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Turalić A, Đeđibegović J, Hegedüs Z, Martinek TA. DPP-4 Cleaves α/β-Peptide Bonds: Substrate Specificity and Half-Lives. Chembiochem 2020; 21:2060-2066. [PMID: 32180303 DOI: 10.1002/cbic.202000050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/19/2020] [Indexed: 11/07/2022]
Abstract
The incorporation of β-amino acids into a peptide sequence has gained particular attention as β- and α/β-peptides have shown remarkable proteolytic stability, even after a single homologation at the scissile bond. Several peptidases have been shown to cleave such bonds with high specificity but at a much slower rate compared to α-peptide bonds. In this study, a series of analogs of dipeptidyl peptidase-4 (DPP-4) substrate inhibitors were synthesized in order to investigate whether β-amino acid homologation at the scissile bond could be a valid approach to improving peptide stability towards DPP-4 degradation. DPP-4 cleaved the α/β-peptide bond after the N-terminal penultimate Pro with a broad specificity and retained full activity regardless of the β3 -amino acid side chain and peptide length. Significantly improved half-lives were observed for β3 Ile-containing peptides. Replacing the penultimate Pro with a conformationally constrained Pro mimetic led to proteolytic resistance. DPP-4 cleavage of α/β-peptide bonds with a broad promiscuity represents a new insight into the stability of peptide analogs containing β-amino acids as such analogs were thought to be stable towards enzymatic degradation.
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Affiliation(s)
- Amila Turalić
- Department of Pharmaceutical Analysis, University of Sarajevo, Faculty of Pharmacy, Zmaja od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Jasmina Đeđibegović
- Department of Pharmaceutical Analysis, University of Sarajevo, Faculty of Pharmacy, Zmaja od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, Faculty of Medicine, 8 Dóm tér, 6720, Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Faculty of Medicine, 8 Dóm tér, 6720, Szeged, Hungary.,MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, Szeged, 6720, Hungary
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2
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Kulkarni K, Habila N, Del Borgo MP, Aguilar MI. Novel Materials From the Supramolecular Self-Assembly of Short Helical β 3-Peptide Foldamers. Front Chem 2019; 7:70. [PMID: 30828574 PMCID: PMC6384263 DOI: 10.3389/fchem.2019.00070] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 11/13/2022] Open
Abstract
Self-assembly is the spontaneous organization of small components into higher-order structures facilitated by the collective balance of non-covalent interactions. Peptide-based self-assembly systems exploit the ability of peptides to adopt distinct secondary structures and have been used to produce a range of well-defined nanostructures, such as nanotubes, nanofibres, nanoribbons, nanospheres, nanotapes, and nanorods. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been reported to undergo supramolecular self-assembly, and have been used to produce materials-such as hydrogels-that are tailored for applications in tissue engineering, cell culture and drug delivery. This review provides an overview of self-assembled peptide nanostructures obtained via the supramolecular self-assembly of short β-peptide foldamers with a specific focus on N-acetyl-β3-peptides and their applications as bio- and nanomaterials.
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Affiliation(s)
| | | | - Mark P. Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute, Monash Univdersity, Melbourne, VIC, Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute, Monash Univdersity, Melbourne, VIC, Australia
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3
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Eddinger GA, Gellman SH. Differential Effects of β 3 - versus β 2 -Amino Acid Residues on the Helicity and Recognition Properties of Bim BH3-Derived α/β-Peptides. Angew Chem Int Ed Engl 2018; 57:13829-13832. [PMID: 30161284 DOI: 10.1002/anie.201806909] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/13/2018] [Indexed: 01/07/2023]
Abstract
Oligomers containing α- and β-amino acid residues (α/β-peptides) have been shown to mimic the α-helical conformation of conventional peptides when the unnatural residues are derived from β3 -amino acids or cyclic β-amino acids, but the impact of incorporating β2 residues has received little attention. The effects of β2 residues on the conformation and recognition behavior of α/β-peptides that mimic an isolated α-helix were investigated. This effort has focused on 26-mers based on the Bim BH3 domain; a set of isomers with identical α/β backbones that differ only in the placement of certain side chains along the backbone (β3 vs. β2 substitution) was compared. Circular dichroism data suggest that β2 residues can be helix-destabilizing relative to β3 residues, although the size of this effect seems to depend on side chain identity. Binding data show that β3 →β2 substitution at sites that contact a partner protein, Bcl-xL , can influence affinity in a way that transcends effects on helicity.
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Affiliation(s)
- Geoffrey A Eddinger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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4
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Eddinger GA, Gellman SH. Differential Effects of β
3
‐ versus β
2
‐Amino Acid Residues on the Helicity and Recognition Properties of Bim BH3‐Derived α/β‐Peptides. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Geoffrey A. Eddinger
- Department of ChemistryUniversity of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Samuel H. Gellman
- Department of ChemistryUniversity of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
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5
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Gadais C, Ballet S. The Neurokinins: Peptidomimetic Ligand Design and Therapeutic Applications. Curr Med Chem 2018; 27:1515-1561. [PMID: 30209994 DOI: 10.2174/0929867325666180913095918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/15/2022]
Abstract
The neurokinins are indisputably essential neurotransmitters in numerous pathoand physiological events. Being widely distributed in the Central Nervous System (CNS) and peripheral tissues, their discovery rapidly promoted them to drugs targets. As a necessity for molecular tools to understand the biological role of this class, endogenous peptides and their receptors prompted the scientific community to design ligands displaying either agonist and antagonist activity at the three main neurokinin receptors, called NK1, NK2 and NK3. Several strategies were implemented for this purpose. With a preference to small non-peptidic ligands, many research groups invested efforts in synthesizing and evaluating a wide range of scaffolds, but only the NK1 antagonist Aprepitant (EMENDT) and its prodrug Fosaprepitant (IVEMENDT) have been approved by the Food Drug Administration (FDA) for the treatment of Chemotherapy-Induced and Post-Operative Nausea and Vomiting (CINV and PONV, respectively). While non-peptidic drugs showed limitations, especially in side effect control, peptidic and pseudopeptidic compounds progressively regained attention. Various strategies were implemented to modulate affinity, selectivity and activity of the newly designed ligands. Replacement of canonical amino acids, incorporation of conformational constraints, and fusion with non-peptidic moieties gave rise to families of ligands displaying individual or dual NK1, NK2 and NK3 antagonism, that ultimately were combined with non-neurokinin ligands (such as opioids) to target enhanced biological impact.
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Affiliation(s)
- Charlène Gadais
- Research Group of Organic Chemistry, Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussels, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussels, Pleinlaan 2, B-1050 Brussels, Belgium
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6
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Gach-Janczak K, Piekielna-Ciesielska J, Adamska-Bartłomiejczyk A, Perlikowska R, Kruszyński R, Kluczyk A, Krzywik J, Sukiennik J, Cerlesi MC, Calo G, Wasilewski A, Zielińska M, Janecka A. Synthesis and activity of opioid peptidomimetics with β 2- and β 3-amino acids. Peptides 2017; 95:116-123. [PMID: 28782637 DOI: 10.1016/j.peptides.2017.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 01/08/2023]
Abstract
Morphiceptin (Tyr-Pro-Phe-Pro-NH2) is a selective ligand of the mu opioid receptor, an important target in pain regulation. In this study, morphiceptin was modified at positions 2 or 3 by introduction of β2- or β3-amino acids and additionally in position 1 by replacing Tyr by Dmt (2',6'-dimethyltyrosine), which resulted in obtaining enzymatically stable analogs with mixed opioid receptor affinity profiles. An analog of the sequence Dmt-d-Ala-(R)-β2-1-Nal-Pro-NH2 [Nal=3-(1-naphthyl)-alanine] showed very high activity at the mu and delta receptors in the calcium mobilization functional test but did not cross the artificial membrane imitating the blood-brain barrier. In the in vivo test this analog induced strong antinociceptive effect in the writhing test in mice after intraperitioneal but also oral administration and inhibited diarrhea similarly to loperamide. Therefore, it may become an interesting lead compound in the development of peripherally restricted drugs for the treatment of gastrointestinal disorders.
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Affiliation(s)
| | | | | | | | - Rafał Kruszyński
- Department of X-ray Crystallography and Crystal Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Alicja Kluczyk
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | | | | | - Maria Camilla Cerlesi
- Department of Medical Sciences, Section of Pharmacology and Italian Institute of Neuroscience, University of Ferrara, 44121 Ferrara, Italy
| | - Girolamo Calo
- Department of Medical Sciences, Section of Pharmacology and Italian Institute of Neuroscience, University of Ferrara, 44121 Ferrara, Italy
| | - Andrzej Wasilewski
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Poland
| | - Marta Zielińska
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Poland
| | - Anna Janecka
- Department of Biomolecular Chemistry, Medical University, Lodz, Poland.
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7
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Xu J, Chen X, Wang M, Zheng P, Song BA, Chi YR. Aminomethylation of Enals through Carbene and Acid Cooperative Catalysis: Concise Access to β2-Amino Acids. Angew Chem Int Ed Engl 2015; 54:5161-5. [DOI: 10.1002/anie.201412132] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/09/2015] [Indexed: 11/09/2022]
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8
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Xu J, Chen X, Wang M, Zheng P, Song BA, Chi YR. Aminomethylation of Enals through Carbene and Acid Cooperative Catalysis: Concise Access to β2-Amino Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412132] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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García-González I, Mata L, Corzana F, Jiménez-Osés G, Avenoza A, Busto JH, Peregrina JM. Synthesis and Conformational Analysis of Hybrid α/β-Dipeptides IncorporatingS-Glycosyl-β2,2-Amino Acids. Chemistry 2014; 21:1156-68. [DOI: 10.1002/chem.201405318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 12/27/2022]
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10
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Greco A, Tani S, De Marco R, Gentilucci L. Synthesis and Analysis of the Conformational Preferences of 5-Aminomethyloxazolidine-2,4-dione Scaffolds: First Examples of β2- and β2, 2-Homo-Freidinger Lactam Analogues. Chemistry 2014; 20:13390-404. [PMID: 25182659 DOI: 10.1002/chem.201402519] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 07/07/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Arianna Greco
- Dept. of Chemistry "G. Ciamician", University of Bologna via Selmi 2, 40126, Bologna (Italy), Fax: (+39) 0512099456
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11
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Ilisz I, Grecsó N, Aranyi A, Suchotin P, Tymecka D, Wilenska B, Misicka A, Fülöp F, Lindner W, Péter A. Enantioseparation of β2-amino acids on cinchona alkaloid-based zwitterionic chiral stationary phases. Structural and temperature effects. J Chromatogr A 2014; 1334:44-54. [DOI: 10.1016/j.chroma.2014.01.075] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
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12
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Le Gall E, Léonel E. A Four-Component Reaction Involving In Situ Generated Organometallic Reagents: Straightforward Access to β-Amino Esters. Chemistry 2013; 19:5238-41. [DOI: 10.1002/chem.201300345] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Indexed: 11/05/2022]
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13
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Hernández-Vázquez LG, Leyva MA, Metta-Magaña AJ, Escalante J. Microwave-Assisted Synthesis ofβ-Lactams and Cyclo-β-dipeptides. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Ben Hamidane H, Vorobyev A, Larregola M, Lukaszuk A, Tourwé D, Lavielle S, Karoyan P, Tsybin Y. Radical Stability Directs Electron Capture and Transfer Dissociation of β-Amino Acids in Peptides. Chemistry 2010; 16:4612-22. [DOI: 10.1002/chem.200902480] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Indexed: 11/08/2022]
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15
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β-Amino acid substitutions and structure-based CoMFA modeling of hepatitis C virus NS3 protease inhibitors. Bioorg Med Chem 2008; 16:5590-605. [DOI: 10.1016/j.bmc.2008.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 03/28/2008] [Accepted: 04/01/2008] [Indexed: 11/19/2022]
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16
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Bandala Y, Aviña J, González T, Rivero IA, Juaristi E. Solid phase synthesis of novelα/β-tetrapeptides, electrospray ionization mass spectrometric evaluation of their metal cation complexation behavior, and conformational analysis using density functional theory (DFT). J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Baruah PK, Gonnade R, Rajamohanan PR, Hofmann HJ, Sanjayan GJ. BINOL-Based FoldamersAccess to Oligomers with Diverse Structural Architectures. J Org Chem 2007; 72:5077-84. [PMID: 17564462 DOI: 10.1021/jo070396y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article, we report on the synthesis and conformation of a new family of aromatic oligoamide foldamers based on binaphthol (BINOL) monomers. A series of oligomers with differing chirality of the individual BINOL building blocks and mixed sequences of alternate BINOL and pyridyl building blocks has been synthesized and structurally characterized. NMR and quantum chemical calculations on the basis of ab initio MO theory were performed to obtain insight into the conformational features of these oligomers. It is shown that the combination of these inherently chiral aromatic building blocks provides a novel access to a wide variety of conformationally ordered synthetic oligomers with diverse and dazzling structural architectures distinct from those classically observed.
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Affiliation(s)
- Pranjal K Baruah
- Division of Organic Synthesis, Central Material Characterization Division, and Central NMR Facility, National Chemical Laboratory, Doctor Homi Bhabha Road, Pune 411 008, India
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18
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Angelici G, Luppi G, Kaptein B, Broxterman QB, Hofmann HJ, Tomasini C. Synthesis and Secondary Structure of Alternate α,β-Hybrid Peptides Containing Oxazolidin-2-one Moieties. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700134] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Seebach D, Jaun B, Sebesta R, Mathad R, Flögel O, Limbach M, Sellner H, Cottens S. Synthesis, and Helix or Hairpin-Turn Secondary Structures of ‘Mixed’α/β-Peptides Consisting of Residues with Proteinogenic Side Chains and of 2-Amino-2-methylpropanoic Acid (Aib). Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690176] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Norgren AS, Büttner F, Prabpai S, Kongsaeree P, Arvidsson PI. β2-Amino Acids in the Design of Conformationally Homogeneous cyclo-Peptide Scaffolds. J Org Chem 2006; 71:6814-21. [PMID: 16930031 DOI: 10.1021/jo060854n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we report studies on the influence of chiral beta(2)-amino acids in the design of conformationally homogeneous cyclic tetrapeptide scaffolds. The cyclic alpha-tetrapeptide cyclo(-Phe-D-Pro-Lys-Phe-) (1) and its four mixed analogues, having one of the alpha-Phe replaced by either an (S)- or an (R)-beta(2)hPhe residue (i.e., cyclo(-(R)-beta(2)hPhe-D-Pro-Lys-Phe) (2a), cyclo(-(S)-beta(2)hPhe-D-Pro-Lys-Phe-) (2b), cyclo(-Phe-D-Pro-Lys-(R)-beta(2)hPhe-) (3a), and cyclo(-Phe-D-Pro-Lys-(R)-beta(2)hPhe-) (3b)), were all synthesized through solid-phase procedures followed by solution-phase cyclization. Initially, all five cyclo-peptides were analyzed by (1)H NMR spectroscopic studies in different solvents and at variable temperatures. Subsequently, a detailed 2D NMR spectroscopic analysis of three of the mixed peptides in water was performed, and the information thus extracted was used as restraints in a computational study on the peptides' conformational preference. An X-ray crystallographic study on the side chain-protected (Boc) 2a revealed the solid-state structure of this peptide. The results presented herein, together with previous literature data on beta(3)-amino acid residues, conclusively demonstrate the potential of beta-amino acids in the design of conformationally homogeneous cyclic peptides that are homologous to peptides with known applications in biomedicinal chemistry and as molecular receptors.
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Affiliation(s)
- Anna S Norgren
- Department of Biochemistry and Organic Chemistry, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
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21
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Moumne R, Lavielle S, Karoyan P. Efficient Synthesis of β2-Amino Acid by Homologation of α-Amino Acids Involving the Reformatsky Reaction and Mannich-Type Imminium Electrophile. J Org Chem 2006; 71:3332-4. [PMID: 16599644 DOI: 10.1021/jo060316a] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Development of new methods for the synthesis of beta-amino acids is important as polymers of these compounds are promising peptidomimetic candidates in medicinal chemistry. We report here our findings on a new and highly efficient general strategy for the synthesis of beta2-amino acids by homologation of alpha-amino acids, involving the Reformatsky reaction and Mannich-type imminium electrophile.
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Affiliation(s)
- Roba Moumne
- Synthèses, Structures et Fonctions des Molécules Bioactives, CNRS/UMR 7613, Université Pierre et Marie Curie, 4, Place Jussieu, 75252, Paris Cedex 05, France
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22
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Aschi M, Mollica A, Lucente G, Paradisi MP, Mazza F. Conformational properties of β-residue-containing oligopeptides in apolar solvent. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Abstract
Intrinsic conformational characteristics of beta-peptides built up from simple achiral and chiral beta-amino acid residues (i.e., HCO-beta-Ala-NH2, HCO-beta-Abu-NH2) were studied using quantum chemical calculations and 1H-NMR spectroscopy. A conformer-based systematic and uniform nomenclature was introduced to differentiate conformers. Geometry optimizations were performed on all homoconformers of both HCO-(beta-Ala)(k)-NH2 and HCO-(beta-Abu)(k)-NH2 (1 < or = k < or = 6) model systems at the RHF/3-21G and RHF/6-311++G(d, p) levels of theory. To test for accuracy and precision, additional computations were carried out at several levels of theory [e.g., RHF/6-31G(d), and B3LYP/6-311++G(d, p)]. To display the folding preference, the relative stability of selected conformers as function of the length of the polypeptide chain was determined. Ab initio population distribution of hexapeptides and the conformational ensemble of synthetic models composed of beta-Ala and beta-Abu studied using 1H-NMR in different solvents were compared at a range of temperatures. Helical preference induced by various steric effects of nonpolar side chains was tested using higher level ab initio methods for well-known model systems such as: HCO-(beta-HVal-beta-HAla-beta-HLeu)2-NH2, HCO-(ACHC)6-NH2, HCO-(trans-ACPC)6-NH2, and HCO-(cis-ACPC)6-NH2. The relative stabilities determined by theoretical methods agreed well with most experimental data, supporting the theory that the local conformational preference influenced by steric effects is a key determining factor of the global fold both in solution and in the gas phase.
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Affiliation(s)
- Tamás Beke
- Department of Organic Chemistry, Eötvös L. Univ., P.O. Box 32, H-1518 Budapest 112, Hungary
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24
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Disney MD, Hook DF, Namoto K, Seeberger PH, Seebach D. N-Linked Glycosylatedβ-Peptides Are Resistant to Degradation by Glycoamidase A. Chem Biodivers 2005; 2:1624-34. [PMID: 17191959 DOI: 10.1002/cbdv.200590132] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Beta-peptides are resistant to degradation by a variety of proteolytic enzymes that rapidly degrade natural alpha-peptides. This is one of many characteristics that make beta-peptides an attractive class of compounds for drug discovery efforts. To further understand the molecular recognition properties of beta-peptides and the ability of enzymes to degrade them, we have synthesized a series of N-linked glycosylated beta- and alpha-peptides, and tested their stability towards a glycosidase. We found that glyco-beta-peptides that contain N-acetylglucosamine (1) or N,N-diacetylchitobiose (2) are completely stable to degradation by glycoamidase A. In comparison, the glyco-alpha-peptides 3 and 4 containing N-acetylglucosamine or N,N-diacetylchitobiose are degraded. Inhibition experiments using increasing concentrations of a glyco-beta-peptide fail to inhibit degradation of the corresponding glyco-alpha-peptide, even when the glyco-beta-peptide is at a 128-fold higher concentration than the glyco-alpha-peptide. Evidently, the glyco-beta-peptides have a much weaker affinity for the active site of the glycosidase than the corresponding glyco-alpha-peptide. These and the results with proteolytic enzymes suggest that the additional CH(2) group introduced into the alpha-amino acid residues causes beta-peptides not to be recognized by hydrolytic enzymes. The results described herein suggest the potential of beta-peptides that are functionalized with carbohydrates for biological and biomedical investigations, without having to be concerned about the carbohydrate being removed.
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Affiliation(s)
- Matthew D Disney
- Laboratorium für Organische Chemie, Department für Chemie und Angewandte Biowissenschaften, Eidgenössische Technische Hochschule Zürich, ETH Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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25
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Sagan S, Quancard J, Lequin O, Karoyan P, Chassaing G, Lavielle S. Conformational analysis of the C-terminal Gly-Leu-Met-NH2 tripeptide of substance P bound to the NK-1 receptor. ACTA ACUST UNITED AC 2005; 12:555-65. [PMID: 15911376 DOI: 10.1016/j.chembiol.2005.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 03/21/2005] [Indexed: 11/20/2022]
Abstract
We examined the effect of simultaneously incorporating proline or proline-amino acid chimeras in positions 9, 10, and/or 11 of substance P, on the affinity for the two NK-1 binding sites and on second-messenger activation. Because these 3-substituted prolines constrain not only the (phi,psi) values of the peptide backbone, but also the chi space of the amino acid side chain, we were able to gather data on the structural requirements for high-affinity binding to the NK-1 receptor. We were able to confirm that this C-terminal component is crucial and that it should adopt an extended conformation close to a polyproline II structure when bound to the receptor. The partial additivity of these constraints, more specifically, for the NK-1M site, suggests that the peptide backbone flexibility around the hinge-point residue Gly9 is essential to subtly position crucial side chains.
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Affiliation(s)
- Sandrine Sagan
- Synthèse, Structure et Fonction de Molécules Bioactives, Unite Mixte de Recherche 7613, Centre National de la Recherche Scientifique-Université Paris 6, Paris, France
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Hook DF, Bindschädler P, Mahajan YR, Sebesta R, Kast P, Seebach D. The Proteolytic Stability of ‘Designed’β-Peptides Containingα-Peptide-Bond Mimics and of Mixedα,β-Peptides: Application to the Construction of MHC-Binding Peptides. Chem Biodivers 2005; 2:591-632. [PMID: 17192006 DOI: 10.1002/cbdv.200590039] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Whereas alpha-peptides are rapidly degraded in vivo and in vitro by a multitude of peptidases, substrates constructed entirely of or incorporating homologated alpha-amino acid (i.e., beta-amino acid) units exhibit a superior stability profile. Efforts made so far to proteolytically hydrolyze a beta-beta peptide bond have not proved fruitful; a study aimed at breaching this proteolytic stability is discussed here. A series of such bonds have been designed with side-chain groups similar in relative positions (constitution) and three-dimensional arrangements (configuration) as found about alpha-peptidic amide bonds. Increasing the prospect for degradation would permit the tuning of beta-peptide stability; here, however, no cleavage was observed (1, 2, 4-6, Table 1). Peptides comprised of alpha- and beta-amino acids (mixed alpha,beta-peptides, 8-11) are expected to benefit from both recognition by a natural receptor and a high level of proteolytic stability, ideal characteristics of pharmacologically active compounds. Beta3-peptides containing alpha-amino acid moieties at the N-terminus are degraded, albeit slowly, by several peptidases. Of particular interest is the ability of pronase to cleave an alpha-beta peptide bond, namely that of alphaAla-beta3 hAla. Significantly, successful hydrolysis is independent of the configuration of the beta-amino acid. Some of the alpha,beta-peptides discussed here are being investigated for their binding affinities to class I MHC proteins. The computer-programming steps required to prepare alpha,beta-peptides on an automated peptide synthesizer are presented.
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Affiliation(s)
- David F Hook
- Departement für Chemie und Angewandte Biowissenschaften, Laboratorium für Organische Chemie der Eidgenössischen Technischen Hochschule, ETH Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich
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Claudel S, Tasseau O, Sagan S, Grison C, Coutrot P, Lavielle S. Incorporation of vinylogous scaffolds in the C-terminal tripeptide of substance P. ACTA ACUST UNITED AC 2005; 64:186-93. [PMID: 15485556 DOI: 10.1111/j.1399-3011.2004.00180.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycine-9 and leucine-10 of substance P (SP) are critical for (NK)-1 receptor recognition and agonist activity. Propsi(Z)-CH=CH(CH3)-CONH)Leu (or Met) and Propsi((E)-CH=CH(CH3)-CONH)Leu (or Met) have been introduced in the sequence of SP, in order to restrict the conformational flexibility of the C-terminal tripeptide, Gly-Leu-Met-NH2, of SP. Propsi((Z)-CH=C(CH2CH(CH3)2)-CONH)Met-NH2, with an isobutyl substituent to mimic the Leu side-chain, was also incorporated in place of the C-terminal tripeptide. The substituted-SP analogs were tested for their affinity to human NK-1 receptor specific binding sites (NK-1M and NK-1m) and their potency to stimulate adenylate cyclase and phospholipase C in Chinese Hamster ovary (CHO) cells transfected with the human NK-1 receptor. The most potent SP analogs [Pro9psi((Z)CH=C(CH3)CONH)Leu10]SP and [Pro9psi ((E)CH=C(CH3)CONH)Leu10]SP, are about 100-fold less potent than SP on both binding sites and second messenger pathways. These vinylogous (Z)- or (E)-CH=C(CH3)- or (Z)-CH=C(CH2CH(CH3)2) moieties hamper the correct positioning of the C-terminal tripeptide of SP within both the NK-1M- and NK-1m-specific binding sites. The origin of these lower potencies is related either to an incorrect peptidic backbone conformation and/or an unfavorable receptor interaction of the methyl or isobutyl group.
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Affiliation(s)
- S Claudel
- Laboratoire de Chimie Organique Biomoléculaire, Institut Nancéien de Chimie Moléculaire, Université H. Poincaré, Vandoeuvre-les-Nancy Cedex, France
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Mezzache S, Pepe C, Karoyan P, Fournier F, Tabet JC. Proton affinity of diastereoisomers of modified prolines using the kinetic method and density functional theory calculations: role of the cis/trans substituent on the endo/exo ring conformation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:2279-83. [PMID: 16021616 DOI: 10.1002/rcm.2049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The proton affinity (PA) of cis/trans-3-prolinoleucines and cis/trans-3-prolinoglutamic acids have been studied by the kinetic method and density functional theory (DFT) calculations. Several conformations of the neutral and the protonated modified prolines, in particular the endo and exo ring conformations, were analyzed with respect to their contribution to the PA values. When the substituent is an alkyl, both the diastereoisomers have the same PA value. However, the PA values for the diastereoisomers are different when the substituted chain contains functional groups (e.g. a carboxyl group). This variation in PA values could be attributed to the existence of intramolecular hydrogen bonds.
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Affiliation(s)
- S Mezzache
- Synthèse, Structure et Fonction de Molécules Bioactives, CNRS, UMR 7613, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris cedex 05, France
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Giordano C, Nalli M, Paradisi MP, Sansone A, Lucente G, Spisani S. Beta-peptido sulfonamides: for-Met-Leu-Phe-OMe analogues containing taurine and chiral beta-amino-ethanesulfonic acid residues. ACTA ACUST UNITED AC 2004; 59:953-63. [PMID: 15598430 DOI: 10.1016/j.farmac.2004.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Accepted: 07/27/2004] [Indexed: 11/21/2022]
Abstract
A series of new beta-peptido sulfonamides, related to the chemotactic tripeptide fMLF-OMe, has been synthesized. The examined 1a,b-7a,b models contain the achiral -HN-(CH(2))(2)-SO(2)- taurine (Tau) residue or the chiral -HN-CH(nBu)-CH(2)-SO(2)- and -HN-CH(iBu)-CH(2)-SO(2)- residues, corresponding to the beta-aminocarboxylic acid counterparts beta(3)-HNle and beta(3)-HLeu, respectively. The biological activity of the new analogues has been determined on human neutrophils and compared with that of the reference ligand as well as that of the previously studied related models. The results are analyzed in terms of structure-activity relationships. The conformational preferences of the new tripeptides 1b and 2b, containing a central chiral beta-amino-ethanesulfonic acid residue, have also been discussed.
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Affiliation(s)
- Cesare Giordano
- Istituto di Chimica Biomolecolare del CNR, Sezione di Roma c/o Dipartimento di Studi Farmaceutici, Università degli Studi di Roma La Sapienza, Piazzale A. Moro 5, 00185 Rome, Italy
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Hook DF, Gessier F, Noti C, Kast P, Seebach D. Probing the Proteolytic Stability of β-Peptides Containing α-Fluoro- and α-Hydroxy-β-Amino Acids. Chembiochem 2004; 5:691-706. [PMID: 15122642 DOI: 10.1002/cbic.200300827] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
One of the benefits of beta-peptides as potential candidates for biological applications is their stability against common peptidases. Attempts have been made to rationalize this stability by altering the electron availability of a given amide carbonyl bond through the introduction of polar substituents at the alpha-position of a single beta-amino acid. Such beta-amino acids (beta-homoglycine, beta-homoalanine), containing one or two fluorine atoms or a hydroxy group in the alpha-position, were prepared in enantiopure form. A versatile method for preparing these alpha-fluoro-beta-amino acids by the homologation of appropriate alpha-amino acids and C-OH->C-F or C=O-->CF(2) substitution with DAST, is described. Consequently, a series of beta-peptides possessing an electronically modified residue at the N terminus or embedded within the chain was synthesized, and their proteolytic stability was investigated against a selection of enzymes. All ten beta-peptides tested were resilient to proteolysis. Introducing a polar, sterically undemanding group, into the alpha-position of beta-amino acids in a beta-peptide chain does not appear to facilitate localized or general enzymatic degradation.
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Affiliation(s)
- David F Hook
- Laboratorium für Organische Chemie, Eidgenössischen Technischen Hochschule, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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Synthesis of (R) and (S) enantiomers of Fmoc-protected 1,2,4-oxadiazole-containing β3-amino acids from Fmoc-(R)-β-HAsp(OtBu)-OH. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)01471-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Quancard J, Karoyan P, Sagan S, Convert O, Lavielle S, Chassaing G, Lequin O. Characterization of the bioactive conformation of the C-terminal tripeptide Gly-Leu-Met-NH2 of substance P using [3-prolinoleucine10]SP analogues. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:2869-78. [PMID: 12823557 DOI: 10.1046/j.1432-1033.2003.03665.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Residue Leu10 of substance P (SP) is critical for NK-1 receptor recognition and agonist activity. In order to probe the bioactive conformation of this residue, cis- and trans-3-substituted prolinoleucines were introduced in position 10 of SP. The substituted SP analogues were tested for their affinity to human NK-1 receptor specific binding sites (NK-1M and NK-1m) and their potency to stimulate adenylate cyclase and phospholipase C in CHO cells transfected with the human NK-1 receptor. [trans-3-prolinoleucine10]SP retained affinity and potency similar to SP whereas [cis-3-prolinoleucine10]SP shows dramatic loss of affinity and potency. To analyze the structural implications of these biological results, the conformational preferences of the SP analogues were analyzed by NMR spectroscopy and minimum-energy conformers of Ac-cis-3-prolinoleucine-NHMe, Ac-trans-3-prolinoleucine-NHMe and model dipeptides were generated by molecular mechanics calculations. From NMR and modeling studies it can be proposed that residue Leu10 of SP adopts a gauche(+) conformation around the chi1 angle and a trans conformation around the chi2 angle in the bioactive conformation. Together with previously published results, our data indicate that the C-terminal SP tripeptide should preferentially adopt an extended conformation or a PPII helical structure when bound to the receptor.
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Affiliation(s)
- Jean Quancard
- UMR 7613 Paris 6-CNRS, Université Pierre et Marie Curie, Paris, France
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