51
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Dutt Konar A, Vass E, Hollósi M, Majer Z, Grüber G, Frese K, Sewald N. Conformational properties of secondary amino acids: replacement of pipecolic acid by N-methyl-l-alanine in efrapeptin C. Chem Biodivers 2013; 10:942-51. [PMID: 23681735 DOI: 10.1002/cbdv.201300086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Indexed: 11/08/2022]
Abstract
The efrapeptins, a family of naturally occurring peptides with inhibitory activities against ATPases, contain several α,α-disubstituted α-amino acids such as α-aminoisobutyric acid (Aib) or isovaline (Iva) besides pipecolic acid (Pip), β-Ala, Leu, Gly, and a C-terminal heterocyclic residue. Secondary α-amino acids such as proline are known to stabilize discrete conformations in peptides. A similar influence is ascribed to N-alkyl α-amino acids. We synthesized two efrapeptin C analogs with replacement of Pip by N-methyl-L-alanine (MeAla) using a combination of solid- and solution-phase techniques in a fragment-condensation strategy to compare the conformational bias of both secondary amino acids. The solution conformation was investigated by vibrational circular dichroism (VCD) to probe whether the analogs adopt a 310 -helical conformation. The MeAla-containing analogs [MeAla(1,3) ]efrapeptin C and [MeAla(1,3,11) ]efrapeptin C inhibit ATP hydrolysis by the A3 B3 complex of A1 A0 -ATP synthase from Methanosarcina mazei Gö1.
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52
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Rigger L, Schmidt RL, Holman KM, Simonović M, Micura R. The synthesis of methylated, phosphorylated, and phosphonated 3'-aminoacyl-tRNA(Sec) mimics. Chemistry 2013; 19:15872-8. [PMID: 24127424 DOI: 10.1002/chem.201302188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Indexed: 11/12/2022]
Abstract
The twenty first amino acid, selenocysteine (Sec), is the only amino acid that is synthesized on its cognate transfer RNA (tRNA(Sec)) in all domains of life. The multistep pathway involves O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS), an enzyme that catalyzes the terminal chemical reaction during which the phosphoseryl-tRNA(Sec) intermediate is converted into selenocysteinyl-tRNA(Sec). The SepSecS architecture and the mode of tRNA(Sec) recognition have been recently determined at atomic resolution. The crystal structure provided valuable insights that gave rise to mechanistic proposals that could not be validated because of the lack of appropriate molecular probes. To further improve our understanding of the mechanism of the biosynthesis of selenocysteine in general and the mechanism of SepSecS in particular, stable tRNA(Sec) substrates carrying aminoacyl moieties that mimic particular reaction intermediates are needed. Here, we report on the accurate synthesis of methylated, phosphorylated, and phosphonated serinyl-derived tRNA(Sec) mimics that contain a hydrolysis-resistant ribose 3'-amide linkage instead of the natural ester bond. The procedures introduced allow for efficient site-specific methylation and/or phosphorylation directly on the solid support utilized in the automated RNA synthesis. For the preparation of (S)-2-amino-4-phosphonobutyric acid-oligoribonucleotide conjugates, a separate solid support was generated. Furthermore, we developed a three-strand enzymatic ligation protocol to obtain the corresponding full-length tRNA(Sec) derivatives. Finally, we developed an electrophoretic mobility shift assay (EMSA) for rapid, qualitative characterization of the SepSecS-tRNA interactions. The novel tRNA(Sec) mimics are promising candidates for further elucidation of the biosynthesis of selenocysteine by X-ray crystallography and other biochemical approaches, and could be attractive for similar studies on other tRNA-dependent enzymes.
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Affiliation(s)
- Lukas Rigger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck (Austria), Fax: (+43) 512 507 57799
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53
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54
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Roodbeen R, Jensen KJ. Synthesis of N-methylated peptides: on-resin methylation and microwave-assisted couplings. Methods Mol Biol 2013; 1047:141-149. [PMID: 23943484 DOI: 10.1007/978-1-62703-544-6_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
N-methylation may positively influence the pharmacokinetic properties of peptides by improving oral availability and in vivo half-life. Additionally, target affinity and specificity may be improved. Here, we describe the solid-phase N-methylation of peptides using direct alkylation. This method allows a rapid N-methyl scan of synthetic, bioactive peptides. Additionally, a microwave-enhanced method for the difficult coupling onto the methylated N terminus is provided.
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Affiliation(s)
- Renée Roodbeen
- Department of Chemistry, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
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55
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Chatterjee J, Rechenmacher F, Kessler H. N-methylation of peptides and proteins: an important element for modulating biological functions. Angew Chem Int Ed Engl 2012; 52:254-69. [PMID: 23161799 DOI: 10.1002/anie.201205674] [Citation(s) in RCA: 330] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Indexed: 11/06/2022]
Abstract
N-Methylation is one of the simplest chemical modifications often occurring in peptides and proteins of prokaryotes and higher eukaryotes. Over years of evolution, nature has employed N-methylation of peptides as an ingenious technique to modulate biological function, often as a mode of survival through the production of antibiotics. This small structural change can not only mobilize large protein complexes (as in the histone methylation), but also inhibits the action of enzymes by selective recognition of protein-protein interaction surfaces. In recent years through the advancement in synthetic approaches, the potential of N-methylation has begun to be revealed, not only in modulating biological activity and selectivity as well as pharmacokinetic properties of peptides, but also in delivering novel drugs. Herein, we summarize the current knowledge of the versatility of N-methylation in modulating biological, structural, and pharmacokinetic properties of peptides.
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Affiliation(s)
- Jayanta Chatterjee
- Genome biology unit, European Molecular Biology Laboratory, Heidelberg, Germany
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56
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Chatterjee J, Rechenmacher F, Kessler H. N-Methylierung von Peptiden und Proteinen: ein wichtiges Element für die Regulation biologischer Funktionen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205674] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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57
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Roodbeen R, Pedersen SL, Hosseini M, Jensen KJ. Microwave Heating in the Solid-Phase Synthesis ofN-Methylated Peptides: When Is Room Temperature Better? European J Org Chem 2012. [DOI: 10.1002/ejoc.201201050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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58
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Haj-Yahya M, Eltarteer N, Ohayon S, Shema E, Kotler E, Oren M, Brik A. N-methylation of isopeptide bond as a strategy to resist deubiquitinases. Angew Chem Int Ed Engl 2012; 51:11535-9. [PMID: 23065695 DOI: 10.1002/anie.201205771] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/23/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Mahmood Haj-Yahya
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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59
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Haj-Yahya M, Eltarteer N, Ohayon S, Shema E, Kotler E, Oren M, Brik A. N-Methylation of Isopeptide Bond as a Strategy to Resist Deubiquitinases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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60
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Georghiou G, Kleiner RE, Pulkoski-Gross M, Liu DR, Seeliger MA. Highly specific, bisubstrate-competitive Src inhibitors from DNA-templated macrocycles. Nat Chem Biol 2012; 8:366-74. [PMID: 22344177 PMCID: PMC3307835 DOI: 10.1038/nchembio.792] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/01/2011] [Indexed: 01/21/2023]
Abstract
Protein kinases are attractive therapeutic targets, but their high sequence and structural conservation complicates the development of specific inhibitors. We recently discovered from a DNA-templated macrocycle library inhibitors with unusually high selectivity among Src-family kinases. Starting from these compounds, we developed and characterized in molecular detail potent macrocyclic inhibitors of Src kinase and its cancer-associated gatekeeper mutant. We solved two co-crystal structures of macrocycles bound to Src kinase. These structures reveal the molecular basis of the combined ATP- and substrate peptide-competitive inhibitory mechanism and the remarkable kinase specificity of the compounds. The most potent compounds inhibit Src activity in cultured mammalian cells. Our work establishes that macrocycles can inhibit protein kinases through a bi-substrate competitive mechanism with high potency and exceptional specificity, reveals the precise molecular basis for their desirable properties, and provides new insights into the development of Src-specific inhibitors with potential therapeutic relevance.
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Affiliation(s)
- George Georghiou
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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61
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Abstract
This protocol presents a detailed description of the synthesis of N-methylated cyclic peptides. N-methylation is a powerful technique to modulate the physicochemical properties of peptides by introducing one or more methyl groups into the peptidic amide bonds. Together with peptide cyclization, this procedure confers unprecedented pharmacokinetic properties to the peptides, including metabolic stability, membrane permeability and even oral bioavailability. Here we describe two simplified methods of N-methylation of linear peptides on solid supports, which can be performed in less than 2 h and are applicable to any amino acid. Finally, we also describe two methods of peptide cyclization, which can be used to obtain the N-methylated cyclic peptide and which are not limited to specific peptide sequences. With this protocol, multiply N-methylated cyclic peptides can be synthesized in as little as 4-5 d.
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Affiliation(s)
- Jayanta Chatterjee
- Institute for Advanced Study and Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Garching, Germany
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62
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Pedersen SL, Tofteng AP, Malik L, Jensen KJ. Microwave heating in solid-phase peptide synthesis. Chem Soc Rev 2012; 41:1826-44. [DOI: 10.1039/c1cs15214a] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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63
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Marcucci E, Tulla-Puche J, Albericio F. Solid-Phase Synthesis of NMe-IB-01212, a Highly N-Methylated Cyclic Peptide. Org Lett 2011; 14:612-5. [DOI: 10.1021/ol203231q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eleonora Marcucci
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
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64
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Demmer O, Dijkgraaf I, Schumacher U, Marinelli L, Cosconati S, Gourni E, Wester HJ, Kessler H. Design, synthesis, and functionalization of dimeric peptides targeting chemokine receptor CXCR4. J Med Chem 2011; 54:7648-62. [PMID: 21905730 DOI: 10.1021/jm2009716] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The chemokine receptor CXCR4 is a critical regulator of inflammation and immune surveillance, and it is specifically implicated in cancer metastasis and HIV-1 infection. On the basis of the observation that several of the known antagonists remarkably share a C(2) symmetry element, we constructed symmetric dimers with excellent antagonistic activity using a derivative of a cyclic pentapeptide as monomer. To optimize the binding affinity, we investigated the influence of the distance between the monomers and the pharmacophoric sites in the synthesized constructs. The affinity studies in combination with docking computations support a two-site binding model. In a final step, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) was introduced as chelator for (radio-)metals, thus allowing to exploit these compounds as a new group of CXCR4-binding peptidic probes for molecular imaging and endoradiotherapeutic purposes. Both the DOTA conjugates and some of their corresponding metal complexes retain good CXCR4 affinity, and one (68)Ga labeled compound was studied as PET tracer.
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Affiliation(s)
- Oliver Demmer
- Institute for Advanced Study, Technische Universität München , Lichtenbergstrasse 4, D-85748 Garching, Germany
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65
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Tal-Gan Y, Freeman NS, Klein S, Levitzki A, Gilon C. Metabolic stability of peptidomimetics: N-methyl and aza heptapeptide analogs of a PKB/Akt inhibitor. Chem Biol Drug Des 2011; 78:887-92. [PMID: 21824328 DOI: 10.1111/j.1747-0285.2011.01207.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Linear peptides suffer from poor pharmacokinetic and pharmacodynamic properties. Peptidomimetics are designed to overcome these pharmacological drawbacks while maintaining the biological effects of the parent peptides. Aza-peptides, in which an alpha carbon is replaced with nitrogen, are promising peptidomimetic analogs; however, little is known about the stability of these analogs toward enzymatic degradation. We performed systematic aza and N-methyl scans of a PKB/Akt inhibitor, PTR6154. We evaluated the stability of the aza-scan and N-methyl scan libraries toward enzymatic degradation by trypsin/chymotrypsin. Our results indicate that the modification site is important for metabolic stability and that aza-peptides have a more global effect than N-methylation, affecting cleavage sites distant from the modification site.
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Affiliation(s)
- Yftah Tal-Gan
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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66
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Erhöhung der αvβ3-Selektivität des Angiogenese hemmenden Wirkstoffs Cilengitid durch N-Methylierung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102971] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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67
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Mas-Moruno C, Beck JG, Doedens L, Frank AO, Marinelli L, Cosconati S, Novellino E, Kessler H. Increasing αvβ3 selectivity of the anti-angiogenic drug cilengitide by N-methylation. Angew Chem Int Ed Engl 2011; 50:9496-500. [PMID: 21948451 DOI: 10.1002/anie.201102971] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/27/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Carlos Mas-Moruno
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, 85747 Garching, Germany
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68
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Chatterjee J, Laufer B, Beck JG, Helyes Z, Pintér E, Szolcsányi J, Horvath A, Mandl J, Reubi JC, Kéri G, Kessler H. N-Methylated sst2 Selective Somatostatin Cyclic Peptide Analogue as a Potent Candidate for Treating Neurogenic Inflammation. ACS Med Chem Lett 2011; 2:509-14. [PMID: 24900340 DOI: 10.1021/ml200032v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/04/2011] [Indexed: 11/29/2022] Open
Abstract
A focused multiply N-methylated library of a cyclic hexapeptidic somatostatin analogue: MK678 cyclo(-MeAYwKVF-) was generated, which resulted in the unexpected observation of an efficacious tetra-N-methylated analogue, cyclo(-MeAYMewMeKVMeF-) with a potent inhibitory action on sensory neuropeptide release in vitro and on acute neurogenic inflammatory response in vivo. The analogue shows selectivity toward somatostatin receptor subtype 2 (sst2). Extensive 2D NMR spectroscopy and molecular dynamics simulation revealed the solution conformation of the analogue, which can be adopted as a lead for the further structure-activity relationship studies targeting neurogenic inflammation.
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Affiliation(s)
- Jayanta Chatterjee
- Institute for Advanced Study and Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Burkhardt Laufer
- Institute for Advanced Study and Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Johannes G. Beck
- Institute for Advanced Study and Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, University of Pécs, H-7624, Hungary
| | - Erika Pintér
- Department of Pharmacology and Pharmacotherapy, University of Pécs, H-7624, Hungary
| | - János Szolcsányi
- Department of Pharmacology and Pharmacotherapy, University of Pécs, H-7624, Hungary
| | - Aniko Horvath
- Pathobiochemistry Research Group of Hungarian Academy of Sciences in Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, H-1094, Hungary
| | - Jozsef Mandl
- Pathobiochemistry Research Group of Hungarian Academy of Sciences in Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, H-1094, Hungary
| | - Jean C. Reubi
- Division of Cell Biology and Experimental Cancer Research, Institute of Pathology, University of Bern, Bern, CH-3010 Switzerland
| | - György Kéri
- Pathobiochemistry Research Group of Hungarian Academy of Sciences in Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, H-1094, Hungary
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
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69
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Ovadia O, Greenberg S, Chatterjee J, Laufer B, Opperer F, Kessler H, Gilon C, Hoffman A. The effect of multiple N-methylation on intestinal permeability of cyclic hexapeptides. Mol Pharm 2011; 8:479-87. [PMID: 21375270 DOI: 10.1021/mp1003306] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent progress in peptide synthesis simplified the synthesis of multiple N-methylation of peptides. To evaluate how multiple N-methylation affects the bioavailability of peptides, a poly alanine cyclic hexapeptide library (n = 54), varying in the number of N-methyl (N-Me) groups (1-5 groups) and their position, was synthesized. The peptides were evaluated for their intestinal permeability in vitro using the Caco-2 model. Further evaluation of the transport route of chosen analogues was performed using rat excised viable intestinal tissue, a novel colorimetric liposomal model and the parallel artificial membrane permeability assay (PAMPA). While most members were found to have poor permeability (permeability coefficient, P(app) < 1 x 10⁻⁶ cm/s, lower than mannitol, the marker for paracellular permeability), 10 analogues were found to have high Caco-2 permeability, (P(app) > 1 x 10⁻⁵ cm/s, similar to testosterone, a marker of transcellular permeability). No correlation was found between the number of N-methylated groups and the enhanced permeability. However, 9/10 permeable peptides in the Caco-2 model included an N-Me placed adjacently to the D-Ala position. While the exact transport route was not fully characterized, the data suggests a facilitated diffusion. It can be concluded that multiple N-methylation of peptides may improve intestinal permeability, and therefore can be utilized in the design of orally available peptide-based therapeutics.
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Affiliation(s)
- Oded Ovadia
- The Institute of Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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70
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Zheng J, Liu C, Sawaya MR, Vadla B, Khan S, Woods RJ, Eisenberg D, Goux WJ, Nowick JS. Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide. J Am Chem Soc 2011; 133:3144-57. [PMID: 21319744 PMCID: PMC3048834 DOI: 10.1021/ja110545h] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This paper describes studies of a series of macrocyclic β-sheet peptides 1 that inhibit the aggregation of a tau-protein-derived peptide. The macrocyclic β-sheet peptides comprise a pentapeptide "upper" strand, two δ-linked ornithine turn units, and a "lower" strand comprising two additional residues and the β-sheet peptidomimetic template "Hao". The tau-derived peptide Ac-VQIVYK-NH(2) (AcPHF6) aggregates in solution through β-sheet interactions to form straight and twisted filaments similar to those formed by tau protein in Alzheimer's neurofibrillary tangles. Macrocycles 1 containing the pentapeptide VQIVY in the "upper" strand delay and suppress the onset of aggregation of the AcPHF6 peptide. Inhibition is particularly pronounced in macrocycles 1a, 1d, and 1f, in which the two residues in the "lower" strand provide a pattern of hydrophobicity and hydrophilicity that matches that of the pentapeptide "upper" strand. Inhibition varies strongly with the concentration of these macrocycles, suggesting that it is cooperative. Macrocycle 1b containing the pentapeptide QIVYK shows little inhibition, suggesting the possibility of a preferred direction of growth of AcPHF6 β-sheets. On the basis of these studies, a model is proposed in which the AcPHF6 amyloid grows as a layered pair of β-sheets and in which growth is blocked by a pair of macrocycles that cap the growing paired hydrogen-bonding edges. This model provides a provocative and appealing target for future inhibitor design.
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Affiliation(s)
- Jing Zheng
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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71
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Fang WJ, Yakovleva T, Aldrich JV. A convenient approach to synthesizing peptide C-terminal N-alkyl amides. Biopolymers 2011; 96:715-22. [PMID: 22252422 PMCID: PMC3924563 DOI: 10.1002/bip.21600] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 01/03/2011] [Accepted: 01/10/2011] [Indexed: 11/10/2022]
Abstract
Peptide C-terminal N-alkyl amides have gained more attention over the past decade due to their biological properties, including improved pharmacokinetic and pharmacodynamic profiles. However, the synthesis of this type of peptide on solid phase by current available methods can be challenging. Here we report a convenient method to synthesize peptide C-terminal N-alkyl amides using the well-known Fukuyama N-alkylation reaction on a standard resin commonly used for the synthesis of peptide C-terminal primary amides, the peptide amide linker-polyethylene glycol-polystyrene (PAL-PEG-PS) resin. The alkylation and oNBS deprotection were conducted under basic conditions and were therefore compatible with this acid labile resin. The alkylation reaction was very efficient on this resin with a number of different alkyl iodides or bromides, and the synthesis of model enkephalin N-alkyl amide analogs using this method gave consistently high yields and purities, demonstrating the applicability of this methodology. The synthesis of N-alkyl amides was more difficult on a Rink amide resin, especially the coupling of the first amino acid to the N-alkyl amine, resulting in lower yields for loading the first amino acid onto the resin. This method can be widely applied in the synthesis of peptide N-alkyl amides.
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Affiliation(s)
| | - Tatyana Yakovleva
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Jane V. Aldrich
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, KS 66045, USA
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72
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Fang WJ, Bennett MA, Aldrich JV. Deletion of Ac-NMePhe(1) from [NMePhe(1) ]arodyn under acidic conditions, part 1: effects of cleavage conditions and N-terminal functionality. Biopolymers 2011; 96:97-102. [PMID: 20560149 PMCID: PMC3412617 DOI: 10.1002/bip.21496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Peptides containing N-methylamino acids can exhibit improved pharmacodynamic and pharmacokinetic profiles compared to nonmethylated peptides, and therefore interest in these N-methylated peptides has been increasing in recent years. Arodyn (Ac[Phe¹,²,³,Arg⁴,D-Ala⁸]Dyn A(1-11)NH₂) is an acetylated dynorphin A(Dyn A) analog that is a potent and selective κ opioid receptor antagonist (Bennett et al., J Med Chem 2002, 45, 5617), and its analog [NMePhe¹]arodyn shows even higher affinity and selectivity for κ opioid receptors (Bennett et al., J Pept Res 2005, 65, 322). During the synthesis of [NMePhe¹]arodyn analogs, the arodyn-(2-11) derivatives were obtained as major products. Analysis indicated that Ac-NMePhe was lost from the completed peptide sequence during acidic cleavage of the peptides from the resin and that the acetyl group played an important role in this side reaction. Different cleavage conditions were evaluated to minimize this side reaction and maximize the yield of pure [NMePhe¹]arodyn analogs. Modifications to the N-terminus of the peptides to prevent the side reaction were also explored. The incorporation of a heteroatom-containing group such as methoxycarbonyl as the N-terminal functionality prevented this side reaction, while the incorporation of a bulky acyl group could not. Substituting NMePhe with the conformationally constrained analog Tic (1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) also prevented the side reaction.
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Affiliation(s)
- Wei-Jie Fang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Marco A. Bennett
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21201, USA
| | - Jane V. Aldrich
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
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73
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Synthetic strategy for side chain mono-N-alkylation of Fmoc-amino acids promoted by molecular sieves. Amino Acids 2010; 41:981-90. [DOI: 10.1007/s00726-010-0798-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 10/25/2010] [Indexed: 11/26/2022]
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74
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Qu H, Magotti P, Ricklin D, Wu EL, Kourtzelis I, Wu YQ, Kaznessis YN, Lambris JD. Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency. Mol Immunol 2010; 48:481-9. [PMID: 21067811 DOI: 10.1016/j.molimm.2010.10.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 10/10/2010] [Indexed: 11/26/2022]
Abstract
Compstatin is a 13-residue disulfide-bridged peptide that inhibits a key step in the activation of the human complement system. Compstatin and its derivatives have shown great promise for the treatment of many clinical disorders associated with unbalanced complement activity. To obtain more potent compstatin analogues, we have now performed an N-methylation scan of the peptide backbone and amino acid substitutions at position 13. One analogue (Ac-I[CVW(Me)QDW-Sar-AHRC](NMe)I-NH(2)) displayed a 1000-fold increase in both potency (IC(50) = 62 nM) and binding affinity for C3b (K(D) = 2.3 nM) over that of the original compstatin. Biophysical analysis using surface plasmon resonance and isothermal titration calorimetry suggests that the improved binding originates from more favorable free conformation and stronger hydrophobic interactions. This study provides a series of significantly improved drug leads for therapeutic applications in complement-related diseases, and offers new insights into the structure-activity relationships of compstatin analogues.
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Affiliation(s)
- Hongchang Qu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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75
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Lanning JD, Hawk AJ, Derryberry J, Meredith SC. Chaperone-like N-methyl peptide inhibitors of polyglutamine aggregation. Biochemistry 2010; 49:7108-18. [PMID: 20583779 DOI: 10.1021/bi1006095] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyglutamine expansion in the exon 1 domain of huntingtin leads to aggregation into beta-sheet-rich insoluble aggregates associated with Huntington's disease. We assessed eight polyglutamine peptides with different permutations of N-methylation of backbone and side chain amides as potential inhibitors of polyglutamine aggregation. Surprisingly, the most effective inhibitor, 5QMe(2) [Anth-K-Q-Q(Me(2))-Q-Q(Me(2))-Q-CONH(2), where Anth is N-methylanthranilic acid and Q(Me(2)) is side chain N-methyl Q], has only side chain methylations at alternate residues, highlighting the importance of side chain interactions in polyglutamine fibrillogenesis. Above a 1:1 stoichiometric ratio, 5QMe(2) can completely prevent fibrillation of a synthetic aggregating peptide, YAQ(12)A; it also shows significant inhibition at substoichiometric ratios. Surface plasmon resonance (SPR) measurements show a moderate K(d) with very fast k(on) and k(off) values. Sedimentation equilibrium analytical ultracentrifugation indicates that 5QMe(2) is predominantly or entirely monomeric at concentrations of <or=1 mM and that it forms a 1:1 stoichiometric complex with a fibril-forming target, YAQ(12)A. 5QMe(2) inhibits not only nucleation of YAQ(12)A but also fibril extension, as shown by the fact that it also inhibits seeded fibril growth where the nucleation steps are bypassed. 5QMe(2) acts on its targets only when they are in the PPII-like conformation, but not after they undergo a transition to beta-sheets. Thus, 5QMe(2) does not disassemble preformed YAQ(12)A; this contrasts with our previously described, backbone N-methylated inhibitors of beta-amyloid aggregation [Gordon, D. J., et al. (2001) Biochemistry 40, 8237-8245; Gordon, D. J., et al. (2002) J. Pept. Res. 60, 37-55]. The mode of action of 5QMe(2) is reminiscent of that of chaperones, because it binds and releases its targets very rapidly and maintains them in a nonaggregation-prone, monomeric state, in this case, the polyproline II (PPII)-like conformation, as shown by circular dichroism spectroscopy.
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Affiliation(s)
- Jennifer D Lanning
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
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76
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Doedens L, Opperer F, Cai M, Beck JG, Dedek M, Palmer E, Hruby VJ, Kessler H. Multiple N-methylation of MT-II backbone amide bonds leads to melanocortin receptor subtype hMC1R selectivity: pharmacological and conformational studies. J Am Chem Soc 2010; 132:8115-28. [PMID: 20496895 PMCID: PMC2895553 DOI: 10.1021/ja101428m] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Multiple N-methylation is a novel technology to improve bioavailability of peptides and increase receptor subtype selectivity. This technique has been applied here to the superpotent but nonselective cyclic peptide MT-II. A library of all possible 31 backbone N-methylated derivatives has been synthesized and tested for binding and activation at melanocortin receptor subtypes 1, 3, 4, and 5. It turned out that selectivity is improved with every introduced N-methyl group, resulting in several N-methylated selective and potent agonists for the hMC1R. The most potent of these derivatives is N-methylated on four out of five amide bonds in the cyclic structure. Its solution structure indicates a strongly preferred backbone conformation that resembles other alpha-MSH analogs but possesses much less flexibility and in addition distinct differences in the spatial arrangement of individual amino acid side chains.
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Affiliation(s)
- Lucas Doedens
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Florian Opperer
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Minying Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Johannes G. Beck
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Matt Dedek
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Erin Palmer
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Victor J. Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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77
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Ovadia O, Greenberg S, Laufer B, Gilon C, Hoffman A, Kessler H. Improvement of drug-like properties of peptides: the somatostatin paradigm. Expert Opin Drug Discov 2010; 5:655-71. [DOI: 10.1517/17460441.2010.493935] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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78
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Leggio A, Belsito EL, De Marco R, Liguori A, Perri F, Viscomi MC. An efficient preparation of N-methyl-alpha-amino acids from N-nosyl-alpha-amino acid phenacyl esters. J Org Chem 2010; 75:1386-92. [PMID: 20121053 DOI: 10.1021/jo901643f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper we describe a simple and efficient solution-phase synthesis of N-methyl-N-nosyl-alpha-amino acids and N-Fmoc-N-methyl-alpha-amino acids. This represents a very important application in peptide synthesis to obtain N-methylated peptides in both solution and solid phase. The developed methodology involves the use of N-nosyl-alpha-amino acids with the carboxyl function protected as a phenacyl ester and the methylating reagent diazomethane. An important aspect of this synthetic strategy is the possibility to selectively deprotect the carboxyl function or alternatively both amino and carboxyl moieties by using the same reagent with a different molar excess and under mild conditions. Furthermore, the adopted procedure keeps unchanged the acid-sensitive side chain protecting groups used in Fmoc-based synthetic strategies.
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Affiliation(s)
- Antonella Leggio
- Dipartimento di Scienze Farmaceutiche, Università della Calabria, Via Ponte P. Bucci Cubo 15/C, I-87036 Arcavacata di Rende (CS), Italy
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79
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Izzo I, Acosta GA, Tulla-Puche J, Cupido T, Martin-Lopez MJ, Cuevas C, Albericio F. Solid-Phase Synthesis of Aza-Kahalalide F Analogues: (2R,3R)-2-Amino-3-azidobutanoic Acid as Precursor of the Aza-Threonine. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901345] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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80
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Tal-Gan Y, Freeman NS, Klein S, Levitzki A, Gilon C. Synthesis and structure–activity relationship studies of peptidomimetic PKB/Akt inhibitors: The significance of backbone interactions. Bioorg Med Chem 2010; 18:2976-85. [DOI: 10.1016/j.bmc.2010.02.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 02/12/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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81
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Laufer B, Frank A, Chatterjee J, Neubauer T, Mas-Moruno C, Kummerlöwe G, Kessler H. The Impact of Amino Acid Side Chain Mutations in Conformational Design of Peptides and Proteins. Chemistry 2010; 16:5385-90. [DOI: 10.1002/chem.201000545] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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82
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Sicherl F, Cupido T, Albericio F. A novel dipeptidomimetic containing a cyclic threonine. Chem Commun (Camb) 2010; 46:1266-8. [PMID: 20449272 DOI: 10.1039/b915220b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient and simple two-step procedure for the formation of hydroxy-Freidinger lactams is presented. The methodology allows assembly of the cyclic threonine motif (cThr) in solution and on solid support during conventional peptide synthesis.
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Affiliation(s)
- Frank Sicherl
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028-Barcelona, Spain.
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83
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Pratim Bose P, Chatterjee U, Nerelius C, Govender T, Norström T, Gogoll A, Sandegren A, Göthelid E, Johansson J, Arvidsson PI. Poly-N-methylated amyloid beta-peptide (Abeta) C-terminal fragments reduce Abeta toxicity in vitro and in Drosophila melanogaster. J Med Chem 2010; 52:8002-9. [PMID: 19908889 DOI: 10.1021/jm901092h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alzheimer's disease (AD), an age related neurodegenerative disorder, threatens to become a major health-economic problem. Assembly of 40- or 42-residue amyloid beta-peptides (Abeta) into neurotoxic oligo-/polymeric beta-sheet structures is an important pathogenic feature in AD, thus, inhibition of this process has been explored to prevent or treat AD. The C-terminal part plays an important role in Abeta aggregation, but most Abeta aggregation inhibitors have targeted the central region around residues 16-23. Herein, we synthesized hexapeptides with varying extents of N-methylation based on residues 32-37 of Abeta, to target its C-terminal region. We measured the peptides' abilities to retard beta-sheet and fibril formation of Abeta and to reduce Abeta neurotoxicity. A penta-N-methylated peptide was more efficient than peptides with 0, 2, or 3 N-methyl groups. This penta-N-methylated peptide moreover increased life span and locomotor activity in Drosophila melanogaster flies overexpressing human Abeta(1-42).
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Affiliation(s)
- Partha Pratim Bose
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
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84
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Synthesis of chemically modified bioactive peptides: recent advances, challenges and developments for medicinal chemistry. Future Med Chem 2009; 1:1289-310. [DOI: 10.4155/fmc.09.97] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although not complying with Lipinski’s rule, peptides are to an increasing extent being developed into new active pharmaceutical ingredients. This is mainly due to novel application routes, formulations and chemical modifications, which confer on the peptides improved uptake and increased metabolic stability. A brief survey of currently approved peptide drugs and the present scope of the application of peptides as drugs is provided. Cyclic peptides are emerging as an interesting class of peptides with conformational rigidity and homogeneity, high receptor affinity and selectivity, increased metabolic stability and – in special cases – even oral availability. Challenges and new methodology for the synthesis of cyclic peptides are outlined and an overview of approaches toward the design of peptide conformation and peptide modification by nonproteinogenic building blocks is given.
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85
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Jamieson AG, Boutard N, Beauregard K, Bodas MS, Ong H, Quiniou C, Chemtob S, Lubell WD. Positional scanning for peptide secondary structure by systematic solid-phase synthesis of amino lactam peptides. J Am Chem Soc 2009; 131:7917-27. [PMID: 19453183 DOI: 10.1021/ja9010628] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incorporation of amino lactams into biologically active peptides has been commonly used to restrict conformational mobility, enhance selectivity, and increase potency. A solid-phase method using a Fmoc-protection strategy has been developed for the systematic synthesis of peptides containing configurationally defined alpha- and beta-amino gamma-lactams. N-Alkylation of N-silyl peptides with five- and six-member cyclic sulfamidates 9 and 8 minimized bis-alkylation and provided N-alkyl peptides, which underwent lactam annulation under microwave heating. Employing this solid-phase protocol on the growth hormone secretagogue GHRP-6, as well as on the allosteric modulator of the IL-1 receptor 101.10, has furnished 16 lactam derivatives and validated the effectiveness of this approach on peptides bearing aliphatic, aromatic, branched, charged, and heteroatomic side chains. The binding affinity IC(50) values of the GHRP-6 lactam analogues on both the GHS-R1a and CD36 receptors are reported as well as inhibition of thymocyte proliferation measurements for the 101.10 lactam analogues. In these cases, lactam analogues were prepared exhibiting similar or improved properties compared with the parent peptide. Considering the potential for amino lactams to induce peptide turn conformations, the effective method described herein for their supported construction on growing peptides, and for the systematical amino lactam scan of peptides, has proven useful for the rapid identification of the secondary structure necessary for peptide biological activity.
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Affiliation(s)
- Andrew G Jamieson
- Chemistry Department, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, Quebec H3C 3J7, Canada
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86
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LeBeau AM, Banerjee SR, Pomper MG, Mease RC, Denmeade SR. Optimization of peptide-based inhibitors of prostate-specific antigen (PSA) as targeted imaging agents for prostate cancer. Bioorg Med Chem 2009; 17:4888-93. [PMID: 19541487 PMCID: PMC3087300 DOI: 10.1016/j.bmc.2009.06.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 06/03/2009] [Accepted: 06/06/2009] [Indexed: 11/30/2022]
Abstract
Prostate-specific antigen (PSA) is a serine protease biomarker that may play a role in prostate cancer development and progression. The inhibition of PSA's enzymatic activity with small molecule inhibitors is an attractive and, as of yet, unexploited target. Previously, we reported a series of peptidyl aldehyde and boronic acid based inhibitors of PSA. In this study, the structural requirements in the P2 and P3 positions of peptide-based PSA inhibitors are explored through the substitution of a series of natural and unnatural amino acids in these positions. This analysis demonstrated a preference for hydrophobic residues in the P2 position and amino acids with the potential to hydrogen bond in the P3 position. Using this information, a peptide boronic acid inhibitor with the sequence Cbz-Ser-Ser-Gln-Nle-(boro)-Leu was identified with a K(i) for PSA of 25nM. The attachment of a bulky metal chelating group to the amino terminal of this peptide did not adversely affect PSA inhibition. This result suggests that a platform of PSA inhibitor chelates could be developed as SPECT or PET-based imaging agents for prostate cancer.
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Affiliation(s)
- Aaron M. LeBeau
- Department of Pharmacology and Molecular Science, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sangeeta R. Banerjee
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Martin G. Pomper
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD
- The Sidney Kimmel Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ronnie C. Mease
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Samuel R. Denmeade
- Department of Pharmacology and Molecular Science, The Johns Hopkins University School of Medicine, Baltimore, MD
- The Sidney Kimmel Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD
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87
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Laufer B, Chatterjee J, Frank AO, Kessler H. Can N-methylated amino acids serve as substitutes for prolines in conformational design of cyclic pentapeptides? J Pept Sci 2009; 15:141-6. [PMID: 18985637 DOI: 10.1002/psc.1076] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The incorporation of proline into cyclic peptides seems to be the most promising way to induce beta-turn structures. Recently, however, it was shown that N-methylated amino acids might be even better suited than proline for introducing turn structures. Another property of proline, the ability to effect cis-peptide bonds, has also been reported for N-methylated amino acids. These findings raise the question if it might be possible to replace a proline by an N-methylated amino acid without altering the desired conformational features. The most important benefit of replacing proline by an N-methylated residue is that one recovers the side-chain functionalities, which could be used for enhancing binding selectivity, or to tune a cyclic peptide concerning its pharmacological properties.Here, we compare cyclic peptides containing one or two prolines or N-methylated alanines and a combination of both with respect to preferred conformations and cis-peptide bonds. In addition, the positions have been investigated where an N-alkylated amino acid has to be incorporated to mimic structural aspects usually introduced by proline residues.
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Affiliation(s)
- Burkhardt Laufer
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747 Germany
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88
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Tulla-Puche J, Marcucci E, Prats-Alfonso E, Bayó-Puxan N, Albericio F. NMe Amide as a Synthetic Surrogate for the Thioester Moiety in Thiocoraline. J Med Chem 2009; 52:834-9. [DOI: 10.1021/jm800784k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Judit Tulla-Puche
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Eleonora Marcucci
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Elisabet Prats-Alfonso
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Núria Bayó-Puxan
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
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89
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Linde Y, Ovadia O, Safrai E, Xiang Z, Portillo FP, Shalev DE, Haskell-Luevano C, Hoffman A, Gilon C. Structure-activity relationship and metabolic stability studies of backbone cyclization and N-methylation of melanocortin peptides. Biopolymers 2008; 90:671-82. [PMID: 18655141 DOI: 10.1002/bip.21057] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Backbone cyclization (BC) and N-methylation have been shown to enhance the activity and/or selectivity of biologically active peptides and improve metabolic stability and intestinal permeability. In this study, we describe the synthesis, structure-activity relationship (SAR) and intestinal metabolic stability of a backbone cyclic peptide library, BL3020, based on the linear alpha-Melanocyte stimulating hormone analog Phe-D-Phe-Arg-Trp-Gly. The drug lead, BL3020-1, selected from the BL3020 library (compound 1) has been shown to inhibit weight gain in mice following oral administration. Another member of the BL3020 library, BL3020-17, showed improved biological activity towards the mMC4R, in comparison to BL3020-1, although neither were selective for MC4R or MC5R. N-methylation, which restrains conformational freedom while increasing metabolic stability beyond that which is imparted by BC, was used to find analogs with increased selectivity. N-methylated backbone cyclic libraries were synthesized based on the BL3020 library. SAR studies showed that all the N-methylated backbone cyclic peptides demonstrated reduced biological activity and selectivity for all the analyzed receptors. N-methylation of active backbone cyclic peptides destabilized the active conformation or stabilized an inactive conformation, rendering the peptides biologically inactive. N-methylation of backbone cyclic peptides maintained stability to degradation by intestinal enzymes.
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Affiliation(s)
- Yaniv Linde
- Institute of Chemistry, Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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90
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A preparation of N-Fmoc-N-methyl-α-amino acids and N-nosyl-N-methyl-α-amino acids. Amino Acids 2008; 38:133-43. [DOI: 10.1007/s00726-008-0221-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
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91
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Chatterjee J, Gilon C, Hoffman A, Kessler H. N-methylation of peptides: a new perspective in medicinal chemistry. Acc Chem Res 2008; 41:1331-42. [PMID: 18636716 DOI: 10.1021/ar8000603] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The potential of peptides as drug candidates is limited by their poor pharmacokinetic properties. Many peptides have a short half-life in vivo and a lack of oral availability. Inspired by the excellent pharmacokinetic profile of cyclosporine, a natural, multiply N-methylated cyclic peptide, we envisioned multiple N-methylation as a promising way to rationally improve key pharmacokinetic characteristics. In this Account, we summarize our efforts toward modulating the properties of peptides by multiple N-methylation. As a first step, we simplified the synthesis of N-methylated amino acids in solution, by employing very mild conditions that could be tolerated by the diverse protecting groups required when working with naturally occurring amino acids. We also report the rapid and inexpensive syntheses of N-methylated peptides on a solid support; this facilitated the N-methyl scanning of bioactive peptides. Because of a lack of information regarding the conformational behavior of multiply N-methylated peptides, a complete library of N-methylated cyclic alanine pentapeptides was synthesized. The library provided valuable insight into the conformational modulation of cyclic peptides by N-methylation. This information is extremely valuable for the design of bioactive peptides and spatial screening of cyclic N-methylated peptides. To demonstrate the applicability of N-methylation to highly active but poorly bioavailable peptides, we performed a full N-methyl scan of the cyclopeptidic somatostatin analog cyclo(-PFwKTF-), known as the Veber-Hirschmann peptide. We show here for the first time that the simple approach of multiple N-methylation can drastically improve the metabolic stability and intestinal permeability of peptides, for example, resulting in 10% oral bioavailability for a tri-N-methylated Veber-Hirschmann peptide analog. In addition, we also describe a designed approach to N-methylated peptide library synthesis, which can accelerate the screening of N-methylated bioactive peptides. Finally, we find that multiple N-methylation of a cyclic hexapeptide integrin antagonist of GPIIb-IIIa (alphaIIb beta3 integrin), cyclo(-GRGDfL-), increases the selectivity of this peptide toward different integrin subtypes. This result demonstrates the utility of multiple N-methylation in elucidating the bioactive conformation of peptides.
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Affiliation(s)
- Jayanta Chatterjee
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Chaim Gilon
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Amnon Hoffman
- Department of Pharmaceutics, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Horst Kessler
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
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92
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Walther T, Arndt HD, Waldmann H. Solid-Support Based Total Synthesis and Stereochemical Correction of Brunsvicamide A. Org Lett 2008; 10:3199-202. [DOI: 10.1021/ol801064d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thilo Walther
- TU Dortmund, Fakultät Chemie, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany, and Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
| | - Hans-Dieter Arndt
- TU Dortmund, Fakultät Chemie, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany, and Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
| | - Herbert Waldmann
- TU Dortmund, Fakultät Chemie, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany, and Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
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93
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Vagner J, Qu H, Hruby VJ. Peptidomimetics, a synthetic tool of drug discovery. Curr Opin Chem Biol 2008; 12:292-6. [PMID: 18423417 PMCID: PMC2515564 DOI: 10.1016/j.cbpa.2008.03.009] [Citation(s) in RCA: 381] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 03/11/2008] [Accepted: 03/14/2008] [Indexed: 10/22/2022]
Abstract
The demand for modified peptides with improved stability profiles and pharmacokinetic properties is driving extensive research effort in this field. Many structural modifications of peptides guided by rational design and molecular modeling have been established to develop novel synthetic approaches. Recent advances in the synthesis of conformationally restricted building blocks and peptide bond isosteres are discussed.
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Affiliation(s)
- Josef Vagner
- Department of Biochemistry and Molecular Biophysics, Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Hongchang Qu
- Department of Chemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Victor J. Hruby
- Department of Chemistry, University of Arizona, Tucson, AZ, 85721, USA
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94
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Demmer O, Dijkgraaf I, Schottelius M, Wester HJ, Kessler H. Introduction of functional groups into peptides via N-alkylation. Org Lett 2008; 10:2015-8. [PMID: 18407647 DOI: 10.1021/ol800654n] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An optimized protocol for the mild and selective Fukuyama-Mitsunobu reaction was used for mono- and di- N-alkylation on solid support. Thereby, nonfunctionalized aliphatic and aromatic residues are quickly introduced into transiently protected, primary amines of a linear peptide. N-Alkylation can also be used to implement alkyl chains carrying (protected) functionalities suited for subsequent modification. Applicability of this method is demonstrated by various N-alkylated analogues of a cyclic CXCR4 receptor antagonist originally developed by Fujii et. al.
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Affiliation(s)
- O Demmer
- Department Chemie, Lehrstuhl II für organische Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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95
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Biron E, Chatterjee J, Ovadia O, Langenegger D, Brueggen J, Hoyer D, Schmid HA, Jelinek R, Gilon C, Hoffman A, Kessler H. Improving oral bioavailability of peptides by multiple N-methylation: somatostatin analogues. Angew Chem Int Ed Engl 2008; 47:2595-9. [PMID: 18297660 DOI: 10.1002/anie.200705797] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Eric Biron
- CIPS at Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747-Garching, Germany
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96
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Biron E, Chatterjee J, Ovadia O, Langenegger D, Brueggen J, Hoyer D, Schmid H, Jelinek R, Gilon C, Hoffman A, Kessler H. Die Verbesserung der oralen Bioverfügbarkeit von Peptiden durch multiple N-Methylierung: Somatostatin-Analoga. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705797] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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97
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Lawrence J, Jourdan M, Vallée Y, Blandin V. Peptide cyclization via ring-closing metathesis: the N-alkenoxy peptide approach. Org Biomol Chem 2008; 6:4575-81. [DOI: 10.1039/b812611a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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98
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Marcucci E, Bayó-Puxan N, Tulla-Puche J, Spengler J, Albericio F. Cysteine-S-trityl a Key Derivative to PrepareN-Methyl Cysteines. ACTA ACUST UNITED AC 2008; 10:69-78. [DOI: 10.1021/cc7001588] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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99
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Chatterjee J, Ovadia O, Zahn G, Marinelli L, Hoffman A, Gilon C, Kessler H. Multiple N-methylation by a designed approach enhances receptor selectivity. J Med Chem 2007; 50:5878-81. [PMID: 17973471 DOI: 10.1021/jm701044r] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An unselective cyclic peptide integrin ligand was sequentially N-methylated by a designed approach, where only the externally oriented (solvent exposed) amide bonds were N-methylated. The N-methylation resulted in tremendous enhancement in selectivity among the different integrin receptor subtypes (alpha5beta1, alphavbeta3, and alphaIIbbeta3). Conformational and docking studies were performed, which suggested that the receptor selectivity is principally caused by reduced backbone flexibility due to N-methylation.
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Affiliation(s)
- Jayanta Chatterjee
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl II für Organische Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching D85747, Germany
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100
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Tantry SJ, Venkataramanarao R, Chennakrishnareddy G, Sureshbabu VV. Total Synthesis of Cyclosporin O by Convergent Approach Employing Fmoc-Amino Acid Chlorides Mediated by Zinc Dust. J Org Chem 2007; 72:9360-3. [DOI: 10.1021/jo701329w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subramanyam J Tantry
- Department of Studies in Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, India
| | - Rao Venkataramanarao
- Department of Studies in Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, India
| | - Gundala Chennakrishnareddy
- Department of Studies in Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, India
| | - Vommina Venkata Sureshbabu
- Department of Studies in Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, India
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