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zeng L, Xu S, Cui S, Zhang F. Three Component Synthesis of β‑Aminoxy Amides. Org Chem Front 2022. [DOI: 10.1039/d2qo00631f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multicomponent reaction for the synthesis of β‑aminoxy amides is described. In this reaction, N-hydroxamic acids, yna-mides and aldehydes could assemble efficiently to deliver structurally diverse β‑aminoxy amides under the...
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2
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Luo Y, Chen CH, Zhu F, Mo DL. Synthesis of α-aminooxy amides through [3 + 3] cycloaddition and Sc(OTf) 3-catalyzed double C-N bond cleavage in a one-pot reaction. Org Biomol Chem 2020; 18:8209-8218. [PMID: 33043956 DOI: 10.1039/d0ob01788d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Various α-aminooxy amides bearing a quaternary carbon at the α-position were prepared in good to excellent yields under mild reaction conditions from N-vinyl nitrones and α-bromohydroxamates. The N-vinyl nitrones tolerate a wide range of N-vinyl fluorenone nitrones and N-vinyl isatin nitrones. Mechanistic studies show that the reaction initially proceeds through [3 + 3] cycloaddition between N-vinyl nitrones and aza-oxyallyl cations generated from α-bromohydroxamates to afford six-membered N,O-heterocycles, followed by double C-N bond cleavage in the presence of the Sc(OTf)3 catalyst. A selective N-O bond cleavage of the obtained α-aminooxy amides is also realized under Fe/NH4Cl conditions. Furthermore, gram-scalable preparations of α-aminooxy amides are easily achieved.
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Affiliation(s)
- Yan Luo
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China; School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Chun-Hua Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China; School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Fan Zhu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China; School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Dong-Liang Mo
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China; School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
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3
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Howard EH, Cain CF, Kang C, Del Valle JR. Synthesis of Enantiopure ε-Oxapipecolic Acid. J Org Chem 2019; 85:1680-1686. [DOI: 10.1021/acs.joc.9b02382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evan H. Howard
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Christopher F. Cain
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Changwon Kang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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4
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Affiliation(s)
- Ajay L. Chandgude
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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5
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Diedrich D, Moita AJR, Rüther A, Frieg B, Reiss GJ, Hoeppner A, Kurz T, Gohlke H, Lüdeke S, Kassack MU, Hansen FK. α-Aminoxy Oligopeptides: Synthesis, Secondary Structure, and Cytotoxicity of a New Class of Anticancer Foldamers. Chemistry 2016; 22:17600-17611. [PMID: 27573537 DOI: 10.1002/chem.201602521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 11/11/2022]
Abstract
α-Aminoxy peptides are peptidomimetic foldamers with high proteolytic and conformational stability. To gain an improved synthetic access to α-aminoxy oligopeptides we used a straightforward combination of solution- and solid-phase-supported methods and obtained oligomers that showed a remarkable anticancer activity against a panel of cancer cell lines. We solved the first X-ray crystal structure of an α-aminoxy peptide with multiple turns around the helical axis. The crystal structure revealed a right-handed 28 -helical conformation with precisely two residues per turn and a helical pitch of 5.8 Å. By 2D ROESY experiments, molecular dynamics simulations, and CD spectroscopy we were able to identify the 28 -helix as the predominant conformation in organic solvents. In aqueous solution, the α-aminoxy peptides exist in the 28 -helical conformation at acidic pH, but exhibit remarkable changes in the secondary structure with increasing pH. The most cytotoxic α-aminoxy peptides have an increased propensity to take up a 28 -helical conformation in the presence of a model membrane. This indicates a correlation between the 28 -helical conformation and the membranolytic activity observed in mode of action studies, thereby providing novel insights in the folding properties and the biological activity of α-aminoxy peptides.
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Affiliation(s)
- Daniela Diedrich
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ana J Rodrigues Moita
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Anja Rüther
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Benedikt Frieg
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Guido J Reiss
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Astrid Hoeppner
- X-Ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Steffen Lüdeke
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Matthias U Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Finn K Hansen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
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6
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Li Z, Lebedyeva I, Zhao D, Myers L, Pillai GG, Hall CD, Katritzky AR. Synthesis of L-Lys-Aminoxy-Goralatide. J Pept Sci 2014; 20:923-7. [PMID: 25331328 DOI: 10.1002/psc.2702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/15/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022]
Abstract
Natural tetrapeptide Goralatide inhibits primitive hematopoietic cell proliferation but reported to be rather unstable in solution (half-life 4.5 min). In this work, we report the synthesis of an aminoxy analog of Goralatide. Aminoxy moiety is expected to provide increased stability and bioavailability of the Goralatide analog.
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Affiliation(s)
- Zhiliang Li
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, PO Box: 117200, Gainesville, FL, 32611-7200, USA
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7
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Avan I, Hall CD, Katritzky AR. Peptidomimetics via modifications of amino acids and peptide bonds. Chem Soc Rev 2014; 43:3575-94. [DOI: 10.1039/c3cs60384a] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Altmayer-Henzien A, Declerck V, Merlet D, Baltaze JP, Farjon J, Guillot R, Aitken DJ. Solution State Conformational Preferences of Dipeptides Derived from N-Aminoazetidinecarboxylic Acid: An Assessment of the Hydrazino Turn. J Org Chem 2013; 78:6031-9. [DOI: 10.1021/jo400736t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amandine Altmayer-Henzien
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Valérie Declerck
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Denis Merlet
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Jean-Pierre Baltaze
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Jonathan Farjon
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Régis Guillot
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
| | - David J. Aitken
- Laboratoire
de Synthèse Organique et Méthodologie, ‡Laboratoire de RMN en Milieu Orienté, and §Services Communs, ICMMO (UMR CNRS 8182), Université Paris Sud, 15 Rue Georges Clemenceau, 91405 Orsay cedex, France
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10
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Baldauf C, Hofmann HJ. Ab initioMO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers ofω-Amino Acids. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200436] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Ma B, Yin C, Yang D, Lin G. Effect of structural modification on the gastrointestinal stability and hepatic metabolism of α-aminoxy peptides. Amino Acids 2012; 43:2073-85. [DOI: 10.1007/s00726-012-1291-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 04/03/2012] [Indexed: 10/28/2022]
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12
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Le Grel P, Salaün A, Mocquet C, Le Grel B, Roisnel T, Potel M. Z/E Isomerism in Nα-Nα-Disubstituted Hydrazides and the Amidoxy Bond: Application to the Conformational Analysis of Pseudopeptides Built of Hydrazinoacids and α-Aminoxyacids. J Org Chem 2011; 76:8756-67. [DOI: 10.1021/jo201390b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Arnaud Salaün
- CBMN, UMR 5248, 2 rue Robert Escarpit, 33 607 Pessac
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13
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Reddy CR, Radhika L, Kumar TP, Chandrasekhar S. First Acid-Catalyzed Entry to O-Alkylated Hydroximides from Benzylic Alcohols. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Ma B, Zha H, Li N, Yang D, Lin G. Effect of Structural Modification of α-Aminoxy Peptides on Their Intestinal Absorption and Transport Mechanism. Mol Pharm 2011; 8:1073-82. [DOI: 10.1021/mp1003866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bin Ma
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Huiyan Zha
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR
| | - Na Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Dan Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR
| | - Ge Lin
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
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15
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Jiao ZG, Chang XW, Ding W, Liu GJ, Song KS, Zhu NY, Zhang DW, Yang D. β NO Turns and Helices Induced by β2-Aminoxy Peptides: Synthesis and Conformational Studies. Chem Asian J 2011; 6:1791-9. [DOI: 10.1002/asia.201000933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 11/07/2022]
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16
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Yang D, Chang XW, Zhang DW, Jiang ZF, Song KS, Zhang YH, Zhu NY, Weng LH, Chen MQ. Chiral alpha-aminoxy acid/achiral cyclopropane alpha-aminoxy acid unit as a building block for constructing the alpha N-O helix. J Org Chem 2010; 75:4796-805. [PMID: 20568786 DOI: 10.1021/jo100810m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The monomer 1 derived from achiral 1-(aminoxy)cyclopropanecarboxylic acid (OAcc) and oligopeptides 2-9 consisting of a chiral alpha-aminoxy acid and an achiral alpha-aminoxy acid such as OAcc were synthesized and their structures characterized. The eight-membered-ring intramolecular hydrogen bond, namely the alpha N-O turn, was formed between adjacent residues independent of their chirality. However, the helix formation was sequence-dependent. Dipeptide 2 bearing chiral alpha-aminoxy acid (d-OAA) at the N-terminus and achiral OAcc at the C-terminus preferentially adopted a right-handed 1.8(8) helical structure, but dipeptide 3 (OAcc-d-OAA) did not. Theoretical calculation results, in good agreement with experimental ones, revealed that the biased handedness of alpha N-O turn found in OAcc residue depends on its preceding chiral residue. It was then found that the helical conformation was destroyed in the case of oligopeptides 6 and 7 [OAA-(OAcc)(n), n = 2, 3]. The crystal structure of tripeptide 8 ((i)PrCO-d-OVal-OAcc-d-OVal-NH(i)Bu) further disclosed the helical structure formed by three consecutive homochiral alpha N-O turns. This study has uncovered achiral aminoxy acid residues such as the OAcc unit as a useful building block to be incorporated into chiral aminoxy peptides to mimic chiral helix structure.
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Affiliation(s)
- Dan Yang
- Department of Chemistry, Fudan University, Shanghai 200433, China.
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17
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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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18
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Zhang YH, Song K, Zhu NY, Yang D. The effect of backbone stereochemistry on the folding of acyclic beta(2, 3)-aminoxy peptides. Chemistry 2010; 16:577-87. [PMID: 19876967 DOI: 10.1002/chem.200901471] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As a new type of foldamer, beta-aminoxy peptides have the ability to adopt novel beta N--O turns or beta N--O helices in solution. Herein, we describe a new subclass of beta-aminoxy peptide, that is, peptides of acyclic beta(2, 3)-aminoxy acids (NH(2)OCHR(1)CHR(2)COOH), in which the presence of two chiral centers provides insight into the effect of backbone stereochemistry on the folding of beta-aminoxy peptides. Acyclic beta(2, 3)-aminoxy peptides with syn and anti configurations have been synthesized and their conformations investigated by NMR, IR, and circular dichroism (CD) spectroscopic, and X-ray crystallographic analysis. The beta N--O turns or beta N--O helices, which feature nine-membered rings with intramolecular hydrogen bonds and have been identified previously in peptides of beta(3)- and beta(2, 2)-aminoxy acids, are also predominantly present in the acyclic beta(2, 3)-aminoxy peptides with a syn configuration and N--O bonds gauche to the C(alpha)--C(beta) bonds in both solution and the solid state. In the acyclic beta(2, 3)-aminoxy peptides with an anti configuration, an extended strand (i.e., non-hydrogen-bonded state) is found in the solid state, and several conformations including non-hydrogen-bonded and intramolecular hydrogen-bonded states are present simultaneously in nonpolar solvents. These results suggest that the backbone stereochemistry does affect the folding of the acyclic beta(2, 3)-aminoxy peptides. Theoretical calculations on the conformations of model acyclic beta(2, 3)-aminoxy peptides with different backbone stereochemistry were also conducted to elucidate structural characteristics. Our present work may provide useful guidelines for the design and construction of new foldamers with predicable structures.
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Affiliation(s)
- Yu-Hui Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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19
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Katritzky AR, Avan I, Tala SR. Efficient Preparation of Aminoxyacyl Amides, Aminoxy Hybrid Peptides, and α-Aminoxy Peptides. J Org Chem 2009; 74:8690-4. [DOI: 10.1021/jo901612j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Ilker Avan
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
- Department of Chemistry, Anadolu University, 26470, Eskişehir, Turkey
| | - Srinivasa R. Tala
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
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20
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Yang D, Liu GJ, Jiao ZG, Zhang DW, Luo Z, Song KS, Chen MQ. Disulfide Bond Creates a Small Connecting Loop in Aminoxy Peptide Backbone. Chemistry 2008; 14:10297-302. [DOI: 10.1002/chem.200800095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Li X, Wu YD, Yang D. Alpha-aminoxy acids: new possibilities from foldamers to anion receptors and channels. Acc Chem Res 2008; 41:1428-38. [PMID: 18785763 DOI: 10.1021/ar8001393] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Naturally occurring peptides serve important functions as enzyme inhibitors, hormones, neurotransmitters, and immunomodulators in many physiological processes including metabolism, digestion, pain sensitivity, and the immune response. However, due to their conformational flexibility and poor bioavailability, such peptides are not generally viewed as useful therapeutic agents in clinical applications. In an effort to solve these problems, chemists have developed peptidomimetic foldamers, unnatural oligomeric molecules that fold into rigid and well-defined secondary structures mimicking the structures and biological functions of these natural peptides. We have designed peptidomimetic foldamers that give predictable, backbone-controlled secondary structures irrespective of the nature of the side chains. This Account presents our efforts to develop a novel class of peptidomimetic foldamers comprising alpha-aminoxy acids and explore their applications in the simulation of ion recognition and transport processes in living systems. Peptides constructed from alpha-aminoxy acids fold according to the following rules: (1) A strong intramolecular eight-membered-ring hydrogen bond forms between adjacent alpha-aminoxy acid residues (the alpha N-O turn). The chirality of the alpha-carbon, not the nature of the side chains, determines the conformation of this chiral N-O turn. (2) While homochiral oligomers of alpha-aminoxy acids form an extended helical structure (1.8 8 helix), heterochiral ones adopt a bent reverse turn structure. (3) In peptides of alternating alpha-amino acids and alpha-aminoxy acids, the seven-membered-ring intramolecular hydrogen bond, that is, the gamma-turn, is initiated by a succeeding alpha N-O turn. Thus, this type of peptide adopts a novel 7/8 helical structure. In investigating the potential applications of alpha-aminoxy acids, we have found that the amide NH units of alpha-aminoxy acids are more acidic than are regular amide NH groups, which makes them better hydrogen bond donors when interacting with anions. This property makes alpha-aminoxy acids ideal building blocks for the construction of anion receptors. Indeed, we have constructed both cyclic and acyclic anion receptors that have strong affinities and good (enantio-)selectivities toward chloride (Cl(-)) and chiral carboxylate ions. Taking advantage of these systems' preference for Cl(-) ions, we have also employed alpha-aminoxy acid units to construct a synthetic Cl(-) channel that can mediate the passage of Cl(-) ions across cell membranes. Continued studies of these peptidomimetic systems built from alpha-aminoxy acids should lead to a broad range of applications in chemistry, biology, medicine, and materials science.
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Affiliation(s)
- Xiang Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Dan Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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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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Sharma GVM, Manohar V, Dutta SK, Subash V, Kunwar AC. Design of a “New Motif” with β-Amino Acids and α-Aminoxy Acids: Synthesis of Hybrid Peptides with 12/10-Helix. J Org Chem 2008; 73:3689-98. [DOI: 10.1021/jo702242q] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gangavaram V. M. Sharma
- D-211, Discovery Laboratory, Organic Chemistry Division III and Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Vennampalli Manohar
- D-211, Discovery Laboratory, Organic Chemistry Division III and Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Samit K. Dutta
- D-211, Discovery Laboratory, Organic Chemistry Division III and Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Velaparthi Subash
- D-211, Discovery Laboratory, Organic Chemistry Division III and Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Ajit C. Kunwar
- D-211, Discovery Laboratory, Organic Chemistry Division III and Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology, Hyderabad 500 007, India
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24
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Le Grel P, Salaün A, Potel M, Le Grel B, Lassagne F. Aza-β3-Cyclohexapeptides: Pseudopeptidic Macrocycles with Interesting Conformational and Configurational Properties Slow Pyramidal Nitrogen Inversion in 24-Membered Rings! J Org Chem 2006; 71:5638-45. [PMID: 16839144 DOI: 10.1021/jo0608467] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among pseudopeptidic foldamers, aza-beta3-peptides have the unique property to possess nitrogen stereocenters instead of carbon stereocenters. As the result of pyramidal inversion at N(alpha)-atoms along the backbone, they behave as a set of C8-based secondary structures in equilibrium. This structural modulation is exploited here to prepare 24-membered macrocycles with great efficiency. Both crystal structures and spectroscopic data establish that aza-beta3-cyclohexapeptides adopt a highly organized conformation where the relative configuration of chiral nitrogen atoms is alternated. This makes them an interesting scaffold as the stereocontrol occurs spontaneously through the cyclization. These compounds reveal an unprecedented slow pyramidal nitrogen inversion in macrocycles. Pyramidal ground state stabilization, hindered rotation, steric crowding, and H-bond cooperativity are proposed to participate in this striking phenomenon. The equilibrium between invertomers of aza-beta3-cyclohexapeptides is reminiscent of the interchange between the two chair forms of cyclohexane.
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Affiliation(s)
- Philippe Le Grel
- ICMV, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc 35042 Rennes Cedex, France.
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25
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Yuan L, Sanford AR, Feng W, Zhang A, Zhu J, Zeng H, Yamato K, Li M, Ferguson JS, Gong B. Synthesis of crescent aromatic oligoamides. J Org Chem 2006; 70:10660-9. [PMID: 16355983 DOI: 10.1021/jo050798a] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structures: see text] This article describes the synthetic procedures for the preparation of crescent (and helical) aromatic oligoamides developed in recent years in our laboratory. The large-scale preparation of a variety of monomers derived from various tetrasubstituted benzenes is presented. Three different strategies for constructing various oligomers consisting of meta- and meta/para-linked benzene residues are discussed. Factors affecting coupling efficiency and yields are analyzed. The developed synthetic methods have provided the basis for the preparation of longer oligomers and for the development of solid-phase synthesis.
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Affiliation(s)
- Lihua Yuan
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, USA
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26
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Abstract
Peptoids of alpha- and beta-peptides (alpha- and beta-peptoids) can be obtained by shifting the amino acid side chains from the backbone carbon atoms of the monomer constituents to the peptide nitrogen atoms. They are, therefore, N-substituted poly-glycines and poly-beta-alanines, respectively. Due to the substituted nitrogen atoms, the ability for hydrogen bond formation between peptide bonds gets lost. It may be very interesting to see whether such non-natural oligomers could be regarded as foldamers, which fold into definite backbone conformers. In this paper, we provide a complete overview on helix formation in alpha- and beta-peptoids on the basis of systematic theoretical conformational analyses employing the methods of ab initio molecular orbital (MO) theory. It can be shown that the alpha- and beta-peptoid structures form helical structures with both trans and cis peptide bonds despite the missing hydrogen bonds. Obviously, the conformational properties of the backbone are more important for folding than the possibility of hydrogen bonding. There are close relationships between the helices of alpha-peptoids and poly-glycine and poly-proline helices of alpha-peptides, whereas the helices of beta-peptoids correspond to the well-known helical structures of beta-peptides as, for instance, the 3(1)-helix of beta-peptides with 14-membered hydrogen-bonded rings. Thus, alpha- and beta-peptoids enrich the field of foldamers and may be used as useful tools in peptide and protein design.
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Affiliation(s)
- Carsten Baldauf
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, D-04103 Leipzig, Germany
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27
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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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28
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Salaün A, Potel M, Roisnel T, Gall P, Le Grel P. Crystal Structures of Aza-β3-peptides, A New Class of Foldamers Relying on a Framework of Hydrazinoturns. J Org Chem 2005; 70:6499-502. [PMID: 16050716 DOI: 10.1021/jo050938g] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystals of aza-beta3-peptides have been obtained. This gives the first opportunity for hydrazino peptides, in the sense of oligomers built exclusively with alpha-hydrazinoacetic units, to be observed in the solid state. The structures make it clear that the H-bond network developed by aza-beta3-peptides differs radically from those of the corresponding beta3-peptides but strongly resembles that of the alpha-aminoxy peptides. Our study contributes to the current interest in hydrazino peptides as an extension of the beta-peptide concept.
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Affiliation(s)
- Arnaud Salaün
- SESO, UMR CNRS 6510, Université de Rennes I, and Laboratoire du Solide et Inorganique Moléculaire, UMR CNRS 6511, 263 avenue du General Leclerc CS 74205, 35042 Rennes Cedex, France
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29
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Wei J, Shao X, Gong M, Zhu B, Cui Y, Gao Y, Wang R. Structure–activity relationships of novel endomorphin-2 analogues with N–O turns induced by α-aminoxy acids. Bioorg Med Chem Lett 2005; 15:2986-9. [PMID: 15984054 DOI: 10.1016/j.bmcl.2005.04.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Endomorphin-2 (H-Tyr-Pro-Phe-Phe-NH2, EM-2) is a putative endogenous mu-opioid receptor ligand. To study the structure-activity relationship against its receptor, we introduced N-O turns into EM-2 and got the analogues with potent affinities for mu-opioid receptor. Our results indicated that N-O turn structures at the Pro2-aminoxy-Phe3 position of EM-2 analogues played important roles for their affinities. These novel analogues with N-O turns provided a new approach to develop potent analgesics related to EM-2.
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Affiliation(s)
- Jie Wei
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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30
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Yuan L, Zeng H, Yamato K, Sanford AR, Feng W, Atreya HS, Sukumaran DK, Szyperski T, Gong B. Helical aromatic oligoamides: reliable, readily predictable folding from the combination of rigidified structural motifs. J Am Chem Soc 2005; 126:16528-37. [PMID: 15600357 DOI: 10.1021/ja046858w] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Factors responsible for the folding of aromatic oligoamides with backbones rigidified by local three-center H-bonds were investigated. The stability of the three-center H-bonds was quantified by the half-lives of amide proton-deuterium exchange reactions, which show that the three-center H-bonds were largely intact at room temperature in the oligomer examined. This result is consistent with our current and previous 2D NMR studies. The overall helical conformation of nonamer 1 was found by variable-temperature NOESY studies to be dynamic. As temperature rose, the end-to-end NOEs rapidly disappeared, while the amide side chain NOEs were still readily detectable, corresponding to the "breath" and stretching of the helix by slightly twisting the local H-bonded rings. Based on the simple repetition of the same structural motif and local conformational preference, undecamer 2 was found to fold into well-defined helical conformation. The predictability of the folding of these backbone-rigidified aromatic oligoamides was demonstrated by a simple modeling method using structural parameters from oligomers with known crystal structures. The reliability and generality of the modeling methods were shown by the excellent agreement between the modeled structures corresponding to 1 and 2 and data from NOESY studies.
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Affiliation(s)
- Lihua Yuan
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, The State University of New York, Buffalo, New York 14260, USA
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31
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Baldauf C, Günther R, Hofmann HJ. Control of Helix Formation in Vinylogous γ-Peptides by (E)- and (Z)-Double Bonds: A Way to Ion Channels and Monomolecular Nanotubes. J Org Chem 2005; 70:5351-61. [PMID: 15989314 DOI: 10.1021/jo0480489] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] A complete overview on the alternative and competitive helices in vinylogous gamma-peptides is given, which was obtained on the basis of a systematic conformational analysis at various levels of ab initio MO theory (HF/6-31G*, DFT/B3LYP/6-31G*, PCM/HF/6-31G*). Contrary to the parent gamma-peptides, there is a strict control of helix formation by the configuration of the double bond between the C(alpha) and C(beta) atoms of the monomer constituents. (E)-Double bonds favor helices with larger pseudocycles beginning with 14- up to 27-membered hydrogen-bonded rings, whereas the (Z)-configuration of the double bonds supports a distinct preference of helices with smaller seven- and nine-membered pseudocycles showing interactions between nearest-neighbor peptide bonds. The rather stable helices of the (E)-vinylogous peptides with 22-, 24-, and 27-membered hydrogen-bonded pseudocycles have inner diameters large enough to let molecules or ions pass. Thus, they could be interesting model compounds for the design of membrane channels and monomolecular nanotubes. Since (E)- and (Z)-vinylogous gamma-amino acids and their oligomers are synthetically accessible, our study may stimulate structure research in this novel field of foldamers.
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Affiliation(s)
- Carsten Baldauf
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
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32
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Baldauf C, Günther R, Hofmann HJ. Side-chain control of folding of the homologous α-, β-, and γ-peptides into “mixed” helices (β-helices). Biopolymers 2005; 80:675-87. [PMID: 15714456 DOI: 10.1002/bip.20249] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A systematic analysis of the substituent influence on the formation of the unique secondary structure type of "mixed" helices in the homologous alpha-, beta-, and gamma-peptides was performed on the basis of ab initio molecular orbital theory. Contrary to the common periodic peptide helices, mixed helices have an alternating periodicity and their hydrogen-bonding pattern is similar to those of beta-sheets. They belong, therefore, to the family of beta-helices. It is shown that folding of peptide sequences into mixed helices is energetically preferred over folding into their periodic counterparts in numerous cases. The influence of entropy and solvents on the formation of the various competitive mixed and periodic helix types is discussed. Among the oligomers of the various homologous amino acids, beta-peptides show the highest tendency to form beta-helices. The rules of substituent influence derived from the analysis of a wide variety of backbone substitution patterns might be helpful for a rational design of mixed helix structures, which could be important for mimicking membrane channels.
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Affiliation(s)
- Carsten Baldauf
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig
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33
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Gao Y, Wu * YD. Theoretical study of the secondary structures of unionized Poly(γ-D-glutamic acid). Mol Phys 2004. [DOI: 10.1080/0026897042000274955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Abstract
A series of chiral beta(3)-aminoxy acids or amides with various side chains have been synthesized via two different approaches. One is the Arndt-Eistert homologation approach, using chiral alpha-aminoxy acids as starting materials. The other approach, utilizing the enantioselective reduction of beta-keto esters catalyzed by baker's yeast or chiral Ru(II) complexes, produces chiral beta(3)-aminoxy acids with nonproteinaceous side chains. The oligomers of beta(3)-aminoxy acids can be readily prepared using EDCI/HOAt as the coupling reagent.
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Affiliation(s)
- Dan Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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35
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Yang X, Yuan L, Yamato K, Brown AL, Feng W, Furukawa M, Zeng XC, Gong B. Backbone-rigidified oligo(m-phenylene ethynylenes). J Am Chem Soc 2004; 126:3148-62. [PMID: 15012145 DOI: 10.1021/ja039416d] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligo(m-phenylene ethynylenes) (oligo(m-PE)) with backbones rigidified by intramolecular hydrogen bonds were found to fold into well-defined conformations. The localized intramolecular hydrogen bond involves a donor and an acceptor from two adjacent benzene rings, respectively, which enforces globally folded conformations on these oligomers. Oligomers with two to seven residues have been synthesized and characterized. The persistence of the intramolecular hydrogen bonds and the corresponding curved conformations were established by ab initio and molecular mechanics calculations, 1D and 2D (1)H NMR spectroscopy, and UV spectroscopy. Pentamer 5, hexamer 6, and heptamer 7 adopt well-defined helical conformations. Such a backbone-based conformational programming should lead to molecules whose conformations are resilient toward structural variation of the side groups. These m-PE oligomers have provided a new approach for achieving folded unnatural oligomers under conditions that are otherwise unfavorable for previously described, solvent-driven folding of m-PE foldamers. Stably folded structures based on the design principle described here can be developed and may find important applications.
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Affiliation(s)
- Xiaowu Yang
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, USA
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36
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Cho MK, Kim SS, Lee MR, Shin J, Lee J, Lim SK, Baik JH, Yoon CJ, Shin I, Lee W. NMR Studies on Turn Mimetic Analogs Derived from Melanocyte-stimulating Hormones. BMB Rep 2003; 36:552-7. [PMID: 14659073 DOI: 10.5483/bmbrep.2003.36.6.552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oligomers with alpha-aminooxy acids are reported to form very stable turn and helix structures, and they are supposed to be useful peptidomimetics for drug design. A recent report suggested that homochiral oxa-peptides form a strong eight-member-ring structure by a hydrogen bond between adjacent aminooxy-acid residues in a CDCl3 solution. In order to design an alpha-MSH analog with a stable turn conformation, we synthesized four tetramers and one pentamer, based on alpha-MSH sequence, and determined the solution structures of the molecules by two-dimensional NMR spectroscopy and simulated annealing calculations. The solution conformations of the three peptidomimetic molecules (TLV, TDV, and TLL) in DMSO-d6 contain a stable 7-membered-ring structure that is similar to a gamma-turn in normal peptides. Newly-designed tetramer TDF and pentamer PDF have a ball-type rigid structure that is induced by strong hydrogen bonds between adjacent amide protons and carbonyl oxygens. In conclusion, the aminooxy acids, easily prepared from natural or unnatural amino acids, can be employed to prepare peptidomimetic analogues with well-defined turn structures for pharmaceutical interest.
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Affiliation(s)
- Min-Kyu Cho
- Department of Biochemistry and Protein Network Research Center, College of Science, Yonsei University, Seoul 120-749, Korea.
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37
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Yang D, Qu J, Li W, Wang DP, Ren Y, Wu YD. A Reverse Turn Structure Induced by a d,l-α-Aminoxy Acid Dimer. J Am Chem Soc 2003; 125:14452-7. [PMID: 14624594 DOI: 10.1021/ja029514j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Our previous work revealed that two adjacent D-alpha-aminoxy acids could form two homochiral N-O turns, with the backbone folding into an extended helical structure (1.8(8)-helix). Here, we report the conformational studies of linear peptides 3-6, which contain a D,L-alpha-aminoxy acid dimer segment. The NMR and X-ray analysis of 3 showed that it folded into a loop conformation with two heterochiral N-O turns. This loop segment can be used to constrain tetrapeptides 4 and 6 to form a reverse turn structure. (1)H NMR dilution studies, DMSO-d6 addition studies, and 2D-NOESY data indicated that tetrapeptides 4 and 6 folded into reverse turn conformations featured by a head-to-tail 16-membered-ring intramolecular hydrogen bond. In contrast, tetrapeptide 5 with L-Ala instead of Gly or D-Ala as the N-terminal amino acid could not form the desired reverse turn structure for steric reasons. Quantum mechanics calculations showed that model pentamide 7, with the same substitution pattern of 4, adopted a novel reverse turn conformation featuring two heterochiral N-O turns (each of an 8-membered ring hydrogen bond), a cross-strand 16-membered ring hydrogen bond, and a 7-membered ring gamma-turn.
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Affiliation(s)
- Dan Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China.
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38
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Li YX, Wu YD. A Theoretical Study on the Structure of Poly((R)-3-hydroxybutanoic acid). J Phys Chem A 2003. [DOI: 10.1021/jp0343741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Xue Li
- Institute of Theoretical and Computational Chemistry, State Key Laboratory of Molecular Dynamics and Stable Structures, College of Chemistry, Peking University, Beijing, China, and Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun-Dong Wu
- Institute of Theoretical and Computational Chemistry, State Key Laboratory of Molecular Dynamics and Stable Structures, College of Chemistry, Peking University, Beijing, China, and Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
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39
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Vanderesse R, Thevenet L, Marraud M, Boggetto N, Reboud M, Corbier C. Alpha-aminoxy acids as building blocks for the oxime and hydroxylamine pseudopeptide links. Application to the synthesis of human elastase inhibitors. J Pept Sci 2003; 9:282-99. [PMID: 12803495 DOI: 10.1002/psc.452] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aminoxy acids NH2-O-C(alpha)HR-CO2H are much more easily obtained in the enantiomerically pure form than the analogous hydrazino acids NH2-NH-C(alpha)HR-CO2H, and it has been shown that the isosteric amidoxy psi[CO-NH-O] and hydrazide psi[CO-NH-NH] amide surrogates Induce two quite similar gamma-like folded structures. An aminoxy acid can also be N-coupled to a peptide aldehyde to give the aldoxime psi[CH = N-O] link or to a peptide ketone to form the ketoxime psi[CR= N-O] link. The former can be further reduced into the hydroxylamine psi[CH2-NH-O] link which gives rise to reduced amidoxy peptides. The structural properties Induced by these amide surrogates were studied, using IR and NMR spectroscopy, paying particular attention to the Z/E-isomerism of the oxime link. In order to investigate their inhibitory potency, the three amide surrogates were introduced in the Pro3-Val4 and Val4-Ala5 position of Z-Ala1-Ala2-Pro3-Val4-Ala5-Ala6-NHiPr, a substrate which is cleaved in the Val4-Ala5 position by human leukocyte elastase (HLE). The [Val4psi[CO-NH-O]Ala5] analogue was still a substrate, while the [Pro3psi[CO-NH-O]Val4] and [Val4psi[CH = N-O]Ala5] pseudopeptides acted as HLE competitive inhibitors.
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Affiliation(s)
- Regis Vanderesse
- LCPM, UMR CNRS-INPL 7568, ENSIC-INPL BP 451, 54001 Nancy, France.
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40
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Abstract
Structural and thermodynamic features of the sheets formed by beta-peptides have been studied by quantum mechanics calculations using peptide models. Calculations using dipeptide models indicate that the intrinsic hydrogen bond strength is great for both parallel and antiparallel sheets and that it is little affected by proper substituents. Heterochiral-beta(2,3)-peptides have much stronger sheet-forming propensity than other types of peptides because their favored backbone conformation is ideal for sheet formation. A planar or ideally pleated strand has a curved geometry, which is unfavorable for the formation of sheets. Thus, sheets have to adopt twisted geometries. There is a large cooperativity in the formation of the hydrogen bond network in the sheets of beta-peptides in the perpendicular direction due to long-range electrostatic attractions because all carbonyl groups are roughly in the same direction, in contrast to the situation in beta-sheets of alpha-peptides.
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Affiliation(s)
- Jin-Qiu Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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41
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Lee HJ, Song JW, Choi YS, Park HM, Lee KB. A theoretical study of conformational properties of N-methyl azapeptide derivatives. J Am Chem Soc 2002; 124:11881-93. [PMID: 12358532 DOI: 10.1021/ja026496x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational properties of azapeptide derivatives, Ac-azaGly-NHMe (1), Ac-azaAla-NHMe (2), Ac-NMe-azaGly-NHMe (3), Ac-NMe-azaAla-NHMe (4), Ac-azaGly-NMe(2) (5), Ac-azaAla-NMe(2) (6), Ac-NMe-azaGly-NMe(2) (7), and Ac-NMe-azaAla-NMe(2) (8), were systematically examined by using ab initio MO and DFT methods. Structural perturbations in azapeptides resulting from cyclic substitution of a methyl group at three N-positions of an azaamino acid were studied on the basis of the structure of the simplest model azapeptide, 1. Potential energy surfaces were generated at the HF/6-31G level for 1-4 and at the HF/6-31G//HF/3-21G level for 5-8 by rotating two key dihedral angles (phi, psi) in increments of 30 degrees. The backbone (phi, psi) angles of the minima for 1-4 are observed at the i + 2 position to form the betaI(I')-, betaII(II')-, betaVI-turns or the polyproline II structure according to the orientation of the acetyl group and the positions of the N-methyl groups. Compounds 5-8 coupled to a secondary amine were found to preferentially adopt polyproline II, betaI(III)-turn, or alpha-helical structure or even extended conformations depending on the orientation of the acetyl group and the positions of the N-methyl groups. Furthermore, N-methyl groups, depending on their positions, were found to affect the orientation of the amide group in the lowest energy conformations, the pyramidality of the N2 atom, and the bond length in azapeptide derivatives. These unique theoretical conformations of N-methyl azapeptide derivatives could be utilized in the definite design of secondary structure for peptides and proteins, and in the development of new drugs and molecular machines.
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Affiliation(s)
- Ho-Jin Lee
- Advanced Analysis Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryangri, Seoul 130-650, Korea
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42
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Yang D, Zhang YH, Zhu NY. beta(2,2)-Aminoxy acids: a new building block for turns and helices. J Am Chem Soc 2002; 124:9966-7. [PMID: 12188642 DOI: 10.1021/ja026966n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational properties of peptides 1-4 built from 3-aminoxy-2,2-dimethyl-propionic acid, a beta2,2-aminoxy acid, were investigated by NMR spectroscopy and X-ray crystallography. A novel beta N-O turn involving a nine-membered-ring intramolecular hydrogen bond between NHi+2 and COi was formed in diamides 1 and 2, which was further stabilized by another six-membered-ring intramolecular hydrogen bond between NHi+2 and NOi+1. Triamides 3 and 4 displayed a well-defined helical structure featuring two consecutive beta N-O turns. The X-ray structure of 4 revealed that the amide carbonyl group at position i+2 was twisted +65.9 degrees from that at i position, suggesting a novel 1.79 helix. Therefore, beta2,2-aminoxy acid can be used as a new building block for turns and helices.
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Affiliation(s)
- Dan Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong.
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43
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Shin I, Park K. Solution-phase synthesis of aminooxy peptoids in the C to N and N to C directions. Org Lett 2002; 4:869-72. [PMID: 11893173 DOI: 10.1021/ol010251s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] Aminooxy peptoids, which are potential peptidomimetics, were synthesized by a stepwise monomer assembly. Ns-protected N-substituted aminooxyacetate tert-butyl esters were used as a monomer in both the C to N and the N to C directions. Submonomer synthesis of aminooxy peptoids is also described.
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Affiliation(s)
- Injae Shin
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea.
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44
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Abstract
The three-center hydrogen bond in diaryl amide 1 was examined by IR and 1H NMR spectroscopy, X-ray crystallography, and ab initio calculations. By comparing 1 with its structural isomers 2, 3 and 4, and with its conformational isomers 1a-c, it was found that the two two-center components of the three-center interaction reinforce each other, that is, the enhanced stability of the three-center hydrogen bond is a result of positive cooperativity between the two components. Substituents not involved in hydrogen bonding have little effect on the strength of the two- and three-center hydrogen bonds. To our knowledge, this is the first three-center hydrogen-bonding system that has been shown to exhibit positive cooperativity. Ab initio calculations of the geometries, vibrational modes, and 1H NMR chemical shifts also support the experimental findings. These results have provided a new insight into the three-center intramolecular hydrogen bonding in a partially rigidified structure and have provided a reliable motif for designing stably folded structures.
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Affiliation(s)
- R D Parra
- Department of Chemistry, Natural Sciences Complex, State University of New York, Buffalo 14260, USA.
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45
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Shireman BT, Miller MJ, Jonas M, Wiest O. Conformational study and enantioselective, regiospecific syntheses of novel aminoxy trans-proline analogues derived from an acylnitroso Diels-Alder cycloaddition. J Org Chem 2001; 66:6046-56. [PMID: 11529730 DOI: 10.1021/jo010284l] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cis/trans isomerization of the proline amide bond has many implications in biological processes. The conformations of representative acylnitroso-derived proline analogues derived from cyclopentadiene were shown to exist exclusively as the E or trans conformation in CD2Cl2. The energetically favored conformations were determined using COSMO self-consistent reaction field calculations at the B3LYP/6-31G level of theory in addition to low temperature 1H NMR studies. The syntheses of the acylnitroso-derived peptides utilized two methods to selectively functionalize either of two chemically similar esters in the acylnitroso-derived amino acids. A novel transpeptidation of the amino acid that controlled the absolute stereochemistry in the acylnitroso Diels-Alder cycloaddition took advantage of an activated aminoxy amide linkage to control regiochemistry. Alternatively, an enantioselective and regiospecific enzymatic resolution of a racemic dimethyl ester provided a novel aminoxy acid.
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Affiliation(s)
- B T Shireman
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556-5670, USA
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46
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Wu YD, Zhao YL. A theoretical study on the origin of cooperativity in the formation of 3(10)- and alpha-helices. J Am Chem Soc 2001; 123:5313-9. [PMID: 11457394 DOI: 10.1021/ja003482n] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By using a simple repeating unit method, we have conducted a theoretical study which delineates the preferences for beta-strand, 2(7)-ribbon, 3(10)-helix, and alpha-helix formation for a series of polyglycine models up to 14 amino acid residues (Ac-(Gly)(n), n = 0, 1, 2,., 14). Interactions among residues, which result in cooperativity, are clearly indicated by variations in calculated energies of the residues. Whereas no cooperativity is found in the formation of beta-strands and 2(7)-ribbons, there is a significant cooperativity in the formation of 3(10)- and alpha-helices, especially for the latter. In the case of alpha-helices, the 14th residue is more stable than the 3rd by about 3 kcal/mol. A good correlation between calculated residue energy and residue dipole moment was uncovered, indicating the importance of long-range electrostatic interactions to the cooperativity. The results of our calculations are compared with those of the AMBER and PM3 methods, and indicate that both methods, AMBER and PM3, need further development in the cooperative view of electrostatic interactions. The result should be of importance in providing insight into protein folding and formation of helical structures in a variety of polymeric compounds. This also suggests a strategy for the development of more consistent molecular mechanics force fields.
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Affiliation(s)
- Y D Wu
- Contribution from the Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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47
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Son HS, Hong BH, Lee CW, Yun S, Kim KS. A new type of helix pattern in polyalanine peptide. J Am Chem Soc 2001; 123:514-5. [PMID: 11456562 DOI: 10.1021/ja0014640] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H S Son
- National Creative Research Initiative Center for Superfunctional Materials, Department of Chemistry Division of Molecular and Life Sciences Pohang University of Science and Technology Hyojadong, Namgu, Pohang 790-784, Korea
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48
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Günther R, Hofmann HJ. Hydrazino peptides as foldamers: an extension of the beta-peptide concept. J Am Chem Soc 2001; 123:247-55. [PMID: 11456510 DOI: 10.1021/ja001066x] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Replacing the C(beta) atoms in the beta-amino acid constituents of beta-peptides by nitrogen atoms leads to hydrazino peptides. A systematic conformation analysis of blocked hydrazino peptide oligomers of the general type I at the HF/6-31G, MP2/6-31G, and DFT/B3LYP/6-31G levels of ab initio MO theory and on the basis of molecular mechanics reveals a wide variety of secondary structures, as for instance various helices and sheet- and turnlike conformers. Some of them are closely related to secondary structure types found in beta-peptides; others represent novel types. Thus, a very stable, novel helix with 14-membered hydrogen-bonded pseudocycles, which occupies a conformation space different from that of helices with 14-membered rings found among the most stable conformers in beta-peptides, is indicated. The most important secondary structure elements are characterized by interactions between peptidic NH and CO groups. The additional hydrazino N(alpha)H group takes part in special structuring effects but is of lesser importance for secondary structure formation. The influence of environmental effects on the existence and stability of the various structure types is discussed. Due to the wide variety of structural possibilities, hydrazino peptides might be a useful tool for peptide and protein design.
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Affiliation(s)
- R Günther
- Contribution from the Institute of Biochemistry, Faculty of Biosciences, Pharmacy, and Psychology, University of Leipzig, Talstrasse 33, D-04103 Leipzig, Germany
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49
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Shin I, Lee M, Lee J, Jung M, Lee W, Yoon J. Synthesis of optically active phthaloyl D-aminooxy acids from L-amino acids or L-hydroxy acids as building blocks for the preparation of aminooxy peptides. J Org Chem 2000; 65:7667-75. [PMID: 11076633 DOI: 10.1021/jo0006573] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- I Shin
- Department of Chemistry and Department of Biochemistry, Yonsei University, Seoul 120-749, Korea.
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