1
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Bonvin E, Personne H, Paschoud T, Reusser J, Gan BH, Luscher A, Köhler T, van Delden C, Reymond JL. Antimicrobial Peptide-Peptoid Hybrids with and without Membrane Disruption. ACS Infect Dis 2023; 9:2593-2606. [PMID: 38062792 PMCID: PMC10714400 DOI: 10.1021/acsinfecdis.3c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Among synthetic analogues of antimicrobial peptides (AMPs) under investigation to address antimicrobial resistance, peptoids (N-alkylated oligoglycines) have been reported to act both by membrane disruption and on intracellular targets. Here we gradually introduced peptoid units into the membrane-disruptive undecapeptide KKLLKLLKLLL to test a possible transition toward intracellular targeting. We found that selected hybrids containing up to five peptoid units retained the parent AMP's α-helical folding, membrane disruption, and antimicrobial effects against Gram-negative bacteria including multidrug-resistant (MDR) strains of Pseudomonas aeruginosa and Klebsiella pneumoniae while showing reduced hemolysis and cell toxicities. Furthermore, some hybrids containing as few as three peptoid units as well as the full peptoid lost folding, membrane disruption, hemolysis, and cytotoxicity but displayed strong antibacterial activity under dilute medium conditions typical for proline-rich antimicrobial peptides (PrAMPs), pointing to intracellular targeting. These findings parallel previous reports that partially helical amphiphilic peptoids are privileged oligomers for antibiotic development.
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Affiliation(s)
- Etienne Bonvin
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hippolyte Personne
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Thierry Paschoud
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jérémie Reusser
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Alexandre Luscher
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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2
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Bahatheg G, Kuppusamy R, Yasir M, Black DS, Willcox M, Kumar N. Short Tryptamine-Based Peptoids as Potential Therapeutics for Microbial Keratitis: Structure-Function Correlation Studies. Antibiotics (Basel) 2022; 11:antibiotics11081074. [PMID: 36009943 PMCID: PMC9404767 DOI: 10.3390/antibiotics11081074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 12/02/2022] Open
Abstract
Peptoids are peptidomimetics that have attracted considerable interest as a promising class of antimicrobials against multi-drug-resistant bacteria due to their resistance to proteolysis, bioavailability, and thermal stability compared to their corresponding peptides. Staphylococcus aureus is a significant contributor to infections worldwide and is a major pathogen in ocular infections (keratitis). S. aureus infections can be challenging to control and treat due to the development of multiple antibiotic resistance. This work describes short cationic peptoids with activity against S. aureus strains from keratitis. The peptoids were synthesized via acid amine-coupling between naphthyl-indole amine or naphthyl-phenyl amine with different amino acids to produce primary amines (series I), mono-guanidines (series II), tertiary amine salts (series III), quaternary ammonium salts (series IV), and di-guanidine (series V) peptoids. The antimicrobial activity of the peptoids was compared with ciprofloxacin, an antibiotic that is commonly used to treat keratitis. All new compounds were active against Staphylococcus aureus S.aureus 38. The most active compounds against S.aur38 were 20a and 22 with MIC = 3.9 μg mL−1 and 5.5 μg mL−1, respectively. The potency of these two active molecules was investigated against 12 S. aureus strains that were isolated from microbial keratitis. Compounds 20a and 22 were active against 12 strains with MIC = 3.2 μg mL−1 and 2.1 μg mL−1, respectively. There were two strains that were resistant to ciprofloxacin (Sa.111 and Sa.112) with MIC = 128 μg mL−1 and 256 μg mL−1, respectively. Compounds 12c and 13c were the most active against E. coli, with MIC > 12 μg mL−1. Cytoplasmic membrane permeability studies suggested that depolarization and disruption of the bacterial cell membrane could be a possible mechanism for antibacterial activity and the hemolysis studies toward horse red blood cells showed that the potent compounds are non-toxic at up to 50 μg mL−1.
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Affiliation(s)
- Ghayah Bahatheg
- School of Chemistry, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Department of Chemistry, Faculty of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Rajesh Kuppusamy
- School of Chemistry, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- School of Optometry and Vision Science, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Correspondence: (R.K.); (N.K.)
| | - Muhammad Yasir
- School of Optometry and Vision Science, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - David StC. Black
- School of Chemistry, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - Naresh Kumar
- School of Chemistry, The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Correspondence: (R.K.); (N.K.)
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3
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Herlan CN, Feser D, Schepers U, Bräse S. Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond. Chem Commun (Camb) 2021; 57:11131-11152. [PMID: 34611672 DOI: 10.1039/d1cc04237h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Dominik Feser
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
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4
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Kim S, Nam HY, Lee J, Seo J. Mitochondrion-Targeting Peptides and Peptidomimetics: Recent Progress and Design Principles. Biochemistry 2019; 59:270-284. [PMID: 31696703 DOI: 10.1021/acs.biochem.9b00857] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondria are multifunctional subcellular organelles whose operations encompass energy production, signal transduction, and metabolic regulation. Given their wide range of roles, they have been studied extensively as a potential therapeutic target for the treatment of various diseases, including cancer, diabetes, and neurodegenerative diseases. Mitochondrion-mediated pathways have been identified as promising targets in the context of these diseases. However, the delivery of specific probes and drugs to the mitochondria is one of the major problems that remains to be solved. Over the past decade, much effort has been devoted to developing mitochondrion-targeted delivery methods based on the membrane characteristics and the protein import machinery of mitochondria. While various methods utilizing small molecules to polymeric particles have been introduced, it is notable that many of these compounds share common structural elements and physicochemical properties for optimal selectivity and efficiency. In this Perspective, we will review the most recently developed mitochondrion-targeting peptides and peptidomimetics to outline the key aspects of structural requirements and design principles. We will also discuss successful and potential applications of mitochondrial delivery to assess opportunities and challenges in the targeting of mitochondria.
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Affiliation(s)
- Soyoung Kim
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
| | - Ho Yeon Nam
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
| | - Jiyoun Lee
- Department of Global Medical Science , Sungshin University , Seoul 01133 , Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
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5
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Bartolowits MD, Gast JM, Hasler AJ, Cirrincione AM, O’Connor RJ, Mahmoud AH, Lill MA, Davisson VJ. Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen. ACS OMEGA 2019; 4:15181-15196. [PMID: 31552364 PMCID: PMC6751697 DOI: 10.1021/acsomega.9b02079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a central factor in DNA replication and repair pathways that plays an essential role in genome stability. The functional roles of PCNA are mediated through an extensive list of protein-protein interactions, each of which transmits specific information in protein assemblies. The flexibility at the PCNA-protein interaction interfaces offers opportunities for the discovery of functionally selective inhibitors of DNA repair pathways. Current fragment-based drug design methodologies can be limited by the flexibility of protein interfaces. These factors motivated an approach to defining compounds that could leverage previously identified subpockets on PCNA that are suitable for fragment-binding sites. Methodologies for screening multiple connected fragment-binding events in distinct subpockets are deployed to improve the selection of fragment combinations. A flexible backbone based on N-alkyl-glycine amides offers a scaffold to combinatorically link multiple fragments for in silico screening libraries that explore the diversity of subpockets at protein interfaces. This approach was applied to discover new potential inhibitors of DNA replication and repair that target PCNA in a multiprotein recognition site. The screens of the libraries were designed to computationally filter ligands based upon the fragments and positions to <1%, which were synthesized and tested for direct binding to PCNA. Molecular dynamics simulations also revealed distinct features of these novel molecules that block key PCNA-protein interactions. Furthermore, a Bayesian classifier predicted 15 of the 16 new inhibitors to be modulators of protein-protein interactions, demonstrating the method's utility as an effective screening filter. The cellular activities of example ligands with similar affinity for PCNA demonstrate unique properties for novel selective synergy with therapeutic DNA-damaging agents in drug-resistant contexts.
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Affiliation(s)
- Matthew D. Bartolowits
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jonathon M. Gast
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ashlee J. Hasler
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Anthony M. Cirrincione
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rachel J. O’Connor
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amr H. Mahmoud
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Markus A. Lill
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Vincent Jo Davisson
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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6
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Shyam R, Charbonnel N, Job A, Blavignac C, Forestier C, Taillefumier C, Faure S. 1,2,3‐Triazolium‐Based Cationic Amphipathic Peptoid Oligomers Mimicking Antimicrobial Helical Peptides. ChemMedChem 2018; 13:1513-1516. [DOI: 10.1002/cmdc.201800273] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/05/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Radhe Shyam
- Université Clermont Auvergne CNRS, SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | | | - Aurélie Job
- Université Clermont Auvergne CNRS, SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | - Christelle Blavignac
- Université Clermont Auvergne Centre Imagerie Cellulaire Santé 63000 Clermont-Ferrand France
| | | | - Claude Taillefumier
- Université Clermont Auvergne CNRS, SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | - Sophie Faure
- Université Clermont Auvergne CNRS, SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
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7
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Schneider AC, Fritz D, Vasquez JK, Vollrath SBL, Blackwell HE, Brasë S. Microwave-Facilitated SPOT-Synthesis of Antibacterial Dipeptoids. ACS COMBINATORIAL SCIENCE 2017; 19:715-737. [PMID: 29035557 PMCID: PMC5931720 DOI: 10.1021/acscombsci.7b00096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With microwave irradiation, the submonomer synthesis of dipeptoids on functionalized cellulose can be accelerated with good yields and purity. Optimization provided a library of 96 dipeptoids. From these, 29 compounds were found with an antibacterial activity against MRSA at a concentration of 25 μM. Large nonpolar residues, such as undecylamine and dehydroabiethylamine, are the key components engendering the observed antibacterial activity of these peptoids.
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Affiliation(s)
- Anne C. Schneider
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Daniel Fritz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Joseph K. Vasquez
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Sidonie B. L. Vollrath
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Stefan Brasë
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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8
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Molchanova N, Hansen PR, Franzyk H. Advances in Development of Antimicrobial Peptidomimetics as Potential Drugs. Molecules 2017; 22:E1430. [PMID: 28850098 PMCID: PMC6151827 DOI: 10.3390/molecules22091430] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 01/19/2023] Open
Abstract
The rapid emergence of multidrug-resistant pathogens has evolved into a global health problem as current treatment options are failing for infections caused by pan-resistant bacteria. Hence, novel antibiotics are in high demand, and for this reason antimicrobial peptides (AMPs) have attracted considerable interest, since they often show broad-spectrum activity, fast killing and high cell selectivity. However, the therapeutic potential of natural AMPs is limited by their short plasma half-life. Antimicrobial peptidomimetics mimic the structure and biological activity of AMPs, but display extended stability in the presence of biological matrices. In the present review, focus is on the developments reported in the last decade with respect to their design, synthesis, antimicrobial activity, cytotoxic side effects as well as their potential applications as anti-infective agents. Specifically, only peptidomimetics with a modular structure of residues connected via amide linkages will be discussed. These comprise the classes of α-peptoids (N-alkylated glycine oligomers), β-peptoids (N-alkylated β-alanine oligomers), β³-peptides, α/β³-peptides, α-peptide/β-peptoid hybrids, α/γ N-acylated N-aminoethylpeptides (AApeptides), and oligoacyllysines (OAKs). Such peptidomimetics are of particular interest due to their potent antimicrobial activity, versatile design, and convenient optimization via assembly by standard solid-phase procedures.
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Affiliation(s)
- Natalia Molchanova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
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9
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Antunes S, Corre JP, Mikaty G, Douat C, Goossens PL, Guichard G. Effect of replacing main-chain ureas with thiourea and guanidinium surrogates on the bactericidal activity of membrane active oligourea foldamers. Bioorg Med Chem 2017; 25:4245-4252. [PMID: 28687228 DOI: 10.1016/j.bmc.2017.04.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/22/2017] [Accepted: 04/28/2017] [Indexed: 12/11/2022]
Abstract
Membrane-active foldamers have recently emerged as potential mimics of antimicrobial peptides (AMPs). Amphiphilic cationic helical N,N'-linked oligoureas are one such class of AMP mimics with activities in vitro against a broad range of bacteria including Bacillus anthracis, a Gram-positive sporulating bacillus and causing agent of anthrax. Here we have used site-selective chemical modifications of the oligourea backbone to gain additional insight into the relationship between structure and function and modulate anthracidal activity. A series of analogues in which urea linkages at selected positions are replaced by thiourea and guanidium surrogates have been prepared on solid support and tested against different bacterial forms of B. anthracis (germinated spores and encapsulated bacilli). Urea→thiourea and urea→guanidinium replacements close to the negative end of the helix dipole led to analogues with increased potency and selectivity for B. anthracis versus mammalian cells.
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Affiliation(s)
- Stéphanie Antunes
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France; CNRS, CBMN, UMR 5248, F-33600 Pessac, France
| | - Jean-Philippe Corre
- HistoPathologie et Modèles Animaux/Pathogénie des Toxi-Infections Bactériennes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France
| | - Guillain Mikaty
- HistoPathologie et Modèles Animaux/Pathogénie des Toxi-Infections Bactériennes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France
| | - Céline Douat
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France; CNRS, CBMN, UMR 5248, F-33600 Pessac, France
| | - Pierre L Goossens
- HistoPathologie et Modèles Animaux/Pathogénie des Toxi-Infections Bactériennes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France.
| | - Gilles Guichard
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France; CNRS, CBMN, UMR 5248, F-33600 Pessac, France.
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10
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Abstract
Each year, the United States spends about $20 billion to treat people who have been infected with antibiotic resistant bacteria. Even so, the development of new antibiotics has slowed considerably since the mid-20th century. As a result, researchers are looking into developing synthetic compounds and materials with antimicrobial activities such as those made by the Schanze and Whitten groups [ACS Appl. Mater. Interfaces 3, 2820 (2011)]. Previously, they have demonstrated that poly(phenylene ethynylene) (PPE) based electrolytes and oligomeric end-only phenylene ethynylene (EO-OPE) based electrolytes possess strong biocidal activity. However, before the PPE and OPE can be used with humans, skin irritation tests are required to ensure their safety. In this work, in vitro skin assays are used to predict in vivo irritation. Tissues were conditioned for 24 h, exposed to test substances for 1 h, and then tested for viability using colorimetric and cytokine assays. Concentrations up to 50 μg/ml were tested. Viability assays and cytokine (IL-1α) assays demonstrated that the two polymers, three symmetric oligomers, and three "end only" oligomers were nonirritants. In addition, electrospun mats consisting of several promising compounds, including poly(caprolactone), were evaluated. Therefore, all test substances are conservatively classified as nonirritants after a 1 h exposure time period.
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11
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Design and Synthesis of a Novel N-(1H-tetrazol-5-yl)methyl Cyclic Peptoid Using Nosyl-protected N-(1-trityl-1H-tetrazol-5-yl)methyl Substituted Glycine. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9581-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Ganesh SD, Saha N, Zandraa O, Zuckermann RN, Sáha P. Peptoids and polypeptoids: biomimetic and bioinspired materials for biomedical applications. Polym Bull (Berl) 2017. [DOI: 10.1007/s00289-016-1902-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Knight AS, Zhou EY, Francis MB, Zuckermann RN. Sequence Programmable Peptoid Polymers for Diverse Materials Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5665-5691. [PMID: 25855478 DOI: 10.1002/adma.201500275] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/13/2015] [Indexed: 06/04/2023]
Abstract
Polymer sequence programmability is required for the diverse structures and complex properties that are achieved by native biological polymers, but efforts towards controlling the sequence of synthetic polymers are, by comparison, still in their infancy. Traditional polymers provide robust and chemically diverse materials, but synthetic control over their monomer sequences is limited. The modular and step-wise synthesis of peptoid polymers, on the other hand, allows for precise control over the monomer sequences, affording opportunities for these chains to fold into well-defined nanostructures. Hundreds of different side chains have been incorporated into peptoid polymers using efficient reaction chemistry, allowing for a seemingly infinite variety of possible synthetically accessible polymer sequences. Combinatorial discovery techniques have allowed the identification of functional polymers within large libraries of peptoids, and newly developed theoretical modeling tools specifically adapted for peptoids enable the future design of polymers with desired functions. Work towards controlling the three-dimensional structure of peptoids, from the conformation of the amide bond to the formation of protein-like tertiary structure, has and will continue to enable the construction of tunable and innovative nanomaterials that bridge the gap between natural and synthetic polymers.
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Affiliation(s)
- Abigail S Knight
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Effie Y Zhou
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Matthew B Francis
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ronald N Zuckermann
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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14
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Lee J, Huang W, Broering JM, Barron AE, Seo J. Prostate tumor specific peptide-peptoid hybrid prodrugs. Bioorg Med Chem Lett 2015; 25:2849-52. [PMID: 26022845 DOI: 10.1016/j.bmcl.2015.04.092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/17/2015] [Accepted: 04/30/2015] [Indexed: 11/30/2022]
Abstract
Inspired by naturally occurring host defense peptides, cationic amphipathic peptoids provide a promising scaffold for anti-cancer therapeutics. Herein, we report a library of peptide-peptoid hybrid prodrugs that can be selectively activated by prostate cancer cells. We have identified several compounds demonstrating potent anti-cancer activity with good to moderate selectivity. We believe that these prodrugs can provide a useful design principle for next generation peptide-peptoid hybrid prodrugs.
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Affiliation(s)
- Jiyoun Lee
- Department of Global Medical Science, Sungshin University, Seoul 142-732, Republic of Korea
| | - Wei Huang
- Department of Bioengineering, Stanford University, Palo Alto, CA 94305, USA
| | - James M Broering
- Department of Bioengineering, Stanford University, Palo Alto, CA 94305, USA
| | - Annelise E Barron
- Department of Bioengineering, Stanford University, Palo Alto, CA 94305, USA.
| | - Jiwon Seo
- Division of Liberal Arts and Sciences and Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan gwagiro, Buk-gu, Gwangju 500-712, Republic of Korea.
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15
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Brooks BD, Brooks AE. Therapeutic strategies to combat antibiotic resistance. Adv Drug Deliv Rev 2014; 78:14-27. [PMID: 25450262 DOI: 10.1016/j.addr.2014.10.027] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 10/20/2014] [Accepted: 10/22/2014] [Indexed: 12/16/2022]
Abstract
With multidrug resistant bacteria on the rise, new antibiotic approaches are required. Although a number of new small molecule antibiotics are currently in the development pipeline with many more in preclinical development, the clinical options and practices for infection control must be expanded. Biologics and non-antibiotic adjuvants offer this opportunity for expansion. Nevertheless, to avoid known mechanisms of resistance, intelligent combination approaches for multiple simultaneous and complimentary therapies must be designed. Combination approaches should extend beyond biologically active molecules to include smart controlled delivery strategies. Infection control must integrate antimicrobial stewardship, new antibiotic molecules, biologics, and delivery strategies into effective combination therapies designed to 1) fight the infection, 2) avoid resistance, and 3) protect the natural microbiome. This review explores these developing strategies in the context of circumventing current mechanisms of resistance.
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Affiliation(s)
| | - Amanda E Brooks
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA; Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND58108, USA.
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16
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Pipkorn R, Braun K, Wiessler M, Waldeck W, Schrenk HH, Koch M, Semmler W, Komljenovic D. A peptide & peptide nucleic acid synthesis technology for transporter molecules and theranostics--the SPPS. Int J Med Sci 2014; 11:697-706. [PMID: 24843319 PMCID: PMC4025169 DOI: 10.7150/ijms.8168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/25/2014] [Indexed: 11/20/2022] Open
Abstract
Advances in imaging diagnostics using magnetic resonance tomography (MRT), positron emission tomography (PET) and fluorescence imaging including near infrared (NIR) imaging methods are facilitated by constant improvement of the concepts of peptide synthesis. Feasible patient-specific theranostic platforms in the personalized medicine are particularly dependent on efficient and clinically applicable peptide constructs. The role of peptides in the interrelations between the structure and function of proteins is widely investigated, especially by using computer-assisted methods. Nowadays the solid phase synthesis (SPPS) chemistry emerges as a key technology and is considered as a promising methodology to design peptides for the investigation of molecular pharmacological processes at the transcriptional level. SPPS syntheses could be carried out in core facilities producing peptides for large-scale scientific implementations as presented here.
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Affiliation(s)
- Ruediger Pipkorn
- 1. German Cancer Research Center, Dept. of Translational Immunology, INF 410, D-69120 Heidelberg, Germany
| | - Klaus Braun
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Manfred Wiessler
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Waldemar Waldeck
- 3. German Cancer Research Center, Division of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Hans-Hermann Schrenk
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Mario Koch
- 1. German Cancer Research Center, Dept. of Translational Immunology, INF 410, D-69120 Heidelberg, Germany
| | - Wolfhard Semmler
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Dorde Komljenovic
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
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Wilde KN, Whitten DG, Canavan HE. In vitro cytotoxicity of antimicrobial conjugated electrolytes: interactions with mammalian cells. ACS APPLIED MATERIALS & INTERFACES 2013; 5:9305-11. [PMID: 24102342 DOI: 10.1021/am402476g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
An estimated 19 000 deaths and $3-4 billion in health care costs per year in the United States are attributed to methicillin-resistant Staphlococcus aureus (MRSA) infections. Certain conjugated phenylene ethynylene (CPE)-based polymers (PPE) and oligomers (OPE) have been demonstrated to exhibit dark and light-activated antimicrobial activity. Until recently, the relative cytotoxicity of these PPEs and OPEs toward mammalian cells haas been unknown, limiting the applications for which they may be used (e.g., reducing and/or preventing the spread of untreatable bacterial strains). In this work, we examine the toxicity of CPEs to mammalian cells using cytotoxicity assays of cellular monolayers. Eight CPEs, two PPEs and six OPEs, were selected for these studies based on their biocidal activity, and diversity of repeat unit number and functional groups. Briefly, two cell types were exposed to CPEs at concentrations ranging from 1-100 ug/mL for 24 h. We find that concentration largely determines the resulting viability of cells, although at intermediate concentrations (5-10 ug/mL), the effect of light on light-activated compounds is very important. Furthermore, we find that the longer-chained compounds are cytotoxic at much higher concentrations, and therefore have the widest range of concentrations available for potential applications.
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Affiliation(s)
- Kristin N Wilde
- Center for Biomedical Engineering, Department of Chemical and Nuclear Engineering, MSC01-1141, University of New Mexico , Albuquerque, New Mexico 87131, United States
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Huang ML, Shin SBY, Benson MA, Torres VJ, Kirshenbaum K. A Comparison of Linear and Cyclic Peptoid Oligomers as Potent Antimicrobial Agents. ChemMedChem 2011; 7:114-22. [DOI: 10.1002/cmdc.201100358] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/08/2011] [Indexed: 01/02/2023]
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Robinson JA. Protein epitope mimetics as anti-infectives. Curr Opin Chem Biol 2011; 15:379-86. [PMID: 21419690 DOI: 10.1016/j.cbpa.2011.02.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/17/2011] [Indexed: 01/09/2023]
Abstract
There is growing interest in the design of synthetic molecules that mimic the structures and functions of epitopes found on the surface of peptides and proteins. Epitope mimetics can provide valuable tools to probe complex biological processes, as well as interesting leads for drug and vaccine discovery. One application of epitope mimetics is reviewed here, focusing on mimetics of the cationic antimicrobial peptides that form part of the innate immune response to microbial and viral infection in many organisms. Mimetics of these naturally occurring peptides and proteins may be useful to explore mechanisms of antimicrobial and immunomodulatory action, and as a potential source of new antibiotics to address one of the most pressing current threats to human health.
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Affiliation(s)
- John A Robinson
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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20
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Godballe T, Nilsson LL, Petersen PD, Jenssen H. Antimicrobial β-Peptides and α-Peptoids. Chem Biol Drug Des 2011; 77:107-16. [DOI: 10.1111/j.1747-0285.2010.01067.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Nandel FS, Saini A. Peptoids with aliphatic sidechains as helical structures without hydrogen bonds and collagen/ inverse-collagen type structures. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/jbpc.2011.21006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Bang JK, Nan YH, Lee EK, Shin SY. A Novel Trp-rich Model Antimicrobial Peptoid with Increased Protease Stability. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.9.2509] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Culf AS, Ouellette RJ. Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives. Molecules 2010; 15:5282-335. [PMID: 20714299 PMCID: PMC6257730 DOI: 10.3390/molecules15085282] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/14/2010] [Accepted: 08/02/2010] [Indexed: 12/02/2022] Open
Abstract
Peptoids (N-substituted polyglycines and extended peptoids with variant backbone amino-acid monomer units) are oligomeric synthetic polymers that are becoming a valuable molecular tool in the biosciences. Of particular interest are their applications to the exploration of peptoid secondary structures and drug design. Major advantages of peptoids as research and pharmaceutical tools include the ease and economy of synthesis, highly variable backbone and side-chain chemistry possibilities. At the same time, peptoids have been demonstrated as highly active in biological systems while resistant to proteolytic decay. This review with 227 references considers the solid-phase synthetic aspects of peptoid preparation and utilization up to 2010 from the instigation, by R. N. Zuckermann et al., of peptoid chemistry in 1992.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute, Moncton, NB, Canada.
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24
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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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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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26
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Levengood MR, Kerwood CC, Chatterjee C, van der Donk WA. Investigation of the substrate specificity of lacticin 481 synthetase by using nonproteinogenic amino acids. Chembiochem 2009; 10:911-9. [PMID: 19222036 PMCID: PMC2737179 DOI: 10.1002/cbic.200800752] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Indexed: 11/10/2022]
Abstract
Lantibiotics are peptide antimicrobial compounds that are characterized by the thioether-bridged amino acids lanthionine and methyllanthionine. For lacticin 481, these structures are installed in a two-step post-translational modification process by a bifunctional enzyme, lacticin 481 synthetase (LctM). LctM catalyzes the dehydration of Ser and Thr residues to generate dehydroalanine or dehydrobutyrine, respectively, and the subsequent intramolecular regio- and stereospecific Michael-type addition of cysteines onto the dehydroamino acids. In this study, semisynthetic substrates containing nonproteinogenic amino acids were prepared by expressed protein ligation and [3+2]-cycloaddition of azide and alkyne-functionalized peptides. LctM demonstrated broad substrate specificity toward substrates containing beta-amino acids, D-amino acids, and N-alkyl amino acids (peptoids) in certain regions of its peptide substrate. These findings showcase its promise for use in lantibiotic and peptide-engineering applications, whereby nonproteinogenic amino acids might impart improved stability or modulated biological activities. Furthermore, LctM permitted the incorporation of an alkyne-containing amino acid that can be utilized for the site-selective modification of mature lantibiotics and used in target identification.
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Affiliation(s)
| | | | | | - Wilfred A. van der Donk
- M.R. Levengood, C.C. Kerwood, C. Chatterjee, Prof. W.A. van der Donk Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 Fax: (217) 244-8533 E-mail:
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27
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Fowler SA, Blackwell HE. Structure-function relationships in peptoids: recent advances toward deciphering the structural requirements for biological function. Org Biomol Chem 2009; 7:1508-24. [PMID: 19343235 DOI: 10.1039/b817980h] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligomers of N-substituted glycine, or peptoids, are versatile tools to probe biological processes and hold promise as therapeutic agents. An underlying theme in the majority of recent peptoid research is the connection between peptoid function and peptoid structure. For certain applications, well-folded peptoids are essential for activity, while unstructured peptoids appear to suffice, or even are superior, for other applications. Currently, these structure-function connections are largely made after the design, synthesis, and characterization process. However, as guidelines for peptoid folding are elucidated and the known biological activities are expanded, we anticipate these connections will provide a pathway toward the de novo design of functional peptoids. In this perspective, we review several of the peptoid structure-function relationships that have been delineated over the past five years.
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Affiliation(s)
- Sarah A Fowler
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
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28
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Messeguer J, Cortés N, García-Sanz N, Navarro-Vendrell G, Ferrer-Montiel A, Messeguer A. Synthesis of a positional scanning library of pentamers of N-alkylglycines assisted by microwave activation and validation via the identification of trypsin inhibitors. ACTA ACUST UNITED AC 2008; 10:974-80. [PMID: 18847288 DOI: 10.1021/cc800144x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A positional scanning library of 625 N-alkylglycine pentamers has been synthesized on solid-phase, employing a set of 10 commercially available primary amines as a source of chemical diversity. The iterative synthetic steps were carried out in tea bags and accelerated by using microwave assisted organic synthesis (MAOS). The reactivity study of the primary amines used as diversity sources led to determine their relative reactivity values and equireactivity factors, which were applied to the library synthesis to ensure comparable concentrations of all final oligomers in the mixtures. This library was validated by the screening, deconvolution, and identification of trypsin inhibitors. These compounds are of potential interest for controlling the intracellular transport of TRPV1 channel.
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Affiliation(s)
- Joaquim Messeguer
- Department of Chemical and Biomolecular Nanotechnology, Instituto de Quimica Avancada de Catalunya (IQAC), CSIC, Jordi Girona 18, 08034 Barcelona, Spain
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29
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Gabriel GJ, Som A, Madkour AE, Eren T, Tew GN. Infectious Disease: Connecting Innate Immunity to Biocidal Polymers. MATERIALS SCIENCE & ENGINEERING. R, REPORTS : A REVIEW JOURNAL 2007; 57:28-64. [PMID: 18160969 PMCID: PMC2153456 DOI: 10.1016/j.mser.2007.03.002] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Infectious disease is a critically important global healthcare issue. In the U.S. alone there are 2 million new cases of hospital-acquired infections annually leading to 90,000 deaths and 5 billion dollars of added healthcare costs. Couple these numbers with the appearance of new antibiotic resistant bacterial strains and the increasing occurrences of community-type outbreaks, and clearly this is an important problem. Our review attempts to bridge the research areas of natural host defense peptides (HDPs), a component of the innate immune system, and biocidal cationic polymers. Recently discovered peptidomimetics and other synthetic mimics of HDPs, that can be short oligomers as well as polymeric macromolecules, provide a unique link between these two areas. An emerging class of these mimics are the facially amphiphilic polymers that aim to emulate the physicochemical properties of HDPs but take advantage of the synthetic ease of polymers. These mimics have been designed with antimicrobial activity and, importantly, selectivity that rivals natural HDPs. In addition to providing some perspective on HDPs, selective mimics, and biocidal polymers, focus is given to the arsenal of biophysical techniques available to study their mode of action and interactions with phospholipid membranes. The issue of lipid type is highlighted and the important role of negative curvature lipids is illustrated. Finally, materials applications (for instance, in the development of permanently antibacterial surfaces) are discussed as this is an important part of controlling the spread of infectious disease.
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Affiliation(s)
- Gregory J Gabriel
- Polymer Science & Engineering Department, University of Massachusetts, 120 Governors Drive, Amherst, MA 01003
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30
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Edwards P. Peptoid positional scanning libraries for identification of multidrug resistance reversal agents. Drug Discov Today 2006. [DOI: 10.1016/j.drudis.2006.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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31
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Ryge TS, Hansen PR. Potent antibacterial lysine-peptoid hybrids identified from a positional scanning combinatorial library. Bioorg Med Chem 2006; 14:4444-51. [PMID: 16524733 DOI: 10.1016/j.bmc.2006.02.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 02/10/2006] [Accepted: 02/17/2006] [Indexed: 10/24/2022]
Abstract
In this paper, we describe the synthesis and screening of a biased positional scanning library made up of peptoids (N-alkylglycines) and lysines. The library consisted of 100 mixtures divided into four sub-libraries; OXXXKKK, XOXXKKK, XXOXKKK, and XXXOKKK, O being a defined peptoid building block and X a mixture of 25 peptoid building blocks. A theoretical number of 390,625 compounds were synthesized. The compound mixtures were screened against the American Type Culture Collection (ATCC) Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922 bacterial strains, and the cytotoxic activities were assessed using a human blood hemolytic assay. The results from each sub-library were examined to identify the most potent amine at each position. On the basis of this knowledge eight new lysine-peptoid hybrids were synthesized and tested in the biological assays. One compound in particular, [N-(cyclohexylmethyl)glycyl]-[N-(1-methylhexyl)glycyl]-[N-(4-methylbenzyl)glycyl]-[N-(2-(3-chlorophenyl)ethyl)glycyl]-lysyl-lysyl-lysine amide, showed high antibacterial activity and low toxicity toward red blood cells.
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Affiliation(s)
- Trine S Ryge
- Department of Natural Sciences, KVL, Frederiksberg, Copenhagen, Denmark
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32
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Abstract
Here we report the design, synthesis and antibacterial activity of 20 lysine-peptoid hybrids. The hybrids are based on the peptoid lead structure [N-(1-naphthalenemethyl)glycyl]-[N-(4-methylbenzyl)glycyl]-[N-(1-naphthalenemethyl)glycyl]-N-(butyl)glycin amide (1) and contain between one and six lysine residues each. The compounds were tested for antibacterial activity against S. aureus ATCC 25923 and E. coli ATCC 25922. Furthermore, the hemolytic activity toward human erythrocytes was assessed. Several compounds with potent antibacterial activity and low hemolytic activity were identified.
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Affiliation(s)
- Trine S Ryge
- Department of Natural Sciences, Section of Bioorganic Chemistry, Royal Veterinary and Agricultural University, Copenhagen, Denmark
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33
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Shuey SW, Delaney WJ, Shah MC, Scialdone MA. Antimicrobial beta-peptoids by a block synthesis approach. Bioorg Med Chem Lett 2005; 16:1245-8. [PMID: 16384703 DOI: 10.1016/j.bmcl.2005.11.075] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 11/18/2005] [Accepted: 11/21/2005] [Indexed: 10/25/2022]
Abstract
Antimicrobial peptides and their mimetics offer a potential new disinfective tool. beta-Peptoids (oligo-N-substituted beta-alanines) were synthesized and investigated for antimicrobial activity. A block approach whereby di- and tri-beta-peptoids were first prepared and then ligated via amide bond formation to synthesize larger beta-peptoids was developed. The beta-peptoids were found to possess moderate activity in an Escheridchia coli assay.
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Affiliation(s)
- Steven W Shuey
- DuPont Central Research and Development, PO Box 80328, Experimental Station, Wilmington, DE 19880-0328, USA.
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Masip I, Cortés N, Abad MJ, Guardiola M, Pérez-Payá E, Ferragut J, Ferrer-Montiel A, Messeguer A. Design and synthesis of an optimized positional scanning library of peptoids: identification of novel multidrug resistance reversal agents. Bioorg Med Chem 2005; 13:1923-9. [PMID: 15727848 DOI: 10.1016/j.bmc.2005.01.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Revised: 01/10/2005] [Accepted: 01/14/2005] [Indexed: 11/30/2022]
Abstract
Herein is reported the optimized solid-phase synthesis of a library of 5,120 trimeric N-alkylglycines (peptoids) using the positional scanning format and the submonomer strategy. Diversity at the N-terminal position was generated from 20 commercially available primary amines, whereas 16 primary amines were employed for the middle and C-terminal positions of the trimers. Formation of undesirable side-products observed in a previous library synthesis (Humet, M. et al. J. Comb. Chem. 2003, 5, 597-605) was averted by restricting the use of primary amines functionalized with tertiary amino groups to the third amination step. Screening of the new library for the identification of chemosensitizers yielded two peptoids, compounds 1 and 2, with potent in vitro activity as multidrug resistance (MDR) reversal agents. The structures of the lead peptoids are consistent with a pharmacophore model generated from the interaction of various known inhibitors with the MDR-implicated transmembrane glycoprotein P-gp.
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Affiliation(s)
- Isabel Masip
- Department of Biological Organic Chemistry, I.I.Q.A.B. (C.S.I.C.), J. Girona, 18, E-08034 Barcelona, Spain
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35
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Tang YC, Deber CM. Aqueous solubility and membrane interactions of hydrophobic peptides with peptoid tags. Biopolymers 2004; 76:110-8. [PMID: 15054891 DOI: 10.1002/bip.10566] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lysine tagging of hydrophobic peptides of parent sequence KKAAALAAAAALAAWAALAAAKKKK-NH(2) has been shown to facilitate their synthesis and purification through water solubilization, yet not impact on the intrinsic properties of the hydrophobic core sequence with respect to its insertion into membranes in an alpha-helical conformation. However, due to their positively charged character, such peptides often become bound to phospholipid head groups in membrane surfaces, which inhibits their transbilayer insertion and/or prevents their transport across cellular bilayers. We sought to develop more neutral peptides of membrane-permeable character by replacing most Lys residues with uncharged peptoid [N-(R)glycyl] residues, which might similarly confer water solubility while retaining membrane-interactive properties of the hydrophobic core. Several "peptoid-tagged" derivatives of the parent peptide were prepared with varying peptoid content, with five of the six Lys residues replaced with peptoids Nala and/or Nval. Conformations of these peptides measured by circular dichroism spectroscopy demonstrated that these water-soluble peptides retain the alpha-helix structure in micelles (lysophosphatidylcholine and sodium dodecyl sulfate) notwithstanding the known helix-breaking capacity of the peptoid tags. Blue shifts in Trp fluorescence spectra and quenching experiments with acrylamide confirmed that peptoid-tagged peptides insert spontaneously into micellar membranes. Results suggest that upon introduction of uncharged tags, the interaction between the membrane and the peptides is dominated by the hydrophobicity of the peptide core rather than the electrostatic interactions between the Lys and the head groups of the lipids. The overall findings indicate that peptoid residues are effective surrogates for Lys as uncharged water-solubilizing tags and, as such, provide a potentially valuable feature of design of membrane-interactive peptides.
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Affiliation(s)
- Yan-Chun Tang
- Division of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
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36
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Murphy MB, Fuller ST, Richardson PM, Doyle SA. An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res 2003; 31:e110. [PMID: 12954786 PMCID: PMC203336 DOI: 10.1093/nar/gng110] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the key components of proteomics initiatives is the production of high affinity ligands or probes that specifically recognize protein targets in assays that detect and capture proteins of interest. Particularly versatile probes with tremendous potential for use as affinity molecules are aptamers. Aptamers are short single-stranded DNA or RNA sequences that are selected in vitro based on affinity for a target molecule. Aptamers offer advantages over traditional antibody-based affinity molecules in their ease of production, regeneration and stability, largely due to the chemical properties of nucleic acids versus amino acids. We describe an improved in vitro selection protocol that relies on magnetic separations for DNA aptamer production that is relatively easy and scalable without the need for expensive robotics. We demonstrate the ability of aptamers that recognize thyroid transcription factor 1 (TTF1) to bind their target protein with high affinity and specificity, and detail their uses in a number of assays. The TTF1 aptamers were characterized using surface plasmon resonance, and shown to be useful for enzyme-linked assays, western blots and affinity purification.
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Affiliation(s)
- Michael B Murphy
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Burkoth TS, Fafarman AT, Charych DH, Connolly MD, Zuckermann RN. Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis. J Am Chem Soc 2003; 125:8841-5. [PMID: 12862480 DOI: 10.1021/ja0352101] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptoids (N-substituted glycines) are an important class of biomimetic oligomers that have made a significant impact in the areas of combinatorial drug discovery, gene therapy, drug delivery, and biopolymer folding in recent years. Sequence-specific peptoid oligomers are easily assembled from primary amines by the solid-phase submonomer method. However, most amines that contain heterocyclic nitrogens in the side chain do not incorporate efficiently. We present here a straightforward revision of the submonomer method that allows efficient incorporation of unprotected imidazoles, pyridines, pyrazines, indoles, and quinolines into oligomers as long as 15 monomers in length. This improved method uses chloroacetic acid instead of bromoacetic acid in the acylation step of the monomer addition cycle, and allows for the incorporation of new side chains that should enable the synthesis of peptoids with entirely new properties.
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Affiliation(s)
- Timothy S Burkoth
- Chiron Corporation, 4560 Horton Street, Emeryville, California 94608, USA
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Tang YC, Deber CM. Hydrophobicity and helicity of membrane-interactive peptides containing peptoid residues. Biopolymers 2002; 65:254-62. [PMID: 12382286 DOI: 10.1002/bip.10236] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Peptoid (N-alkylglycyl) residues in peptides have been studied in a variety of applications, but their behavior in membrane environments has not been systematically investigated. We have synthesized a series of membrane-interactive peptides of prototypic structure KKAAAXAAAAAXAAWAAXAAAKKKK-amide, where X corresponds to the peptoid residues Nala (= sarcosine), Nval, Nile, Nleu, Nphe, and Ntrp. Investigation of their relative hydrophobic character by high-performance liquid chromatography indicated an order of hydrophobicity Ntrp > Nphe > Nleu > Nile > Nval > Nala-largely parallel to the relative scale for these side-chains in natural amino acids, although all values were significantly more "hydrophilic" than their amino acid correspondents. Conformations of peptoid-containing peptides measured by circular dichroism spectroscopy were unordered in the presence of SDS micelles but helical for peptides with X = the corresponding amino acids, suggesting a general helix-breaking tendency for the peptoid residues. However, peptides were able to form helical structures in the solvent n-butanol, indicating that this conformation is possible if peptides became inserted into micellar phases. The latter notion was confirmed by increasing hydrophobic content of the peptides by embedding peptoid Nala residues in Leu-rich rather than Ala-rich sequences, which promoted peptide insertion and helical structure in micelles. The overall results suggest that judicious interspersing of amino acid and peptoid residues in peptide sequences can produce hydrophobic water-soluble materials with membrane-partitioning capacity.
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Affiliation(s)
- Yan-Chun Tang
- Division of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
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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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Ruijtenbeek R, Kruijtzer JAW, van de Wiel W, Fischer MJE, Flück M, Redegeld FAM, Liskamp RMJ, Nijkamp FP. Peptoid-Peptide Hybrids That Bind Syk SH2 Domains Involved in Signal Transduction. Chembiochem 2001. [DOI: 10.1002/1439-7633(20010302)2:3%3c171::aid-cbic171%3e3.0.co;2-b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ruijtenbeek R, Kruijtzer JA, van de Wiel W, Fischer MJ, Flück M, Redegeld FA, Liskamp RM, Nijkamp FP. Peptoid - peptide hybrids that bind Syk SH2 domains involved in signal transduction. Chembiochem 2001; 2:171-9. [PMID: 11828442 DOI: 10.1002/1439-7633(20010302)2:3<171::aid-cbic171>3.0.co;2-b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peptoid-peptide hybrids are oligomeric peptidomimetics that contain one or more N-substituted glycine residues. In these hybrids, the side chains of one or several amino acids are "shifted" from the alpha-carbon atom to the amide nitrogen atom. A library of phosphorylated peptoid-peptide hybrids derived from the sequence pTyr-Glu-Thr-Leu was synthesized and tested for binding to the tandem SH2 domain of the protein tyrosine kinase Syk. A considerable influence of the side chain position was observed. Compounds 19-21, 24, and 25 comprising a peptoid NpTyr and/or NGlu residue did not show any binding. Compounds 22, 23, and 26 containing an NhThr (hThr=homothreonine) and/or NLeu peptoid residue showed binding with IC(50) values that were only five to eight times higher than that of the tetrapeptide lead compound 18. These data show that side chain shifting is possible with retention of binding capacity, but only at the two C-terminal residues of the tetramer. This method of a peptoid scan using peptoid-peptide hybrids appears to be very useful to explore to what extent a peptide sequence can be transformed into a peptoid while retaining its affinity.
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Affiliation(s)
- R Ruijtenbeek
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, PO Box 80.082, 3508 TB Utrecht, The Netherlands
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