1
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Ericson MD, Freeman KT, Haskell-Luevano C. Peptoid NPhe 4 in AGRP-Based c[Pro 1-Arg 2-Phe 3-Phe 4-Xxx 5-Ala 6-Phe 7-DPro 8] Scaffolds Maintain Mouse MC4R Antagonist Potency. ACS Med Chem Lett 2020; 11:1942-1948. [PMID: 33062177 DOI: 10.1021/acsmedchemlett.9b00641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/26/2020] [Indexed: 01/12/2023] Open
Abstract
The melanocortin receptors are involved in numerous physiological functions and are regulated by agonists derived from the proopiomelanocortin gene transcript and two endogenous antagonists, agouti and agouti-related protein (AGRP). The key binding and functional determinant of AGRP, an MC3R and MC4R antagonist, is an Arg-Phe-Phe tripeptide sequence located on an exposed hexapeptide (Arg-Phe-Phe-Asn-Ala-Phe) loop. It has previously been observed that cyclizing this sequence through a DPro-Pro motif (c[Pro1-Arg2-Phe3-Phe4-Asn5-Ala6-Phe7-DPro8]) resulted in a macrocyclic scaffold with MC4R antagonist activity, with increased MC4R potency when a diaminopropionic acid (Dap) residue is substituted at position 5. In this report, a series of 11 single-peptoid substitutions were performed in the AGRP-derived macrocycles. While most peptoid substitutions decreased MC4R antagonist potency, it was observed that NPhe4 (compounds 4 and 11) or NDab5 (diaminobutyric acid, compound 7) maintained MC4R antagonist potency. The NPhe4 substitutions also resulted in MC5R antagonist and inverse agonist activity equipotent to the parent scaffolds. These data may be used in the design of future MC4R and MC5R antagonist leads and probes that possess increased metabolic stability due to the presence of peptoid residues.
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Affiliation(s)
- Mark D. Ericson
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katie T. Freeman
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carrie Haskell-Luevano
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Tsuchie R, Shimosato M, Hamasaki K. Hydrophobic Association of a Side Chains Induces Reversible Helix Folding in a Dual Aromatic Ring Tagged Short Peptide. CHEM LETT 2018. [DOI: 10.1246/cl.180601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryusuke Tsuchie
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-5-7 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Mayu Shimosato
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-5-7 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Keita Hamasaki
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-5-7 Toyosu, Koto-ku, Tokyo 135-8548, Japan
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3
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Ren J, Mann YS, Zhang Y, Browne MD. Synthesis and Mass Spectrometry Analysis of Oligo-peptoids. J Vis Exp 2018. [PMID: 29553518 DOI: 10.3791/56652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific;
| | | | - Yuntao Zhang
- Department of Chemistry, University of the Pacific
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4
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 655] [Impact Index Per Article: 93.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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5
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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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6
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Karna N, Dębowski D, Łęgowska A, Bąchor R, Szewczuk Z, Rolka K. Peptide splicing in a double-sequence analogue of trypsin inhibitor SFTI-1 substituted in the P₁ positions by peptoid monomers. Biopolymers 2015; 104:206-12. [PMID: 25904562 DOI: 10.1002/bip.22659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/13/2015] [Accepted: 04/14/2015] [Indexed: 11/12/2022]
Abstract
Recently, we described a process of trypsin-assisted peptide splicing of analogs of trypsin inhibitor SFTI-1, that seems to be very similar to proteasome-catalyzed peptide splicing. Here, we show, for the first time, that a peptide-peptoid hybrid (peptomer) can also be spliced by trypsin. Incubation of a double sequence SFTI-1 analog, containing two peptoid monomers, with equimolar amount of trypsin leads to formation of monocyclic peptomer as the main product. We proved that the peptide bond formed by a peptoid monomer is not only digested by trypsin but also participates in the enzyme-assisted splicing process.
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Affiliation(s)
- Natalia Karna
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952, Gdansk, Poland
| | - Dawid Dębowski
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952, Gdansk, Poland
| | - Anna Łęgowska
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952, Gdansk, Poland
| | - Remigiusz Bąchor
- Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383, Wroclaw, Poland
| | - Zbigniew Szewczuk
- Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383, Wroclaw, Poland
| | - Krzysztof Rolka
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952, Gdansk, Poland
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7
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The identification of high-affinity G protein-coupled receptor ligands from large combinatorial libraries using multicolor quantum dot-labeled cell-based screening. Future Med Chem 2015; 6:809-23. [PMID: 24941874 DOI: 10.4155/fmc.14.38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs), which are involved in virtually every biological process, constitute the largest family of transmembrane receptors. Many top-selling and newly approved drugs target GPCRs. In this review, we aim to recapitulate efforts and progress in combinatorial library-assisted GPCR ligand discovery, particularly focusing on one-bead-one-compound library synthesis and quantum dot-labeled cell-based assays, which both effectively enhance the rapid identification of GPCR ligands with higher affinity and specificity.
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8
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Bogdanov B, Zhao X, Robinson DB, Ren J. Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1202-1216. [PMID: 24845348 DOI: 10.1007/s13361-014-0869-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.
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Affiliation(s)
- Bogdan Bogdanov
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
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9
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Abstract
Peptoids (oligomers of N-substituted glycine residues) and peptide-peptoid hybrid polymers (peptomers) are interesting classes of compounds mimicking structure and function of biologically active peptides. The oligomeric peptidomimetics such as peptoids are particularly important compounds since they provide access to an enormous molecular diversity, by variation of the building blocks. The modular structure of peptoids, ease of synthesis, and high compatibility with existing peptide chemistry synthetic protocols, make peptoids and peptoid-containing peptidomimetics ideal tools for structure-activity and drug discovery related studies.
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10
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Sergeev ME, Voyushina TL, Sergeeva OA, Belozerskaya GG. Efficient enzyme-catalyzed synthesis of peptide secondary amides for use as serine proteinase inhibitors. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Liu F, Park JE, Qian WJ, Lim D, Scharow A, Berg T, Yaffe MB, Lee KS, Burke TR. Peptoid-Peptide hybrid ligands targeting the polo box domain of polo-like kinase 1. Chembiochem 2012; 13:1291-6. [PMID: 22570300 PMCID: PMC4536914 DOI: 10.1002/cbic.201200206] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Indexed: 11/10/2022]
Abstract
We replaced the amino terminal Pro residue of the Plk1 polo-box-domain-binding pentapeptide (PLHSpT) with a library of N-alkyl-Gly "peptoids", and identified long-chain tethered phenyl moieties giving greater than two-orders-of-magnitude affinity enhancement. Further simplification by replacing the peptoid residue with appropriate amides gave low-nanomolar affinity N-acylated tetrapeptides. Binding of the N-terminal long-chain phenyl extension was demonstrated by X-ray co-crystal data.
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Affiliation(s)
- Fa Liu
- Chemical Biology Laboratory, Frederick National Lab, NCI, NIH, Frederick, MD 21702 (USA), Fax: (+1) 301-846-6033
| | - Jung-Eun Park
- Laboratory of Metabolism, National Cancer Institute, NIH, Bethesda, MD 20892 (USA)
| | - Wen-Jian Qian
- Chemical Biology Laboratory, Frederick National Lab, NCI, NIH, Frederick, MD 21702 (USA), Fax: (+1) 301-846-6033
| | - Dan Lim
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (USA)
| | - Andrej Scharow
- Institute of Organic Chemistry, University of Leipzig, 04103 Leipzig (Germany)
| | - Thorsten Berg
- Institute of Organic Chemistry, University of Leipzig, 04103 Leipzig (Germany)
| | - Michael B. Yaffe
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (USA)
| | - Kyung S. Lee
- Laboratory of Metabolism, National Cancer Institute, NIH, Bethesda, MD 20892 (USA)
| | - Terrence R. Burke
- Chemical Biology Laboratory, Frederick National Lab, NCI, NIH, Frederick, MD 21702 (USA), Fax: (+1) 301-846-6033
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12
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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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13
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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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14
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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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15
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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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16
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Ovadia O, Linde Y, Haskell-Luevano C, Dirain ML, Sheynis T, Jelinek R, Gilon C, Hoffman A. The effect of backbone cyclization on PK/PD properties of bioactive peptide-peptoid hybrids: The melanocortin agonist paradigm. Bioorg Med Chem 2010; 18:580-9. [DOI: 10.1016/j.bmc.2009.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/02/2009] [Accepted: 12/03/2009] [Indexed: 10/20/2022]
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17
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Kawakami T, Murakami H, Suga H. Ribosomal Synthesis of Polypeptoids and Peptoid−Peptide Hybrids. J Am Chem Soc 2008; 130:16861-3. [DOI: 10.1021/ja806998v] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takashi Kawakami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Murakami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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18
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Lee BC, Chu TK, Dill KA, Zuckermann RN. Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J Am Chem Soc 2008; 130:8847-55. [PMID: 18597438 DOI: 10.1021/ja802125x] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the long-term goals in developing advanced biomaterials is to generate protein-like nanostructures and functions from a completely nonnatural polymer. Toward that end, we introduced a high-affinity zinc-binding function into a peptoid (N-substituted glycine polymer) two-helix bundle. Borrowing from well-understood zinc-binding motifs in proteins, thiol and imidazole moieties were positioned within the peptoid such that both helices must align in close proximity to form a binding site. We used fluorescence resonance energy transfer (FRET) reporter groups to measure the change of the distance between the two helical segments and to probe the binding of zinc. We systematically varied the position and number of zinc-binding residues, as well as the sequence and size of the loop that connects the two helical segments. We found that certain peptoid two-helix bundles bind zinc with nanomolar affinities and high selectivity compared to other divalent metal ions. Our work is a significant step toward generating biomimetic nanostructures with enzyme-like functions.
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Affiliation(s)
- Byoung-Chul Lee
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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19
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Ross TM, Zuckermann RN, Reinhard C, Frey WH. Intranasal administration delivers peptoids to the rat central nervous system. Neurosci Lett 2008; 439:30-3. [DOI: 10.1016/j.neulet.2008.04.097] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Revised: 04/08/2008] [Accepted: 04/22/2008] [Indexed: 11/30/2022]
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20
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Peptide backbone modifications on the C-terminal hexapeptide of neurotensin. Bioorg Med Chem Lett 2008; 18:2013-8. [DOI: 10.1016/j.bmcl.2008.01.110] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 01/28/2008] [Accepted: 01/29/2008] [Indexed: 11/23/2022]
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21
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Schröder T, Niemeier N, Afonin S, Ulrich AS, Krug HF, Bräse S. Peptoidic Amino- and Guanidinium-Carrier Systems: Targeted Drug Delivery into the Cell Cytosol or the Nucleus. J Med Chem 2008; 51:376-9. [DOI: 10.1021/jm070603m] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tina Schröder
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Nicole Niemeier
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anne S. Ulrich
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Harald F. Krug
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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22
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Liu F, Stephen AG, Adamson C, Gousset K, Aman MJ, Freed EO, Fisher RJ, Burke TR. Hydrazone- and hydrazide-containing N-substituted glycines as peptoid surrogates for expedited library synthesis: application to the preparation of Tsg101-directed HIV-1 budding antagonists. Org Lett 2007; 8:5165-8. [PMID: 17048869 PMCID: PMC2547129 DOI: 10.1021/ol0622211] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacing the Pro6 in the p6(Gag)-derived 9-mer "P-E-P-T-A-P-P-E-E" with N-substituted glycine (NSG) residues is problematic. However, incorporation of hydrazone amides ("peptoid hydrazones") can be readily achieved in library fashion. Furthermore, reduction of these hydrazones to N-substituted "peptoid hydrazides" affords a facile route to library diversification. This approach is demonstrated by application to Tsg101-binding compounds designed as potential HIV budding antagonists. [reaction: see text]
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Affiliation(s)
- Fa Liu
- Laboratory of Medicinal Chemistry, CCR, NCI-Frederick, NIH, Bldg. 376 Boyles St., Frederick, MD 21702
| | | | | | | | - M. Javad Aman
- U.S. Army Medical Research Institute for Infectious Diseases, Frederick, MD
| | | | | | - Terrence R. Burke
- Laboratory of Medicinal Chemistry, CCR, NCI-Frederick, NIH, Bldg. 376 Boyles St., Frederick, MD 21702
- e-mail:
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23
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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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24
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Ying J, Gu X, Cai M, Dedek M, Vagner J, Trivedi DB, Hruby VJ. Design, synthesis, and biological evaluation of new cyclic melanotropin peptide analogues selective for the human melanocortin-4 receptor. J Med Chem 2007; 49:6888-96. [PMID: 17154518 PMCID: PMC1764620 DOI: 10.1021/jm060768f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intensive efforts have been made to develop potent and selective ligands for certain human melanocortin receptors as possible treatments for obesity and sexual dysfunction due to the role of these receptors in feeding behavior, energy homeostasis, sexual function, etc. A number of novel alpha-MSH analogues were designed and synthesized primarily on the basis of our previous MTII NMR structure. In these peptide analogues, a disulfide or lactam bridge between residues at positions 5 and 8 was used as a conformational constraint to enhance the beta-turn spanning His6 and D-Phe7, while the pharmacophore group in Arg8 was mimicked via Nalpha-alkylation of residues 8 or 9 with the guanidinylbutyl group. Biological assays for binding affinities and adenylate cyclase activities for the hMC1R, hMC3R, hMC4R, and hMC5R showed that three analogues have good binding affinity for the hMC4R (0.7-4.1 nM), but have no binding affinity up to 10 microM at the other three melanocortin receptors. Interestingly, the three hMC4R selective analogues display only 50% binding efficiency, suggesting there is allosteric modulation of the melanocortin-4 receptor. These analogues were found to act as antagonists of the hMC4R. This result represents a discovery of very selective peptide-based antagonists for the hMC4R. The high selectivity may be due to the strong conformational constraint via ring contraction as compared to MTII, and the rigid conformation preferred by these new ligands allows them to recognize only the hMC4R, but not to activate the second messenger. The MTII NMR structure-based design thus not only examined the structural model of melanocortin ligands, but also yielded new biologically unique alpha-MSH analogues.
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MESH Headings
- Adenylyl Cyclases/metabolism
- Allosteric Regulation
- Binding, Competitive
- Cell Line
- Drug Design
- Humans
- Ligands
- Magnetic Resonance Spectroscopy
- Molecular Conformation
- Peptides, Cyclic/chemical synthesis
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/pharmacology
- Protein Structure, Secondary
- Radioligand Assay
- Receptor, Melanocortin, Type 4/agonists
- Receptor, Melanocortin, Type 4/antagonists & inhibitors
- Receptor, Melanocortin, Type 4/metabolism
- Structure-Activity Relationship
- alpha-MSH/analogs & derivatives
- alpha-MSH/chemical synthesis
- alpha-MSH/chemistry
- alpha-MSH/pharmacology
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Affiliation(s)
- Jinfa Ying
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
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