1
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Wilson S, Panagabko C, Laleye T, Robinson M, Jagas S, Bowman D, Atkinson J. Synthesis of a photocleavable bola-phosphatidylcholine. Bioorg Med Chem 2023; 93:117465. [PMID: 37688997 DOI: 10.1016/j.bmc.2023.117465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/11/2023]
Abstract
Phosphatidylinositol transfer proteins (PITPs) are ubiquitous in eukaryotes and are involved in the regulation of phospholipid metabolism, membrane trafficking, and signal transduction. Sec14 is a yeast PITP that has been shown to transfer phosphatidylinositol (PI) or phosphatidylcholine (PC) from the endoplasmic reticulum to the Golgi. It is now believed that Sec14 may play a greater role than just shuttling PI and PC throughout the cell. Genetic evidence suggests that retrieval of membrane-bound PI by Sec14 also manages to present PI to the phosphatidylinositol-4-kinase, Pik1, to generate phosphatidylinositol-4-phosphate, PI(4)P. To test this hypothetical model, we designed a photocleavable bolalipid to span the entire membrane, having one phosphatidylcholine or phosphatidylinositol headgroup on each leaflet connected by a photocleavable diacid. Sec14 should not be able to present the bola-PI to Pik1 for phosphorylation as the head group will be difficult to lift from the bilayer as it is tethered on the opposite leaflet. After photocleavage the two halves would behave as a normal phospholipid, thus phosphorylation by Pik1 would resume. We report here the synthesis of a photocleavable bola-PC, a precursor to the desired bola-PI. The mono-photocleavable bola-PC lipid was designed to contain two glycerol molecules with choline head groups connected through a phosphodiester bond at the sn3 position. Each glycerol was acylated with palmitic acid at the sn1 position. These two glycerol moieties were then connected through their respective sn2 hydroxyls via a photocleavable dicarboxylic acid containing a nitrophenyl ethyl photolabile protecting group. The bola-PC and its precursors were found to undergo efficient photocleavage when irradiated in solution or in vesicles with 365 nm light for two minutes. Treatment of the bola-PC with a mutant phospholipase D and myo-inositol produced a mono-inositol bola-PC-PI.
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Affiliation(s)
- Sean Wilson
- Department of Chemistry, Brock University, Ontario, Canada
| | | | - Tayo Laleye
- Department of Chemistry, Brock University, Ontario, Canada
| | | | - Samuel Jagas
- Department of Chemistry, Brock University, Ontario, Canada
| | - David Bowman
- Advanced Biomanufacturing Centre, Brock University, Ontario, Canada
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2
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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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3
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Ghosh P, Rozenberg I, Maayan G. Sequence-function relationship within water-soluble Peptoid Chelators for Cu 2. J Inorg Biochem 2021; 217:111388. [PMID: 33618230 DOI: 10.1016/j.jinorgbio.2021.111388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022]
Abstract
Chelation of Cu2+ by synthetic molecules is an emerging therapeutic approach for treating several illnesses in human body such as Wilson disease, cancer and more. Among synthetic metal chelators, those based on peptoids - N-substituted glycine oligomers - are advantageous due to their structural similarity to peptides, ease of synthesis on solid support and versatile controlled sequences. Tuning peptoid sequences, via systematically changing at least one side chain, can facilitate and control their function. Along these lines, this work aims to explore the role of the non-coordinating side chain within peptoid chelators in order to understand the factors that control the selectivity of these chelators to Cu2+ in water medium. To this aim, a set of peptoid trimers having a pyridine group at the acetylated N-terminal, a 2,2'-bipyridine group at the second position and a non-coordinating group at the C-terminus, where the latter is systematically varied between aromatic, aliphatic, chiral or non-chiral, were investigated as selective chelators for Cu2+. The effect of the position of the non-coordinating group on the selectivity of the peptoid to Cu2+ was also tested. Based on extensive spectroscopic data, we found that the choice of the non-coordinating group along with its position dramatically influences the selectivity of the peptoids to Cu2+. We showed that peptoids having bulky chiral groups at the C-terminus enable high selectivity to Cu2+. We further demonstrated the ability of one of the selective chelators to remove Cu2+ from the natural copper binding protein metallothionein in HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) buffer medium.
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Affiliation(s)
- Pritam Ghosh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 3200008, Israel
| | - Ido Rozenberg
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 3200008, Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 3200008, Israel.
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4
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Ghosh P, Maayan G. A Water‐Soluble Peptoid that Can Extract Cu
2+
from Metallothionein via Selective Recognition. Chemistry 2020; 27:1383-1389. [DOI: 10.1002/chem.202003711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/27/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Pritam Ghosh
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Technion City Haifa 3200008 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Technion City Haifa 3200008 Israel
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5
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Wellhöfer I, Frydenvang K, Kotesova S, Christiansen AM, Laursen JS, Olsen CA. Functionalized Helical β-Peptoids. J Org Chem 2019; 84:3762-3779. [DOI: 10.1021/acs.joc.9b00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Isabelle Wellhöfer
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Simona Kotesova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Andreas M. Christiansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jonas S. Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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6
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Gimenez D, Zhou G, Hurley MFD, Aguilar JA, Voelz VA, Cobb SL. Fluorinated Aromatic Monomers as Building Blocks To Control α-Peptoid Conformation and Structure. J Am Chem Soc 2019; 141:3430-3434. [PMID: 30739443 DOI: 10.1021/jacs.8b13498] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptoids are peptidomimetics of interest in the fields of drug development and biomaterials. However, obtaining stable secondary structures is challenging, and designing these requires effective control of the peptoid tertiary amide cis/trans equilibrium. Herein, we report new fluorine-containing aromatic monomers that can control peptoid conformation. Specifically, we demonstrate that a fluoro-pyridine group can be used to circumvent the need for monomer chirality to control the cis/trans equilibrium. We also show that incorporation of a trifluoro-methyl group ( NCF3Rpe) rather than a methyl group ( NRpe) at the α-carbon of a monomer gives rise to a 5-fold increase in cis-isomer preference.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry , Durham University , South Road , Durham DH1 3LE , U.K
| | - Guangfeng Zhou
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Matthew F D Hurley
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Juan A Aguilar
- Department of Chemistry , Durham University , South Road , Durham DH1 3LE , U.K
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Steven L Cobb
- Department of Chemistry , Durham University , South Road , Durham DH1 3LE , U.K
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7
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Gimenez D, Aguilar JA, Bromley EHC, Cobb SL. Stabilising Peptoid Helices Using Non‐Chiral Fluoroalkyl Monomers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Diana Gimenez
- Department of ChemistryDurham University South Road Durham DH1 3LE UK
| | - Juan A. Aguilar
- Department of ChemistryDurham University South Road Durham DH1 3LE UK
| | | | - Steven L. Cobb
- Department of ChemistryDurham University South Road Durham DH1 3LE UK
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8
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Gimenez D, Aguilar JA, Bromley EHC, Cobb SL. Stabilising Peptoid Helices Using Non-Chiral Fluoroalkyl Monomers. Angew Chem Int Ed Engl 2018; 57:10549-10553. [PMID: 29846037 PMCID: PMC6099454 DOI: 10.1002/anie.201804488] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/18/2018] [Indexed: 01/15/2023]
Abstract
Stability towards protease degradation combined with modular synthesis has made peptoids of considerable interest in the fields of chemical biology, medicine, and biomaterials. Given their tertiary amide backbone, peptoids lack the capacity to hydrogen-bond, and as such, controlling secondary structure can be challenging. The incorporation of bulky, charged, or chiral aromatic monomers can be used to control conformation but such building blocks limit applications in many areas. Through NMR and X-ray analysis we demonstrate that non-chiral neutral fluoroalkyl monomers can be used to influence the Kcis/trans equilibria of peptoid amide bonds in model systems. The cis-isomer preference displayed is highly unprecedented given that neither chirality nor charge is used to control the peptoid amide conformation. The application of our fluoroalkyl monomers in the design of a series of linear peptoid oligomers that exhibit stable helical structures is also reported.
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Affiliation(s)
- Diana Gimenez
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Juan A. Aguilar
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
| | | | - Steven L. Cobb
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
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9
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Young SC. A Systematic Review of Antiamyloidogenic and Metal-Chelating Peptoids: Two Structural Motifs for the Treatment of Alzheimer's Disease. Molecules 2018; 23:E296. [PMID: 29385058 PMCID: PMC6017092 DOI: 10.3390/molecules23020296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 11/17/2022] Open
Abstract
Alzheimer's disease (AD) is an incurable form of dementia affecting millions of people worldwide and costing billions of dollars in health care-related payments, making the discovery of a cure a top health, societal, and economic priority. Peptide-based drugs and immunotherapies targeting AD-associated beta-amyloid (Aβ) aggregation have been extensively explored; however, their therapeutic potential is limited by unfavorable pharmacokinetic (PK) properties. Peptoids (N-substituted glycine oligomers) are a promising class of peptidomimetics with highly tunable secondary structures and enhanced stabilities and membrane permeabilities. In this review, the biological activities, structures, and physicochemical properties for several amyloid-targeting peptoids will be described. In addition, metal-chelating peptoids with the potential to treat AD will be discussed since there are connections between the dysregulation of certain metals and the amyloid pathway.
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Affiliation(s)
- Sherri C Young
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, PA 18104, USA.
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10
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Martínez-Quiroz M, Ochoa-Terán A, Aguilar-Martínez M, García-Elías J, Santacruz Ortega H, Miranda-Soto V, Pina-Luis G. New fluorescent metal receptors based on 4,4′-carbonyl bis(carbamoylbenzoic) acid analogues with naphthalene fluorophore. Supramol Chem 2017. [DOI: 10.1080/10610278.2016.1277585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marisela Martínez-Quiroz
- Centro de Graduados e Investigación en Química, Instituto Tecnológico de Tijuana, Tijuana, Mexico
| | - Adrián Ochoa-Terán
- Centro de Graduados e Investigación en Química, Instituto Tecnológico de Tijuana, Tijuana, Mexico
| | | | - José García-Elías
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Hisila Santacruz Ortega
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
| | - Valentín Miranda-Soto
- Centro de Graduados e Investigación en Química, Instituto Tecnológico de Tijuana, Tijuana, Mexico
| | - Georgina Pina-Luis
- Centro de Graduados e Investigación en Química, Instituto Tecnológico de Tijuana, Tijuana, Mexico
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11
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Nalband DM, Warner BP, Zahler NH, Kirshenbaum K. Rapid identification of metal-binding peptoid oligomers by on-resin X-ray fluorescence screening. Biopolymers 2016; 102:407-15. [PMID: 25059748 DOI: 10.1002/bip.22528] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 12/18/2022]
Abstract
N-Substituted glycine peptoid oligomers have recently attracted attention for their metal binding capabilities. Due to their efficient synthesis on solid phase, peptoids are well suited for generation of compound libraries, followed by screening for molecular recognition and other diverse functional attributes. Ideally, peptoids could be simultaneously screened for binding to a number of metal species. Here, we demonstrate the use of bench-top X-ray fluorescence (XRF) instrumentation to screen rapidly, on solid support, a library of peptoid oligomers incorporating metal-binding functionalities. A subset of the peptoid sequences exhibited significant metal binding capabilities, including a peptoid pentamer and a nonamer that were shown to selectively bind nickel. The binding capabilities were validated by colorimetric assay and by depletion of Ni(2+) ion concentration from solution, establishing bench-top XRF as a rapid, practicable high-throughput screening technique for peptoid oligomers. This protocol will facilitate discovery of metallopeptoids with unique material properties.
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12
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Knight AS, Zhou EY, Francis MB. Development of Peptoid-Based Ligands for the Removal of Cadmium from Biological Media. Chem Sci 2015; 7:4042-4048. [PMID: 26918113 PMCID: PMC4762606 DOI: 10.1039/c5sc00676g] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
To address the lack of current therapeutic strategies for cadmium poisoning, peptoid-based ligands are identified using combinatorial chemistry that can selectively coordinate cadmium in a complex biological sample matrix.
Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate the significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.
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Affiliation(s)
- Abigail S Knight
- Department of Chemistry, University of California, Berkeley, CA, 94720
| | - Effie Y Zhou
- Department of Chemistry, University of California, Berkeley, CA, 94720
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, CA, 94720; The Molecular Foundry at Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
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13
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Knight AS, Zhou EY, Pelton JG, Francis MB. Selective chromium(VI) ligands identified using combinatorial peptoid libraries. J Am Chem Soc 2013; 135:17488-93. [PMID: 24195610 PMCID: PMC4136388 DOI: 10.1021/ja408788t] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a worldwide water contaminant that is currently without cost-effective and efficient remediation strategies. This is in part due to a lack of ligands that can bind it amid an excess of innocuous ions in aqueous solution. We present herein the design and application of a peptoid-based library of ligand candidates for toxic metal ions. A selective screening process was used to identify members of the library that can bind to Cr(VI) species at neutral pH and in the presence of a large excess of spectator ions. There were 11 sequences identified, and their affinities were compared using titrations monitored with UV-vis spectroscopy. To identify the interactions involved in coordination and specificity, we evaluated the effects of sequence substitutions and backbone variation in the highest affinity structure. Additional characterization of the complex formed between this sequence and Cr(VI) was performed using NMR spectroscopy. To evaluate the ability of the developed sequences to remediate contaminated solutions, the structures were synthesized on a solid-phase resin and incubated with environmental water samples that contained simulated levels of chromium contamination. The synthetic structures demonstrated the ability to reduce the amount of toxic chromium to levels within the range of the EPA contamination guidelines. In addition to providing some of the first selective ligands for Cr(VI), these studies highlight the promise of peptoid sequences as easily prepared components of environmental remediation materials.
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Affiliation(s)
- Abigail S. Knight
- Department of Chemistry, University of California, Berkeley, CA, 94720
| | - Effie Y. Zhou
- Department of Chemistry, University of California, Berkeley, CA, 94720
| | - Jeffrey G. Pelton
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, CA, 94720
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
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14
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Park SH, Szleifer I. Structural and dynamical characteristics of peptoid oligomers with achiral aliphatic side chains studied by molecular dynamics simulation. J Phys Chem B 2011; 115:10967-75. [PMID: 21819112 PMCID: PMC3177600 DOI: 10.1021/jp2025957] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All-atom molecular dynamics simulations of N-substituted glycine peptoid oligomers with methyl and methoxyethyl side chains have been carried out for chain lengths of 5, 10, 20, and 50 residues in aqueous phase at room temperature. The (ϕ, ψ) backbone dihedral angle distributions in the Ramachandran plots show that helical structures, similar to polyproline type I and type II helices, are the most favorable conformations in most peptoid oligomers studied. The left-handed helical structures are shown to be increasingly favored as the oligomer chain length grows. A significant population of cis amide bond configurations has been identified in the peptoid oligomers. By combining the analysis of ϕ and ω backbone dihedral angles, we determined the relative composition of the four major conformations favored by the backbone dihedral angles. The trans α(D) conformation is found to be most favored for all peptoid oligomers studies. The time correlation functions of the end-to-end distance highlight a rigid backbone structure relative to side chains for peptoid oligomers. The transition between right-handed and left-handed helical conformations is found to be very rare and between cis and trans isomerism in the amide bond completely absent in the simulation time scale. The radii of gyration for all peptoid oligomers have been found to be consistently larger in comparison to the peptide counterparts, suggesting slightly open structures for peptoids relative to peptides, whereas the fluctuations in the radius of gyration support a rigid backbone structure of peptoids.
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Affiliation(s)
- Sung Hyun Park
- Department of Biomedical Engineering and Chemistry of Life Processes, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, U.S.A
| | - Igal Szleifer
- Department of Biomedical Engineering and Chemistry of Life Processes, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, U.S.A
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15
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Fuller AA, Seidl FJ, Bruno PA, Plescia MA, Palla KS. Use of the environmentally sensitive fluorophore 4-N,N-dimethylamino-1,8-naphthalimide to study peptoid helix structures. Biopolymers 2011; 96:627-38. [DOI: 10.1002/bip.21605] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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16
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Guo L, Li J, Brown Z, Ghale K, Zhang D. Synthesis and characterization of cyclic and linear helical poly(α-peptoid)s by N-heterocyclic carbene-mediated ring-opening polymerizations of N-substituted N-carboxyanhydrides. Biopolymers 2011; 96:596-603. [DOI: 10.1002/bip.21597] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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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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18
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Gorske BC, Stringer JR, Bastian BL, Fowler SA, Blackwell HE. New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems. J Am Chem Soc 2010; 131:16555-67. [PMID: 19860427 DOI: 10.1021/ja907184g] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Controlling the equilibria between backbone cis- and trans-amides in peptoids, or N-substituted glycine oligomers, constitutes a significant challenge in the construction of discretely folded peptoid structures. Through the analysis of a set of monomeric peptoid model systems, we have developed new and general strategies for controlling peptoid conformation that utilize local noncovalent interactions to regulate backbone amide rotameric equilibria, including n-->pi*, steric, and hydrogen bonding interactions. The chemical functionalities required to implement these strategies are typically confined to the peptoid side chains, preserve chirality at the side chain N-alpha-carbon known to engender peptoid structure, and are fully compatible with standard peptoid synthesis techniques. Our examinations of peptoid model systems have also elucidated how solvents affect various side chain-backbone interactions, revealing fundamental aspects of these noncovalent interactions in peptoids that were largely uncharacterized previously. As validation of our monomeric model systems, we extended the scope of this study to include peptoid oligomers and have now demonstrated the importance of local steric and n-->pi* interactions in dictating the structures of larger, folded peptoids. This new, modular design strategy has guided the construction of peptoids containing 1-naphthylethyl side chains, which we show can be utilized to effectively eliminate trans-amide rotamers from the peptoid backbone, yielding the most conformationally homogeneous class of peptoid structures yet reported in terms of amide rotamerism. Overall, this research has afforded a valuable and expansive set of design tools for the construction of both discretely folded peptoids and structurally biased peptoid libraries and should shape our understanding of peptoid folding.
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Affiliation(s)
- Benjamin C Gorske
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, USA
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Stair JL, White BR, Rowland A, Holcombe JA. Quantitative Determination of Single-Bead Metal Content from a Peptide Combinatorial Library. ACTA ACUST UNITED AC 2006; 8:929-34. [PMID: 17096583 DOI: 10.1021/cc060100m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An electrothermal vaporizer inductively coupled plasma mass spectrometer (ETV-ICPMS) was used to quantitatively screen metals bound to single polystyrene (TentaGel) beads with immobilized oligopeptides. Tests were performed using ETV-ICPMS to screen a series of identical beads as well as a series of combinatorial library beads exposed to a multimetal solution composed of Mg2+, Mn2+, Ni2+, Cu2+, Cd2+, Eu2+, and Pb2+. The residual metal content remaining bound to the beads after acid extractions was also analyzed by solid sampling of the entire bead using oxygen ashing in the ETV. Nine beads (80 mesh, 0.25 mmol g(-1) nominal capacity) containing covalently attached polyaspartic acid (PLAsp; n = 20) showed metal extract concentrations in the range of 4-130 ng mL(-1). After normalizing by bead volume, the precision of capacity measurements in a single bead (7-14%) was primarily dictated by analysis error and contributions from bead diameter measurement with negligible contributions, surprisingly, from variations in site density from bead to bead. A sample combinatorial library of the sequence GXXGXXGXXGXX (X = cysteine, aspartic acid, or glutamic acid and G = glycine) (60 mesh, 0.25 mmol g(-1) nominal capacity) was also used to demonstrate the utility of this method. Metal extract concentrations ranged from 1 to 1300 ng mL(-1) with significant concentration variation between beads, indicating the individual selectivity on each bead. For these larger beads, analysis precision (i.e., capacity precision) was further improved to 3-10% due to the overall increase in bead metal content. Through metal extract determinations, ETV-ICPMS was shown to be a viable nondestructive tool for full metal characterization of "hit" sequences belonging to a combinatorial library.
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Affiliation(s)
- Jacqueline L Stair
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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Sawicki M, Siaugue JM, Jacopin C, Moulin C, Bailly T, Burgada R, Meunier S, Baret P, Pierre JL, Taran F. Discovery of powerful uranyl ligands from efficient synthesis and screening. Chemistry 2006; 11:3689-97. [PMID: 15809989 DOI: 10.1002/chem.200401056] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
New tripodal gem-(bis-phosphonates) uranophiles were discovered by a screening method that allowed for the selection of ligands with strong uranyl-binding properties in a convenient microtiter-plate format. The method is based on competitive uranium binding by using Sulfochlorophenol S as chromogenic chelate. This dye compound was found to present high uranyl complexation properties and allowed to highlight ligands presenting association constants for UO(2+)(2) up to 10(18) at pH 7.4 and 10(20) at pH 9. A collection of 40 known ligands including polycarboxylate, hydroxamate, catecholate, hydroxypyridonate and hydroxyquinoline derivatives was tested. Also screened was a combinatorial library prepared from seven amine scaffolds and eight acrylates bearing diverse chelating moieties. Among these 96 tested candidates, a tripod derivative bearing gem-bis-phosphonates moieties was found to present the highest complexation properties over a wide range of pH and was further studied.
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Affiliation(s)
- Marcin Sawicki
- Service de Marquage Moléculaire et de Chimie Bio-organique, DBJC/DSV CEA-Saclay, Gif sur Yvette, France
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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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Abstract
The split-pool diversity orientated synthesis method, which requires some form of encoding to track the synthesis of discrete compounds, has been the lynchpin of most combinatorial synthesis efforts. The use of encoding methods in combinatorial chemistry has matured, and depending on their level of resources, chemists now have a diverse choice of encoding methods available. New methods of encoding have been developed that are inexpensive, simple to incorporate into any laboratory, and utilize analytical equipment such as MS, FTIR and NMR that are readily available to most organic chemists.
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Affiliation(s)
- Nicholas J Ede
- Mimotopes Pty. Ltd, 11 Duerdin Street, Clayton, Victoria 3168, Australia.
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