1
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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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2
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Mizuno A, Matsui K, Shuto S. From Peptides to Peptidomimetics: A Strategy Based on the Structural Features of Cyclopropane. Chemistry 2017. [PMID: 28632330 DOI: 10.1002/chem.201702119] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptidomimetics, non-natural mimicries of bioactive peptides, comprise an important class of drug molecules. The essence of the peptidomimetic design is to mimic the key conformation assumed by the bioactive peptides upon binding to their targets. Regulation of the conformation of peptidomimetics is important not only to enhance target binding affinity and selectivity, but also to confer cell-membrane permeability for targeting protein-protein interactions in cells. The rational design of peptidomimetics with suitable three-dimensional structures is challenging, however, due to the inherent flexibility of peptides and their dynamic conformational changes upon binding to the target biomolecules. In this Minireview, a three-dimensional structural diversity-oriented strategy based on the characteristic structural features of cyclopropane to address this challenging issue in peptidomimetic chemistry is described.
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Affiliation(s)
- Akira Mizuno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Kouhei Matsui
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka, 561-0825, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
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3
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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4
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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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5
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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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6
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Sallmann M, Oldenburg F, Braun B, Réglier M, Simaan AJ, Limberg C. Ein funktionelles Strukturmodell für die 1-Aminocyclopropan- 1-carbonsäure-Oxidase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Sallmann M, Oldenburg F, Braun B, Réglier M, Simaan AJ, Limberg C. A structural and functional model for the 1-aminocyclopropane-1-carboxylic acid oxidase. Angew Chem Int Ed Engl 2015; 54:12325-8. [PMID: 26190407 DOI: 10.1002/anie.201502529] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/22/2015] [Indexed: 11/06/2022]
Abstract
The hitherto most realistic low-molecular-weight analogue for the 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) is reported. The ACCOs 2-His-1-carboxylate iron(II) active site was mimicked by a TpFe moiety, to which the natural substrate ACC could be bound. The resulting complex [Tp(Me,Ph) FeACC] (1), according to X-ray diffraction analysis performed for the nickel analogue, represents an excellent structural model, featuring ACC coordinated in a bidentate fashion-as proposed for the enzymatic substrate complex-as well as a vacant coordination site that forms the basis for the first successful replication also of the ACCO function: 1 is the first known ACC complex that reacts with O2 to produce ethylene. As a FeOOH species had been suggested as intermediate in the catalytic cycle, H2 O2 was tested as the oxidant, too, and indeed evolution of ethylene proceeded even more rapidly to give 65 % yield.
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Affiliation(s)
- Madleen Sallmann
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, 12489 Berlin (Germany) http://www.chemie.hu-berlin.de/aglimberg
| | - Fabio Oldenburg
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, 12489 Berlin (Germany) http://www.chemie.hu-berlin.de/aglimberg
| | - Beatrice Braun
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, 12489 Berlin (Germany) http://www.chemie.hu-berlin.de/aglimberg
| | - Marius Réglier
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, (France) http://ism2.univ-amu.fr/pages-bleues/index2.htm
| | - A Jalila Simaan
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, (France) http://ism2.univ-amu.fr/pages-bleues/index2.htm.
| | - Christian Limberg
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, 12489 Berlin (Germany) http://www.chemie.hu-berlin.de/aglimberg.
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8
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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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9
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Crisma M, De Zotti M, Moretto A, Peggion C, Drouillat B, Wright K, Couty F, Toniolo C, Formaggio F. Single and multiple peptide γ-turns: literature survey and recent progress. NEW J CHEM 2015. [DOI: 10.1039/c4nj01564a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Published data on peptide isolated and repetitive γ-turns are reviewed. Advancements in our laboratories on these 3D-structures are also presented.
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Affiliation(s)
- Marco Crisma
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | - Marta De Zotti
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | | | | | - Bruno Drouillat
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Karen Wright
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - François Couty
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Claudio Toniolo
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
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10
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Synthesis and evaluation of C8-substituted 4.5-spiro lactams as Glycogen Phosphorylase a inhibitors. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Characterization of Cu(II)-ACC complexes and conversion of the bound ACC into ethylene in the presence of hydrogen peroxide. detection of a brown intermediate at low temperature. Bioinorg Chem Appl 2011:43424. [PMID: 18274607 PMCID: PMC2216062 DOI: 10.1155/2007/43424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 07/16/2007] [Indexed: 11/23/2022] Open
Abstract
Two copper(II)-ACC complexes were prepared and characterized: [Cu(bpy)(ACC)(H2O)]⋅CO4 (1) and [Cu(ACC)2]3⋅4H2O (2). Their crystallographic structures are described and analyzed. Spectroscopic characterizations (UV-visible and EPR) confirm that the structure is maintained in solution. These complexes are able to produce ethylene in the presence of hydrogen peroxide
in an “ACC Oxidase-like” reaction in water and in methanol. The conversion of ACC into ethylene depends on the amount of base, and, in methanol, 3 equivalents of NaOH are needed for optimum activity. The base is proposed to play a role in H2O2 deprotonation. The presence of an exogenic ligand (bpy) is important for the reactivity and may stabilize a reaction intermediate. Indeed, a brown intermediate with an absorption band centered at 433 nm can be detected at low temperature when 1 is treated with 10 equivalents
of H2O2.
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12
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LaPlante SR, Gillard JR, Jakalian A, Aubry N, Coulombe R, Brochu C, Tsantrizos YS, Poirier M, Kukolj G, Beaulieu PL. Importance of ligand bioactive conformation in the discovery of potent indole-diamide inhibitors of the hepatitis C virus NS5B. J Am Chem Soc 2011; 132:15204-12. [PMID: 20942454 DOI: 10.1021/ja101358s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Significant advances have led to receptor induced-fit and conformational selection models for describing bimolecular recognition, but a more comprehensive view must evolve to also include ligand shape and conformational changes. Here, we describe an example where a ligand's "structural hinge" influences potency by inducing an "L-shape" bioactive conformation, and due to its solvent exposure in the complex, reasonable conformation-activity-relationships can be qualitatively attributed. From a ligand design perspective, this feature was exploited by successful linker hopping to an alternate "structural hinge" that led to a new and promising chemical series which matched the ligand bioactive conformation and the pocket bioactive space. Using a combination of X-ray crystallography, NMR and modeling with support from binding-site resistance mutant studies and photoaffinity labeling experiments, we were able to derive inhibitor-polymerase complexes for various chemical series.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard St., Laval, Quebec, Canada, H7S2G5.
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13
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Crisma M, Moretto A, Peggion C, Panella L, Kaptein B, Broxterman QB, Formaggio F, Toniolo C. Chiral, fully extended helical peptides. Amino Acids 2011; 41:629-41. [DOI: 10.1007/s00726-011-0839-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/19/2011] [Indexed: 11/24/2022]
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14
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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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15
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Flores-Ortega A, Casanovas J, Assfeld X, Alemán C. Protonation of the Side Group in β- and γ-Aminated Proline Analogues: Effects on the Conformational Preferences. J Org Chem 2009; 74:3101-8. [DOI: 10.1021/jo900169s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Jordi Casanovas
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Xavier Assfeld
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
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16
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FABIANO N, VALLE G, CRISMA M, TONIOLO C, SAVIANO M, LOMBARDI A, ISERNIA C, PAVONE V, BLASIO B, PEDONE C, BENEDETTI E. Conformational versatility of the Nα-acylated tripeptide amide tail of oxytocin. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1993.tb00155.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Ballano G, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids. J Phys Chem B 2008; 112:13101-15. [PMID: 18811190 DOI: 10.1021/jp8032116] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.
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Affiliation(s)
- Gema Ballano
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, Zaragoza, Spain
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18
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Ghattas W, Giorgi M, Mekmouche Y, Tanaka T, Rockenbauer A, Réglier M, Hitomi Y, Simaan AJ. Identification of a Copper(I) Intermediate in the Conversion of 1-Aminocyclopropane Carboxylic Acid (ACC) into Ethylene by Cu(II)−ACC Complexes and Hydrogen Peroxide. Inorg Chem 2008; 47:4627-38. [DOI: 10.1021/ic702303g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wadih Ghattas
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - Michel Giorgi
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - Yasmina Mekmouche
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - Tsunehiro Tanaka
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - Antal Rockenbauer
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - Marius Réglier
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - Yutaka Hitomi
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
| | - A. Jalila Simaan
- Institut des Sciences Moléculaires de Marseille, ISM2/BiosCiences UMR-CNRS 6263, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Service 342, 13397 Marseille cedex 20, France, Spectropôle, Aix-Marseille Université, Centre Scientifique de Saint-Jérôme, Av. Escadrille Normandie-Niémen, 13397 Marseille cedex 20, France, Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsuta, Kyoto 615-8510, Japan, and Chemical Research Center, Hungarian
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19
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Meneghetti F, Artali R. Structural and Conformational Studies on Two Diastereomeric Dihydroisoxazolyl Cyclopropane Derivatives. HETEROCYCLES 2008. [DOI: 10.3987/com-07-11261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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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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21
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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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22
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Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid. J Phys Chem B 2007; 110:21264-71. [PMID: 17048955 DOI: 10.1021/jp062804s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have used quantum mechanical calculations at the B3LYP/6-311G(d,p) level to determine the conformational preferences of the N-acetyl-N'-methylamide derivative of 1-aminocyclopentane-1-carboxylic acid in the gas phase, chloroform solution, and water solution. The backbone conformation of this dipeptide has been described through the dihedral angles varphi and psi, while the pseudorotational phase angle was used to define the conformation of the cyclopentane ring. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different conformations depending on the polarity of the environment. The potential energy of the pseudorotation was also studied as a function of the backbone conformation. Interestingly, the conformation of the cyclic side chain depends on the backbone arrangement. Furthermore, the number of pseudorotational states accessible at room temperature is high in all the investigated environments, especially in aqueous solution. Finally, a set of force-field parameters for classical molecular mechanics calculations was developed for the investigated amino acid. Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters.
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Affiliation(s)
- Carlos Aleman
- 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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23
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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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24
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de Meijere A, Kozhushkov SI, Schill H. Three-Membered-Ring-Based Molecular Architectures. Chem Rev 2006; 106:4926-96. [PMID: 17165680 DOI: 10.1021/cr0505369] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Armin de Meijere
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstrasse 2, D-37077 Göttingen, Germany
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25
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Meneghetti F, Roda G, Ragone S, Artali R. Structural studies and NMDA activity of an enantiopure dihydroisoxazole derivative. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.tetasy.2006.11.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Kohrt JT, Filipski KJ, Cody WL, Bigge CF, La F, Welch K, Dahring T, Bryant JW, Leonard D, Bolton G, Narasimhan L, Zhang E, Peterson JT, Haarer S, Sahasrabudhe V, Janiczek N, Desiraju S, Hena M, Fiakpui C, Saraswat N, Sharma R, Sun S, Maiti SN, Leadley R, Edmunds JJ. The discovery of glycine and related amino acid-based factor Xa inhibitors. Bioorg Med Chem 2006; 14:4379-92. [PMID: 16529937 DOI: 10.1016/j.bmc.2006.02.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Revised: 02/17/2006] [Accepted: 02/21/2006] [Indexed: 10/24/2022]
Abstract
Herein, we report on the identification of three potent glycine and related amino acid-based series of FXa inhibitors containing a neutral P1 chlorophenyl pharmacophore. A X-ray crystal structure has shown that constrained glycine derivatives with optimized N-substitution can greatly increase hydrophobic interactions in the FXa active site. Also, the substitution of a pyridone ring for a phenylsulfone ring in the P4 sidechain resulted in an inhibitor with enhanced oral bioavailability.
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Affiliation(s)
- Jeffrey T Kohrt
- Pfizer Global Research and Development, Michigan Labs, Ann Arbor, 48105, USA.
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27
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Judas N, Raos N. Self-Assembly of cis and trans Forms of the Copper(II) Complex with 1-Aminocyclopropane-1-carboxylate into Discrete Trimers in the Solid State. Inorg Chem 2006; 45:4892-4. [PMID: 16780308 DOI: 10.1021/ic060780y] [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
A copper(II) complex with 1-aminocyclopropane-1-carboxylic acid assembles by apical Cu...O bonds and hydrogen-bonding interactions into discrete trimeric units that exhibit both cis and trans binding modes.
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Affiliation(s)
- Nenad Judas
- Laboratory of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia.
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28
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Ghattas W, Gaudin C, Giorgi M, Rockenbauer A, Simaan AJ, Réglier M. ACC-Oxidase like activity of a copper (ii)–ACC complex in the presence of hydrogen peroxide. Detection of a reaction intermediate at low temperature. Chem Commun (Camb) 2006:1027-9. [PMID: 16491198 DOI: 10.1039/b515374c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A Cu(II)-ACC complex [(Bpy)Cu(ACC)(H2O)]ClO4 (1) was prepared and its treatment with hydrogen peroxide gave rise to ethylene production in an ACC-Oxidase like activity. A brown species that could be a key intermediate in the reaction was detected at low temperature.
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Affiliation(s)
- Wadih Ghattas
- Laboratoire de Bioinorganique Structurale, UMR CNRS 6517, Université Paul Cézanne Aix-Marseille III, Service 432 Faculté des Sciences et Techniques, 13397 Marseille cedex 20, France
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29
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Crisma M, Deschamps JR, George C, Flippen-Anderson JL, Kaptein B, Broxterman QB, Moretto A, Oancea S, Jost M, Formaggio F, Toniolo C. A topographically and conformationally constrained, spin-labeled, alpha-amino acid: crystallographic characterization in peptides. ACTA ACUST UNITED AC 2005; 65:564-79. [PMID: 15885116 DOI: 10.1111/j.1399-3011.2005.00258.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC) is a topographically and conformationally restricted, nitroxide containing, C(alpha)-tetrasubstituted alpha-amino acid. Here, we describe the molecular and crystal structures, as determined by X-ray diffraction analyses, of a TOAC terminally protected derivative, the cyclic dipeptide c(TOAC)(2).1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) solvate, and five TOAC-containing, terminally protected, linear peptides ranging in length from tetra- to hepta-peptides. Incipient and fully developed, regular or distorted 3(10)-helical structures are formed by the linear peptides. A detailed discussion on the average geometry and preferred conformation for the TOAC piperidine ring is also reported. The X-ray diffraction structure of an intramolecularly cyclized side product resulting from a C-activated TOAC residue has also been determined.
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Affiliation(s)
- M Crisma
- Department of Chemistry, Institute of Biomolecular Chemistry, CNR, University of Padova, 35131 Padova, Italy
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30
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Cetina M, Dzolić Z, Mrvos-Sermek D, Hergold-Brundić A, Nagl A, Mintas M. Synthesis and X-ray study of the 6-(N-pyrrolyl)purine and thymine derivatives of 1-aminocyclopropane-1-carboxylic acid. ACTA ACUST UNITED AC 2004; 63:391-8. [PMID: 15140156 DOI: 10.1111/j.1399-3011.2004.00133.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The novel purine and pyrimidine derivatives of 1-aminocyclopropane-1-carboxylic acid 1 and 2 were obtained by alkylation of 6-(N-pyrrolyl)purine and thymine with methyl 1-benzamido-2-chloromethylcyclopropanecarboxylate. X-ray crystal structure analysis shows that the cyclopropane rings in 1 and 2 posses Z-configuration. The cyclopropane ring atoms and attached atoms of the benzamido and methoxycarbonyl moiety of both molecules are disposed perpendicularly to each other. The carbonyl oxygen of the methoxycarbonyl moiety adopts in both compounds a synperiplanar conformation with respect to the midpoint of the distal bond of the cyclopropane ring. The torsion angles Phi and psi for the 1-aminocyclopropane-1-carboxylic acid residue in 1 and 2 correspond to a folded conformation, while the torsion angles omega define antiperiplanar conformation. Intermolecular hydrogen bonds connect the molecules of 1 into dimers. Each dimer is hydrogen-bonded with four ethanol molecules, thus forming discrete unit. On the contrary, intermolecular hydrogen bonds link the molecules of 2 generating three-dimensional network.
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Affiliation(s)
- M Cetina
- Faculty of Textile Technology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
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31
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Casanovas J, Jiménez AI, Cativiela C, Pérez JJ, Alemán C. N-acetyl-N'-methylamide derivative of (2S,3S)-1-amino-2,3-diphenylcyclopropanecarboxylic acid: theoretical analysis of the conformational impact produced by the incorporation of the second phenyl group to the cyclopropane analogue of phenylalanine. J Org Chem 2003; 68:7088-91. [PMID: 12946154 DOI: 10.1021/jo034720a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intrinsic conformational preferences of (2S,3S)-1-amino-2,3-diphenylcyclopropanecarboxylic acid, a phenylalanine cyclopropane analogue bearing two phenyl substituents, have been examined theoretically. For this purpose, its N-acetyl-N'-methylamide derivative, Ac-(2S,3S)c(3)diPhe-NHMe, has been investigated by using ab initio HF and DFT methods. Results have been compared with those previously reported for other cyclopropane analogues of phenylalanine, and with experimental data available for c(3)diPhe-containing peptides.
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Affiliation(s)
- Jordi Casanovas
- Departament de Química, Escola Universitària Politècnica, Universitat de Lleida, c/Jaume II No. 69, 25001 Lleida, Spain.
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32
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Cetina M, Hergold-Brundić A, Raos N, Žuža-Mak L. Crystal and molecular structure and conformational analysis of (1RS, 2SR)-1-[N-(tert-butoxycarbonyl)amino]-2-hydroxymethylcyclopropane-1-carboxylic acid. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00389-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Džolić Z, Cetina M, Kovaček D, Hergold-Brundić A, Mrvoš-Sermek D, Nagl A, Slade N, Pavelić K, Balzarini J, Clercq ED, Zerbe O, Folkers G, Scapozza L, Mintas M. Molecular structures and ab initio molecular orbital calculations of the optically active derivatives of 1-aminocyclopropane-1-carboxylic acid. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00255-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Peggion C, Formaggio F, Crisma M, Toniolo C, Jiménez AI, Cativiela C, Kaptein B, Broxterman QB, Saviano M, Benedetti E. Folding of peptides characterized by c3Val, a highly constrained analogue of valine. Biopolymers 2003; 68:178-91. [PMID: 12548622 DOI: 10.1002/bip.10295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Using a combined chemical/chiral chromatographic approach we synthesized an N-protected derivative of (R)-c(3)Val, a severely conformationally restricted C(alpha)-tetrasubstituted alpha-amino acid characterized by a C(beta,beta)-dimethylated cyclopropane system. A set of terminally protected derivatives and model peptides (to the heptamer level), containing one or two (R)-c(3)Val residues in combination with either Aib or Gly residues, was prepared by solution methods. A detailed solution and crystal-state conformational investigation, based on Fourier transform infrared (FTIR) absorption, (1)H-NMR, and x-ray diffraction techniques, performed in comparison with a similar study on related derivatives and peptides rich in (alphaMe)Val, the prototype of C(alpha)-tetrasubstituted alpha-amino acids of this subfamily, allowed us to conclude the following: (a) c(3)Val is a good beta-bend and helix former, although less efficient than (alphaMe)Val. (b) The relationship between alpha-carbon chirality and screw sense of the folded structure formed is the same as that of (alphaMe)Val, i.e., the (R)-enantiomer has a strong left-handed bias. (c) c(3)Val seems more prone than (alphaMe)Val to fold into a gamma-bend conformation. The conformational propensities of C(beta,beta)-disubstituted Ac(3)c residues are also discussed in comparison with those of the parent cyclopropane residue.
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Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy
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35
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Alemán C, Jiménez AI, Cativiela C, Perez JJ, Casanovas J. Influence of the Phenyl Side Chain on the Conformation of Cyclopropane Analogues of Phenylalanine. J Phys Chem B 2002. [DOI: 10.1021/jp026381f] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain, and Departament de Química, Escola Universitària Politècnica, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Ana I. Jiménez
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain, and Departament de Química, Escola Universitària Politècnica, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Carlos Cativiela
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain, and Departament de Química, Escola Universitària Politècnica, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Juan J. Perez
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain, and Departament de Química, Escola Universitària Politècnica, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Jordi Casanovas
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain, and Departament de Química, Escola Universitària Politècnica, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
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Cativiela C, Diaz-de-Villegas MD, Marraud M, Oliveros L. Efficient access to all four stereoisomers of phenylalanine cyclopropane analogues by chiral HPLC. Chirality 1999; 11:583-90. [PMID: 10423286 DOI: 10.1002/(sici)1520-636x(1999)11:7<583::aid-chir11>3.0.co;2-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Bonded polysaccharide-derived chiral stationary phases were found to be useful for the preparation of the four stereoisomers of the cyclopropane analogue of phenylalanine (c(3)Phe) as well as for the direct determination of the enantiomeric purity of c(3)Phe derivatives by HPLC. Three chiral stationary phases, consisting of cellulose and amylose derivatives chemically bonded on allylsilica gel, were tested. The mixed 10-undecenoate/3, 5-dimethylphenylcarbamate of cellulose, 10-undecenoate/3, 5-dimethylphenylcarbamate of amylose and 10-undecenoate/p-methylbenzoate of cellulose were the starting polysaccharide derivatives for CSP-1, CSP-2, and CSP-3, respectively. Using mixtures of n-hexane/chloroform/2-propanol as mobile phase on a semi-preparative column (150 mm x 20 mm ID) containing CSP-2, we separated about 1.7 g of racemic cis-methyl 1-tert-butoxycarbonylamino-2-phenylcyclopropanecarboxylate (cis-6) and 1.2 g of racemic trans-methyl-1-tert-butoxycarbonylamino-2-phenylcycloprop-anecarboxyl ate (trans-6) by successive injections. Copyright 1999 Wiley-Liss, Inc.
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Affiliation(s)
- C Cativiela
- Departamento de Quimica Organica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
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Gomez-Catalan J, Perez JJ, Jimenez AI, Cativiela C. Study of the conformational profile of selected unnatural amino acid residues derived from L-phenylalanine. J Pept Sci 1999; 5:251-62. [PMID: 10463780 DOI: 10.1002/(sici)1099-1387(199906)5:6<251::aid-psc190>3.0.co;2-k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The present work reports the results of a conformational study performed on seven unnatural amino acid residues and on its natural precursor, investigated by means of computational methods at the molecular mechanics level. Amino acid residues selected for the present study are derivatives of L-phenylalanine substituted at the alpha and/or beta carbons. This series is composed of different linear analogs, including alpha-methyl, beta-methyl and beta-phenyl substituted with different stereochemistry. Analysis of the Ramachandran maps of the corresponding dipeptides in vacuo reveals their conformational preferences, to be used as guidance for the synthesis of constrained peptide analogs with desired conformational propensities. The available conformational space for every dipeptide is also analysed.
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Affiliation(s)
- J Gomez-Catalan
- Dept. de Toxicologia, Facultat de Farmacia, Universitat de Barcelona, Spain
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Palacin S, Chin DN, Simanek EE, MacDonald JC, Whitesides GM, McBride MT, Palmore GTR. Hydrogen-Bonded Tapes Based on Symmetrically Substituted Diketopiperazines: A Robust Structural Motif for the Engineering of Molecular Solids. J Am Chem Soc 1997. [DOI: 10.1021/ja962905b] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Serge Palacin
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
| | - Donovan N. Chin
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
| | - Eric E. Simanek
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
| | - John C. MacDonald
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
| | - George M. Whitesides
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
| | - Mary T. McBride
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
| | - G. Tayhas R. Palmore
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 01238, and Department of Chemistry, University of California, Davis, California 95616
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Khalil EM, Subasinghe NL, Johnson RL. An efficient and high yield method for the N-tert-butoxycarbonyl protection of sterically hindered amino acids. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)00589-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Formaggio F, Toniolo C, Crisma M, Valle G, Kaptein B, Schoemaker HE, Kamphuis J, Di Blasio B, Maglio O, Fattorusso R. The preferred solid-state conformation of (alpha Me)Trp peptides. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1995; 45:70-7. [PMID: 7775010 DOI: 10.1111/j.1399-3011.1995.tb01569.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The two Z-L-Ala-DL-(alpha Me)Trp-NH2 diastereomeric dipeptides were synthesized from (Z-L-Ala)2(O) and H-DL-(alpha Me)Trp-NH2. The latter racemate, prepared by phase-transfer catalyzed alkylation of the N alpha-benzylidene derivative of alanine amide followed by acidic hydrolysis of the resulting Schiff base, was characterized by X-ray diffraction. The molecular and crystal structure of Z-L-Ala-L-(alpha Me)Trp-NH2, separated from its diastereomer by silica-gel column chromatography, was determined by X-ray diffraction analysis. Both independent molecules in the asymmetric unit of the dipeptide adopt a type-II beta-bend conformation. However, only the more regularly folded conformation of molecule B is stabilized by a 1<--4 C = O...H--N intramolecular H bond. The present results indicate that: (i) the C alpha-methylated (alpha Me)Trp residue is a strong beta-bend and helix former, and (ii) the relationship between (alpha Me)Trp chirality and helix screw sense tends to be opposite to that of protein amino acids. The implications for the use of the (alpha Me)Trp residue in designing conformationally restricted analogs of bioactive peptides are briefly discussed.
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Affiliation(s)
- F Formaggio
- C.N.R. Department of Organic Chemistry, University of Padova, Italy
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Crisma M, Moretto V, Valle G, Formaggio F, Toniolo C. First characterization at atomic resolution of the C-activating groups in a peptide synthesis acid chloride, acid azide and carboxylic-carboxylic mixed anhydride. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1993; 42:378-83. [PMID: 8244633 DOI: 10.1111/j.1399-3011.1993.tb00508.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The X-ray diffraction structures of three N alpha-protected, C alpha-activated MeAib derivatives are reported. They are Tos-MeAib-Cl, Tos-MeAib-N3 and Tos-MeAib-O-Piv. The geometry and conformation of these classical carboxyl activating groups, which have been characterized at atomic resolution for the first time, are discussed.
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Affiliation(s)
- M Crisma
- C.N.R., Department of Organic Chemistry, University of Padova, Italy
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Toniolo C, Crisma M, Formaggio F, Valle G, Cavicchioni G, Precigoux G, Aubry A, Kamphuis J. Structures of peptides from alpha-amino acids methylated at the alpha-carbon. Biopolymers 1993; 33:1061-72. [PMID: 8343585 DOI: 10.1002/bip.360330708] [Citation(s) in RCA: 211] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The structural preferences of peptides (and depsipeptides) from the achiral MeAib and Hib residues, and the chiral Iva, (alpha Me) Val, (alpha Me) Leu, and (alpha Me) Phe residues, as determined by conformational energy computations, x-ray diffraction analyses, and 1H-nmr and spectroscopic studies, are reviewed and compared with literature data on Aib-containing peptides. The results obtained indicate that helical structures are preferentially adopted by peptides rich in these alpha-amino acids methylated at the alpha-carbon. Intriguing experimental findings on the impact of the chirality of Iva, (alpha Me) Val, and (alpha Me) Phe residues on helix screw sense are illustrated.
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Affiliation(s)
- C Toniolo
- Department of Organic Chemistry, University of Padova, Italy
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Di Blasio B, Pavone V, Lombardi A, Pedone C, Benedetti E. Noncoded residues as building blocks in the design of specific secondary structures: symmetrically disubstituted glycines and beta-alanine. Biopolymers 1993; 33:1037-49. [PMID: 8343584 DOI: 10.1002/bip.360330706] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Structural changes can be induced in a peptide by selective substitution of coded alpha-amino acid residues by noncoded alpha-amino acid residues and the consequent production of analogues with modified structure and conformational preferences. In this review article we summarize the solid state structural results and the conformational preferences of two classes of "building blocks": (a) the linear and cyclic symmetrically alpha, alpha-disubstituted glycines in which either two identical n-alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side-chain system is formed by linking the two alpha-carbon side chains, respectively; and (b) the beta-alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given.
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Affiliation(s)
- B Di Blasio
- Department of Chemistry, University of Naples Federico II, Italy
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Valle G, Crisma M, Toniolo C, Sudhanand, Rao RB, Sukumar M, Balaram P. Stereochemistry of peptides containing 1-aminocycloheptane-1-carboxylic acid (Ac7c). INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1991; 38:511-8. [PMID: 1819586 DOI: 10.1111/j.1399-3011.1991.tb01534.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The crystal structures of four peptides incorporating 1-aminocycloheptane-1-carboxylic acid (Ac7c) are described. Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe adopt beta-turn conformations stabilized by an intramolecular 4----1 hydrogen bond, the former folding into a type-I/III beta-turn and the latter into a type-II beta-turn. In the dipeptide esters, Boc-Aib-Ac7c-OMe and Boc-Pro-Ac7c-OMe, the Ac7c and Aib residues adopt helical conformations, while the Pro residue remains semi-extended in both the molecules of Boc-Pro-Ac7c-OMe found in the asymmetric unit. The cycloheptane ring of Ac7c residues adopts a twist-chair conformation in all the peptides studied. 1H-NMR studies in CDCl3 and (CD3)2SO and IR studies in CDCl3 suggest that Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe maintain the beta-turn conformations in solution.
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Affiliation(s)
- G Valle
- Department of Organic Chemistry, University of Padova, Italy
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Matsui S, Srivastava VP, Holt EM, Taylor EW, Stammer CH. Synthesis and conformational analysis of L-aspartylproline and L-aspartyl-2,3-methanoproline propyl esters. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1991; 37:306-14. [PMID: 1894445 DOI: 10.1111/j.1399-3011.1991.tb00744.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- S Matsui
- Department of Chemistry, School of Chemical Sciences, University of Georgia, Athens
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