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Ueda A, Makura Y, Kakazu S, Kato T, Umeno T, Hirayama K, Doi M, Oba M, Tanaka M. E-Selective Ring-Closing Metathesis in α-Helical Stapled Peptides Using Carbocyclic α,α-Disubstituted α-Amino Acids. Org Lett 2022; 24:1049-1054. [PMID: 35073100 DOI: 10.1021/acs.orglett.1c04256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an E-selective ring-closing metathesis reaction in α-helical stapled peptides at positions i and i + 4. The use of two chiral carbocyclic α,α-disubstituted α-amino acids, (1S,3S)-Ac5c3OAll and (1R,3S)-Ac5c3OAll, provides a high E-selectivity of a ≤59:1 E:Z ratio, while mixtures with E:Z ratios of 2.1-0.5:1 were produced with standard acyclic (S)-(4-pentenyl)alanine amino acids. A stapled octapeptide composed of (1S,3S)- and (1R,3S)-Ac5c3OAll amino acids showed a right-handed α-helical crystal structure.
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Affiliation(s)
- Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yui Makura
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Sana Kakazu
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Tomohiro Umeno
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kazuhiro Hirayama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
- Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 606-0823, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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2
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Makura Y, Ueda A, Kato T, Iyoshi A, Higuchi M, Doi M, Tanaka M. X-ray Crystallographic Structure of α-Helical Peptide Stabilized by Hydrocarbon Stapling at i, i + 1 Positions. Int J Mol Sci 2021; 22:ijms22105364. [PMID: 34069753 PMCID: PMC8160927 DOI: 10.3390/ijms22105364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Hydrocarbon stapling is a useful tool for stabilizing the secondary structure of peptides. Among several methods, hydrocarbon stapling at i,i + 1 positions was not extensively studied, and their secondary structures are not clarified. In this study, we investigate i,i + 1 hydrocarbon stapling between cis-4-allyloxy-l-proline and various olefin-tethered amino acids. Depending on the ring size of the stapled side chains and structure of the olefin-tethered amino acids, E- or Z-selectivities were observed during the ring-closing metathesis reaction (E/Z was up to 8.5:1 for 17–14-membered rings and up to 1:20 for 13-membered rings). We performed X-ray crystallographic analysis of hydrocarbon stapled peptide at i,i + 1 positions. The X-ray crystallographic structure suggested that the i,i + 1 staple stabilizes the peptide secondary structure to the right-handed α-helix. These findings are especially important for short oligopeptides because the employed stapling method uses two minimal amino acid residues adjacent to each other.
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Affiliation(s)
- Yui Makura
- Graduate School of Biomedical Sciences, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki 852-8521, Japan; (Y.M.); (A.I.); (M.H.)
| | - Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki 852-8521, Japan; (Y.M.); (A.I.); (M.H.)
- Correspondence: (A.U.); (M.T.); Tel.: +81-95-819-2425 (A.U.); +81-95-819-2423 (M.T.)
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan; (T.K.); (M.D.)
| | - Akihiro Iyoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki 852-8521, Japan; (Y.M.); (A.I.); (M.H.)
| | - Mei Higuchi
- Graduate School of Biomedical Sciences, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki 852-8521, Japan; (Y.M.); (A.I.); (M.H.)
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan; (T.K.); (M.D.)
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki 852-8521, Japan; (Y.M.); (A.I.); (M.H.)
- Correspondence: (A.U.); (M.T.); Tel.: +81-95-819-2425 (A.U.); +81-95-819-2423 (M.T.)
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Ueda A, Higuchi M, Sato K, Umeno T, Tanaka M. Design and Synthesis of Helical N-Terminal L-Prolyl Oligopeptides Possessing Hydrocarbon Stapling. Molecules 2020; 25:E4667. [PMID: 33066194 PMCID: PMC7594088 DOI: 10.3390/molecules25204667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 01/17/2023] Open
Abstract
We designed and synthesized helical short oligopeptides with an L-proline on the N-terminus and hydrocarbon stapling on the side chain. Side-chain stapling is a frequently used method for the development of biologically active peptides. Side-chain stapling can stabilize the secondary structures of peptides, and, therefore, stapled peptides may be applicable to peptide-based organocatalysts. Olefin-tethered cis-4-hydroxy-L-proline 1 and L-serine 2 and 8, and (R)-α-allyl-proline 18 were used as cross-linking motifs and incorporated into helical peptide sequences. The Z- and E-selectivities were observed for the ring-closing metathesis reactions of peptides 3 and 11 (i,i+1 series), respectively, while no E/Z-selectivity was observed for that of 19 (i,i+3 series). The stapled peptide B' catalyzed the Michael addition reaction of 1-methylindole to α,β-unsaturated aldehyde, which was seven times faster than that of unstapled peptide B. Furthermore, the high catalytic activity was retained even at lower catalyst loadings (5 mol %) and lower temperatures (0 °C). The circular dichroism spectra of stapled peptide B' showed a right-handed helix with a higher intensity than that of unstapled peptide B. These results indicate that the introduction of side-chain stapling is beneficial for enhancing the catalytic activity of short oligopeptide catalysts.
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Affiliation(s)
- Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan; (M.H.); (K.S.); (T.U.)
| | | | | | | | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan; (M.H.); (K.S.); (T.U.)
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4
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Koba Y, Ueda A, Oba M, Doi M, Kato T, Demizu Y, Tanaka M. Left-Handed Helix of Three-Membered Ring Amino Acid Homopeptide Interrupted by an N-H···Ethereal O-Type Hydrogen Bond. Org Lett 2018; 20:7830-7834. [PMID: 30499676 DOI: 10.1021/acs.orglett.8b03331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A chiral three-membered ring Cα,α-disubstituted α-amino acid ( R, R)-Ac3cdMOM, in which the α-carbon is not a chiral center, but two side chain β-carbons are chiral centers, was synthesized from dimethyl l-(+)-tartrate, and its homopeptides were prepared. X-ray crystallographic analysis of ( R, R)-Ac3cdMOM pentapeptide showed bent left-handed ( M) 310-helical structures with an unusual intramolecular hydrogen bond of the N-H···O (ethereal) type. The left-handedness of the bent helices was exclusively controlled by the side-chain β-carbon chiral centers.
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Affiliation(s)
- Yurie Koba
- Graduate School of Biomedical Sciences , Nagasaki University , 1-14 Bukyo-machi , Nagasaki 852-8521 , Japan
| | - Atsushi Ueda
- Graduate School of Biomedical Sciences , Nagasaki University , 1-14 Bukyo-machi , Nagasaki 852-8521 , Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences , Nagasaki University , 1-14 Bukyo-machi , Nagasaki 852-8521 , Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences , Osaka 569-1094 , Japan
| | - Takuma Kato
- Osaka University of Pharmaceutical Sciences , Osaka 569-1094 , Japan
| | - Yosuke Demizu
- Division of Organic Chemistry , National Institute of Health Sciences , Kawasaki 210-9501 , Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences , Nagasaki University , 1-14 Bukyo-machi , Nagasaki 852-8521 , Japan
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5
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Eto R, Oba M, Ueda A, Uku T, Doi M, Matsuo Y, Tanaka T, Demizu Y, Kurihara M, Tanaka M. Diastereomeric Right- and Left-Handed Helical Structures with Fourteen (R)-Chiral Centers. Chemistry 2017; 23:18120-18124. [PMID: 29134704 DOI: 10.1002/chem.201705306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Indexed: 12/31/2022]
Abstract
The relationship between chiral centers and the helical-screw control of their peptides has already been reported, but it has yet to be elucidated in detail. A chiral four-membered ring α,α-disubstituted α-amino acid with a (R,R)-butane-2,3-diol acetal moiety at the γ-position, but no α-chiral carbon, was synthesized. X-ray crystallographic analysis unambiguously revealed that its homo-chiral heptapeptide formed right-handed (P) and left-handed (M) 310 -helical structures at a ratio of 1:1. They appeared to be enantiomeric at the peptide backbone, but diastereomeric with fourteen (R)-configuration chiral centers. Conformational analyses of homopeptides in solution also indicated that diastereomeric (P) and (M) helices existed at approximately equal amounts, with a slight preference toward right-handedness, and they quickly interchanged at room temperature. The circumstances of chiral centers are important for the control of their helical-screw direction.
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Affiliation(s)
- Ryo Eto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Tsubasa Uku
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, Osaka, 569-1094, Japan
| | - Yosuke Matsuo
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Takashi Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Yosuke Demizu
- National Institute of Health Sciences, Tokyo, 158-8501, Japan
| | - Masaaki Kurihara
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare, Ohtawara, 324-8501, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
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6
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [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] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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7
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Ueda A, Umeno T, Doi M, Akagawa K, Kudo K, Tanaka M. Helical-Peptide-Catalyzed Enantioselective Michael Addition Reactions and Their Mechanistic Insights. J Org Chem 2016; 81:6343-56. [PMID: 27384597 DOI: 10.1021/acs.joc.6b00982] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Helical peptide foldamer catalyzed Michael addition reactions of nitroalkane or dialkyl malonate to α,β-unsaturated ketones are reported along with the mechanistic considerations of the enantio-induction. A wide variety of α,β-unsaturated ketones, including β-aryl, β-alkyl enones, and cyclic enones, were found to be catalyzed by the helical peptide to give Michael adducts with high enantioselectivities (up to 99%). On the basis of X-ray crystallographic analysis and depsipeptide study, the amide protons, N(2)-H and N(3)-H, at the N terminus in the α-helical peptide catalyst were crucial for activating Michael donors, while the N-terminal primary amine activated Michael acceptors through the formation of iminium ion intermediates.
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Affiliation(s)
- Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Tomohiro Umeno
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences , Osaka 569-1094, Japan
| | - Kengo Akagawa
- Institute of Industrial Science, The University of Tokyo , Tokyo 153-8505, Japan
| | - Kazuaki Kudo
- Institute of Industrial Science, The University of Tokyo , Tokyo 153-8505, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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8
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Demizu Y, Doi M, Yamashita H, Misawa T, Oba M, Kurihara M, Suemune H, Tanaka M. The side-chain hydroxy groups of a cyclic α,α-disubstituted α-amino acid promote oligopeptide 310 -helix packing in the crystalline state. Biopolymers 2016; 106:757-68. [PMID: 27237543 DOI: 10.1002/bip.22881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/09/2016] [Accepted: 05/23/2016] [Indexed: 01/08/2023]
Abstract
A single chiral cyclic α,α-disubstituted amino acid with side-chain methoxymethyl (MOM) protecting groups, (3S,4S)-1-amino-(3,4-dimethoxymethoxy)cyclopentanecarboxylic acid [(S, S)-Ac5 c(dOMOM) ], or side-chain hydroxy groups, (3S,4S)-1-amino-(3,4-dihydroxy)cyclopentanecarboxylic acid [(S, S)-Ac5 c(dOH) ], was attached to the N-terminal or C-terminal position of α-aminoisobutyric acid (Aib) tetrapeptide segments; i.e., we designed and synthesized four pentapeptides, Cbz-[(S, S)-Ac5 c(dOMOM) ]-(Aib)4 -OEt (1), Cbz-[(S, S)-Ac5 c(dOH) ]-(Aib)4 -OEt (2), Cbz-(Aib)4 -[(S, S)-Ac5 c(dOMOM) ]-OMe (3), and Cbz-(Aib)4 -[(S, S)-Ac5 c(dOH) ]-OMe (4). We then analyzed the peptides' structures in the crystalline state. The four peptides all folded into 310 -helical structures; 1 formed a left-handed (M) 310 -helix, 2 formed a mixture of right-handed (P) and (M) 310 -helices, 3 formed a mixture of (P) and (M) 310 -helices, and 4 formed a (P) 310 -helix, respectively. In packing mode, the molecules of peptides 1 and 3, which both possessed an Ac5 c(dOMOM) residue, were connected by intermolecular hydrogen bonds along the peptide backbone (NH···O type). On the other hand, the packing of peptides 2 and 4, which both contained an Ac5 c(dOH) residue, was based on intermolecular hydrogen bonds derived from both the peptide backbone and the side-chain hydroxy groups of the amino acid Ac5 c(dOH) (OH···O type). © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 757-768, 2016.
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Affiliation(s)
- Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Tokyo, 158-8501, Japan.
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, Osaka, 569-1094, Japan
| | - Hiroko Yamashita
- Division of Organic Chemistry, National Institute of Health Sciences, Tokyo, 158-8501, Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences, Tokyo, 158-8501, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-Machi, Nagasaki, 852-8521, Japan
| | - Masaaki Kurihara
- Division of Organic Chemistry, National Institute of Health Sciences, Tokyo, 158-8501, Japan
| | - Hiroshi Suemune
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-Machi, Nagasaki, 852-8521, Japan
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Furukawa K, Oba M, Opiyo GO, Doi M, Tanaka M. Cyclic α,α-Disubstituted α-Amino Acids with Menthone in Their Side-Chains Linked through an Acetal Moiety and Helical Structures of Their Peptides. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kaori Furukawa
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - George Ouma Opiyo
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences; 569-1094 Osaka Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
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10
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Crisma M, Toniolo C. Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids. Biopolymers 2016; 104:46-64. [PMID: 25363510 DOI: 10.1002/bip.22581] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/14/2014] [Accepted: 10/24/2014] [Indexed: 01/09/2023]
Abstract
The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131, Padova, Italy
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11
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Demizu Y, Okitsu K, Yamashita H, Doi M, Misawa T, Oba M, Tanaka M, Kurihara M. α-Helical Structures of Oligopeptides with an Alternating l-Leu-Aib Segment. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yosuke Demizu
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Koyo Okitsu
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Hiroko Yamashita
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences; 569-1094 Osaka Japan
| | - Takashi Misawa
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - Masaaki Kurihara
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
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12
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Maffucci I, Clayden J, Contini A. Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides. J Phys Chem B 2015; 119:14003-13. [PMID: 26457452 DOI: 10.1021/acs.jpcb.5b07050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mechanisms behind the propensity of chiral constrained Cα-tetrasubstituted amino acids (cCTAAs) to induce one particular helical screw sense, when included in the Ac-Aib2-cCTAA-Aib2-NHMe peptide model, were studied through replica exchange molecular dynamics, potential of mean force, and quantum theory of atoms in molecules calculations. We observed that cCTAAs exert their effect on helical screw sense selectivity through the positioning of the side chain to generate steric hindrance in either the (-x, +y, +z) or (+x, +y, -z) sectors of a right-handed 3D Cartesian space, where the z axis corresponds to the axis of the helix and the Cα lies on the +y semiaxis (0, +y, 0). The different strengthening of the noncovalent interactions, also comprising C-H···O interactions, exerted by the cCTAA in the right-handed or left-handed helix was also found important to define the preference of a cCTAA for a particular helix screw sense.
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Affiliation(s)
- 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
| | - Jonathan Clayden
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, U.K
| | - 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
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13
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Yamashita H, Demizu Y, Misawa T, Shoda T, Kurihara M. Synthesis of a bis-cationic α,α-disubstituted amino acid (9-amino-bispidine-9-carboxylic acid) and its effects on the conformational properties of peptides. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.02.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Structural development of stapled short helical peptides as vitamin D receptor (VDR)–coactivator interaction inhibitors. Bioorg Med Chem 2015; 23:1055-61. [DOI: 10.1016/j.bmc.2015.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/05/2015] [Accepted: 01/05/2015] [Indexed: 11/23/2022]
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15
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Demizu Y, Yamashita H, Misawa T, Doi M, Tanaka M, Kurihara M. Effects of D-Leu Residues on the Helical Secondary Structures of L-Leu-Based Nonapeptides. Chem Pharm Bull (Tokyo) 2015; 63:218-24. [DOI: 10.1248/cpb.c14-00760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences
| | - Hiroko Yamashita
- Division of Organic Chemistry, National Institute of Health Sciences
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences
| | | | | | - Masaaki Kurihara
- Division of Organic Chemistry, National Institute of Health Sciences
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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16
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Oba M, Takazaki H, Kawabe N, Doi M, Demizu Y, Kurihara M, Kawakubo H, Nagano M, Suemune H, Tanaka M. Helical Peptide-Foldamers Having a Chiral Five-Membered Ring Amino Acid with Two Azido Functional Groups. J Org Chem 2014; 79:9125-40. [DOI: 10.1021/jo501493x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makoto Oba
- Graduate
School of Biomedical Sciences, Nagasaki University, 1-14 Bukyo-machi, Nagasaki 852-8521, Japan
| | - Hiroomi Takazaki
- Graduate
School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Naomi Kawabe
- Graduate
School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, Osaka 569-1094, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Hiromu Kawakubo
- Department
of Pharmaceutical Sciences, Nihon Pharmaceutical University, Saitama 362-0806, Japan
| | - Masanobu Nagano
- Graduate
School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroshi Suemune
- Graduate
School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masakazu Tanaka
- Graduate
School of Biomedical Sciences, Nagasaki University, 1-14 Bukyo-machi, Nagasaki 852-8521, Japan
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17
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De Poli M, Byrne L, Brown RA, Solà J, Castellanos A, Boddaert T, Wechsel R, Beadle JD, Clayden J. Engineering the Structure of an N-Terminal β-Turn To Maximize Screw-Sense Preference in Achiral Helical Peptide Chains. J Org Chem 2014; 79:4659-75. [DOI: 10.1021/jo500714b] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Matteo De Poli
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Liam Byrne
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Robert A. Brown
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jordi Solà
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | | | - Thomas Boddaert
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Romina Wechsel
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jonathan D. Beadle
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jonathan Clayden
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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18
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Yamashita H, Demizu Y, Shoda T, Sato Y, Oba M, Tanaka M, Kurihara M. Amphipathic short helix-stabilized peptides with cell-membrane penetrating ability. Bioorg Med Chem 2014; 22:2403-8. [DOI: 10.1016/j.bmc.2014.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 02/28/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
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19
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Demizu Y, Yamashita H, Yamazaki N, Sato Y, Doi M, Tanaka M, Kurihara M. Oligopeptides with Equal Amounts of l- and d-Amino Acids May Prefer a Helix Screw Sense. J Org Chem 2013; 78:12106-13. [DOI: 10.1021/jo402133e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yosuke Demizu
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Hiroko Yamashita
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
- Graduate
School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Norikazu Yamazaki
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yukiko Sato
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Mitsunobu Doi
- Osaka
University of Pharmaceutical Sciences, Osaka 569-1094, Japan
| | - Masakazu Tanaka
- Graduate
School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Masaaki Kurihara
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
- Graduate
School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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20
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Yamazaki N, Demizu Y, Sato Y, Doi M, Kurihara M. Helical Foldamer Containing a Combination of Cyclopentane-1,2-diamine and 2,2-Dimethylmalonic Acid. J Org Chem 2013; 78:9991-4. [DOI: 10.1021/jo401505b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norikazu Yamazaki
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yukiko Sato
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, Osaka 569-1094, Japan
| | - Masaaki Kurihara
- Division
of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan
- Graduate
School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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21
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Development of stapled short helical peptides capable of inhibiting vitamin D receptor (VDR)–coactivator interactions. Bioorg Med Chem Lett 2013; 23:4292-6. [DOI: 10.1016/j.bmcl.2013.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 05/27/2013] [Accepted: 06/01/2013] [Indexed: 11/19/2022]
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22
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Thorat VH, Ingole TS, Vijayadas KN, Nair RV, Kale SS, Ramesh VVE, Davis HC, Prabhakaran P, Gonnade RG, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. The Ant-Pro Reverse-Turn Motif. Structural Features and Conformational Characteristics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201739] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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23
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Sharma GVM, Kodeti SR, Dutta SK, Velaparthi S, Narsimulu K, Anjaiah G, Basha SJ, Kunwar AC. Chirality and Template-Mediated Induction of Helical Preferences in Achiral β-Peptides. Chemistry 2012; 18:16046-60. [DOI: 10.1002/chem.201201892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/20/2012] [Indexed: 11/06/2022]
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24
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Anan K, Demizu Y, Oba M, Kurihara M, Doi M, Suemune H, Tanaka M. Helical Structures of Bicyclicα-Amino Acid Homochiral Oligomers with the Stereogenic Centers at the Side-Chain Fused-Ring Junctions. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200403] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Demizu Y, Nagoya S, Doi M, Sato Y, Tanaka M, Kurihara M. Twisted structure of a cyclic hexapeptide containing a combination of alternating L-Leu-D-Leu-Aib segments. J Org Chem 2012; 77:9361-5. [PMID: 23006337 DOI: 10.1021/jo301509c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We designed and synthesized a C(2)-symmetric cyclic hexapeptide, cyclo(L-Leu-D-Leu-Aib)(2) (2), which contains L- and D-amino acids and achiral Aib residues. The conformation of 2 was analyzed in the crystalline state and in solution, which was a unique figure-eight-shaped conformation.
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Affiliation(s)
- Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan.
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26
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Demizu Y, Yabuki YU, Doi M, Sato Y, Tanaka M, Kurihara M. Conformations of helical Aib peptides containing a pair of l-amino acid and d-amino acid. J Pept Sci 2012; 18:466-75. [PMID: 22619002 DOI: 10.1002/psc.2418] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 04/18/2012] [Accepted: 04/20/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Yosuke Demizu
- Division of Organic Chemistry; National Institute of Health Sciences; 1-18-1, Kamiyoga, Setagaya; Tokyo; 158-8501; Japan
| | - Yu-u Yabuki
- Division of Organic Chemistry; National Institute of Health Sciences; 1-18-1, Kamiyoga, Setagaya; Tokyo; 158-8501; Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences; Osaka; 569-1094; Japan
| | - Yukiko Sato
- Division of Organic Chemistry; National Institute of Health Sciences; 1-18-1, Kamiyoga, Setagaya; Tokyo; 158-8501; Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences; Nagasaki University; 1-14 Bunkyo-machi; Nagasaki; 852-8521; Japan
| | - Masaaki Kurihara
- Division of Organic Chemistry; National Institute of Health Sciences; 1-18-1, Kamiyoga, Setagaya; Tokyo; 158-8501; Japan
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28
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Demizu Y, Doi M, Kurihara M, Maruyama T, Suemune H, Tanaka M. One-Handed Helical Screw Direction of Homopeptide Foldamer Exclusively Induced by Cyclic α-Amino Acid Side-Chain Chiral Centers. Chemistry 2012; 18:2430-9. [DOI: 10.1002/chem.201102902] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Indexed: 11/11/2022]
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29
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Enantioselective epoxidation of α,β-unsaturated ketones catalyzed by stapled helical l-Leu-based peptides. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.075] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Jiménez AI, Vaquero V, Cabezas C, López JC, Cativiela C, Alonso JL. The Singular Gas-Phase Structure of 1-Aminocyclopropanecarboxylic Acid (Ac3c). J Am Chem Soc 2011; 133:10621-8. [DOI: 10.1021/ja2033603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana I. Jiménez
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - Vanesa Vaquero
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cabezas
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Juan C. López
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cativiela
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - José L. Alonso
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
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31
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Demizu Y, Doi M, Sato Y, Tanaka M, Okuda H, Kurihara M. Effect of one D-Leu residue on right-handed helical -L-Leu-Aib- peptides in the crystal state. J Pept Sci 2011; 17:420-6. [DOI: 10.1002/psc.1332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/15/2010] [Accepted: 10/18/2010] [Indexed: 11/11/2022]
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32
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Yamagata N, Demizu Y, Sato Y, Doi M, Tanaka M, Nagasawa K, Okuda H, Kurihara M. Design of a stabilized short helical peptide and its application to catalytic enantioselective epoxidation of (E)-chalcone. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.12.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Demizu Y, Doi M, Kurihara M, Okuda H, Nagano M, Suemune H, Tanaka M. Conformational studies on peptides containing α,α-disubstituted α-amino acids: chiral cyclic α,α-disubstituted α-amino acid as an α-helical inducer. Org Biomol Chem 2011; 9:3303-12. [DOI: 10.1039/c0ob01146k] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Demizu Y, Tanaka M, Doi M, Kurihara M, Okuda H, Suemune H. Conformations of peptides containing a chiral cyclic α, α-disubstituted α-amino acid within the sequence of Aib residues. J Pept Sci 2010; 16:621-6. [DOI: 10.1002/psc.1273] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Nagano M, Tanaka M, Doi M, Demizu Y, Kurihara M, Suemune H. Helical-screw directions of diastereoisomeric cyclic alpha-amino acid oligomers. Org Lett 2010; 11:1135-7. [PMID: 19191578 DOI: 10.1021/ol802963a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two series of homooligomers composed of diastereoisomeric cyclic alpha-amino acids having two chiral centers at the alpha-carbon and the side chain were synthesized, and their preferred secondary structures were studied in solution and in the crystal state. The oligomers are a new class of helical-foldamers possessing two kinds of chiral centers on the helical backbone and at the lateral surface of the helix.
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Affiliation(s)
- Masanobu Nagano
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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36
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Revilla-López G, Torras J, Curcó D, Casanovas J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Grodzinski P, Alemán C. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. J Phys Chem B 2010; 114:7413-22. [PMID: 20455555 PMCID: PMC2896893 DOI: 10.1021/jp102092m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/ Jaume II n°69, Lleida E-25001, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Piotr Grodzinski
- Alliance for Nanotechnology in Cancer, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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Alemán C, Jiménez AI, Cativiela C, Nussinov R, Casanovas J. Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue. J Org Chem 2009; 74:7834-43. [PMID: 19772338 PMCID: PMC2771318 DOI: 10.1021/jo901594e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of the restricted phenylalanine analogue generated by including the alpha and beta carbon atoms into a cyclohexane ring (1-amino-2-phenylcyclohexanecarboxylic acid, c(6)Phe) have been determined using quantum mechanical calculations. Specifically, the conformational profile of the N-acetyl-N'-methylamide derivative of the c(6)Phe stereoisomers exhibiting either a cis or a trans relative orientation between the amino and phenyl substituents has been analyzed in different environments (gas phase, chloroform, and aqueous solutions). Calculations were performed using B3LYP, MP2, and HF methods combined with the 6-31+G(d,p) and 6-311++G(d,p) basis sets, and a self-consistent reaction-field (SCRF) method was applied to analyze the influence of the solvent. The amino acids investigated can be viewed as constrained phenylalanine analogues with a rigidly oriented aromatic side chain that may interact with the peptide backbone not only sterically but also electronically through the aromatic pi orbitals. Their conformational propensities have been found to be strongly influenced by the specific orientation of the aromatic substituent in each stereoisomer and the conformation adopted by the cyclohexane ring, as well as by the environment.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n 69, Lleida E-25001, Spain
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38
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Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 2009; 49:1623-9. [PMID: 19548653 DOI: 10.1021/ci9001487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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39
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Revilla-López G, Torras J, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue. J Org Chem 2009; 74:2403-12. [PMID: 19236034 PMCID: PMC2682113 DOI: 10.1021/jo802704h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of the nonproteinogenic amino acids constructed by incorporating the arginine side chain in the beta position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated by using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c(5)Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N'-methylamide derivatives of cis- and trans-c(5)Arg have been examined in the gas phase and in solution by using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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40
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Ousaka N, Sato T, Kuroda R. Total Helical-Sense Bias of an Achiral Peptide Main Chain Induced by a Chiral Side-Chain Bridge. J Am Chem Soc 2009; 131:3820-1. [DOI: 10.1021/ja8091714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naoki Ousaka
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo 153-0041, Japan, and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tomohiro Sato
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo 153-0041, Japan, and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Reiko Kuroda
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo 153-0041, Japan, and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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41
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Cativiela C, Ordóñez M. Recent Progress on the Stereoselective Synthesis of Cyclic Quaternary alpha-Amino Acids. TETRAHEDRON, ASYMMETRY 2009; 20:1-63. [PMID: 20300486 PMCID: PMC2839256 DOI: 10.1016/j.tetasy.2009.01.002] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The most recent papers describing the stereoselective synthesis of cyclic quaternary alpha-amino acids are collected in this review. The diverse synthetic approaches are classified according to the size of the ring and taking into account the bond that is formed to complete the quaternary skeleton.
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Affiliation(s)
- Carlos Cativiela
- Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza (Spain)
| | - Mario Ordóñez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, 62209 Cuernavaca, Morelos (México)
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42
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King ED, Tao P, Sanan TT, Hadad CM, Parquette JR. Photomodulated Chiral Induction in Helical Azobenzene Oligomers. Org Lett 2008; 10:1671-4. [DOI: 10.1021/ol8004722] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric D. King
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Peng Tao
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Toby T. Sanan
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | | | - Jon R. Parquette
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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43
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Clayden J, Lemiègre L, Pickworth M, Jones L. Conformation and stereodynamics of 2,2′-disubstituted N,N′-diaryl ureas. Org Biomol Chem 2008; 6:2908-13. [DOI: 10.1039/b802673d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Casanovas J, Jiménez AI, Cativiela C, Nussinov R, Alemán C. 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue. J Org Chem 2007; 73:644-51. [PMID: 18081347 DOI: 10.1021/jo702107s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DFT calculations at the B3LYP/6-311G(d,p) level have been used to investigate the intrinsic conformational preferences of 1-amino-2-phenylcyclopentane-1-carboxylic acid (c5Phe), a constrained analogue of phenylalanine in which the alpha and beta carbons are included in a cyclopentane ring. Specifically, the N-acetyl-N'-methylamide derivatives of the cis and trans stereoisomers, where cis and trans refer to the relative position between the amino group and the phenyl ring, have been calculated. Solvent effects have been examined using a self-consistent reaction field (SCRF) method. Results indicate that the conformational space of the cis stereoisomer is much more restricted than that of the trans derivative both in the gas phase and in solution.
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Affiliation(s)
- Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II No. 69, Lleida E-25001, Spain.
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45
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Maity P, König B. Enantio- and diastereoselective syntheses of cyclic Cα-tetrasubstituted α-amino acids and their use to induce stable conformations in short peptides. Biopolymers 2007; 90:8-27. [DOI: 10.1002/bip.20902] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Brackmann F, de Meijere A. Natural Occurrence, Syntheses, and Applications of Cyclopropyl-Group-Containing α-Amino Acids. 1. 1-Aminocyclopropanecarboxylic Acid and Other 2,3-Methanoamino Acids. Chem Rev 2007; 107:4493-537. [DOI: 10.1021/cr078376j] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farina Brackmann
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Armin de Meijere
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
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47
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Abstract
[Structure: see text] The self-assembly in the crystal state of the terminally protected, linear dipeptide Boc-(S,S)c3diPhe-(R,R)c3diPhe-NHiPr (1) through intermolecular hydrogen bonds leads to the formation of a supramolecular helix of large diameter (18 A), internally decorated with phenyl rings. As a result, a hollow helical channel large enough to accommodate guest molecules is observed. This supramolecular structure differs from previous examples of peptide nanotubes. Compound 1 incorporates a highly restricted cyclopropane phenylalanine analogue (c3diPhe) with remarkable conformational properties.
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Affiliation(s)
- Marco Crisma
- Department of Organic Chemistry, ICMA, University of Zaragoza-CSIC, 50009 Zaragoza, Spain.
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48
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Maity P, Zabel M, König B. Tetrahydrofuran Calpha-tetrasubstituted amino acids: two consecutive beta-turns in a crystalline linear tripeptide. J Org Chem 2007; 72:8046-53. [PMID: 17877403 DOI: 10.1021/jo701423w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of tetrahydrofuran Calpha-tetrasubstituted amino acids (TAAs) and their effect on the conformation in small peptides are reported. The synthesis starts from the protein amino acid methionine, which is protected at the C and N terminus and converted into the corresponding sulfonium salt by alkylation. Simple base treatment in the presence of an aryl aldehyde leads to the formation of tetrahydrofuran tetrasubstituted Calpha-amino acids in a highly diastereoselective (trans/cis ratio up to 97:3) reaction with moderate to good yields (35-78%) depending on the aldehyde used. Palladium-catalyzed coupling reactions allow a subsequent further functionalization of the TAA. The R,S,S-TAA-Ala dipeptide amide adopts a beta-turn type I conformation, whereas its S,R,S isomer does not. The R,S,S-Gly-TAA-Ala tripeptide amide shows in the solid state and in solution a conformation of two consecutive beta-turn type III structures, stabilized by i+3-->i intramolecular hydrogen bonds.
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Affiliation(s)
- Prantik Maity
- Institut für Organische Chemie, Universität Regensburg, D-93040 Regensburg, Germany
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49
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Casanovas J, Jiménez AI, Cativiela C, Pérez JJ, Aleman C. Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents. J Phys Chem B 2007; 110:5762-6. [PMID: 16539522 DOI: 10.1021/jp0542569] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical methods have been used to investigate the intrinsic conformational preferences of 1-amino-2,2-diphenylcyclopropanecarboxylic acid (c(3)Dip), a cyclopropane analogue of phenylalanine bearing two phenyl substituents on the same beta-carbon. Geometries, energies, and frequencies were calculated on the N-acetyl-N'-methylamide derivative at the HF and B3LYP levels using the 6-31G(d), 6-311G(d), and 6-31+G(d,p) basis sets. Four minimum energy conformations were characterized: axial C(7), equatorial C(7), right-handed helix, and polyproline II. Analysis of the whole results, which are fully consistent with available experimental data, indicates that c(3)Dip tends to promote gamma-turn conformations.
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Affiliation(s)
- Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II N 69, 25001 Lleida, Spain.
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50
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Crisma M, De Borggraeve WM, Peggion C, Formaggio F, Royo S, Jiménez AI, Cativiela C, Toniolo C. Preferred 3D-structure of peptides rich in a severely conformationally restricted cyclopropane analogue of phenylalanine. Chemistry 2007; 12:251-60. [PMID: 16281320 DOI: 10.1002/chem.200500865] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Terminally blocked, homo-peptide amides of (R,R)-1-amino-2,3-diphenylcyclopropane-1-carboxylic acid (c3diPhe), a chiral member of the family of Calpha-tetrasubstituted alpha-amino acids, from the dimer to the tetramer, and diastereomeric co-oligopeptides of (R,R)- or (S,S)-c3diPhe with (S)-alanine residues to the trimer level were prepared in solution and fully characterized. The synthetic effort was extended to terminally protected co-oligopeptide esters to the hexamer, where c3diPhe residues are combined with achiral alpha-aminoisobutyric acid residues. The preferred conformations of the peptides were assessed in solution by FT-IR absorption, NMR, and CD techniques, and for seven oligomers in the crystal state (by X-ray diffraction) as well. This study clearly indicates that c3diPhe, a sterically demanding cyclopropane analogue of phenylalanine, tends to fold peptides into beta-turn and 3(10)-helix conformations. However, when c3diPhe is in combination with other chiral residues, the conformation preferred by the resulting peptides is also dictated by the chiral sequence of the amino acid building blocks. The (S,S)-enantiomer of this alpha-amino acid, unusually lacking asymmetry in the main chain, strongly favors the left-handedness of the turn/helical peptides formed.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova via Marzolo 1, 35131 Padova, Italy
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