1
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Katoh T, Suga H. Consecutive Ribosomal Incorporation of α-Aminoxy/α-Hydrazino Acids with l/d-Configurations into Nascent Peptide Chains. J Am Chem Soc 2021; 143:18844-18848. [PMID: 34731572 DOI: 10.1021/jacs.1c09270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
α-Aminoxy and α-hydrazino acids are β-amino acid analogs with β-carbons replaced by oxygen and nitrogen, respectively. Such heteroatoms dictate the folding of peptides into specific secondary structures called pseudo-γ-turns. Achiral α-aminoxyacetic acid (NOGly) and l-α-hydrazinophenylalanine (l-NNPhe) have been shown to be suitable for single incorporation during ribosomal translation, but whether ribosomes tolerate other types of α-aminoxy/α-hydrazino acids with l/d-configurations is unknown. Moreover, whether multiple or consecutive incorporations are possible remains unclear. We show, for the first time, multiple and consecutive incorporations of α-aminoxy/α-hydrazino acids with l/d-configurations into various model peptides, including macrocyclic peptide scaffolds.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Mikami R, Tsukagoshi S, Oda Y, Arai K. S-Denitrosylase-like Activity of Cyclic Diselenides Conjugated with Xaa-His Dipeptide: Role of Proline Spacer as a Key Activity Booster. Chembiochem 2021; 23:e202100394. [PMID: 34350692 DOI: 10.1002/cbic.202100394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 11/05/2022]
Abstract
This study developed dipeptide-conjugated 1,2-diselenan-4-amine (1), i.e., 1-Xaa-His, as a new class of S-denitrosylase mimic. The synthesized compounds, especially 1-Pro-His, remarkably promoted S-denitrosylation of nitrosothiols (RSNO) via a catalytic cycle involving the reversible redox reaction between the diselenide and its corresponding diselenol ([SeH,SeH]) form with coexisting reductant thiols (R'SH), during which the [SeH,SeH] form as a key reactive species reduces RSNO to the corresponding thiol (RSH). Structural analyses of 1-Pro-His suggested that the peptide backbone of [SeH,SeH] is rigidly bent to form a γ-turn, possibly including an NH···Se hydrogen bond between the imidazole ring of His and selenol group, thus stabilizing the [SeH,SeH] form thermodynamically, and dramatically enhancing the catalytic activity. Furthermore, the synthetic compounds were found to prohibit S-nitrosylation-induced protein misfolding in the presence of RSNO, eventually implying their potential as a drug seed for misfolding diseases caused by the dysregulation of the S-denitrosylation system.
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Affiliation(s)
- Rumi Mikami
- Tokai University - Shonan Campus: Tokai Daigaku, Chemistry, Kitakaname, 259-1292, Hiratsuka-shi, JAPAN
| | - Shunsuke Tsukagoshi
- Tokai University - Shonan Campus: Tokai Daigaku, Chemistry, Kitakaname, 259-1292, Hiratsuka-shi, JAPAN
| | - Yoshiki Oda
- Tokai University - Shonan Campus: Tokai Daigaku, Technology Joint Management Office, Kitakaname, 259-1292, Hiratsuka-shi, JAPAN
| | - Kenta Arai
- Tokai University, Chemistry, Kitakaname, 259-1292, Hiratsuka-shi, JAPAN
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3
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Clarke D, Wu G, Wu C, Scherman OA. Host-Guest Induced Peptide Folding with Sequence-Specific Structural Chirality. J Am Chem Soc 2021; 143:6323-6327. [PMID: 33860670 PMCID: PMC8154536 DOI: 10.1021/jacs.1c00342] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 12/31/2022]
Abstract
Controlling the spatial and temporal behavior of peptide segments is essential in the fabrication of functional peptide-based materials and nanostructures. To achieve a desired structure, complex sequence design is often required, coupled with the inclusion of unnatural amino acids or synthetic modifications. Herein, we investigate the structural properties of 1:1 inclusion complexes between specific oligopeptides and cucurbit[8]uril (CB[8]), inducing the formation of turns, and by alteration of the peptide sequence, tunable structural chirality. We also explore extended peptide sequence binding with CB[8], demonstrating a simple approach to construct a peptide hairpin.
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Affiliation(s)
| | | | - Ce Wu
- Melville Laboratory for Polymer
Synthesis, Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Oren A. Scherman
- Melville Laboratory for Polymer
Synthesis, Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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4
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Sinatra L, Kolano L, Icker M, Fritzsche SR, Volke D, Gockel I, Thieme R, Hoffmann R, Hansen FK. Hybrid Peptides Based on α-Aminoxy Acids as Antimicrobial and Anticancer Foldamers. Chempluschem 2021; 86:827-835. [PMID: 33656810 DOI: 10.1002/cplu.202000812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/18/2021] [Indexed: 12/31/2022]
Abstract
α-Aminoxy peptides represent an interesting group of peptidomimetics with high proteolytic stability and the ability to fold into specific, predictable secondary structures. Here, we present a series of hybrid peptides consisting of α-aminoxy acids and α-amino acids with cationic and aromatic, hydrophobic side chains in an alternating manner synthesized using an efficient protocol that combines solution- and solid-phase synthesis. 2D ROESY experiments with a representative hexamer suggested the presence of a 7/8 helical conformation in solution. Biological evaluation revealed a significant impact of the peptide chain length and the N-terminal cap on the antimicrobial and anticancer properties of this series of hybrid peptides. The Fmoc-capped peptide 6e displayed the most potent antimicrobial activity against a panel of Gram-negative and Gram-positive bacterial strains (e. g. against E. Coli: MIC=8 mg/L; S. aureus: MIC=4 mg/L).
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Affiliation(s)
- Laura Sinatra
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstr. 34, 04103, Leipzig, Germany
| | - Lisa Kolano
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Maik Icker
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Stefan R Fritzsche
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstr. 34, 04103, Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
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5
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Yuan F, Tian Y, Qin W, Li J, Yang D, Zhao B, Yin F, Li Z. Evaluation of topologically distinct constrained antimicrobial peptides with broad-spectrum antimicrobial activity. Org Biomol Chem 2019; 16:5764-5770. [PMID: 30004546 DOI: 10.1039/c8ob00483h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antimicrobial peptides (AMPs) are short cationic peptides with a high affinity for membranes and emerged as a promising therapeutic approach with potential for treating infectious diseases. Chemical stabilization of short peptides proved to be a successful approach for enhancing their bio-physical properties. Herein, we designed and synthesized a panel of conformationally constrained antimicrobial peptides with either α-helical or β-hairpin conformation using templating strategies. These synthetic short constrained peptides possess different topological distributions of hydrophobic and hydrophilic residues and displayed distinct antimicrobial activity. Notably, the conformationally constrained α-helical peptides displayed a faster internalization into the bacteria cells compared to their β-hairpin analogues. These synthetic short constrained peptides showed killing effects on a broad spectrum of microorganisms mainly through pore formation and membrane damage which provided a potentially promising skeleton for the next generation of stabilized antimicrobial peptides.
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Affiliation(s)
- Fang Yuan
- Institute of Scientific and Technical Information of China, Beijing, 100038, China
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6
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Bucci R, Contini A, Clerici F, Pellegrino S, Gelmi ML. From glucose to enantiopure morpholino β-amino acid: a new tool for stabilizing γ-turns in peptides. Org Chem Front 2019. [DOI: 10.1039/c8qo01116h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
“Environmentally sustainable” synthesis of a new enantiopure morpholino β-amino acid from glucose: a new tool for exotic peptide architectures.
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Affiliation(s)
- Raffaella Bucci
- DISFARM-Sez
- Chimica Generale e Organica “A. Marchesini”
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Alessandro Contini
- DISFARM-Sez
- Chimica Generale e Organica “A. Marchesini”
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Francesca Clerici
- DISFARM-Sez
- Chimica Generale e Organica “A. Marchesini”
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Sara Pellegrino
- DISFARM-Sez
- Chimica Generale e Organica “A. Marchesini”
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Maria Luisa Gelmi
- DISFARM-Sez
- Chimica Generale e Organica “A. Marchesini”
- Università degli Studi di Milano
- 20133 Milano
- Italy
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7
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Vijayadas KN, Kotmale AS, Thorat SH, Gonnade RG, Nair RV, Rajamohanan PR, Sanjayan GJ. Reversal of H-bonding direction by N-sulfonation in a synthetic reverse-turn peptide motif. Org Biomol Chem 2015; 13:3064-9. [PMID: 25624112 DOI: 10.1039/c4ob02438a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication depicts an intriguing example of hydrogen-bonding reversal upon introduction of a sulfonamide linkage at the N-terminus of a synthetic reverse-turn peptide motif. The ready availability of two sulfonyl oxygen atoms, as hydrogen-bonding acceptors, combined with the inherent twisted conformation of sulfonamides are seen to act as switches that engage/disengage the hydrogen-bond at the sticky ends/termini.
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Affiliation(s)
- Kuruppanthara N Vijayadas
- Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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8
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Moussodia RO, Acherar S, Romero E, Didierjean C, Jamart-Grégoire B. Evidence of Nanotubular Self-Organization in Solution and Solid States of Heterochiral Cyclo 1:1 [α/α-Nα-Bn-hydrazino]mers Series. J Org Chem 2015; 80:3022-9. [DOI: 10.1021/jo502684g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ralph-Olivier Moussodia
- Laboratoire
de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375, 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Samir Acherar
- Laboratoire
de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375, 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Eugénie Romero
- Laboratoire
de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375, 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Claude Didierjean
- Laboratoire de Crystallographie, Résonance Magnétique
et Modélisations (CRM2), Université de Lorraine-CNRS, UMR 7036, Faculté des Sciences et Technologies, BP 20239, 54506 Vandœuvre-lès-Nancy cedex, France
| | - Brigitte Jamart-Grégoire
- Laboratoire
de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375, 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
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9
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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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10
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Chandrasekhar S, Rao KVM, Seenaiah M, Naresh P, Devi AS, Jagadeesh B. Formation of Periodicγ-Turns inα/β-Hybrid Peptides: DFT and NMR Experimental Evidence. Chem Asian J 2013; 9:457-61. [DOI: 10.1002/asia.201301068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 11/08/2022]
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11
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Acherar S, Salaün A, Le Grel P, Le Grel B, Jamart-Grégoire B. Conformational Behavior of 1:1 [α/α-Hydrazino]mer, 1:1 [α/Aza-β3-amino]mer and 1:1 [Aza-β3-amino/α]mer Series: Three Series of Foldamers. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Dutt Konar A. Conformational studies of γ-turn in pseudopeptides containing α-amino acid and conformationally constrained meta amino benzoic acid/meta nitro aniline. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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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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14
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Moussodia RO, Acherar S, Bordessa A, Vanderesse R, Jamart-Grégoire B. An expedient and short synthesis of chiral α-hydrazinoesters: synthesis and conformational analysis of 1:1 [α/α-Nα-hydrazino]mers. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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16
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De Marco R, Tolomelli A, Campitiello M, Rubini P, Gentilucci L. Expedient synthesis of pseudo-Pro-containing peptides: towards constrained peptidomimetics and foldamers. Org Biomol Chem 2012; 10:2307-17. [DOI: 10.1039/c2ob07172j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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17
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Ma Y, Yang D, Ma Y, Zhang YH. Novel Cell-Penetrating Peptides Based on α-Aminoxy Acids. Chembiochem 2011; 13:73-9. [DOI: 10.1002/cbic.201100682] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Indexed: 11/06/2022]
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18
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Extraordinary metabolic stability of peptides containing α-aminoxy acids. Amino Acids 2011; 43:499-503. [DOI: 10.1007/s00726-011-1095-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 09/19/2011] [Indexed: 11/26/2022]
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19
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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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20
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Roy A, Prabhakaran P, Baruah PK, Sanjayan GJ. Diversifying the structural architecture of synthetic oligomers: the hetero foldamer approach. Chem Commun (Camb) 2011; 47:11593-611. [DOI: 10.1039/c1cc13313f] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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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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22
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Guo L, Almeida AM, Zhang W, Reidenbach AG, Choi SH, Guzei IA, Gellman SH. Helix formation in preorganized beta/gamma-peptide foldamers: hydrogen-bond analogy to the alpha-helix without alpha-amino acid residues. J Am Chem Soc 2010; 132:7868-9. [PMID: 20491510 DOI: 10.1021/ja103233a] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first high-resolution structural data for the beta/gamma-peptide 13-helix (i,i+3 C=O...H-N H-bonds), a secondary structure that is formed by oligomers with a 1:1 alternation of beta- and gamma-amino acid residues. Our characterization includes both crystallographic and 2D NMR data. Previous studies suggested that beta/gamma-peptides constructed from conformationally flexible residues adopt a different helical secondary structure in solution. Our design features preorganized beta- and gamma-residues, which strongly promote 13-helical folding by the 1:1 beta/gamma backbone.
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Affiliation(s)
- Li Guo
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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23
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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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24
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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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25
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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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26
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Gorske BC, Stringer JR, Bastian BL, Fowler SA, Blackwell HE. New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems. J Am Chem Soc 2010; 131:16555-67. [PMID: 19860427 DOI: 10.1021/ja907184g] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Controlling the equilibria between backbone cis- and trans-amides in peptoids, or N-substituted glycine oligomers, constitutes a significant challenge in the construction of discretely folded peptoid structures. Through the analysis of a set of monomeric peptoid model systems, we have developed new and general strategies for controlling peptoid conformation that utilize local noncovalent interactions to regulate backbone amide rotameric equilibria, including n-->pi*, steric, and hydrogen bonding interactions. The chemical functionalities required to implement these strategies are typically confined to the peptoid side chains, preserve chirality at the side chain N-alpha-carbon known to engender peptoid structure, and are fully compatible with standard peptoid synthesis techniques. Our examinations of peptoid model systems have also elucidated how solvents affect various side chain-backbone interactions, revealing fundamental aspects of these noncovalent interactions in peptoids that were largely uncharacterized previously. As validation of our monomeric model systems, we extended the scope of this study to include peptoid oligomers and have now demonstrated the importance of local steric and n-->pi* interactions in dictating the structures of larger, folded peptoids. This new, modular design strategy has guided the construction of peptoids containing 1-naphthylethyl side chains, which we show can be utilized to effectively eliminate trans-amide rotamers from the peptoid backbone, yielding the most conformationally homogeneous class of peptoid structures yet reported in terms of amide rotamerism. Overall, this research has afforded a valuable and expansive set of design tools for the construction of both discretely folded peptoids and structurally biased peptoid libraries and should shape our understanding of peptoid folding.
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Affiliation(s)
- Benjamin C Gorske
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, USA
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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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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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Fischer L, Didierjean C, Jolibois F, Semetey V, Manuel Lozano J, Briand JP, Marraud M, Poteau R, Guichard G. Propensity for local folding induced by the urea fragment in short-chain oligomers. Org Biomol Chem 2008; 6:2596-610. [PMID: 18600281 DOI: 10.1039/b801139g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examination of local folding and H-bonding patterns in model compounds can be extremely informative to gain insight into the propensity of longer-chain oligomers to adopt specific folding patterns (i.e. foldamers) based on remote interactions. Using a combination of experimental techniques (i.e. X-ray diffraction, FT-IR absorption and NMR spectroscopy) and theoretical calculations at the density functional theory (DFT) level, we have examined the local folding patterns induced by the urea fragment in short-chain aza analogues of beta- and gamma-amino acid derivatives. We found that the urea-turn, a robust C(8) conformation based on 1<--3 H-bond interaction, is largely populated in model ureidopeptides (I-IV) obtained by replacing the alpha-carbon of a beta-amino acid by a nitrogen. This H-bonding scheme is likely to compete with remote H-bond interactions, thus preventing the formation of secondary structures based on remote intrastrand interactions in longer oligomers. In related oligomers obtained by the addition of a methylene in the main chain (V-VIII), nearest-neighbour H-bonded interactions are unfavourable i.e. the corresponding C9 folding pattern is hardly populated. In this series, folding based on remote intrastrand interactions becomes possible for longer oligomers. We present spectroscopic evidence that tetraurea VIII is likely to be the smallest unit capable of reproducing the H-bonded motif found in 2.5-helical N,N'-linked oligoureas.
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Affiliation(s)
- Lucile Fischer
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Immunologie et Chimie Thérapeutiques, 15, rue Descartes, F-67000, Strasbourg, France
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Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic Characterization of Helical Secondary Structures in α/β-Peptides with 1:1 Residue Alternation. J Am Chem Soc 2008; 130:6544-50. [DOI: 10.1021/ja800355p] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Lara C. Spencer
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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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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Kendhale AM, Gonnade R, Rajamohanan PR, Hofmann HJ, Sanjayan GJ. Foldamers with unusual structural architecture from spirobi(indane) building blocks. Chem Commun (Camb) 2008:2541-3. [DOI: 10.1039/b800825f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Choi SH, Guzei IA, Gellman SH. Crystallographic characterization of the alpha/beta-peptide 14/15-helix. J Am Chem Soc 2007; 129:13780-1. [PMID: 17949002 DOI: 10.1021/ja0753344] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Zhu J, Lin JB, Xu YX, Shao XB, Jiang XK, Li ZT. Hydrogen-Bonding-Mediated Anthranilamide Homoduplexes. Increasing Stability through Preorganization and Iterative Arrangement of a Simple Amide Binding Site. J Am Chem Soc 2006; 128:12307-13. [PMID: 16967982 DOI: 10.1021/ja064218i] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes the assembly of two new series of self-complementary duplexes by making use of amide units, the simplest assembling units of hydrogen bonding, as binding sites. All the new monomers possess a rigidified anthranilamide skeleton, which is stabilized by intramolecular hydrogen bonding. Amide units are iteratively introduced to one side of the preorganized skeletons to facilitate the formation of intermolecular hydrogen bonding. Compounds 2 and 3 bear two and three CONH(2) units, respectively, while 4, 6, and 7 are incorporated with two, three, and four AcNH units, respectively. For comparison, compound 5, which is similar to 4 but contains one AcNH and one CF(3)CONH unit, is also prepared. X-ray diffraction analysis of 2, 4, and 5 revealed homodimeric motifs in the solid state which are stabilized by two or more intermolecular hydrogen bonds. (1)H NMR investigations in CDCl(3) indicated that all the compounds form hydrogen-bonded homoduplexes. Duplexes 3.3, 6.6, and 7.7 are highly stable in CDCl(3), with a lower K(assoc) limit of 2.3 x 10(5) M(-1). The K(assoc) values of the three duplexes in more polar CDCl(3)/CD(3)CN (9:1, v/v) were determined with the (1)H NMR dilution method. The result opens the way for the development of new polymeric duplexes of well-ordered structures.
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Affiliation(s)
- Jiang Zhu
- 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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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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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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Hou JL, Shao XB, Chen GJ, Zhou YX, Jiang XK, Li ZT. Hydrogen Bonded Oligohydrazide Foldamers and Their Recognition for Saccharides. J Am Chem Soc 2004; 126:12386-94. [PMID: 15453772 DOI: 10.1021/ja047436p] [Citation(s) in RCA: 212] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the synthesis and characterization of the first series of hydrogen bonding-driven hydrazide foldamers and their recognition for alkyl saccharides in chloroform. Oligomers 1, 2-4, 5, 6, and 7, which contain one, two, four, six, or twelve repeated dibenzoyl hydrazide residues, respectively, have been prepared. The rigid and planar conformations of 1 and 2 or 4 have been established with X-ray analysis and (1)H NMR spectroscopy, whereas the folding and helical conformations of 5-7 have been evidenced by the 1D and 2D (1)H NMR and IR spectroscopy and molecular mechanics calculations. Molecular mechanics calculations also revealed that 5, 6, and 7 possess a rigid cavity with size of ca. 10.6 to 11.1 A, and half of the carbonyl groups in the folding conformations are orientated inwardly inside the cavity. (1)H NMR and CD experiments revealed that 5-7 efficiently complex alkylated mono- and disaccharides 32-35 in chloroform. The association constants (K(assoc)) of the complexes have been determined with the (1)H NMR and fluorescent titration methods. The energy-minimized conformation of 6.34 has been obtained with molecular mechanics calculation. The hydrazide-based folding structures described here represent novel examples of hydrogen bonding-driven foldamers that act as artificial receptors for selective molecular recognition.
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Affiliation(s)
- Jun-Li Hou
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China
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Su S, Giguere JR, Schaus SE, Porco JA. Synthesis of complex alkoxyamines using a polymer-supported N-hydroxyphthalimide. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.05.109] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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