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Wang S, Wu K, Tang YJ, Deng H. Dehydroamino acid residues in bioactive natural products. Nat Prod Rep 2024; 41:273-297. [PMID: 37942836 PMCID: PMC10880069 DOI: 10.1039/d3np00041a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Indexed: 11/10/2023]
Abstract
Covering: 2000 to up to 2023α,β-Dehydroamino acids (dhAAs) are unsaturated nonproteinogenic amino acids found in a wide array of naturally occurring peptidyl metabolites, predominantly those from bacteria. Other organisms, such as fungi, higher plants and marine invertebrates, have also been found to produce dhAA-containing peptides. The α,β-unsaturation in dhAAs has profound effects on the properties of these molecules. They display significant synthetic flexibility, readily undergoing reactions such as Michael additions, transition-metal-catalysed cross-couplings, and cycloadditions. These residues in peptides/proteins also exhibit great potential in bioorthogonal applications using click chemistry. Peptides containing contiguous dhAA residues have been extensively investigated in the field of foldamers, self-assembling supermolecules that mimic biomacromolecules such as proteins to fold into well-defined conformations. dhAA residues in these peptidyl materials tend to form a 2.05-helix. As a result, stretches of dhAA residues arrange in an extended conformation. In particular, peptidyl foldamers containing β-enamino acid units display interesting conformational, electronic, and supramolecular aggregation properties that can be modulated by light-dependent E-Z isomerization. Among approximately 40 dhAAs found in the natural product inventory, dehydroalanine (Dha) and dehydrobutyrine (Dhb) are the most abundant. Dha is the simplest dehydro-α-amino acid, or α-dhAA, without any geometrical isomers, while its re-arranged isomer, 3-aminoacrylic acid (Aaa or ΔβAla), is the simplest dehydro-β-amino acid, or β-enamino acid, and displays E/Z isomerism. Dhb is the simplest α-dhAA that exhibits E/Z isomerism. The Z-isomer of Dhb (Z-Dhb) is sterically favourable and is present in the majority of naturally occurring peptides containing Dhb residues. Dha and Z-Dhb motifs are commonly found in ribosomally synthesized and post-translationally modified peptides (RiPPs). In the last decade, the formation of Dha and Dhb motifs in RiPPs has been extensively investigated, which will be briefly discussed in this review. The formation of other dhAA residues in natural products (NPs) is, however, less understood. In this review, we will discuss recent advances in the biosynthesis of peptidyl NPs containing unusual dhAA residues and cryptic dhAA residues. The proposed biosynthetic pathways of these natural products will also be discussed.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Kewen Wu
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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2
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Liu D, Robin S, Gloaguen E, Brenner V, Mons M, Aitken DJ. Effects of sulfoxide and sulfone sidechain-backbone hydrogen bonding on local conformations in peptide models. Chem Commun (Camb) 2024; 60:2074-2077. [PMID: 38293794 DOI: 10.1039/d3cc05933b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
We examine peptide model systems designed to probe short-range N-H⋯OS sidechain-backbone hydrogen bonding involving amino acid residues with sidechain sulfoxide or sulfone functional groups and its effects on local conformations. A strong 7-membered ring hydrogen bond of this type accompanies an intra-residue N-H⋯OC interaction and stabilizes an extended backbone conformation in preference to classical folded structures.
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Affiliation(s)
- Dayi Liu
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.
| | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.
- Université Paris Cité, Faculté de Pharmacie, Paris 75006, France
| | - Eric Gloaguen
- Université Paris-Saclay, CNRS, ISMO, Orsay 91400, France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, DRF, Gif-sur-Yvette 91191, France
| | - Michel Mons
- Université Paris-Saclay, CEA, LIDYL, Gif-sur-Yvette 91191, France.
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.
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3
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Takeuchi N, Taniguchi M, Kato Y, Takata R, Osaka I, Nakajima N, Hamada M, Koyama Y. Synthesis and Conformational Behaviors of Unnatural Peptides Alternating Chiral and Achiral α,α-Disubstituted α-Amino Acid Units. Macromol Rapid Commun 2023; 44:e2300323. [PMID: 37668077 DOI: 10.1002/marc.202300323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The development of peptidomimetics to modulate the conformational profile of peptides has been extensively studied in the fields of biological and medicinal chemistry. However, large-scale synthesis of peptidomimetics with both an ordered sequence and a controlled secondary structure is highly challenging. In this paper, the framework of peptidomimetics has been designed to be alternating an achiral α,α-disubstituted α-amino acid unit and a chiral α-methylphenylalanine unit. The polymers are synthesized via invented Ugi reaction-based polycondensation technique. The chiral higher-order structures of the alternating peptides are evaluated mainly through circular dichroism (CD) spectroscopy. The UV-Vis and CD spectra of the polymers in three solvents are systematically measured at various temperatures. The anisotropic factors of CD (gCD ) values are calculated to know the chiroptical response. The results indicate the characteristic conformational behaviors. In a polar solvent, the hydrogen bonds between the N-H group of MePhe unit and the C=O of α,α-diphenylglycine unit outweigh the intraresidue hydrogen bonds in α,α-diphenylglycine unit, leading to the formation of a prevailing preferred-handed 310 -helical conformation. On the other hand, in a less polar solvent, the intrachain hydrogen bonds switch to intraresidue hydrogen bonds in α,α-diphenylglycine unit, which make the polymer adopting a prevailing extended planar C5 -conformation.
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Affiliation(s)
- Nanami Takeuchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masataka Taniguchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yuki Kato
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Riko Takata
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Noriyuki Nakajima
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masahiro Hamada
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhito Koyama
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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4
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Liu D, Bardaud JX, Imani Z, Robin S, Gloaguen E, Brenner V, Aitken DJ, Mons M. Length-Dependent Transition from Extended to Folded Shapes in Short Oligomers of an Azetidine-Based α-Amino Acid: The Critical Role of NH···N H-Bonds. Molecules 2023; 28:5048. [PMID: 37446709 DOI: 10.3390/molecules28135048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.05-helix, formed by successive C5 H-bonds, is an elusive secondary structure. Using a combination of theoretical chemistry and spectroscopic studies in both the gas phase and solution phase, we have demonstrated that derivatives of 3-amino-1-methylazetidine-3-carboxylic acid, Aatc(Me) can form sidechain-backbone N-H···N C6γ H-bonds that accompany-and thereby stabilize-C5 H-bonds. In the capped trimer of Aatc(Me), extended C5/C6γ motifs are sufficiently robust to challenge classical 310-helix formation in solution and the fully-extended 2.05-helix conformer has been characterized in the gas phase. Concurrent H-bonding support for successive C5 motifs is a new axiom for stabilizing the extended backbone secondary structure in short peptides.
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Affiliation(s)
- Dayi Liu
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | | | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
- Université Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
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5
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Santi S, Biondi B, Cardena R, Bisello A, Schiesari R, Tomelleri S, Crisma M, Formaggio F. Helical versus Flat Bis-Ferrocenyl End-Capped Peptides: The Influence of the Molecular Skeleton on Redox Properties. Molecules 2022; 27:6128. [PMID: 36144860 PMCID: PMC9503075 DOI: 10.3390/molecules27186128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022] Open
Abstract
Despite the fact that peptide conjugates with a pendant ferrocenyl (Fc) have been widely investigated, bis-ferrocenyl end-capped peptides are rarely synthetized. In this paper, in addition to the full characterization of the Fc-CO-[L-Dap(Boc)]n-NH-Fc series, we report a comparison of the three series of bis-ferrocenyl homopeptides synthesized to date, to gain insights into the influence of α-amino isobutyric (Aib), 2,3-diamino propionic (Dap) and Cα,β-didehydroalanine (ΔAla) amino acids on the peptide secondary structure and on the ferrocene redox properties. The results obtained by 2D NMR analysis and X-ray crystal structures, and further supported by electrochemical data, evidence different behaviors depending on the nature of the amino acid; that is, the formation of 310-helices or fully extended (2.05-helix) structures. In these foldamers, the orientation of the carbonyl groups in the peptide helix yields a macrodipole with the positive pole on the N-terminal amino acid and the negative pole on the C-terminal amino acid, so that oxidation of the Fc moieties takes place more or less easily depending on the orientation of the macrodipole moment as the peptide chain grows. Conversely, the fully extended conformation adopted by ΔAla flat peptides neither generates a macrodipole nor affects Fc oxidation. The utilization as electrochemical and optical (Circular Dichroism) probes of the two terminal Fc groups, bound to the same peptide chain, makes it possible to study the end-to-end effects of the positive charges produced by single and double oxidations, and to evidence the presence "exciton-coupled" CD among the two intramolecularly interacting Fc groups of the L-Dap(Boc) series.
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Affiliation(s)
- Saverio Santi
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Roberta Cardena
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Annalisa Bisello
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Renato Schiesari
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Silvia Tomelleri
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
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6
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Pierri G, Schettini R, Summa FF, De Riccardis F, Monaco G, Izzo I, Tedesco C. Right- and left-handed PPI helices in cyclic dodecapeptoids. Chem Commun (Camb) 2022; 58:5253-5256. [PMID: 35388839 DOI: 10.1039/d2cc00682k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enantiomorphic right- and left-handed polyproline type I helices in four cyclic dodecapeptoids with methoxyethyl and propargyl side chains are observed for the first time by single crystal X-ray diffraction. The peculiar absence of NH⋯OC hydrogen bonds in peptoids unveils the role of intramolecular backbone-to-backbone CO⋯CO interactions and CH⋯OC hydrogen bonds in the stabilization of the macrocycle conformation. Moreover, intramolecular backbone-side chain C5 CH⋯OC hydrogen bonds emerge as a stabilizing factor.
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Affiliation(s)
- Giovanni Pierri
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Rosaria Schettini
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Francesco F Summa
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Guglielmo Monaco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Consiglia Tedesco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
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7
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Mundlapati VR, Imani Z, D'mello VC, Brenner V, Gloaguen E, Baltaze JP, Robin S, Mons M, Aitken DJ. N-H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives. Chem Sci 2021; 12:14826-14832. [PMID: 34820098 PMCID: PMC8597926 DOI: 10.1039/d1sc05014a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom. In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.![]()
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Affiliation(s)
| | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France
| | - Viola C D'mello
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France .,Université de Paris, Faculté de Pharmacie 75006 Paris France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
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Biondi B, Cardena R, Bisello A, Schiesari R, Cerveson L, Facci M, Rancan M, Formaggio F, Santi S. Flat, Ferrocenyl‐Conjugated Peptides: A Combined Electrochemical and Spectroscopic Study. ChemElectroChem 2021. [DOI: 10.1002/celc.202100597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Barbara Biondi
- Institute of Biomolecular Chemistry Padova Unit, CNR via Marzolo 1 35131 Padova Italy
| | - Roberta Cardena
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
| | - Annalisa Bisello
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
| | - Renato Schiesari
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
| | - Laura Cerveson
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
| | - Martino Facci
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
| | - Marzio Rancan
- Institute of Condensed Matter Chemistry and Technologies for Energy (ICMATE), CNR Via Marzolo, 1 35131 Padova Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry Padova Unit, CNR via Marzolo 1 35131 Padova Italy
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
| | - Saverio Santi
- Department of Chemical Sciences University of Padova via Marzolo 1 35131 Padova Italy
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Santi S, Bisello A, Cardena R, Tomelleri S, Schiesari R, Biondi B, Crisma M, Formaggio F. Flat, C α,β -Didehydroalanine Foldamers with Ferrocene Pendants: Assessing the Role of α-Peptide Dipolar Moments. Chempluschem 2021; 86:723-730. [PMID: 33825347 DOI: 10.1002/cplu.202100072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/22/2021] [Indexed: 12/28/2022]
Abstract
The foldamer field is continuously expanding as it allows to produce molecules endowed with 3D-structures and functions never observed in nature. We synthesized flat foldamers based on the natural, but non-coded, Cα,β -didehydroalanine α-amino acid, and covalently linked to them two ferrocene (Fc) moieties, as redox probes. These conjugates retain the flat and extended conformation of the 2.05 -helix, both in solution and in the crystal state (X-ray diffraction). Cyclic voltammetry measurements agree with the adoption of the 2.05 -helix, characterized by a negligible dipole moment. Thus, elongated α-peptide stretches of this type are insulators rather than charge conductors, the latter being constituted by peptide α-helices. Also, our homo-tetrapeptide has a N-to-C length of about 18.2 Å, almost double than that (9.7 Å) of an α-helical α-tetrapeptide.
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Affiliation(s)
- Saverio Santi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Annalisa Bisello
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Roberta Cardena
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Silvia Tomelleri
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Renato Schiesari
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
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10
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Imani Z, Mundlapati VR, Goldsztejn G, Brenner V, Gloaguen E, Guillot R, Baltaze JP, Le Barbu-Debus K, Robin S, Zehnacker A, Mons M, Aitken DJ. Conformation control through concurrent N-H⋯S and N-H⋯O[double bond, length as m-dash]C hydrogen bonding and hyperconjugation effects. Chem Sci 2020; 11:9191-9197. [PMID: 34123167 PMCID: PMC8163419 DOI: 10.1039/d0sc03339a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In addition to the classical N-H⋯O[double bond, length as m-dash]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N-H⋯S interactions (C6γ), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H⋯O[double bond, length as m-dash]C interactions (C5) to provide a C5-C6γ feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6γ features in the planar dimer implicate an unprecedented three-centre H-bond of the type C[double bond, length as m-dash]O⋯H(N)⋯SR2, while the trimer adopts two C5-C6γ features separated by a Ramachandran α-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.
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Affiliation(s)
- Zeynab Imani
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Gildas Goldsztejn
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Jean-Pierre Baltaze
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Sylvie Robin
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France .,Faculté de Pharmacie, Université de Paris 75006 Paris France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Michel Mons
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - David J Aitken
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
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11
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Kubyshkin V, Budisa N. Anticipating alien cells with alternative genetic codes: away from the alanine world! Curr Opin Biotechnol 2019; 60:242-249. [DOI: 10.1016/j.copbio.2019.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/07/2019] [Indexed: 12/24/2022]
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