1
|
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.
Collapse
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
| |
Collapse
|
2
|
De Zotti M, Clayden J. Extended Diethylglycine Homopeptides Formed by Desulfurization of Their Tetrahydrothiopyran Analogues. Org Lett 2019; 21:2209-2212. [PMID: 30859838 DOI: 10.1021/acs.orglett.9b00501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Diethylglycine (Deg) homopeptides adopt the rare 2.05-helical conformation, the longest three-dimensional structure that a peptide of a given sequence can adopt. Despite this unique conformational feature, Deg is rarely used in peptide design because of its poor reactivity. In this paper, we show that reductive desulfurization of oligomers formed from more reactive tetrahydrothiopyran-containing precursors provides a practical way to build the longest Deg homopeptides so far made, and we detail some conformational studies of the Deg oligomers and their heterocyclic precursors.
Collapse
Affiliation(s)
- Marta De Zotti
- Department of Chemistry , University of Padova , Via Marzolo 1 , 35131 Padova , Italy
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| |
Collapse
|
3
|
Rathore RS. Conformational investigations on analogs of inflammation response inducing chemotactic tripeptide fMLP. Biopolymers 2005; 80:651-64. [PMID: 15648091 DOI: 10.1002/bip.20231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformations of three analogs of for-L-Met-L-Leu-L-Phe-OH (fMLP), which initiates inflammatory response by interaction with the formyl peptide receptor (FPR), have been investigated by the application of the X-ray crystallographic technique. The investigated analogs of fMLP peptides are as follows: for-L-Met-1-amino-1-cyclooctane-carbonyl(Ac8c)-L-Phe-OMe; for-L-Met-L-Leu-L-p-iodo-Phe-OH; and for-L-Met-di-n-propylglycyl(Dpg)-L-Phe-OMe. The peptide backbone in and is constrained at position of fMLP by the introduction of Calpha,alpha-disubstituted glycines. In peptide, Phe-OMe is substituted by p-iodo-Phe-OH. Crystal structures reveal an overall folded conformation adopted by and. The former is folded in the type II beta-turn, which is stabilized by an intramolecular 1<--4 (formyl) C==O...H--N (Phe) hydrogen bond, whereas the latter is folded in an open turn without any intramolecular hydrogen bond. On the other hand, peptide has an extended conformation, and two different molecules in a crystallographic asymmetric unit form an antiparallel beta-sheet-like structure. In and, residues Ac8c and Dpg adopt left-handed helical and fully extended (C5) conformations, respectively. The cyclooctane ring in Ac8c acquires a boat-chair conformation. Crystal packing of is characterized by the association of aliphatic-aromatic rings via a C--H...pi interaction. In the crystal of, contrary to the usual observations, peptides are interlinked via networks of head-to-tail hydrogen bond and pi...pi interactions, which are generally observed to be mutually exclusive. The structure-function mechanism of the ligand-receptor interaction is discussed.
Collapse
|
4
|
Toniolo C, Crisma M, Formaggio F, Peggion C. Control of peptide conformation by the Thorpe-Ingold effect (C alpha-tetrasubstitution). Biopolymers 2002; 60:396-419. [PMID: 12209474 DOI: 10.1002/1097-0282(2001)60:6<396::aid-bip10184>3.0.co;2-7] [Citation(s) in RCA: 576] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The preferred conformations of peptides heavily based on the currently extensively exploited achiral and chiral alpha-amino acids with a quaternary alpha-carbon atom, as determined by conformational energy computations, crystal-state (x-ray diffraction) analyses, and solution ((1)H-NMR and spectroscopic) investigations, are reviewed. It is concluded that 3(10)/alpha-helical structures and the fully extended (C(5)) conformation are preferentially adopted by peptide sequences characterized by this family of amino acids, depending upon overall bulkiness and nature (e.g., whether acyclic or C(alpha) (i) <--> C(alpha) (i) cyclized) of their side chains. The intriguing relationship between alpha-carbon chirality and bend/helix handedness is also illustrated. gamma-Bends and semiextended conformations are rarely observed. Formation of beta-sheet structures is prevented.
Collapse
Affiliation(s)
- C Toniolo
- Department of Organic Chemistry, University of Padova, Institute of Biomolecular Chemistry, CNR, 35131 Padova, Italy.
| | | | | | | |
Collapse
|
5
|
Spisani S, Traniello S, Cavicchioni G, Formaggio F, Crisma M, Toniolo C. Probing structural requirements of fMLP receptor: on the size of the hydrophobic pocket corresponding to residue 2 of the tripeptide. J Pept Sci 2002; 8:56-65. [PMID: 11860029 DOI: 10.1002/psc.369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The conformationally constrained f-L-Met-Ac(n)c-L-Phe-OMe (n = 4,9-12) tripeptides, analogues of the chemoattractant f-L-Met-L-Leu-L-Phe-OH, were synthesized in solution by classical methods and fully characterized. These compounds and the published f-L-Met-Xxx-L-Phe-OMe (Xxx = Aib and Ac(n)c where n = 3, 5-8) analogues were compared to determine the combined effect of backbone preferred conformation and side-chain bulkiness at position 2 on the relation of 3D-structure to biological activity. A conformational study of all the analogues was performed in solution by FT-IR absorption and 1H-NMR techniques. In parallel, each peptide was tested for its ability to induce chemotaxis, superoxide anion production and lysozyme secretion from human neutrophils. The biological and conformational data are discussed in relation to the proposed model of the chemotactic receptor on neutrophils, in particular of the hydrophobic pocket accommodating residue 2 of the tripeptide.
Collapse
Affiliation(s)
- Susanna Spisani
- Department of Biochemistry and Molecular Biology, University of Ferrara, Italy
| | | | | | | | | | | |
Collapse
|
6
|
|
7
|
Wolf WM, Stasiak M, Leplawy MT, Bianco A, Formaggio F, Crisma M, Toniolo C. Destabilization of the 310-Helix in Peptides Based on Cα-Tetrasubstituted α-Amino Acids by Main-Chain to Side-Chain Hydrogen Bonds. J Am Chem Soc 1998. [DOI: 10.1021/ja982194c] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wojciech M. Wolf
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| | - Marcin Stasiak
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| | - Miroslav T. Leplawy
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| | - Alberto Bianco
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| | - Marco Crisma
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Contribution from the Institute of General and Ecological Chemistry and the Institute of Organic Chemistry, Technical University, 90-924 Lodz, Poland, and the Department of Organic Chemistry and Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy
| |
Collapse
|
8
|
Torrini I, Paglialunga Paradisi M, Pagani Zecchini G, Lucente G, Gavuzzo E, Mazza F, Pochetti G, Traniello S, Spisani S. Synthesis, conformation, and biological activity of two fMLP-OMe analogues containing the new 2-[2'-(methylthio)ethyl]methionine residue. Biopolymers 1997; 42:415-26. [PMID: 9283291 DOI: 10.1002/(sici)1097-0282(19971005)42:4<415::aid-bip5>3.0.co;2-t] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The new C alpha-tetrasubstituted alpha-amino acid residue 2-[2'-(methylthio)ethyl]methionine (Dmt) has been introduced into the reference chemotactic tripeptide HCO-Met-Leu-Phe-OMe (fMLP-OMe) in place of the leucine or methionine, respectively. The biological activity of the new analogues [Dmt2]fMLP-OMe (2) and [Dmt1]fMLP-OMe (3) has been determined; whereas 2 is active toward human neutrophils, stimulating directed migration, superoxide anion generation, and lysozyme release, 3 results practically inactive in all tested assays. A conformational analysis on 2 and 3 has been performed in solution by using ir absorption and 1H-nmr. The conformation of 2 was also examined in the crystal by x-ray diffraction methods. Both 2 and 3 adopt fully extended conformation in correspondence with the Dmt residue. Biological and conformational results are discussed and compared with related previously studied models.
Collapse
Affiliation(s)
- I Torrini
- Dipartimento di Studi Farmaceutici, Università La Sapienza, Roma, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Pagani Zecchini G, Paglialunga Paradisi M, Torrini I, Lucente G, Mastropietro G, Paci M, Spisani S. Chemotactic peptide analogues. Centrally constrained chemotactic N-formyltripeptides: synthesis, conformation, and activity of two new analogues. Arch Pharm (Weinheim) 1996; 329:517-23. [PMID: 9038418 DOI: 10.1002/ardp.19963291202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The role exercised by the central residue of the chemotactic N-formyltripeptide HCO-Met-Leu-Phe-OMe (fMLP-OMe) in controlling both the backbone conformation and the biochemical activity is the subject of recent interest. Here, two new centrally constrained fMLP-OMe analogues, namely HCO-Met-azaPro-Phe-OMe (4) and HCO-Met-(gamma-lactam)-Phe-OMe (6) have been synthesized and their CDCI3 solution conformation and activity have been studied. The azapeptide 4 adopts beta-folded conformation with the azaPro residue at the i+2 position and an intramolecular H-bond involving the formylic oxygen and the Phe NH. The gamma-lactam tripeptide 6 prefers a semi-extended backbone conformation. When tested on human neutrophils both the new models were found practically devoid of biological activity. The role exerted by the NH groups as well as by the conformational preferences is discussed.
Collapse
Affiliation(s)
- G Pagani Zecchini
- Dipartimento di Studi Farmaceutici, Università La Sapienza, Roma, Italy
| | | | | | | | | | | | | |
Collapse
|