-peptides, ranging in length from 5 to 11 residues, and six new crystal structures of 1:2 alpha/beta-peptides, ranging in length from 6 to 10 residues. All 10 of these new structures are fully helical, and all helices display the i,i+3 CO...H-N hydrogen bonding pattern. These crystallographic data sets, collectively, provide high structural definition for the i,i+3 hydrogen-bonded helical secondary structures available to these foldamer backbones.
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Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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26
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Abraham E, Bailey CW, Claridge TD, Davies SG, Ling KB, Odell B, Rees TL, Roberts PM, Russell AJ, Smith AD, Smith LJ, Storr HR, Sweet MJ, Thompson AL, Thomson JE, Tranter GE, Watkin DJ. A systematic study of the solid state and solution phase conformational preferences of β-peptides derived from transpentacin. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Yang D, Liu GJ, Hao Y, Li W, Dong ZM, Zhang DW, Zhu NY. Conformational Studies on Peptides of α-Aminoxy Acids with Functionalized Side Chains. Chem Asian J 2010; 5:1356-63. [DOI: 10.1002/asia.200900636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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28
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Afarinkia K, Royappa M, Scowen IJ, Steed JW, Yu HW. A synthesis of oligomeric α-hydroxy phenylphosphinates and a study of the conformational preferences of the dimers. Org Biomol Chem 2010; 8:600-6. [DOI: 10.1039/b917737j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Davies SG, Durbin MJ, Hartman SJ, Matsuno A, Roberts PM, Russell AJ, Smith AD, Thomson JE, Toms SM. Parallel kinetic resolution of tert-butyl (RS)-6-alkyl-cyclohex-1-ene-carboxylates for the asymmetric synthesis of 6-alkyl-substituted cishexacin derivatives. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.11.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Wu YD, Han W, Wang DP, Gao Y, Zhao YL. Theoretical analysis of secondary structures of beta-peptides. Acc Chem Res 2008; 41:1418-27. [PMID: 18828608 DOI: 10.1021/ar800070b] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Unlike alpha-amino acids, peptides formed from beta-amino acids (beta-peptides) display stability toward enzymatic degradation and may form turns and helices with as few as four residues. Because both the C alpha and C beta of the beta-amino acid may bear substituents, a large number of beta-amino acids can be synthesized. Beta-peptides form various well-defined secondary structures, including 14-helix, 12-helix, 10/12-helix, 10-helix, 8-helix, turn structures, sheets, and hairpins. For all of these reasons, beta-amino acids have been increasingly used as building blocks for molecular design and pharmaceutical applications. To explain the conformational features of beta-peptides, several quantum mechanics and molecular dynamics studies that rationalize the observed conformational features have been reported. However, a systematic account that unifies various factors critical to the conformational features is still lacking. In this Account, we present a detailed analysis of the conformational features of various beta-peptides. We start by studying the basic local conformational features of beta-peptides using di- and tripeptide models. Then, various secondary structures of unsubstituted beta-peptides with differing numbers of residues are investigated using a repeating unit approach to derive the intrinsic backbone conformational features. We find that the 10/12-helix is intrinsically most stable for the beta-peptide backbone. The 14-helix, 12-helix, and 10-helix structures have similar stabilities for beta-peptide backbones of four to six residues. The substituent effects on the stabilities of beta-peptide secondary structures are then analyzed. Combined with the substituent effect and the intrinsic backbone preferences, all experimental observations of secondary structure formation can be understood. For example, the 10/12-helix is favored for like-beta(2)/beta(3)-peptides, unlike-beta(3)/beta(3)-peptides, and beta(3)/beta-hGly-peptides because these substitution patterns do not cause steric problems for the 10/12-helix. Beta(3)-peptides, beta(2)-peptides, and beta (2,3)-peptides favor the 14-helix because the substituents in these peptides benefit the 14-helix the most but significantly destabilize the 10/12-helix. Because the 10/12-helix is intrinsically favored and has two favorable positions in each residue for substituents, many more hybrid beta-peptides are predicted to exist in this secondary structure, which suggests the need for further experiments. These results are valuable for determining the best use of these building blocks in the design of well-structured molecules with desirable chemical functions.
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Affiliation(s)
- Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei Han
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - De-Ping Wang
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yi Gao
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yi-Lei Zhao
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
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31
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Norgren AS, Arvidsson PI. Design and Synthesis of Glycosylated β3-Peptides Capable of Folding into the 314-Helical Conformation in Water. J Org Chem 2008; 73:5272-8. [DOI: 10.1021/jo8003265] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna S. Norgren
- Department of Biochemistry and Organic Chemistry, Uppsala University, Box 576, S-75123 Uppsala, Sweden, and Medicinal Chemistry, Discovery CNS & Pain Control, AstraZeneca R&D, Södertälje S-15185, Sweden
| | - Per I. Arvidsson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Box 576, S-75123 Uppsala, Sweden, and Medicinal Chemistry, Discovery CNS & Pain Control, AstraZeneca R&D, Södertälje S-15185, Sweden
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32
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Affiliation(s)
- Manisha Sathe
- a Discovery Centre, Process Technology Development Division , Defence Research and Development Establishment , Gwalior , India
| | - Hitendra N. Karade
- a Discovery Centre, Process Technology Development Division , Defence Research and Development Establishment , Gwalior , India
| | - M. P. Kaushik
- a Discovery Centre, Process Technology Development Division , Defence Research and Development Establishment , Gwalior , India
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33
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Chopra D, Guru Row TN. Evaluation of the interchangeability of C–H and C–F groups: insights from crystal packing in a series of isomeric fluorinated benzanilides. CrystEngComm 2008. [DOI: 10.1039/b709938j] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Angelici G, Luppi G, Kaptein B, Broxterman QB, Hofmann HJ, Tomasini C. Synthesis and Secondary Structure of Alternate α,β-Hybrid Peptides Containing Oxazolidin-2-one Moieties. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700134] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Goodman CM, Choi S, Shandler S, DeGrado WF. Foldamers as versatile frameworks for the design and evolution of function. Nat Chem Biol 2007; 3:252-62. [PMID: 17438550 PMCID: PMC3810020 DOI: 10.1038/nchembio876] [Citation(s) in RCA: 759] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Foldamers are sequence-specific oligomers akin to peptides, proteins and oligonucleotides that fold into well-defined three-dimensional structures. They offer the chemical biologist a broad pallet of building blocks for the construction of molecules that test and extend our understanding of protein folding and function. Foldamers also provide templates for presenting complex arrays of functional groups in virtually unlimited geometrical patterns, thereby presenting attractive opportunities for the design of molecules that bind in a sequence- and structure-specific manner to oligosaccharides, nucleic acids, membranes and proteins. We summarize recent advances and highlight the future applications and challenges of this rapidly expanding field.
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Affiliation(s)
- Catherine M Goodman
- Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104-6059, USA
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36
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Sathe M, Ghorpade R, Kaushik MP. Highly Efficient Methanolysis of Bicyclic β-Lactams to β-Amino Ester Using Silica Chloride. CHEM LETT 2006. [DOI: 10.1246/cl.2006.1004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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37
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Edwards AA, Sanjayan GJ, Hachisu S, Tranter GE, Fleet GW. A novel series of oligomers from 4-aminomethyl-tetrahydrofuran-2-carboxylates with 2,4-cis and 2,4-trans stereochemistry. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.05.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Ghosh S, Maitra U. Adaptive Dendron: A Bile Acid Oligomer Behaving asBothNormal and Inverse Micellar Mimic. Org Lett 2006; 8:399-402. [PMID: 16435844 DOI: 10.1021/ol052631+] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
[reaction: see text]. The normal and inverse micellar property of a bile-acid-based dendritic structure was established through dye solubilization studies in both polar and nonpolar media.
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Affiliation(s)
- Sanjib Ghosh
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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39
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Menegazzo I, Fries A, Mammi S, Galeazzi R, Martelli G, Orena M, Rinaldi S. Synthesis and structural characterisation as 12-helix of the hexamer of a β-amino acid tethered to a pyrrolidin-2-one ring. Chem Commun (Camb) 2006:4915-7. [PMID: 17136245 DOI: 10.1039/b612071g] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Starting from (3S,4R,1'S)-3-amino-2-oxo-1-[1'-(4-methoxyphenylethyl)]pyrrolidine carboxylic acid (2), the first synthesis of a beta-foldamer containing pyrrolidin-2-one rings is described, whose 12-helix conformation is assigned by NMR analysis and confirmed by molecular dynamics (MD) simulations.
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Affiliation(s)
- Ileana Menegazzo
- Dipartimento di Scienze Chimiche, Università di Padova, ICB-CNR, Via Marzolo 1, I-35131 Padova, Italy
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40
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Abstract
This Feature Article summarizes our efforts in developing a new family of foldamers from alpha-, beta- and gamma-aminoxy acids. From a series of conformational studies, we demonstrate that peptides consisting of aminoxy acids adopt several well-defined secondary structures, such as alpha N-O turns (which feature an eight-membered-ring hydrogen bond), beta N-O turns (a nine-membered-ring hydrogen bond), gamma N-O turns (a ten-membered-ring hydrogen bond), 1.8(8) helices (consecutive homochiral alpha N-O turns), 7/8 helices (alternating alpha N-O turns and gamma-turns), 1.7(9) helices (consecutive beta N-O turns), reverse turns (consecutive heterochiral alpha N-O turns) and sheet-like structures.
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Affiliation(s)
- Xiang Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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41
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Abstract
The principal secondary structural motifs adopted by peptides assembled from beta-amino acid units are discussed: the 14-, 12-, 10-, 12/10-, and 8-helices, as well as the hairpin turn, extended structures, stacks, and sheets. Features that promote a particular folding propensity are outlined and illustrated by structures determined in solution (NMR) and in the solid-state (x-ray). The N-C(beta)-C(alpha)-CO dihedral angles from molecular dynamics simulations, which are indicative of a particular secondary structure, are presented. A brief description of a helix and a turn of gamma-peptides is also given.
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Affiliation(s)
- Dieter Seebach
- Laboratorium für Organische Chemie der Eidgenössischen Technischen Hochschule Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.
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42
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Stephens OM, Kim S, Welch BD, Hodsdon ME, Kay MS, Schepartz A. Inhibiting HIV fusion with a beta-peptide foldamer. J Am Chem Soc 2005; 127:13126-7. [PMID: 16173723 PMCID: PMC2873035 DOI: 10.1021/ja053444+] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Linear peptides derived from the HIV gp41 C-terminus (C-peptides), such as the 36-residue Fuzeon, are potent HIV fusion inhibitors. These molecules bind to the N-peptide region of gp41 and inhibit an intramolecular protein-protein interaction that powers fusion of the viral and host cell membranes. The N-peptide region contains a surface pocket that is occupied in the post-fusion state by three alpha-helical residues found near the gp41 C-terminus: Trp628, Trp631, and Ile635-the WWI epitope. Here, we describe a set of beta3-decapeptides (betaWWI-1-4) in which the WWI epitope is presented on one face of a short 14-helix stabilized by macrodipole neutralization and side chain-side chain salt bridges. betaWWI-1-4 bind in vitro to IZN17, a validated gp41 model, and inhibit syncytia formation in cell culture. Molecules lacking a complete WWI functional epitope neither bind IZN17 nor inhibit syncytia formation. These results provide evidence that short beta-peptide 14-helices can inhibit an intramolecular protein-protein interaction in vivo. Molecules related to betaWWI-1-4 could represent starting points for the development of highly potent inhibitors or antigens effective against HIV or other viruses, including SARS, Ebola, HRSV, and influenza, that employ common fusion mechanisms.
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43
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English EP, Chumanov RS, Gellman SH, Compton T. Rational development of beta-peptide inhibitors of human cytomegalovirus entry. J Biol Chem 2005; 281:2661-7. [PMID: 16275647 DOI: 10.1074/jbc.m508485200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a pervasive and significant pathogen. At present, there is no HCMV vaccine, and the available drugs target only replication events. Thus, new therapeutic strategies are needed. HCMV fusion appears to require interactions of alpha-helical regions in viral surface glycoproteins gB and gH. Oligomers of beta-amino acids ("beta-peptides") are attractive unnatural scaffolds for mimicry of specific protein surfaces, because beta-peptides adopt predictable helical conformations and resist proteolysis. Here, we report the development of beta-peptides designed to mimic the gB heptad repeat and block HCMV entry. The most potent beta-peptide inhibits HCMV infection in a cell based-assay with an IC50 of approximately 30 microm. Consistent with our structure-based design strategy, inhibition is highly specific for HCMV relative to other related viruses. Mechanistic studies indicate that inhibitory beta-peptides act by disrupting membrane fusion. Our findings raise the possibility that beta-peptides may provide a general platform for development of a new class of antiviral agents and that inhibitory beta-peptides will constitute new tools for elucidating viral entry mechanisms.
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Affiliation(s)
- Emily Payne English
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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44
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Stephens OM, Kim S, Welch BD, Hodsdon ME, Kay MS, Schepartz A. Inhibiting HIV fusion with a beta-peptide foldamer. J Am Chem Soc 2005. [PMID: 16173723 DOI: 10.1021/ja053444] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linear peptides derived from the HIV gp41 C-terminus (C-peptides), such as the 36-residue Fuzeon, are potent HIV fusion inhibitors. These molecules bind to the N-peptide region of gp41 and inhibit an intramolecular protein-protein interaction that powers fusion of the viral and host cell membranes. The N-peptide region contains a surface pocket that is occupied in the post-fusion state by three alpha-helical residues found near the gp41 C-terminus: Trp628, Trp631, and Ile635-the WWI epitope. Here, we describe a set of beta3-decapeptides (betaWWI-1-4) in which the WWI epitope is presented on one face of a short 14-helix stabilized by macrodipole neutralization and side chain-side chain salt bridges. betaWWI-1-4 bind in vitro to IZN17, a validated gp41 model, and inhibit syncytia formation in cell culture. Molecules lacking a complete WWI functional epitope neither bind IZN17 nor inhibit syncytia formation. These results provide evidence that short beta-peptide 14-helices can inhibit an intramolecular protein-protein interaction in vivo. Molecules related to betaWWI-1-4 could represent starting points for the development of highly potent inhibitors or antigens effective against HIV or other viruses, including SARS, Ebola, HRSV, and influenza, that employ common fusion mechanisms.
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Affiliation(s)
- Olen M Stephens
- Department of Chemistry, , Yale University, New Haven, Connecticut 06520-8107, USA
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45
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Li C, Ren SF, Hou JL, Yi HP, Zhu SZ, Jiang XK, Li ZT. F⋅⋅⋅HN Hydrogen Bonding Driven Foldamers: Efficient Receptors for Dialkylammonium Ions. Angew Chem Int Ed Engl 2005; 44:5725-9. [PMID: 16078281 DOI: 10.1002/anie.200500982] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chuang Li
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China
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46
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Li C, Ren SF, Hou JL, Yi HP, Zhu SZ, Jiang XK, Li ZT. F⋅⋅⋅HN Hydrogen Bonding Driven Foldamers: Efficient Receptors for Dialkylammonium Ions. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500982] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Szakonyi Z, Gyónfalvi S, Forró E, Hetényi A, De Kimpe N, Fülöp F. Synthesis of 3- and 4-Hydroxy-2-aminocyclohexanecarboxylic Acids by Iodocyclization. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500297] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Kritzer JA, Tirado-Rives J, Hart SA, Lear JD, Jorgensen WL, Schepartz A. Relationship between side chain structure and 14-helix stability of beta3-peptides in water. J Am Chem Soc 2005; 127:167-78. [PMID: 15631466 PMCID: PMC2873033 DOI: 10.1021/ja0459375] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.
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Affiliation(s)
- Joshua A. Kritzer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | | | - Scott A. Hart
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - James D. Lear
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | | | - Alanna Schepartz
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107
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49
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Kritzer JA, Stephens OM, Guarracino DA, Reznik SK, Schepartz A. beta-Peptides as inhibitors of protein-protein interactions. Bioorg Med Chem 2005; 13:11-6. [PMID: 15582447 PMCID: PMC2853017 DOI: 10.1016/j.bmc.2004.09.009] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 09/08/2004] [Indexed: 01/10/2023]
Abstract
We became interested several years ago in exploring whether 14-helical beta-peptide foldamers could bind protein surfaces and inhibit protein-protein interactions, and if so, whether their affinities and specificities would compare favorably with those of natural or miniature proteins. This exploration was complicated initially by the absence of a suitable beta-peptide scaffold, one that possessed a well-defined 14-helical structure in water and tolerated the diverse sequence variation required to generate high-affinity protein surface ligands. In this perspective, we describe our approach to the design of adaptable beta-peptide scaffolds with high levels of 14-helix structure in water, track the subsequent development of 14-helical beta-peptide protein-protein interaction inhibitors, and examine the potential of this strategy for targeting other therapeutically important proteins.
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Affiliation(s)
| | - Olen M. Stephens
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Samuel K. Reznik
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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50
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Yang D, Zhang DW, Hao Y, Wu YD, Luo SW, Zhu NY. β2,3-Cyclic Aminoxy Acids: Rigid and Ring-Size-Independent Building Blocks of Foldamers. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200454140] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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