1
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Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [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: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
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Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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2
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Fiore KE, Patist MJ, Giannakoulias S, Huang CH, Verma H, Khatri B, Cheng RP, Chatterjee J, Petersson EJ. Structural impact of thioamide incorporation into a β-hairpin. RSC Chem Biol 2022; 3:582-591. [PMID: 35656485 PMCID: PMC9092430 DOI: 10.1039/d1cb00229e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
The thioamide is a naturally-occurring single atom substitution of the canonical amide bond. The exchange of oxygen to sulfur alters the amide's physical and chemical characteristics, thereby expanding its functionality. Incorporation of thioamides in prevalent secondary structures has demonstrated that they can either have stabilizing, destabilizing, or neutral effects. We performed a systematic investigation of the structural impact of thioamide incorporation in a β-hairpin scaffold with nuclear magnetic resonance (NMR). Thioamides as hydrogen bond donors did not increase the foldedness of the more stable "YKL" variant of this scaffold. In the less stable "HPT" variant of the scaffold, the thioamide could be stabilizing as a hydrogen bond donor and destabilizing as a hydrogen bond acceptor, but the extent of the perturbation depended upon the position of incorporation. To better understand these effects we performed structural modelling of the macrocyclic folded HPT variants. Finally, we compare the thioamide effects that we observe to previous studies of both side-chain and backbone perturbations to this β-hairpin scaffold to provide context for our observations.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Martijn J Patist
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Cheng-Hsin Huang
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Richard P Cheng
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
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3
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Zimnicka MM. Conformational Features of Thioamide-Containing Dipeptoids and Peptoid–Peptide Hybrids—Computational and Experimental Approaches. J Phys Chem A 2018; 122:7819-7831. [DOI: 10.1021/acs.jpca.8b05456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Magdalena M. Zimnicka
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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4
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De Zotti M, Peggion C, Biondi B, Crisma M, Formaggio F, Toniolo C. Endothioxopeptides: A conformational overview. Biopolymers 2016; 106:697-713. [DOI: 10.1002/bip.22899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/08/2016] [Accepted: 06/25/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Marta De Zotti
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Cristina Peggion
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Claudio Toniolo
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
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5
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Wang YJ, Szantai-Kis DM, Petersson EJ. Semi-synthesis of thioamide containing proteins. Org Biomol Chem 2016; 13:5074-81. [PMID: 25811732 DOI: 10.1039/c5ob00224a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our laboratory has shown that the thioamide, a single atom O-to-S substitution, can be a versatile fluorescence quenching probe that is minimally-perturbing when placed at many locations in a protein sequence. In order to make these and other thioamide experiments applicable to full-sized proteins, we have developed methods for incorporating thioamides by generating thiopeptide fragments through solid phase synthesis and ligating them to protein fragments expressed in E. coli. To install donor fluorophores, we have adapted unnatural amino acid mutagenesis methods, including the generation of new tRNA synthetases for the incorporation of small, intrinsically fluorescent amino acids. We have used a combination of these two methods, as well as chemoenzymatic protein modification, to efficiently install sidechain and backbone modifications to generate proteins labeled with fluorophore/thioamide pairs.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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6
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Formaggio F, Crisma M, Toniolo C, Peggion C. All-Thioamidated Homo-α-Peptides: Synthesis and Conformation. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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De Zotti M, Biondi B, Peggion C, De Poli M, Fathi H, Oancea S, Toniolo C, Formaggio F. Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity. Beilstein J Org Chem 2012; 8:1161-71. [PMID: 23019444 PMCID: PMC3458734 DOI: 10.3762/bjoc.8.129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/21/2012] [Indexed: 02/04/2023] Open
Abstract
Backbone modification is a common chemical tool to control the conformation of linear peptides and to explore potentially useful effects on their biochemical and biophysical properties. The thioamide, ψ[CS-NH], group is a nearly isosteric structural mimic of the amide (peptide) functionality. In this paper, we describe the solution synthesis, chemical characterization, preferred conformation, and membrane and biological activities of three, carefully selected, peptide analogues of the lipopeptaibiotic [Leu11-OMe] trichogin GA IV. In each analogue, a single thioamide replacement was incorporated. Sequence positions near the N-terminus, at the center, and near the C-terminus were investigated. Our results indicate that (i) a thioamide linkage is well tolerated in the overall helical conformation of the [Leu11-OMe] lipopeptide analogue and (ii) this backbone modification is compatible with the preservation of its typical membrane leakage and antibiotic properties, although somewhat attenuated.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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8
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Batjargal S, Wang YJ, Goldberg JM, Wissner RF, Petersson EJ. Native chemical ligation of thioamide-containing peptides: development and application to the synthesis of labeled α-synuclein for misfolding studies. J Am Chem Soc 2012; 134:9172-82. [PMID: 22468862 PMCID: PMC3415603 DOI: 10.1021/ja2113245] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Thioamide modifications of the peptide backbone are used to perturb secondary structure, to inhibit proteolysis, as photoswitches, and as spectroscopic labels. Thus far, their incorporation has been confined to single peptides synthesized on solid phase. We have generated thioamides in C-terminal thioesters or N-terminal Cys fragments and examined their compatibility with native chemical ligation conditions. Most sequence variants can be coupled in good yields with either TCEP or DTT as the reductant, though some byproducts are observed with prolonged TCEP incubations. Furthermore, we find that thioamides are compatible with thiazolidine protection of an N-terminal Cys, so that multiple ligations can be used to construct larger proteins. Since the acid-lability of the thioamide prohibits on-resin thioester synthesis using Boc chemistry, we devised a method for the synthesis of thioamide peptides with a masked C-terminal thioester that is revealed in situ. Finally, we have shown that thioamidous peptides can be coupled to expressed protein fragments to generate large proteins with backbone thioamide labels by synthesizing labeled versions of the amyloid protein α-synuclein for protein folding studies. In a proof-of-principle experiment, we demonstrated that quenching of fluorescence by thioamides can be used to track conformational changes during aggregation of labeled α-synuclein.
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Affiliation(s)
- Solongo Batjargal
- University of Pennsylvania, Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323 USA
| | - Yanxin J. Wang
- University of Pennsylvania, Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323 USA
| | - Jacob M. Goldberg
- University of Pennsylvania, Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323 USA
| | - Rebecca F. Wissner
- University of Pennsylvania, Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323 USA
| | - E. James Petersson
- University of Pennsylvania, Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323 USA
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9
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Worth AC, Needham CE, Franklin DB, Lampkins AJ. Facile Synthesis of Lipophilic δ-Amino Acid Conjugates from 4-Alkoxy-dithionaphthoic Acids. SYNTHETIC COMMUN 2012. [DOI: 10.1080/00397911.2011.565142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Anna C. Worth
- a Department of Chemistry and Biochemistry , Samford University , Birmingham , Alabama , USA
| | - Catherine E. Needham
- a Department of Chemistry and Biochemistry , Samford University , Birmingham , Alabama , USA
- b McWhorter School of Pharmacy, Department of Pharmaceutical, Social, and Administrative Sciences , Samford University , Birmingham , Alabama , USA
| | - Donald B. Franklin
- a Department of Chemistry and Biochemistry , Samford University , Birmingham , Alabama , USA
| | - Andrew J. Lampkins
- a Department of Chemistry and Biochemistry , Samford University , Birmingham , Alabama , USA
- b McWhorter School of Pharmacy, Department of Pharmaceutical, Social, and Administrative Sciences , Samford University , Birmingham , Alabama , USA
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10
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Vishwanatha TM, Narendra N, Chattopadhyay B, Mukherjee M, Sureshbabu VV. Synthesis of Selenoxo Peptides and Oligoselenoxo Peptides Employing LiAlHSeH. J Org Chem 2012; 77:2689-702. [DOI: 10.1021/jo2024703] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- T. M. Vishwanatha
- Peptide Research Laboratory,
Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore
560001, India
| | - N. Narendra
- Peptide Research Laboratory,
Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore
560001, India
| | - Basab Chattopadhyay
- Department
of Solid State Physics, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata 700032, India
| | - Monika Mukherjee
- Department
of Solid State Physics, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata 700032, India
| | - Vommina V. Sureshbabu
- Peptide Research Laboratory,
Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore
560001, India
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11
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Zimnicka M, Gregersen JA, Tureček F. A Stable Aminothioketyl Radical in the Gas Phase. J Am Chem Soc 2011; 133:10290-301. [DOI: 10.1021/ja203611x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Magdalena Zimnicka
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 981195-1700, United States
| | - Joshua A. Gregersen
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 981195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 981195-1700, United States
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12
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Nandel FS, Sahrawat TR. Conformational study of poly-ΔAbu peptides and construction of amphipathic nanostructure. Biopolymers 2009; 92:44-51. [DOI: 10.1002/bip.21118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Huang Y, Cong Z, Yang L, Dong S. A photoswitchable thioxopeptide bond facilitates the conformation-activity correlation study of insect kinin. J Pept Sci 2008; 14:1062-8. [PMID: 18523967 DOI: 10.1002/psc.1042] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thioxopeptide bond psi[CS-N], a nearly isosteric modification of the native peptide bond, was introduced into insect kinin active core pentapeptide to evaluate the impact of backbone cis/trans photoswitching on bioactivity. The thioxo analog Phe(1)-Tyr(2)-psi[CS-N]-Pro(3)-Trp(4)-Gly(5)-NH(2) (psi[CS-N](2)-kinin), was synthesized by Fmoc solid-phase peptide strategy. The reversible photoswitching property was characterized via spectroscopic methods and HPLC, which showed that the cis conformer increased from 15.7 to 47.7% after 254 nm UV irradiation. A slow thermal reisomerization (t(1/2) = 40 min) permitted us to determine the cockroach hindgut myotropic activity of the thioxopeptide in the photostationary state. The results indicated that the activity increased significantly after UV irradiation and recovered to the ground level after thermal re-equilibration. In the present study, by utilizing the phototriggered isomerization in a specific position of peptide backbone, we revealed that the cis psi[CS-N](2)-kinin conformer is the active conformation when interacting with kinin receptor on cockroach hindgut.
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Affiliation(s)
- Yun Huang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
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14
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Aravinda S, Shamala N, Balaram P. Aib Residues in Peptaibiotics and Synthetic Sequences: Analysis of Nonhelical Conformations. Chem Biodivers 2008; 5:1238-62. [PMID: 18649312 DOI: 10.1002/cbdv.200890112] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Nandel FS, Jaswal R. New Type of Helix and 27 Ribbon Structure Formation in Poly ΔLeu Peptides: Construction of a Single-Handed Template. Biomacromolecules 2007; 8:3093-101. [PMID: 17883275 DOI: 10.1021/bm700504h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
alpha,beta-Dehydroamino acid residues due to the presence of Calpha = Cbeta double bond influences the main chain and the side chain conformations. These residues have interesting chemical features including the increased resistance to enzymatic degradation. The chain length dependent conformational behavior of poly alpha,beta-dehydroleucine (DeltaLeu) peptides in both the pure forms Z and E and their various combinations like alternate ZE/EZ etc. have been investigated by using quantum mechanical method PCILO (perturbative configuration interaction of localized orbitals). The conformational states in alternate Z and E forms, with Phi, Psi values of -10 degrees , 105 degrees /1 degrees , -88 degrees for Z form and 35 degrees , 22 degrees /-34 degrees , -27 degrees for the E form are found to be the most stable and degenerate than the states in pure Z and E forms and the EZ form etc. The repeated Phi, Psi values give rise to altogether new types of left and right handed helices, and their stability increases with increasing chain length. These structures are stabilized by intramolecular hydrogen bonding, carbonyl-carbonyl interactions and hydrophobic interactions between the side chains of DeltaZLeu and DeltaELeu residues. The 2(7) ribbon structure (seven-membered hydrogen-bonded ring involving two consecutive amino acid residues) is found to be most stable and degenerate in the pentapeptide Ac-DeltaELeu5-NHMe, due to the formation of maximum hydrogen bonds. A right-handed template from achiral DeltaLeu peptides has been achieved by incorporating L-Leu at the C-terminal or D-Leu at the N-terminal.
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Affiliation(s)
- Fateh S Nandel
- Department of Biophysics, Panjab University, Chandigarh, India.
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16
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Affiliation(s)
- Thomas Hoeg-jensen
- a Chemistry Department , Royal Veterinary and Agricultural University , Thorvaldsensvej 40, DK-1871, Frederiksberg, C, Denmark
- b Thomas Hoeg-Jensen, Ph.D., Insulin Research , Novo Nordisk 6B 2.54, DK-2880, Bagsvaerd, Denmark
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17
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Hollósi M, Kollát E, Kajtár J, Kajtár M, Fasman GD. Chiroptical labeling of folded polypeptide conformations: The thioamide probe. Biopolymers 2004. [DOI: 10.1002/bip.360301107] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Nandel FS, Khare B. Conformation of peptides constructed from achiral amino acid residues Aib and ?ZPhe: Computational study of the effect ofL/D- Leu at terminal positions. Biopolymers 2004; 77:63-73. [PMID: 15593284 DOI: 10.1002/bip.20128] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conformational studies of the peptides constructed from achiral amino acid residues Aib and Delta(Z)Phe (I) Ac-Aib-Delta(Z)Phe-NHMe (II), and Ac-(Aib-Delta(Z)Phe)(3)-NHMe; peptides III-VI having L-Leu or D-Leu at either the N- or the C-terminal position and of peptides VII-X having Leu residues in different enantiomeric combinations at both the N- and the C-terminal positions in peptide II have been studied to design the peptide with the required helical sense. Peptide II, as expected, adopts degenerate left- and right-handed helical structures. It has been shown that the peptides IV and VI having D-Leu at either the N or the C terminus can be realized in the right-handed helical structure with the phi,psi values of -20 degrees and -60 degrees for the Aib/Delta(Z)Phe residues. L-Leu and D- Leu at both the terminals in peptides VII and VIII, respectively, have hardly any effect as both the left- and the right-handed structures are found to be degenerate. Peptides III and IX can be realized in right- and left-handed helical structures, respectively, in solvents of low polarity whereas peptides V and X are predicted to be in the right-handed helical structures stabilized by carbonyl-carbonyl interactions without the formation of hydrogen bonds. The conformational states with the phi,psi values of 0 degrees and -85 degrees in peptide V are characterized by rise per residue of 2.03 A, rotation per residue of 117.5 degrees , and 3.06 residues per turn. In all peptides having Leu residue at the N terminus, the methyl moiety of the acetyl group is involved in the CH/pi interactions with the Cepsilon--Cdelta edge of the aromatic ring of Delta(Z)Phe (3) and the amino group NH of Delta(Z)Phe is involved in the NH/pi interactions with its own aromatic ring. The CH(3) groups of the Aib residues are also involved in CH/pi interactions with the i + 1th and i + 3th Delta(Z)Phe's aromatic side chains.
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20
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Miwa JH, Pallivathucal L, Gowda S, Lee KE. Conformational stability of helical peptides containing a thioamide linkage. Org Lett 2002; 4:4655-7. [PMID: 12489953 DOI: 10.1021/ol027056d] [Citation(s) in RCA: 62] [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
[structure: see text] Thioxo peptide analogues of the alpha-helical peptide GCN4-p1 were synthesized and evaluated for helicity and oligomeric state. Sedimentation equilibrium and CD measurements indicate that the thioxo peptides fold into parallel alpha-helical coiled coil structures essentially identical to the native structure. This work marks the first incorporation of a thioamide linkage into the backbone of an alpha-helix and demonstrates that a thioamide linkage is compatible with positions within the helix as well as near the C-terminus.
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Affiliation(s)
- Julia H Miwa
- Department of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, USA.
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21
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Miwa JH, Patel AK, Vivatrat N, Popek SM, Meyer AM. Compatibility of the thioamide functional group with beta-sheet secondary structure: incorporation of a thioamide linkage into a beta-hairpin peptide. Org Lett 2001; 3:3373-5. [PMID: 11594837 DOI: 10.1021/ol0166092] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text]. We report the incorporation of a thioamide linkage between the i + 2 and i + 3 residues of the type II' beta-turn of a peptide known to fold into a beta-hairpin conformation. Two-dimensional NMR spectroscopy and circular dichroism spectroscopy indicate that the thioxo peptide adopts a hairpin conformation similar to that of the oxo peptide and that the hairpin conformation persists at elevated temperatures. The results show that a thioamide linkage is compatible with beta-sheet secondary structure.
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Affiliation(s)
- J H Miwa
- Department of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, USA.
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22
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Tran TT, Treutlein H, Burgess AW. Conformational analysis of thiopeptides: (?,?) maps of thio-substituted dipeptides. J Comput Chem 2001. [DOI: 10.1002/jcc.1063] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Albert R, Knecht H, Andersen E, Hungerford V, Schreier MH, Papageorgiou C. Isoxazolylthioamides as potential immunosuppressants a combinatorial chemistry approach. Bioorg Med Chem Lett 1998; 8:2203-8. [PMID: 9873513 DOI: 10.1016/s0960-894x(98)00365-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A library of thioamide derivatives of leflunomide 1a and of its bioactive metabolite 1b has been synthesised on solid phase. Thus, para-substituted phenylacetic acids were coupled to TentaGel and were subsequently reacted with aromatic isothiocyanates. Treatment of the resulting enaminothioamides with hydroxylamine led to their simultaneous cyclisation and cleavage from the resin affording 2-25. Their in vitro profiling demonstrated that the amide-thioamide isologous substitution was detrimental of the biological activity.
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Affiliation(s)
- R Albert
- Novartis Pharma AG, Basel, Switzerland.
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24
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Schutkowski M, Jakob M, Landgraf G, Born I, Neubert K, Fischer G. Probing substrate backbone function in prolyl oligopeptidase catalysis--large positional effects of peptide bond monothioxylation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 245:381-5. [PMID: 9151967 DOI: 10.1111/j.1432-1033.1997.00381.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Site-specific effects on the catalytic activity of prolyl oligopeptidase from human placenta were studied using oligopeptide substrates in which a peptide bond has been replaced by a thioxo peptide bond. Two series of tetrapeptide-4-nitroanilides, Ala-Gly-Pro-Phe-NH-Np and Ala-Ala-Pro-Phe-NH-Np, along with all possible monothioxylated derivatives, were synthesised and k(cat) and Km values were determined for proteolytic cleavage at the Pro-Phe bond. Regardless of either Gly or Ala in the P2 subsite, tetrapeptides were rendered uncleavable by thioxylation at the Pro-Phe linkage. As a result, Ala-Xaa-Pro-psi[CS-NH]-Phe-NH-Np (Xaa = Gly or Ala) displayed competitive inhibition with Ki-values of 12 microM and 44 microM, respectively. Furthermore, in controlling proteolytic susceptibility of the substrates, cooperation of the P3-P2 thioxylation site and the side chain at the P2 subsite was obtained. Thioxylation at this position enhanced k(cat)/Km fivefold in the Gly series, but led to a 1.7-fold decrease in the Ala series of substrates. With respect to the Xaa-Pro peptide bond, all of the substrates underwent cis/trans isomerisation, thus presenting two stable conformers to the protease. However, the magnitudes of the isomerisation constants suggested that neither isomerisation rates nor cis/trans equilibria can explain the effect of thioxylation on the steady-state constants of proteolysis.
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Affiliation(s)
- M Schutkowski
- Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V., Forschungstelle Enzymologie der Proteinfaltung, Halle, Germany
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25
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Tryptophan-derived peptides. 1: Crystal structure and solution conformation of Boc-Gly-Trp-Ala-OtBu. Struct Chem 1996. [DOI: 10.1007/bf02278735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Schutkowski M, Neubert K, Fischer G. Influence on proline-specific enzymes of a substrate containing the thioxoaminoacyl-prolyl peptide bond. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 221:455-61. [PMID: 7909521 DOI: 10.1111/j.1432-1033.1994.tb18758.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Dipeptidyl peptidase IV from porcine kidney and aminopeptidase P from Escherichia coli can utilize thioxoalanyl-proline 4-nitroanilide but with decreased kinetic constants compared to the normal substrates. Product analysis showed that exclusively thioxoalanyl-proline was liberated in the case of dipeptidyl peptidase IV catalysis and thioxo-alanine in the case of aminopeptidase-P-mediated thioxo peptide bond hydrolysis. For the proline-specific aminopeptidase P the kcat/Km value for the thioxo peptide is 1100-fold lower than for the corresponding oxo peptide. This difference is entirely due to kcat. Because the rotation about the thioxo amide bond is about 12.5 kJ mol-1 more difficult than rotation about an amide bond, these data support a mechanism involving rate-limiting rotation about the scissile peptide bond. It was found that the specificity rate constant for the reaction of thioxoalanyl-proline 4-nitroanilide and dipeptidyl peptidase IV is 100-1000-fold lower compared to the corresponding rate constant for alanyl-proline 4-nitroanilide. This remarkable effect is interpreted in terms of a distorted binding of the transition state for the thioxo substrate. The hydrolysis of the thioxo substrate by dipeptidyl peptidase IV is isomer-specific. The conformation about the nonscissile P2-P1 thioxo amide bond has to be in trans for successful cleavage of the scissile peptide bond. We can now directly compare the rotational energy barrier of the prolyl peptide bond for the oxo and the thioxo form.
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Affiliation(s)
- M Schutkowski
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biochemie, Fachbereich Biochemie/Biotechnologie, Germany
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27
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Czugler M, Kálmán A, Kajtár-Peredy M, Kollát E, Kajtár J, Majer Z, Farkas Ö, Hollósi M. Reverse turn conformation of N-thioacetyl thioprolyl glycine N′-methylamide in the crystal and in solution. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)81836-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Approaches to the synthesis of endothiopeptides: Synthesis of a thioamide-containing C-terminal bombesin nonapeptide. Tetrahedron 1992. [DOI: 10.1016/s0040-4020(01)89436-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Anwer MK, Sherman DB, Spatola AF. Backbone modifications in cyclic peptides. Conformational analysis of a cyclic pseudopentapeptide containing a thiomethylene ether amide bond replacement. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1990; 36:392-9. [PMID: 2079394 DOI: 10.1111/j.1399-3011.1990.tb01299.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
NMR and X-ray crystallographic studies have shown that cyclic pentapeptides of the general structure cyclo(D-Xxx-Pro-Gly-Pro-Gly) possess beta- and gamma-turn intramolecular hydrogen bonds. As part of our continuing series surveying the compatibility of various amide bond replacements on peptide structure, we have synthesized cyclo(D-Phe-Pro psi[CH2S]Gly-Pro-Gly). The pseudopeptide was prepared by solid phase methods and cleaved from the resin by a new procedure involving phase transfer catalysis using K2CO3 and tetrabutylammonium hydrogen sulfate. Cyclization was carried out with the use of DPPA, HOBt, and DMAP to afford the product in 69% yield. The conformational behavior of the pseudopeptide was analyzed by 1H and 13C (1D and 2D) NMR techniques. The backbone modification replaced the amide bond that is involved in a gamma-turn intramolecular hydrogen bond in the all-amide structure. In CDCl3, the pseudopeptide adopted the same all-trans conformation as its parent, although the remaining beta-turn hydrogen bond was weaker according to delta delta/delta TNH measurements. In DMSO-d6, the all-trans conformer and a second conformer were observed in a ratio of 55:45. These conformers, which slowly interconverted on the NMR time scale, could be separately assigned; peaks due to chemical exchange were readily distinguishable by the ROESY technique as reported earlier by others. 13C and ROESY experiments suggested the minor conformer contained one cis amide bond at the Gly1-Pro2 position. Thus, both the location and type of amide surrogate are important determinants affecting the compatibility of the replacement with a particular conformational feature.
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Affiliation(s)
- M K Anwer
- Department of Chemistry, University of Louisville, KY
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30
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Hollósi M, Zewdu M, Kollát E, Majer Z, Kajtár M, Batta G, Kövér K, Sándor P. Intramolecular H-bonds and thioamide rotational isomerism in thiopeptides. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1990; 36:173-81. [PMID: 2272753 DOI: 10.1111/j.1399-3011.1990.tb00963.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mono- and dithionated N-acyl amino acid and dipeptide N'-methylamides were synthesized using Lawesson's reagent and S-thioacetyl thioglycolic acid. The conformation of the thionated models was characterized by IR, 13C, and 1H NMR spectroscopy, including NOE experiments. The formation of -C = S...H-N-C = X (X = O or S) intramolecular H-bonds of the type 2----2, 1----3 and 1----4 was evidenced by the characteristic shifts of the IR stretching frequencies of the NH group. Act-Pro-NHCH3(4) and Act-Prot-NHCH3(5) were found to be present as mixtures of rotational isomers about the CS-N bond. 13C chemical shifts of the gamma- and beta-carbons of the proline ring elucidated the conformation (Z or E) of the tertiary thioamide group. Our results suggest that the conformation of thiopeptides is determined by two factors: 1) the H-bond donating and accepting ability of the thioamide group and 2) the repulsion between the thiocarbonyl sulfur atom and the side chain groups of the neighbouring amino acid residues.
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Affiliation(s)
- M Hollósi
- Institute of Organic Chemistry, L. Eötvös University, Budapest, Hungary
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31
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Sherman DB, Spatola AF, Wire WS, Burks TF, Nguyen TM, Schiller PW. Biological activities of cyclic enkephalin pseudopeptides containing thioamides as amide bond replacements. Biochem Biophys Res Commun 1989; 162:1126-32. [PMID: 2764921 DOI: 10.1016/0006-291x(89)90790-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Analogs of H-Tyr-cyclo(N epsilon-D-Lys-Gly-Phe-Leu) have been prepared which contain thioamides at the 3-4 position (monothio), 3-4 and 5-2 positions (dithio), and 2-3, 3-4, and 5-2 positions (trithio). These compounds have been tested for opioid activity in mu- and delta-receptor selective bio- and binding assays. As the number of sulfurs increased, the biological activities dropped on the guinea pig ileum and fluctuated modestly on the mouse vas deferens assay. Surprisingly, the compounds displayed increasing delta selectivity as the number of sulfurs increased. In the binding assay, the thioamide analogs tended to retain affinity toward the mu receptor. The mono- and dithio-analogs were more mu selective than the parent, while the trithio-analog was more delta selective. These results suggest that the subtle exchange of sulfur for oxygen can have a significant impact on receptor selectivity and affinity, and probably reflect the different conformation/structural requirements for binding vs. the biological transduction event.
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Affiliation(s)
- D B Sherman
- Department of Chemistry, University of Louisville, KY 40292
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32
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Toniolo C. Structure of conformationally constrained peptides: from model compounds to bioactive peptides. Biopolymers 1989; 28:247-57. [PMID: 2720107 DOI: 10.1002/bip.360280125] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The use of backbone conformational constraints has acquired increasing importance in the design and synthesis of structurally restricted agonists and antagonists of bioactive peptides. Here I discuss the preferred conformations of four among the most popular types of such peptide surrogates: (a) Peptides from C alpha, alpha-dialkylated residues, (b) tetrazolyl peptides, (c) (gamma- and delta-) lactam-containing peptides, and (d) thiated peptides. Emphasis is given to conformational energy computations and x-ray diffraction analyses of selected model compounds and analogues of small bioactive peptides such as the formylmethionyl tripeptide chemoattractant and MIF.
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