1
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Cameron AJ, Squire CJ, Edwards PJB, Harjes E, Sarojini V. Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides. Chem Asian J 2017; 12:3195-3202. [PMID: 29098772 DOI: 10.1002/asia.201701422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/30/2017] [Indexed: 12/31/2022]
Abstract
Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.
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Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
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2
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Tomsett M, Maffucci I, Le Bailly BAF, Byrne L, Bijvoets SM, Lizio MG, Raftery J, Butts CP, Webb SJ, Contini A, Clayden J. A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal. Chem Sci 2017; 8:3007-3018. [PMID: 28451368 PMCID: PMC5380885 DOI: 10.1039/c6sc05474a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/24/2017] [Indexed: 11/21/2022] Open
Abstract
Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.
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Affiliation(s)
- Michael Tomsett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Bryden A F Le Bailly
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Liam Byrne
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Stefan M Bijvoets
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - M Giovanna Lizio
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - James Raftery
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Craig P Butts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Simon J Webb
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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3
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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4
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Suzuki Y, Miyagi Y, Shiotsuki M, Inai Y, Masuda T, Sanda F. Synthesis and helical structures of poly(ω-alkynamide)s having chiral side chains: effect of solvent on their screw-sense inversion. Chemistry 2014; 20:15131-43. [PMID: 25264082 DOI: 10.1002/chem.201402628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Indexed: 11/06/2022]
Abstract
New ω-alkynamides, (S)-HC≡CCH2CONHCH2CH(CH3)CH2CH3 (1) and (S)-HC≡CCH2CH2CONHCH(CH3)CH2CH2CH2CH2CH3 (2) were synthesized and polymerized with a rhodium catalyst in CHCl3 to obtain cis-stereoregular poly(ω-alkynamide)s (poly(1) and poly(2)). Polarimetric, CD, and IR spectroscopic studies revealed that in solution the polymers adopted predominantly one-handed helical structures stabilized by intramolecular hydrogen bonds between the pendent amide groups. This behavior was similar to that of the corresponding poly(N-alkynylamide) counterparts (poly(3) and poly(4)) reported previously, whereas the helical senses were opposite to each other. The helical structures of the poly(ω-alkynamide)s were stable upon heating similar to those of the poly(N-alkynylamide)s, but the solvent response was completely different. An increase in MeOH content in CHCl3/MeOH resulted in inversion of the predominant screw-sense for poly(1) and poly(2). Conversely, poly(3) was transformed into a random coil, and poly(4) maintained the predominant screw-sense irrespective of MeOH content. The solvent dependence of predominant screw-sense for poly(1) and poly(2) was reasonably explained by molecular orbital studies using the conductor-like screening model (COSMO).
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Affiliation(s)
- Yuji Suzuki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510 (Japan)
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5
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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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6
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Lisowski M, Jaremko Ł, Jaremko M, Mazur A, Latajka R, Makowski M. Effect of the ΔPhe residue configuration on a didehydropeptides conformation: A combined CD and NMR study. Biopolymers 2010; 93:1055-64. [DOI: 10.1002/bip.21522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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7
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Latajka R, Jewginski M, Makowski M, Krezel A. Conformational studies of hexapeptides containing two dehydroamino acid residues in positions 3 and 5 in peptide chain. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Latajka R, Jewginski M, Makowski M, Pawełczak M, Huber T, Sewald N, Kafarski P. Pentapeptides containing two dehydrophenylalanine residues--synthesis, structural studies and evaluation of their activity towards cathepsin C. J Pept Sci 2008; 14:1084-95. [PMID: 18523964 DOI: 10.1002/psc.1045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Synthesis, structural and biological studies of pentapeptides containing two DeltaPhe residues (Z and E isomers) in position 2 and 4 in peptide chain were performed. All the investigated peptides adopted bent conformation and majority of them could exist as two different conformers in solution. Only pentapeptides, containing free N-termini appeared to act as weak inhibitors of cathepsin C with the slow-binding, competitive mechanism of inhibition, free acids being bound slightly better than their methyl esters. Results of molecular modeling suggested significant difference between peptides, depending of the type of amino acid residue in position 5 in peptide chain. Dehydropeptides containing Gly residue in this position may act as competitive slow-reacting substrates and therefore exhibit inhibitory-like properties.
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Affiliation(s)
- R Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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9
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Lisowski M, Latajka R, Picur B, Lis T, Bryndal I, Rospenk M, Makowski M, Kafarski P. Combined effect of the ΔPhe or ΔAla residue and thep-nitroanilide group on a didehydropeptides conformation. Biopolymers 2008; 89:220-34. [DOI: 10.1002/bip.20897] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Latajka R, Jewginski M, Makowski M, Krezel A, Paluch S. Conformational studies of hexapeptides containing two dehydroamino acid residues in positions 2 and 5 in peptide chain. Biopolymers 2008; 89:691-9. [DOI: 10.1002/bip.20994] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Inai Y, Oshikawa T, Yamashita M, Tagawa K, Hirabayashi T. Crystal structure of achiral nonapeptide Boc-(Aib-?zPhe)4-Aib-OMe at atomic resolution: Evidence for a 310-helix. Biopolymers 2003; 70:310-22. [PMID: 14579304 DOI: 10.1002/bip.10390] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An x-ray crystallographic analysis was carried out for Boc-(Aib-DeltaZPhe)4-Aib-OMe (1: Boc = t-butoxycarbonyl; Aib = alpha-aminoisobutyric acid; DeltaZPhe = Z-alpha,beta-didehydrophenylalanine) to provide the precise conformational parameters of the octapeptide segment -(Aib-DeltaZPhe)4-. Peptide 1 adopted a typical 3(10)-helical conformation characterized by <phi> = +/-55.8 degrees (50 degrees -65 degrees), <psi> = +/-26.7 degrees (15 degrees -45 degrees), and <omega> = +/-179.5 degrees (168 degrees -188 degrees) for the average values of the -(Aib-DeltaZPhe)4- segment (the range of the eight values). The 3(10)-helix contains 3.1 residues per turn, being close to the "perfect 3(10)-helix" characterized by 3.0 residues per turn. NMR and Fourier transform infrared (FTIR) spectroscopy revealed that the 3(10)-helical conformation at the atomic resolution is essentially maintained in solution. Energy minimization of peptide 1 by semiempirical molecular orbital calculation converged to a 3(10)-helical conformation similar to the x-ray crystallographic 3(10)-helix. The preference for a 3(10)-helix in the -(Aib-DeltaZPhe)4- segment is ascribed to strong inducers of the 3(10)-helix inherent in Aib and DeltaZPhe residues-in particular, the Aib residues tend to stabilize a 3(10)-helix more effectively. Therefore, the -(Aib-DeltaZPhe)4- segment is useful to rationally design an optically inactive 3(10)-helical backbone, which will be of great importance to provide novel insights into noncovalent and covalent chiral interactions of a helical peptide with a chiral molecule.
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Affiliation(s)
- Yoshihito Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.
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12
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Inai Y, Kurokawa Y, Kojima N. Screw sense preference of non-polarL-amino acid residues second from the N-terminal position. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b206664e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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