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Synthesis of Tetrapeptides Containing Dehydroalanine, Dehydrophenylalanine and Oxazole as Building Blocks for Construction of Foldamers and Bioinspired Catalysts. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092611. [PMID: 35565962 PMCID: PMC9102237 DOI: 10.3390/molecules27092611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022]
Abstract
The incorporation of dehydroamino acid or fragments of oxazole into peptide chain is accompanied by a distorted three-dimensional structure and additionally enables the introduction of non-typical side-chain substituents. Thus, such compounds could be building blocks for obtaining novel foldamers and/or artificial enzymes (artzymes). In this paper, effective synthetic procedures leading to such building blocks-tetrapeptides containing glycyldehydroalanine, glycyldehydrophenylalanine, and glycyloxazole subunits-are described. Peptides containing serine were used as substrates for their conversion into peptides containing dehydroalanine and aminomethyloxazole-4-carboxylic acid while considering possible requirements for the introduction of these fragments into long-chain peptides at the last steps of synthesis.
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2
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The oxydiacetate and iminodiacetate complexes of oxidovanadium(IV) as the new series of the catalysts for the oligomerization of beta-olefin derivatives. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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3
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Drzeżdżon J, Malinowski J, Sikorski A, Gawdzik B, Rybiński P, Chmurzyński L, Jacewicz D. Iminodiacetate complex of cobalt(II) – Structure, physicochemical characteristics, biological properties and catalytic activity for 2-chloro-2-propen-1-ol oligomerization. Polyhedron 2020. [DOI: 10.1016/j.poly.2019.114168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Joaquin D, Lee MA, Kastner DW, Singh J, Morrill ST, Damstedt G, Castle SL. Impact of Dehydroamino Acids on the Structure and Stability of Incipient 3 10-Helical Peptides. J Org Chem 2019; 85:1601-1613. [PMID: 31730750 DOI: 10.1021/acs.joc.9b02747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A comparative study of the impact of small, medium-sized, and bulky α,β-dehydroamino acids (ΔAAs) on the structure and stability of Balaram's incipient 310-helical peptide (1) is reported. Replacement of the N-terminal Aib residue of 1 with a ΔAA afforded peptides 2a-c that maintained the 310-helical shape of 1. In contrast, installation of a ΔAA in place of Aib-3 yielded peptides 3a-c that preferred a β-sheet-like conformation. The impact of the ΔAA on peptide structure was independent of size, with small (ΔAla), medium-sized (Z-ΔAbu), and bulky (ΔVal) ΔAAs exerting similar effects. The proteolytic stabilities of 1 and its analogs were determined by incubation with Pronase. Z-ΔAbu and ΔVal increased the resistance of peptides to proteolysis when incorporated at the 3-position and had negligible impact on stability when placed at the 1-position, whereas ΔAla-containing peptides degraded rapidly regardless of position. Exposure of peptides 2a-c and 3a-c to the reactive thiol cysteamine revealed that ΔAla-containing peptides underwent conjugate addition at room temperature, while Z-ΔAbu- and ΔVal-containing peptides were inert even at elevated temperatures. These results suggest that both bulky and more accessible medium-sized ΔAAs should be valuable tools for bestowing rigidity and proteolytic stability on bioactive peptides.
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Affiliation(s)
- Daniel Joaquin
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Michael A Lee
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - David W Kastner
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Jatinder Singh
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Shardon T Morrill
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Gracie Damstedt
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Steven L Castle
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
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Drzeżdżon J, Jacewicz D, Sielicka A, Chmurzyński L. A review of new approaches to analytical methods to determine the structure and morphology of polymers. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory. Struct Chem 2019. [DOI: 10.1007/s11224-019-01387-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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DFT calculations and NMR measurements applied to the conformational analysis of cis and trans -3-phenylaminocyclohexyl N,N -dimethylcarbamates. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Saavedra CJ, Hernández D, Boto A. Metal-Free, Site-Selective Peptide Modification by Conversion of “Customizable” Units into β-Substituted Dehydroamino Acids. Chemistry 2017; 24:599-607. [DOI: 10.1002/chem.201703758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología, CSIC (Spanish Research Council); Avda. Astrofísico Fco. Sánchez 3 38206 La Laguna Tenerife SPAIN
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología, CSIC (Spanish Research Council); Avda. Astrofísico Fco. Sánchez 3 38206 La Laguna Tenerife SPAIN
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología, CSIC (Spanish Research Council); Avda. Astrofísico Fco. Sánchez 3 38206 La Laguna Tenerife SPAIN
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Jiang J, Ma Z, Castle SL. Bulky α,β-dehydroamino acids: their occurrence in nature, synthesis, and applications. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Parlak C, Gökce M, Tursun M, Rhyman L, Ramasami P. Conformational, vibrational and electronic properties of CH3(CH2)3CX2NH2 (X = H, F, Cl or Br): Halogen and solvent effects. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The effects of varying halogen and solvent, in terms of vibrational and electronic properties, on the different conformers of 1-pentanamine [ CH 3( CH 2)4 NH 2] and 1,1-dihalogeno-pentan-1-amines [ CH 3( CH 2)3 CX 2 NH 2; X = F , Cl or Br ] were investigated by employing the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The B3LYP functional was used with the 6-31++G(d,p) basis set. Computations were focused on the 10 conformational isomers of the compounds in the gas phase and both in non-polar (benzene) and polar (methanol) solvents. The present work explores the effects of the halogen and the medium on the conformational preference, and geometrical parameter, dipole moment, NH 2 vibrational frequency, UV spectrum, highest occupied and lowest unoccupied molecular orbitals (HOMO–LUMO) orbital and DOS diagram of the conformers. The atypical characteristics of fluorine and bromine affecting the electrical bandgap, chemical hardness, electronegativity, PDOS or OPDOS plots and the absorption band are observed correspondingly. The findings of this work can be useful to those systems involving changes in the conformations analogous to the compounds studied.
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Affiliation(s)
- Cemal Parlak
- Department of Physics, Dumlupinar University, Kütahya 43100, Turkey
| | - Münevver Gökce
- Department of Physics, Dumlupinar University, Kütahya 43100, Turkey
| | - Mahir Tursun
- Department of Physics, Dumlupinar University, Kütahya 43100, Turkey
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
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Kaur H, Sasidhar YU. Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study. J Mol Model 2015; 21:88. [PMID: 25773700 DOI: 10.1007/s00894-015-2621-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 02/15/2015] [Indexed: 11/29/2022]
Abstract
Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the neighboring residues. The solution NMR of the parent helical sequence, sans its protein context, showed no inherent tendency to adopt a particular secondary structure in pure water but showed α-helical propensity in TFE/water and SDS micelles. In this study we investigate the conformational preference of the 'parent' and 'duplicate' sequences, sans the protein context, in pure water and an apolar TFE/water solution. Apolar TFE/water solution is a model for non-polar protein context. We performed MD simulations of the two peptides, in explicit water and 80% (v/v) TFE/water, using GROMOS 53a6 force field, at 300 K and 1 bar (under NPT conditions). We show that in TFE/water mixture, salt bridges are stabilized by apolar TFE molecules and main chain-main chain hydrogen bonds promote the α-helical conformation, particularly in the duplicate peptide. Solvent exposure, in pure water, resulted in an α→β transition to form a triple stranded β-sheet structure in the 'duplicate' sequence, with a rare psi-loop topology, while a mixture of turn/bend conformations were adopted by the 'parent' sequence. Thus the differences in conformational preference of the parent and duplicate sequence sans protein context, in pure water and TFE/water, implicate the importance of the environment polarity in dictating the peptide conformation. Mechanism of folding of the observed psi-loop in the duplicate sequence gives insights into folding of this rare β-sheet topology.
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Affiliation(s)
- Harpreet Kaur
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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Tursun M, Rhyman L, Parlak C, Ramasami P, Şenyel M. Conformation and NH stretching of 1,1-dihalogenoheptan-1-amines [CH₃(CH₂)₅CX₂NH₂; X=F, Cl or Br]: halogen and solvent effects. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 139:171-178. [PMID: 25556341 DOI: 10.1016/j.saa.2014.11.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 11/24/2014] [Indexed: 06/04/2023]
Abstract
The effects of halogen and solvent on the conformation and NH stretching of 1,1-dihalogeno-heptan-1-amines [CH3(CH2)5CX2NH2; X=F, Cl or Br] were investigated using the density functional theory method. The functional used was B3LYP employing the 6-31++G(d,p) basis set for all atoms. Computations were carried out for ten possible conformational isomers of the compounds, in the gas phase and both in a non-polar solvent (benzene) and in a polar solvent (methanol). This research work indicates that both the halogen and the medium affect conformational preference, geometrical parameters and NH vibrational frequency. The findings of this work can be useful to those systems involving changes in the conformations analogous to the compounds studied.
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Affiliation(s)
- Mahir Tursun
- Department of Physics, Dumlupinar University, Kütahya 43100, Turkey
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, Mauritius
| | - Cemal Parlak
- Department of Physics, Dumlupinar University, Kütahya 43100, Turkey
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, Mauritius.
| | - Mustafa Şenyel
- Department of Physics, Science Faculty, Anadolu University, Eskişehir 26470, Turkey
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Lenartowicz P, Makowski M, Zarychta B, Ejsmont K. Crystal structure of N-(tert-but-oxy-carbon-yl)phenyl-alanylde-hydro-alanine isopropyl ester (Boc-Phe-ΔAla-OiPr). Acta Crystallogr Sect E Struct Rep Online 2014; 70:599-602. [PMID: 25553003 PMCID: PMC4257372 DOI: 10.1107/s1600536814025197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/17/2014] [Indexed: 11/29/2022]
Abstract
In the crystal structure of the dehydrodipeptide (Boc-Phe-ΔAla-OiPr), the molecule has a trans configuration of the N-methylamide group. Its geometry is different from saturated peptides but is in excellent agreement with other dehydroalanine compounds. In the crystal, an N—H⋯O hydrogen bond links the molecules in a herringbone packing arrangement. In the title compound, the dehydrodipeptide (Boc–Phe–ΔAla–OiPr, C20H28N2O5), the molecule has a trans conformation of the N-methylamide group. The geometry of the dehydroalanine moiety is to some extent different from those usually found in simple peptides, indicating conjugation between the H2C=C group and the peptide bond. The bond angles around dehydroalanine have unusually high values due to the steric hindrance, the same interaction influencing the slight distortion from planarity of the dehydroalanine. The molecule is stabilized by intramolecular interactions between the isopropyl group and the N atoms of the peptide main chain. In the crystal, an N—H⋯O hydrogen bond links the molecules into ribbons, giving a herringbone head-to-head packing arrangement extending along the [100] direction. In the stacks, the molecules are linked by weak C—H⋯O hydrogen-bonding associations.
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Affiliation(s)
- Paweł Lenartowicz
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Maciej Makowski
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Bartosz Zarychta
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Krzysztof Ejsmont
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
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Jewgiński M, Krzciuk-Gula J, Makowski M, Latajka R, Kafarski P. Conformation of dehydropentapeptides containing four achiral amino acid residues - controlling the role of L-valine. Beilstein J Org Chem 2014; 10:660-6. [PMID: 24778717 PMCID: PMC3999861 DOI: 10.3762/bjoc.10.58] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/05/2014] [Indexed: 12/01/2022] Open
Abstract
Structural studies of pentapeptides containing an achiral block, built from two dehydroamino acid residues (ΔZPhe and ΔAla) and two glycines, as well as one chiral L-Val residue were performed using NMR spectroscopy. The key role of the L-Val residue in the generation of the secondary structure of peptides is discussed. The obtained results suggest that the strongest influence on the conformation of peptides arises from a valine residue inserted at the C-terminal position. The most ordered conformation was found for peptide Boc-Gly-ΔAla-Gly-ΔZPhe-Val-OMe (3), which adopts a right-handed helical conformation.
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Affiliation(s)
- Michał Jewgiński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Krzciuk-Gula
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Makowski
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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Siodłak D, Bujak M, Staś M. Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Jaremko M, Jaremko L, Mazur A, Makowski M, Lisowski M. Enhanced β-turn conformational stability of tripeptides containing ΔPhe in cis over trans configuration. Amino Acids 2013; 45:865-75. [PMID: 23812673 DOI: 10.1007/s00726-013-1534-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/07/2013] [Indexed: 11/28/2022]
Abstract
Conformations of three pairs of dehydropeptides with the opposite configuration of the ΔPhe residue, Boc-Gly-Δ(Z/E)Phe-Phe-p-NA (Z- p -NA and E- p -NA), Boc-Gly-Δ(Z/E)Phe-Phe-OMe (Z-OMe and E-OMe), and Boc-Gly-Δ(Z/E)Phe-Phe-OH (Z-OH and E-OH) were compared on the basis of CD and NMR studies in MeOH, TFE, and DMSO. The CD results were used as the additional input data for the NMR-based calculations of the detailed solution conformations of the peptides. It was found that Z- p -NA, E- p -NA, Z-OMe, and Z-OH adopt the β-turn conformations and E-OMe and E-OH are unordered. There are two overlapping type III β-turns in Z- p -NA, type II' β-turn in E- p -NA, and type II β-turn in Z-OMe and Z-OH. The results obtained indicate that in the case of methyl esters and peptides with a free carboxyl group, Δ(Z)Phe is a much stronger inducer of ordered conformations than Δ(E)Phe. It was also found that temperature coefficients of the amide protons are not reliable indicators of intramolecular hydrogen bonds donors in small peptides.
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Affiliation(s)
- Mariusz Jaremko
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany,
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