1
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Zou J, Zhou M, Xiao X, Liu R. Advance in Hybrid Peptides Synthesis. Macromol Rapid Commun 2022; 43:e2200575. [PMID: 35978269 DOI: 10.1002/marc.202200575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/24/2022] [Indexed: 11/08/2022]
Abstract
Hybrid peptides with heterogeneous backbone are a class of peptide mimics with adjustable proteolytic stability obtained from incorporating unnatural amino acid residues into peptide backbone. α/β-peptides and peptide/peptoid hybrids are two types of hybrid peptides that are widely studied for diverse applications, and several synthetic methods have been developed. In this mini review, the advance in hybrid peptide synthesis is summarized, including solution-phase method, solid-phase method, and novel polymerization method. Conventional solution-phase method and solid-phase method generally result in oligomers with defined sequences, while polymerization methods have advantages in preparing peptide hybrid polymers with high molecular weight with simple operation and low cost. In addition, the future development of polymerization method to realize the control of the peptide hybrid polymer sequence is discussed.
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Affiliation(s)
- Jingcheng Zou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Min Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ximian Xiao
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Runhui Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
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2
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Ren J, Tian Y, Hossain E, Connolly MD. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:646-661. [PMID: 26832347 DOI: 10.1007/s13361-016-1341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/07/2016] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry. Graphical Abstract ᅟ.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
| | - Yuan Tian
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ekram Hossain
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael D Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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3
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Jobin S, Vézina-Dawod S, Herby C, Derson A, Biron E. Preparation of N-Substituted N-Arylsulfonylglycines and Their Use in Peptoid Synthesis. Org Lett 2015; 17:5626-9. [DOI: 10.1021/acs.orglett.5b02862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steve Jobin
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Simon Vézina-Dawod
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Claire Herby
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Antoine Derson
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Eric Biron
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
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4
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Park S, Kwon YU. Facile solid-phase parallel synthesis of linear and cyclic peptoids for comparative studies of biological activity. ACS COMBINATORIAL SCIENCE 2015; 17:196-201. [PMID: 25602927 DOI: 10.1021/co5001647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of linear and cyclic peptoids, which were expected to possess better pharmacokinetic properties and biological activities for blocking the interaction between apolipoprotein E and amyloid-β, were designed and synthesized as possible therapeutic agents. Peptoids were easily synthesized on solid-phase by the submonomer strategy and polar side chain-containing amines were effectively introduced under the modified reaction conditions. For the synthesis of cyclic peptoids, β-alanine protected with the 2-phenylisopropyl group, which could be selectively removed by 2% TFA, was used as a primary amine to afford a complete peptoid unit. The macrolactamization between the carboxylic acid of β-alanine moiety and terminal amine of peptoids was successfully performed in the presence of the PyAOP coupling agent on solid-phase in all the cases, providing various sizes of cyclic peptoids. In particular, some cyclic peptoids prepared in this study are the largest in size among cyclic peptoids reported to date. The synthetic strategy which was adopted in this study can also provide a robust platform for solid-phase construction of cyclic peptoid libraries. Currently, synthetic peptoids have been used to test interesting biological activities including the ApoE/Aβ interaction inhibition, nontoxicity, the blood-brain barrier permeability, etc.
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Affiliation(s)
- Shinae Park
- Department
of Chemistry and
Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Yong-Uk Kwon
- Department
of Chemistry and
Nano Science, Ewha Womans University, Seoul 120-750, Korea
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5
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René A, Martinez J, Cavelier F. N-Substituted Glycines with Functional Side-Chains for Peptoid Synthesis. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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6
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Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC. Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J Am Chem Soc 2014; 136:15422-37. [PMID: 25314576 PMCID: PMC4227725 DOI: 10.1021/ja5088216] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We describe a strategy for rendering peptides resistant to proteolysis by formulating them as high-density brush polymers. The utility of this approach is demonstrated by polymerizing well-established cell-penetrating peptides (CPPs) and showing that the resulting polymers are not only resistant to proteolysis but also maintain their ability to enter cells. The scope of this design concept is explored by studying the proteolytic resistance of brush polymers composed of peptides that are substrates for either thrombin or a metalloprotease. Finally, we demonstrate that the proteolytic susceptibility of peptide brush polymers can be tuned by adjusting the density of the polymer brush and offer in silico models to rationalize this finding. We contend that this strategy offers a plausible method of preparing peptides for in vivo use, where rapid digestion by proteases has traditionally restricted their utility.
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Affiliation(s)
- Angela P Blum
- Department of Chemistry & Biochemistry, ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
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7
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Lee KJ, Lim HS. Facile Method To Sequence Cyclic Peptides/Peptoids via One-Pot Ring-Opening/Cleavage Reaction. Org Lett 2014; 16:5710-3. [DOI: 10.1021/ol502788e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Kang Ju Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
- Department of Biochemistry and Molecular
Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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8
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Lee YH, Park N, Park YB, Hwang YJ, Kang C, Kim JS. Organelle-selective fluorescent Cu2+ ion probes: revealing the endoplasmic reticulum as a reservoir for Cu-overloading. Chem Commun (Camb) 2014; 50:3197-200. [PMID: 24519529 DOI: 10.1039/c4cc00091a] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two novel Cu(2+) sensors, 1 and 2, bearing naphthalimide and a DPA moiety were synthesized to study copper accumulation in organelles by selective Cu(2+) sensing. The ER-selective Cu(2+) sensor 1 that we developed serves as a valuable tool for understanding the subcellular compartmentalization and roles of copper ions in physiology and pathophysiology.
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Affiliation(s)
- Yun Hak Lee
- Department of Chemistry, Korea University, Seoul 136-701, Korea.
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9
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Park M, Wetzler M, Jardetzky TS, Barron AE. A readily applicable strategy to convert peptides to peptoid-based therapeutics. PLoS One 2013; 8:e58874. [PMID: 23555603 PMCID: PMC3605428 DOI: 10.1371/journal.pone.0058874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/07/2013] [Indexed: 01/23/2023] Open
Abstract
Incorporation of unnatural amino acids and peptidomimetic residues into therapeutic peptides is highly efficacious and commonly employed, but generally requires laborious trial-and-error approaches. Previously, we demonstrated that C20 peptide has the potential to be a potential antiviral agent. Herein we report our attempt to improve the biological properties of this peptide by introducing peptidomimetics. Through combined alanine, proline, and sarcosine scans coupled with a competitive fluorescence polarization assay developed for identifying antiviral peptides, we enabled to pinpoint peptoid-tolerant peptide residues within C20 peptide. The synergistic benefits of combining these (and other) commonly employed methods could lead to a easily applicable strategy for designing and refining therapeutically-attractive peptidomimetics.
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Affiliation(s)
- Minyoung Park
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Modi Wetzler
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, California, United States of America
| | - Theodore S. Jardetzky
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Annelise E. Barron
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
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10
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Kraskouskaya D, Duodu E, Arpin CC, Gunning PT. Progress towards the development of SH2 domain inhibitors. Chem Soc Rev 2013; 42:3337-70. [DOI: 10.1039/c3cs35449k] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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11
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Lis LG, Smart MA, Luchniak A, Gupta ML, Gurvich VJ. Synthesis and Biological Evaluation of a Biotinylated Paclitaxel With an Extra-Long Chain Spacer Arm. ACS Med Chem Lett 2012; 3:745-748. [PMID: 23259031 DOI: 10.1021/ml300149z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
A biotinylated paclitaxel derivative with an extra-long-chain (LC-LC-Biotin) spacer arm was synthesized using an improved synthetic reaction sequence. The biotinylated paclitaxel analogue retained excellent microtubule stabilizing activity in vitro. Furthermore, it was shown that this analogue can simultaneously engage streptavidin and the binding site on microtubules, making it suitable for localization studies or for the attachment of paclitaxel to solid substrates via a streptavidin linkage.
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Affiliation(s)
- Lev. G. Lis
- Institute for Therapeutics Discovery
and Development and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414,
United States
| | - Mary A. Smart
- Institute for Therapeutics Discovery
and Development and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414,
United States
| | - Anna Luchniak
- Department
of Molecular Genetics
and Cell Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Mohan L. Gupta
- Department
of Molecular Genetics
and Cell Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Vadim J. Gurvich
- Institute for Therapeutics Discovery
and Development and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414,
United States
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12
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Lee MH, Kim JY, Han JH, Bhuniya S, Sessler JL, Kang C, Kim JS. Direct Fluorescence Monitoring of the Delivery and Cellular Uptake of a Cancer-Targeted RGD Peptide-Appended Naphthalimide Theragnostic Prodrug. J Am Chem Soc 2012; 134:12668-74. [DOI: 10.1021/ja303998y] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Min Hee Lee
- Department of Chemistry, Korea University, Seoul, 136-701, Korea
| | - Jin Young Kim
- The School of East-West Medical
Science, Kyung Hee University, Yongin,
446-701, Korea
| | - Ji Hye Han
- The School of East-West Medical
Science, Kyung Hee University, Yongin,
446-701, Korea
| | | | - Jonathan L. Sessler
- Department
of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-0165,
United States
- Department
of Chemistry, Yonsei University, 262 Seonsanno
Sinchon-dong, Seodaemun-gu,
Seoul 120-749, Korea
| | - Chulhun Kang
- The School of East-West Medical
Science, Kyung Hee University, Yongin,
446-701, Korea
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul, 136-701, Korea
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13
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Andreini M, Felten AS, Thien HTT, Taillefumier C, Pellegrini-Moïse N, Chapleur Y. Synthesis of new C-glycosyl aza-β3-amino acids building blocks. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.03.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Shahnaz G, Iqbal J, Rahmat D, Perera G, Laffleur F, Rossi D, Bernkop-Schnürch A. Development and in vivo characterization of a novel peptide drug delivery system providing extended plasma half life. J Control Release 2012; 157:375-82. [DOI: 10.1016/j.jconrel.2011.09.092] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 09/22/2011] [Accepted: 09/24/2011] [Indexed: 10/17/2022]
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15
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Andreasen M, Nielsen SB, Mittag T, Bjerring M, Nielsen JT, Zhang S, Nielsen EH, Jeppesen M, Christiansen G, Besenbacher F, Dong M, Nielsen NC, Skrydstrup T, Otzen DE. Modulation of fibrillation of hIAPP core fragments by chemical modification of the peptide backbone. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:274-85. [DOI: 10.1016/j.bbapap.2011.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/14/2011] [Accepted: 10/24/2011] [Indexed: 11/30/2022]
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16
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Liskamp RMJ, Rijkers DTS, Kruijtzer JAW, Kemmink J. Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics. Chembiochem 2011; 12:1626-53. [PMID: 21751324 DOI: 10.1002/cbic.201000717] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 12/17/2022]
Abstract
Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.
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Affiliation(s)
- Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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17
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Einsiedel J, Held C, Hervet M, Plomer M, Tschammer N, Hübner H, Gmeiner P. Discovery of Highly Potent and Neurotensin Receptor 2 Selective Neurotensin Mimetics. J Med Chem 2011; 54:2915-23. [DOI: 10.1021/jm200006c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jürgen Einsiedel
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Cornelia Held
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Maud Hervet
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Manuel Plomer
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Nuska Tschammer
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
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18
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Ruttekolk IR, Chakrabarti A, Richter M, Duchardt F, Glauner H, Verdurmen WPR, Rademann J, Brock R. Coupling to polymeric scaffolds stabilizes biofunctional peptides for intracellular applications. Mol Pharmacol 2011; 79:692-700. [PMID: 21247935 DOI: 10.1124/mol.110.068296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we demonstrate that coupling to N-hydroxypropyl methacrylamide (HPMA) copolymer greatly enhances the activity of apoptosis-inducing peptides inside cells. Peptides corresponding to the BH3 domain of Bid were coupled to a thioester-activated HPMA (28.5 kDa) via native chemical ligation in a simple one-pot synthesis. Peptides and polymer conjugates were introduced into cells either by electroporation or by conjugation to the cell-penetrating peptide nona-arginine. The molecular basis of the increased activity is elucidated in detail. Loading efficiency and intracellular residence time were assessed by confocal microscopy. Fluorescence correlation spectroscopy was used as a separation-free analytical technique to determine proteolytic degradation in crude cell lysates. HPMA conjugation strongly increased the half-life of the peptides in crude cell lysates and inside cells, revealing proteolytic protection as the basis for higher activity.
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Affiliation(s)
- Ivo R Ruttekolk
- Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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19
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Caporale A, Schievano E, Peggion E. Peptide-peptoid hybrids based on (1-11)-parathyroid hormone analogs. J Pept Sci 2010; 16:480-5. [PMID: 20629116 DOI: 10.1002/psc.1265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A series of peptide-peptoid hybrids, containing N-substituted glycines, were synthesized based on the H-Aib-Val-Aib-Glu-Ile-Gln-Leu-Nle-His-Gln-Har-NH(2) (Har = Homoarginine) as the parent parathyroid hormone (1-11) analog. The compounds were pharmacologically characterized in their agonistic activity at the parathyroid hormone 1 receptor.
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Affiliation(s)
- A Caporale
- Department of Chemical Sciences, Institute of Biomolecular Chemistry, CNR, University of Padova, Padova, Italy.
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20
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Abstract
Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area of research within the field of peptidomimetic science.
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Affiliation(s)
- Christian A Olsen
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, Copenhagen, 2100 Denmark.
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21
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Messeguer J, Masip I, Montolio M, del Rio JA, Soriano E, Messeguer A. Peptoids bearing tertiary amino residues in the n-alkyl side chains: synthesis of a potent inhibitor of Semaphorin 3A. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Dekker FJ, DE Mol NJ, Liskamp RMJ. Thermodynamics of phosphotyrosine peptide-peptoid hybrids binding to the p56lck SH2 domain. J Pept Sci 2010; 16:322-8. [DOI: 10.1002/psc.1242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Kuil J, van Wandelen LT, de Mol NJ, Liskamp RM. Switching between low and high affinity for the Syk tandem SH2 domain by irradiation of azobenzene containing ITAM peptidomimetics. J Pept Sci 2009; 15:685-91. [DOI: 10.1002/psc.1173] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Pflantz R, Christoffers J. Diaminoterephthalates: Scaffolds for Combinatorial Chemistry. Chemistry 2009; 15:2200-9. [DOI: 10.1002/chem.200802151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Kuil J, Branderhorst HM, Pieters RJ, de Mol NJ, Liskamp RMJ. ITAM-derived phosphopeptide-containing dendrimers as multivalent ligands for Syk tandem SH2 domain. Org Biomol Chem 2009; 7:4088-94. [DOI: 10.1039/b905938e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Capone S, Walde P, Seebach D, Ishikawa T, Caputo R. pH-sensitive vesicles containing a lipidic beta-amino acid with two hydrophobic chains. Chem Biodivers 2008; 5:16-30. [PMID: 18205118 DOI: 10.1002/cbdv.200890006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The lipidic beta-amino acid 2-(aminomethyl)-2-pentadecylheptadecanoic acid (1) was synthesized via the alkylation of the C(alpha)-atom of fully protected beta-alanine. Mixed large unilamellar vesicles with a diameter between 100 and 200 nm containing POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and 1 at a molar ratio of 9 : 1 were prepared and found to have a surface charge which is dependent on pH. At slightly acidic pH, the vesicles were positively charged, and at alkaline pH negatively charged. Dynamic light scattering, zeta potential, and cryo-transmission electron-microscopy measurements indicated that the mixed vesicles fused at pH 4-5 with negatively charged mixed vesicles composed of POPC and POPG (9.8 : 1, molar ratio), POPG being 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)].
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Affiliation(s)
- Stefania Capone
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH-Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich
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27
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Eberhard H, Seitz O. N→O-Acyl shift in Fmoc-based synthesis of phosphopeptides. Org Biomol Chem 2008; 6:1349-55. [DOI: 10.1039/b718568e] [Citation(s) in RCA: 15] [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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28
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Pflantz R, Tielmann P, Rössle M, Hoenke C, Christoffers J. Eight-Membered-Ring Lactams – New Scaffolds for Combinatorial Chemistry Prepared by Ring-Expansion of 1,4-Diketones with Primary Amines. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700263] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Elgersma RC, Mulder GE, Kruijtzer JAW, Posthuma G, Rijkers DTS, Liskamp RMJ. Transformation of the amyloidogenic peptide amylin(20–29) into its corresponding peptoid and retropeptoid: Access to both an amyloid inhibitor and template for self-assembled supramolecular tapes. Bioorg Med Chem Lett 2007; 17:1837-42. [PMID: 17276062 DOI: 10.1016/j.bmcl.2007.01.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 01/12/2007] [Accepted: 01/13/2007] [Indexed: 10/23/2022]
Abstract
The highly amyloidogenic peptide sequence of amylin(20-29) was transformed into its corresponding peptoid and retropeptoid sequences to design a novel class of beta-sheet breaker peptides as amyloid inhibitors. This report describes the synthesis of the chiral peptoid building block of L-isoleucine, the solid phase synthesis of the peptoid and retropeptoid sequences of amylin(20-29), and the structural analysis of these amylin derivatives in solution by infrared spectroscopy, circular dichroism, and transmission electron microscopy. It was found that the peptoid sequence did not form amyloid fibrils or any other secondary structures and was able to inhibit amyloid formation of native amylin(20-29). Although the retropeptoid did not form amyloid fibrils it had only modest amyloid inhibitor properties since supramolecular tapes were formed.
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Affiliation(s)
- Ronald C Elgersma
- Department of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, PO Box 80082, 3508 TB Utrecht, The Netherlands
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Gorske BC, Blackwell HE. Interception of quorum sensing in Staphylococcus aureus: a new niche for peptidomimetics. Org Biomol Chem 2006; 4:1441-5. [PMID: 16604206 DOI: 10.1039/b517681f] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pathogenesis in Staphylococcus aureus is dependent on local cell density and is regulated in part by small macrocyclic peptides. Natural and artificial peptide inhibitors of this quorum sensing response have been synthesized and evaluated in structure-activity relationship studies. These investigations have illuminated the quorum sensing mechanism and set the stage for the design of biostable, peptidomimetic inhibitors that could be developed ultimately as therapeutics.
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Affiliation(s)
- Benjamin C Gorske
- Depatment of Chemistry, University of Wisconsin-Madison, 53706-1322, USA
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31
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de Mol NJ, Catalina MI, Dekker FJ, Fischer MJE, Heck AJR, Liskamp RMJ. Protein Flexibility and Ligand Rigidity: A Thermodynamic and Kinetic Study of ITAM-Based Ligand Binding to Syk Tandem SH2. Chembiochem 2005; 6:2261-70. [PMID: 16252296 DOI: 10.1002/cbic.200500141] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Syk tandem Src homology 2 domain (Syk tSH2) constitutes a flexible protein module involved in the regulation of Syk kinase activity. The Syk tSH2 domain is assumed to function by adapting the distance between its two SH2 domains upon bivalent binding to diphosphotyrosine ligands. A thermodynamic and kinetic analysis of ligand binding was performed by using surface plasmon resonance (SPR). Furthermore, the effect of binding on the Syk tSH2 structural dynamics was probed by hydrogen/deuterium exchange and electrospray mass spectrometry (ESI-MS). Two ligands were studied: 1, a flexible peptide derived from the tSH2 recognition ITAM sequence at the gamma chain of the FcepsilonRI-receptor, and 2, a ligand in which the amino acids between the two SH2 binding motifs in ligand 1 have been replaced by a rigid linker of comparable length. Both ligands display comparable affinity for Syk tSH2 at 25 degrees C, yet a major difference in thermodynamics is observed. Upon binding of the rigid ligand, 2, the expected entropy advantage is not realized. On the contrary, 2 binds with a considerably higher entropy price of approximately 9 kcal mol-1, which is attributed to a further decrease in protein flexibility upon binding to this rigid ligand. The significant reduction in deuterium incorporation in the Syk tSH2 protein upon binding of either 1 or 2, as monitored by ESI-MS, indicates a major reduction in protein dynamics upon binding. The results are consistent with a two-step binding model: after an initial binding step, a rapid structural change of the protein occurs, followed by a second binding step. Such a bivalent binding model allows high affinity and fast dissociation kinetics, which are very important in transient signal-transduction processes.
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Affiliation(s)
- Nico J de Mol
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University (UIPS), Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
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Kruijtzer JAW, Nijenhuis WAJ, Wanders N, Gispen WH, Liskamp RMJ, Adan RAH. Peptoid-peptide hybrids as potent novel melanocortin receptor ligands. J Med Chem 2005; 48:4224-30. [PMID: 15974575 DOI: 10.1021/jm0490033] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
All possible peptoid-peptide hybrids of an MC4 receptor agonist were synthesized and investigated on cells expressing different melanocortin (MC) receptor subtypes and for rat grooming behavior. In general, receptor selectivity remained while affinity and potency were decreased. The length of the functional group of Trp was more important for MC3 and MC5 than for MC4 receptor binding. In general, the potency of the peptoid-peptide hybrids to increase rat excessive grooming behavior correlated well with MC4 receptor pharmacology.
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Affiliation(s)
- John A W Kruijtzer
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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33
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Holder JR, Bauzo RM, Xiang Z, Scott J, Haskell-Luevano C. Design and pharmacology of peptoids and peptide–peptoid hybrids based on the melanocortin agonists core tetrapeptide sequence. Bioorg Med Chem Lett 2003; 13:4505-9. [PMID: 14643357 DOI: 10.1016/j.bmcl.2003.08.078] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A series of N-substituted glycine oligomers (peptoids) and peptide-peptoid hybrids were synthesized based on the Ac-His-Phe-Arg-Trp-NH(2) tetrapeptide template. The compounds were pharmacologically characterized at the mouse melanocortin receptors (MC1R, MC3R-MC5R) for agonist activity.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cell Line
- Drug Design
- Glycine/analogs & derivatives
- Humans
- Kinetics
- Ligands
- Mice
- Models, Molecular
- Oligopeptides/chemistry
- Peptides/chemical synthesis
- Peptides/chemistry
- Peptides/pharmacology
- Peptoids/chemical synthesis
- Peptoids/chemistry
- Peptoids/pharmacology
- Receptor, Melanocortin, Type 3/agonists
- Receptor, Melanocortin, Type 3/chemistry
- Receptor, Melanocortin, Type 3/drug effects
- Receptor, Melanocortin, Type 4/agonists
- Receptor, Melanocortin, Type 4/chemistry
- Receptor, Melanocortin, Type 4/drug effects
- Recombinant Proteins/agonists
- Recombinant Proteins/chemistry
- Recombinant Proteins/drug effects
- Structure-Activity Relationship
- Transfection
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Affiliation(s)
- Jerry Ryan Holder
- Department of Medicinal Chemistry, University of Florida, PO Box 100485, Gainesville, FL 32610, USA
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Dekker FJ, de Mol NJ, Fischer MJE, Liskamp RMJ. Amino propynyl benzoic acid building block in rigid spacers of divalent ligands binding to the Syk SH2 domains with equally high affinity as the natural ligand. Bioorg Med Chem Lett 2003; 13:1241-4. [PMID: 12657254 DOI: 10.1016/s0960-894x(03)00117-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The construction of rigid spacers composed of amino propynyl benzoic acid building blocks is described. These spacers were used to link two phosphopeptide ligand sites towards obtaining divalent ligands with a high affinity for Syk tandem SH2 domains, which are important in signal transduction. The spacer containing two of those rigid building blocks led to a ligand which was as active as the natural ligand, indicating that this building block can be used in the design and synthesis of high affinity divalent constructs that can successfully interfere with crucial protein-protein interactions.
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Affiliation(s)
- Frank J Dekker
- Department of Medicinal Chemistry, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, The Netherlands
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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36
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Bultinck P, Augustynen S, Hilbers HW, Moret EE, Tollenaere JP. Generate: a program for 3-D structure generation and conformational analysis of peptides and peptidomimetics. J Comput Chem 2002; 23:746-54. [PMID: 11948593 DOI: 10.1002/jcc.10081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The program Generate, aimed at generating 3-D structures for peptides and peptidomimetics, is presented. The algorithm is based on a build-up procedure, using a library of conformations of amino acid residues. This library is built from conformational analysis of amino acids placed in a di- or tripeptide environment to mimic the surroundings of the amino acid in a true peptide, considering different positions of the residue in the peptide chain (peptidyl fragment, NH(+)(3)-terminus or COO(-)-terminus). Cis-trans isomerism in the amide bonds is taken into account by construction of rotamer libraries for different isomers. Water solvation is included through the GB/SA model. New amino acid residues can easily be added to the libraries, making it possible to generate conformations of peptidomimetics.
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Affiliation(s)
- Patrick Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium.
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37
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Waizenegger T, Fischer R, Brock R. Intracellular concentration measurements in adherent cells: a comparison of import efficiencies of cell-permeable peptides. Biol Chem 2002; 383:291-9. [PMID: 11934267 DOI: 10.1515/bc.2002.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A protocol was developed for performing intracellular concentration measurements in flat adherent tissue culture cells by fluorescence correlation microscopy (FCM). Determination of the number of molecules in the confocal detection volume had to account for background fluorescence caused by molecules adsorbed to the surface of the measurement chamber. Such a background signal leads to a decrease in the amplitude of the autocorrelation function, and thereby to the calculation of an erroneously high number of molecules. Because of the spatial heterogeneity of the background intensity, a method was devised by which its contribution to the total fluorescence could be determined directly from each individual autocorrelation measurement. This method was applied to a comparison of the import efficiencies of different cell-permeable peptides at nanomolar concentrations. The Antennapedia homeodomain-derived peptide penetratin was imported about three times as efficient as the basic fibroblast growth factor-derived MTS peptide. Both peptides equilibrated between cytoplasm and nucleus. A relatively high mobility of these molecules inside the cells indicated that they may be rapidly degraded by cytosolic proteases. Based on these results, it will be possible to determine intracellular concentrations of inhibitors linked to import peptides directly by FCM at nanomolar concentrations and to optimise such constructs for proteolytic stability.
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Affiliation(s)
- Thomas Waizenegger
- Center for Bioinformatics Tübingen, Institute for Cell Biology, University of Tübingen, Germany
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38
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Ruijtenbeek R, Versluis C, Heck AJR, Redegeld FAM, Nijkamp FP, Liskamp RMJ. Characterization of a phosphorylated peptide and peptoid and peptoid-peptide hybrids by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:47-55. [PMID: 11813310 DOI: 10.1002/jms.245] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nano-electrospray tandem mass spectrometry (nano-ES-MS/MS) was used to record collision-induced dissociation (CID) spectra of a set of peptoid-peptide hybrids and the complete peptoid derived from the phosphopeptide Ac-pTyr-Glu-Thr-Leu-NH(2) (1). The presence of B and Y''-type fragment ions in the tandem mass spectra of the protonated molecular ions [M + H](+) allowed confirmation of sequence similar to mass spectrometric sequence analysis in peptides. In the isomeric peptoid compounds studied, one or several amino acid residues were replaced by peptoid residues (N-substituted glycine residues), which resulted in characteristic tandem mass spectra with differently increased relative abundances of Y''-and B-type fragment ions. The increment of a particular Y''-ion was directly correlated to the position of a peptoid residue present. In addition to these increased peak intensities, other characteristic peaks were also observed compared with the spectrum of reference peptide 1. When a peptoid phosphotyrosine was incorporated, the presence of this residue was apparent from the occurrence of a relatively intense peak at m/z 187 representing the positively charged side-chain of phosphotyrosine, which was almost absent in the spectrum of the reference peptide 1. Since the threonine side-chain had to be translated into the homo peptoid analog this substitution was apparent from the presence of [M + H](+) and fragment ions 14 mass units higher than observed in the spectrum of the reference phosphopeptide 1. The presence of an NLeu peptoid residue could be confirmed by the specific fragmentation of the immonium ion showing an intense peak in its tandem mass spectrum at m/z 57, which results from the loss of an neutral imine molecule leading to a positively charged [C(4)H(9)](+) ion. By means of these mass spectrometric characteristics, all isomeric peptoid compounds could be distinguished from each other and characterized. The methods used appear to be very useful in future studies of peptoids and peptoid-peptide hybrids.
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Affiliation(s)
- Rob Ruijtenbeek
- Department of Pharmacology and Pathophysiology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
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