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Angera IJ, Wright MM, Del Valle JR. Beyond N-Alkylation: Synthesis, Structure, and Function of N-Amino Peptides. Acc Chem Res 2024; 57:1287-1297. [PMID: 38626119 DOI: 10.1021/acs.accounts.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics.Substitution of the backbone amide in peptides represents a subtle chemical modification with profound effects on conformation and stability. Studies focused on N-alkylation have already led to broad-ranging applications in peptidomimetic design. Inspired by nonribosomal peptide natural products harboring amide N-oxidations, we envisioned that main-chain hydrazide and hydroxamate bonds would impose distinct conformational preferences and offer unique opportunities for backbone diversification. This Account describes our exploration of peptide N-amination as a strategy for stabilizing canonical protein folds and for the structure-based design of soluble amyloid mimics.We developed a general synthetic protocol to access N-amino peptides (NAPs) on solid support. In an effort to stabilize β-strand conformation, we designed stitched peptidomimetics featuring covalent tethering of the backbone N-amino substituent to the preceding residue side chain. Using a combination of NMR, X-ray crystallography, and molecular dynamics simulations, we discovered that backbone N-amination alone could significantly stabilize β-hairpin conformation in multiple models of folding. Our studies revealed that the amide NH2 substituent in NAPs participates in cooperative noncovalent interactions that promote β-sheet secondary structure. In contrast to Cα-substituted α-hydrazino acids, we found that N-aminoglycine and its N'-alkylated derivatives instead stabilize polyproline II (PPII) conformation. The reactivity of hydrazides also allows for late-stage peptide macrocyclization, affording novel covalent surrogates of side-chain-backbone H-bonds.The pronounced β-sheet propensity of Cα-substituted α-hydrazino acids prompted us to target amyloidogenic proteins using NAP-based β-strand mimics. Backbone N-amination was found to render aggregation-prone lead sequences soluble and resistant to proteolysis. Inhibitors of Aβ and tau identified through N-amino scanning blocked protein aggregation and the formation of mature fibrils in vitro. We further identified NAP-based single-strand and cross-β tau mimics capable of inhibiting the prion-like cellular seeding activity of recombinant and patient-derived tau fibrils.Our studies establish backbone N-amination as a valuable addition to the peptido- and proteomimetic tool kit. α-Hydrazino acids show particular promise as minimalist β-strand mimics that retain side-chain information. Late-stage derivatization of hydrazides also provides facile entry into libraries of backbone-edited peptides. We anticipate that NAPs will thus find applications in the development of optimally constrained folds and modulators of PPIs.
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Affiliation(s)
- Isaac J Angera
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Madison M Wright
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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2
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Anwar AF, Cain CF, Garza MJ, Degen D, Ebright RH, Del Valle JR. Stabilizing Pseudouridimycin: Synthesis, RNA Polymerase Inhibitory Activity, and Antibacterial Activity of Dipeptide-Modified Analogues. ChemMedChem 2024; 19:e202300474. [PMID: 37751316 PMCID: PMC10843019 DOI: 10.1002/cmdc.202300474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 09/28/2023]
Abstract
Pseudouridimycin (PUM) is a microbially produced C-nucleoside dipeptide that selectively targets the nucleotide addition site of bacterial RNA polymerase (RNAP) and that has a lower rate of spontaneous resistance emergence relative to current drugs that target RNAP. Despite its promising biological profile, PUM undergoes relatively rapid decomposition in buffered aqueous solutions. Here, we describe the synthesis, RNAP-inhibitory activity, and antibacterial activity of chemically stabilized analogues of PUM. These analogues feature targeted modifications that mitigate guanidine-mediated hydroxamate bond scission. A subset of analogues in which the central hydroxamate is replaced with amide or hydrazide isosteres retain the antibacterial activity of the natural product.
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Affiliation(s)
- Avraz F Anwar
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Christopher F Cain
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael J Garza
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Juan R Del Valle
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
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3
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Eastwood JRB, Weisberg EI, Katz D, Zuckermann RN, Kirshenbaum K. Guidelines for designing peptoid structures: Insights from the
Peptoid Data Bank. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
| | | | - Dana Katz
- Department of Chemistry New York University New York New York USA
| | | | - Kent Kirshenbaum
- Department of Chemistry New York University New York New York USA
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4
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Yang W, Seo J, Kim JH. Protein-mimetic peptoid nanoarchitectures for pathogen recognition and neutralization. NANOSCALE 2023; 15:975-986. [PMID: 36541218 DOI: 10.1039/d2nr05326h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent outbreaks of both new and existing infectious pathogens have threatened healthcare systems around the world. Therefore, it is vital to detect and neutralize pathogens to prevent their spread and treat infected patients. This consideration has led to the development of biosensors and antibiotics inspired by the structure and function of antibodies and antimicrobial peptides (AMPs), which constitute adaptive and innate immunity, efficiently protecting the human body against invading pathogens. Herein, we provide an overview of recent advances in the detection and neutralization of pathogens using protein-mimetic peptoid nanoarchitectures. Peptoids are bio-inspired and sequence-defined polymers composed of repeating N-substituted glycine units. They can spontaneously fold into well-defined three-dimensional nanostructures that encode chemical information depending on their sequences. Loop-functionalized peptoid nanosheets have been constructed by mimicking antibodies containing chemically variable loops as binding motifs for their respective target pathogen. Furthermore, by mimicking the cationic amphipathic features of natural AMPs, helical peptoids and their assemblies have been developed to achieve selective anti-infective activity owing to their intrinsic ability to interact with bacterial membranes and viral envelopes. We believe that this mini-review furnishes in-depth insight into how to construct protein-like nanostructures via the self-assembly of peptoids for application in the detection of pathogens and the treatment of infectious diseases for future healthcare applications.
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Affiliation(s)
- Woojin Yang
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Jae Hong Kim
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
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5
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Angelici G, Bhattacharjee N, Pypec M, Jouffret L, Didierjean C, Jolibois F, Perrin L, Roy O, Taillefumier C. Unveiling the conformational landscape of achiral all- cis tert-butyl β-peptoids. Org Biomol Chem 2022; 20:7907-7915. [PMID: 36173021 DOI: 10.1039/d2ob01351g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and conformational study of N-substituted β-alanines with tert-butyl side chains is described. The oligomers prepared by submonomer synthesis and block coupling methods are up to 15 residues long and are characterised by amide bonds in the cis-conformation. A conformational study comprising experimental solution NMR spectroscopy, X-ray crystallography and molecular modeling shows that despite their intrinsic higher conformational flexibility compared to their α-peptoid counterparts, this family of achiral oligomers adopt preferred secondary structures including a helical conformation close to that described with (1-naphthyl)ethyl side chains but also a novel ribbon-like conformation.
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Affiliation(s)
- Gaetano Angelici
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | - Nicholus Bhattacharjee
- Université de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - Maxime Pypec
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | - Laurent Jouffret
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | | | - Franck Jolibois
- Université de Toulouse-INSA-UPS, LPCNO, CNRS UMR 5215, 135 av. Rangueil, F-31077, Toulouse, France
| | - Lionel Perrin
- Université de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - Olivier Roy
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | - Claude Taillefumier
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
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6
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Purushotham M, Paul B, Govindachar DM, Singh AK, Periyasamy G, Peter SC. Ortho-halogen effects: n→π* interactions, halogen bonding, and deciphering chiral attributes in N-aryl glycine peptoid foldamers. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Pypec M, Jouffret L, Taillefumier C, Roy O. First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation. Beilstein J Org Chem 2022; 18:845-854. [PMID: 35923157 PMCID: PMC9296984 DOI: 10.3762/bjoc.18.85] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022] Open
Abstract
The synthesis and conformational analysis of the first series of peptoid oligomers composed of consecutive N-(alkylamino)glycine units is investigated. We demonstrate that N-(methylamino)glycine homooligomers can be readily synthesized in solution using N-Boc-N-methylhydrazine as a peptoid submonomer and stepwise or segment coupling methodologies. Their structures were analyzed in solution by 1D and 2D NMR, in the solid state by X-ray crystallography (dimer 2), and implicit solvent QM geometry optimizations. N-(Methylamino)peptoids were found to preferentially adopt trans amide bonds with the side chain N–H bonds oriented approximately perpendicular to the amide plane. This orientation is conducive to local backbone stabilization through intra-residue hydrogen bonds but also to intermolecular associations. The high capacity of N-(methylamino)peptoids to establish intermolecular hydrogen bonds was notably deduced from pronounced concentration-dependent N–H chemical shift variation in 1H NMR and the antiparallel arrangement of mirror image molecules held together via two hydrogen bonds in the crystal lattice of dimer 2.
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Affiliation(s)
- Maxime Pypec
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont–Ferrand, France
| | - Laurent Jouffret
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont–Ferrand, France
| | - Claude Taillefumier
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont–Ferrand, France
| | - Olivier Roy
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont–Ferrand, France
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8
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Kalita D, Sahariah B, Mookerjee SP, Sarma BK. Strategies to Control the cis-trans Isomerization of Peptoid Amide Bonds. Chem Asian J 2022; 17:e202200149. [PMID: 35362652 DOI: 10.1002/asia.202200149] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/30/2022] [Indexed: 11/11/2022]
Abstract
Peptoids are oligomers of N-substituted glycine units. They structurally resemble peptides but, unlike natural peptides, the side chains of peptoids are present on the amide nitrogen atoms instead of the α-carbons. The N-substitution improves cell-permeability of peptoids and enhance their proteolytic stability over natural peptides. Therefore, peptoids are ideal peptidomimetic candidates for drug discovery, especially for intracellular targets. Unfortunately, most peptoid ligands discovered so far possess moderate affinity towards their biological targets. The moderate affinity of peptoids for biomacromolecules is linked to their conformational flexibility, which causes substantial entropic loss during the peptoid-biomacromolecule binding process. The conformational flexibility of peptoids is caused by the lack of backbone chirality, absence of hydrogen bond donors (NH) in their backbone to form CO···HN hydrogen bonds and the facile cis-trans isomerization of their tertiary amide bonds. In recent years, many investigators have shown that the incorporation of specific side chains with unique steric and stereoelectronic features can favourably shift the cis-trans equilibria of peptoids towards one of the two isomeric forms. Such strategies are helpful to design homogenous peptoid oligomers having well defined secondary structures. Herein, we discuss the strategies developed over the years to control the cis-trans isomerization of peptoid amide bonds.
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Affiliation(s)
- Debajit Kalita
- Jawaharlal Nehru Centre for Advanced Scientific Research, New Chemistry Unit, INDIA
| | - Biswajit Sahariah
- Jawaharlal Nehru Centre for Advanced Scientific Research, New Chemistry Unit, INDIA
| | | | - Bani Kanta Sarma
- Jawaharlal Nehru Centre for Advanced Scientific Research, New Chemistry Unit, Rachenahalli Lake Road, Jakkur, 560064, India, 560064, Bangalore, INDIA
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9
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Abstract
Azapeptides undergo on-resin, late-stage N-alkylations to install side chains with high chemoselectivity for the hydrazide nitrogen atoms. The major product is the N1-alkylated "azapeptoid", with only small amounts (<10%) of alkylation occurring at the other aza-amino acid nitrogen (N2). Dialkylations are also possible and afford highly functionalized, disubstituted azapeptides with side chains installed on both aza-amino acid nitrogen atoms. The site-selectivity was determined using Edman degradation, MS/MS sequencing, and comparative LCMS and NMR analyses.
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Affiliation(s)
- Maxwell O Bowles
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Caroline Proulx
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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10
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Del Valle J, Cain CF, Scott AM, Sarnowski MP. Total synthesis and chemical stability of pseudouridimycin. Chem Commun (Camb) 2022; 58:2351-2354. [DOI: 10.1039/d1cc07059b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the chemical synthesis of pseudouridimycin (1), an antimicrobial natural product that potently and selectively inhibits bacterial RNA polymerase. Chemical stability studies revealed intramolecular hydroxamate bond scission to be...
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11
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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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12
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Davern CM, Lowe BD, Rosfi A, Ison EA, Proulx C. Submonomer synthesis of peptoids containing trans-inducing N-imino- and N-alkylamino-glycines. Chem Sci 2021; 12:8401-8410. [PMID: 34221321 PMCID: PMC8221195 DOI: 10.1039/d1sc00717c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/09/2021] [Indexed: 11/21/2022] Open
Abstract
The use of hydrazones as a new type of submonomer in peptoid synthesis is described, giving access to peptoid monomers that are structure-inducing. A wide range of hydrazones were found to readily react with α-bromoamides in routine solid phase peptoid submonomer synthesis. Conditions to promote a one-pot cleavage of the peptoid from the resin and reduction to the corresponding N-alkylamino side chains were also identified, and both the N-imino- and N-alkylamino glycine residues were found to favor the trans-amide bond geometry by NMR, X-ray crystallography, and computational analyses.
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Affiliation(s)
- Carolynn M Davern
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Brandon D Lowe
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Adam Rosfi
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Elon A Ison
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Caroline Proulx
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
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13
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Study of the cyclization of N-hydroxy- and N-methoxy-N-(2-oxoalkyl)amides. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01673-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Richaud AD, Roche SP. Structure-Property Relationship Study of N-(Hydroxy)Peptides for the Design of Self-Assembled Parallel β-Sheets. J Org Chem 2020; 85:12329-12342. [PMID: 32881524 DOI: 10.1021/acs.joc.0c01441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The design of novel and functional biomimetic foldamers remains a major challenge in creating mimics of native protein structures. Herein, we report the stabilization of a remarkably short β-sheet by incorporating N-(hydroxy)glycine (Hyg) residues into the backbone of peptides. These peptide-peptoid hybrids form unique parallel β-sheet structures by self-assembly upon hydrogenation. Our spectroscopic and crystallographic data suggest that the local conformational perturbations induced by N-(hydroxy)amides are outweighed by a network of strong interstrand hydrogen bonds.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States.,Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
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15
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Fuller AA, Jimenez CJ, Martinetto EK, Moreno JL, Calkins AL, Dowell KM, Huber J, McComas KN, Ortega A. Sequence Changes Modulate Peptoid Self-Association in Water. Front Chem 2020; 8:260. [PMID: 32391314 PMCID: PMC7191062 DOI: 10.3389/fchem.2020.00260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/17/2020] [Indexed: 01/15/2023] Open
Abstract
Peptoids, N-substituted glycine oligomers, are a class of diverse and sequence-specific peptidomimetics with wide-ranging applications. Advancing the functional repertoire of peptoids to emulate native peptide and protein functions requires engineering peptoids that adopt regular secondary and tertiary structures. An understanding of how changes to peptoid sequence change structural features, particularly in water-soluble systems, is underdeveloped. To address this knowledge gap, five 15-residue water-soluble peptoids that include naphthalene-functionalized side chains were designed, prepared, and subjected to a structural study using a palette of techniques. Peptoid sequence designs were based on a putative amphiphilic helix peptoid bearing structure-promoting (S)-N-(1-naphthylethyl)glycine residues whose self-association in water has been studied previously. New peptoid variants reported here include sequence changes that influenced peptoid conformational flexibility, functional group patterning (amphiphilicity), and hydrophobicity. Peptoid structures were evaluated and compared using circular dichroism spectroscopy, fluorescence spectroscopy, and size exclusion chromatography. Spectral data confirmed that sequence changes alter peptoids' degree of assembly and the organization of self-assembled structures in aqueous solutions. Insights gained in these studies will inform the design of new water-soluble peptoids with regular structural features, including desirable higher-order (tertiary and quaternary) structural features.
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Affiliation(s)
- Amelia A Fuller
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Christian J Jimenez
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Ella K Martinetto
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Jose L Moreno
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Anna L Calkins
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Kalli M Dowell
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Jonathan Huber
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Kyra N McComas
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Alberto Ortega
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
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16
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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17
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Rzeigui M, Traikia M, Jouffret L, Kriznik A, Khiari J, Roy O, Taillefumier C. Strengthening Peptoid Helicity through Sequence Site-Specific Positioning of Amide cis-Inducing NtBu Monomers. J Org Chem 2020; 85:2190-2201. [PMID: 31873018 DOI: 10.1021/acs.joc.9b02916] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The synthesis of biomimetic helical secondary structures is sought after for the construction of innovative nanomaterials and applications in medicinal chemistry such as the development of protein-protein interaction modulators. Peptoids, a sequence-defined family of oligomers, enable a peptidomimetic strategy, especially considering the easily accessible monomer diversity and peptoid helical folding propensity. However, cis-trans isomerization of the backbone tertiary amides may impair the peptoid's adoption of stable secondary structures, notably the all-cis polyproline I-like helical conformation. Here, we show that cis-inducing NtBu achiral monomers strategically positioned within chiral sequences may reinforce the degree of peptoid helicity, although with a reduced content of chiral side chains. The design principles presented here will undoubtedly help achieve more conformationally stable helical peptoids with desired functions.
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Affiliation(s)
- Maha Rzeigui
- Université Clermont Auvergne , CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand , France.,Université de Carthage , Faculté Des Sciences de Bizerte, Laboratoire de Chimie Organique et Analytique, ISEFC, 2000 Bardo , Tunisie
| | - Mounir Traikia
- Université Clermont Auvergne , CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand , France
| | - Laurent Jouffret
- Université Clermont Auvergne , CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand , France
| | - Alexandre Kriznik
- Université de Lorraine , CNRS, IMoPA, F-54000 Nancy , France.,Université de Lorraine , CNRS, Inserm, UMS2008 IBSLor, Biophysics and Structural Biology Core Facility, F-54000 Nancy , France
| | - Jameleddine Khiari
- Université de Carthage , Faculté Des Sciences de Bizerte, Laboratoire de Chimie Organique et Analytique, ISEFC, 2000 Bardo , Tunisie
| | - Olivier Roy
- Université Clermont Auvergne , CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand , France
| | - Claude Taillefumier
- Université Clermont Auvergne , CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand , France
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18
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Sarnowski MP, Del Valle JR. N-Hydroxy peptides: solid-phase synthesis and β-sheet propensity. Org Biomol Chem 2020; 18:3690-3696. [DOI: 10.1039/d0ob00664e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Backbone amide hydroxylation of peptide strands enhances β-hairpin folding.
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Affiliation(s)
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry
- University of Notre Dame
- Notre Dame
- USA
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19
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Howard EH, Cain CF, Kang C, Del Valle JR. Synthesis of Enantiopure ε-Oxapipecolic Acid. J Org Chem 2019; 85:1680-1686. [DOI: 10.1021/acs.joc.9b02382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evan H. Howard
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Christopher F. Cain
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Changwon Kang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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20
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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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21
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Roe LT, Pelton JG, Edison JR, Butterfoss GL, Tresca BW, LaFaye BA, Whitelam S, Wemmer DE, Zuckermann RN. Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution. Biopolymers 2019; 110:e23267. [PMID: 30835821 DOI: 10.1002/bip.23267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/29/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022]
Abstract
Conformational control in peptoids, N-substituted glycines, is crucial for the design and synthesis of biologically-active compounds and atomically-defined nanomaterials. While there are a growing number of structural studies in solution, most have been performed with conformationally-constrained short sequences (e.g., sterically-hindered sidechains or macrocyclization). Thus, the inherent degree of heterogeneity of unconstrained peptoids in solution remains largely unstudied. Here, we explored the folding landscape of a series of simple peptoid tetramers in aqueous solution by NMR spectroscopy. By incorporating specific 13 C-probes into the backbone using bromoacetic acid-2-13 C as a submonomer, we developed a new technique for sequential backbone assignment of peptoids based on the 1,n-Adequate pulse sequence. Unexpectedly, two of the tetramers, containing an N-(2-aminoethyl)glycine residue (Nae), had preferred conformations. NMR and molecular dynamics studies on one of the tetramers showed that the preferred conformer (52%) had a trans-cis-trans configuration about the three amide bonds. Moreover, >80% of the ensemble contained a cis amide bond at the central amide. The backbone dihedral angles observed fall directly within the expected minima in the peptoid Ramachandran plot. Analysis of this compound against similar peptoid analogs suggests that the commonly used Nae monomer plays a key role in the stabilization of peptoid structure via a side-chain-to-main-chain interaction. This discovery may offer a simple, synthetically high-yielding approach to control peptoid structure, and suggests that peptoids have strong intrinsic conformational preferences in solution. These findings should facilitate the predictive design of folded peptoid structures, and accelerate application in areas ranging from drug discovery to biomimetic nanoscience.
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Affiliation(s)
- Leah T Roe
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - John R Edison
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Blakely W Tresca
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan
| | - Bridgette A LaFaye
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Stephen Whitelam
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California
| | - David E Wemmer
- Department of Chemistry, University of California, Berkeley, California
| | - Ronald N Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California
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22
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Battigelli A. Design and preparation of organic nanomaterials using self‐assembled peptoids. Biopolymers 2019; 110:e23265. [DOI: 10.1002/bip.23265] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Alessia Battigelli
- School of Engineering, Center for Biomedical Engineering, Institute for Molecular and Nanoscale Innovation, Brown University Providence Rhode Island
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23
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de la Torre AF, Ali A, Concepcion O, Montero-Alejo AL, Muñiz FM, Jiménez CA, Belmar J, Velázquez-Libera JL, Hernández-Rodríguez EW, Caballero J. A study of the cis–trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone. NEW J CHEM 2019. [DOI: 10.1039/c9nj02234a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The current work provides a study on the cis–trans isomerization behaviour of N-alkylated peptides decorated with phosphonate ester groups.
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Affiliation(s)
- Alexander F. de la Torre
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | - Akbar Ali
- Department of Chemistry
- University of Sargodha
- Pakistan
| | - Odette Concepcion
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | | | - Francisco M. Muñiz
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | - Claudio A. Jiménez
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | - Julio Belmar
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | | | | | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Universidad de Talca
- Talca
- Chile
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24
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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25
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017; 56:2083-2086. [DOI: 10.1002/anie.201609395] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/12/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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26
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Lee YJ, Chung S, Ahn YD, Kang B, Lee JY, Seo J. Self-assembling Helical Rod-Coil Peptoid Amphiphiles. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.11042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yen Jea Lee
- Department of Chemistry, School of Physics and Chemistry; Gwangju Institute of Science and Technology; Gwangju 61005 Republic of Korea
| | - Solchan Chung
- School of Materials Science and Engineering; Gwangju Institute of Science and Technology; Gwangju 61005 Republic of Korea
| | - Young Deok Ahn
- Department of Chemistry, School of Physics and Chemistry; Gwangju Institute of Science and Technology; Gwangju 61005 Republic of Korea
| | - Boyeong Kang
- Department of Chemistry, School of Physics and Chemistry; Gwangju Institute of Science and Technology; Gwangju 61005 Republic of Korea
| | - Jae Young Lee
- School of Materials Science and Engineering; Gwangju Institute of Science and Technology; Gwangju 61005 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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27
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Gangloff N, Ulbricht J, Lorson T, Schlaad H, Luxenhofer R. Peptoids and Polypeptoids at the Frontier of Supra- and Macromolecular Engineering. Chem Rev 2015; 116:1753-802. [DOI: 10.1021/acs.chemrev.5b00201] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Niklas Gangloff
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Juliane Ulbricht
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Thomas Lorson
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Helmut Schlaad
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Robert Luxenhofer
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
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28
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Mukherjee S, Zhou G, Michel C, Voelz VA. Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential. J Phys Chem B 2015; 119:15407-17. [PMID: 26584227 DOI: 10.1021/acs.jpcb.5b09625] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone φ-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consistent with experiment. We validate our results against both QM calculations and NMR experiments. For this latter task, we make quantitative comparisons to sparse NOE data using the Bayesian Inference of Conformational Populations (BICePs) algorithm, a method we have recently developed for this purpose. We then performed extensive REMD simulations of Nspe oligomers as a function of chain length and temperature to probe the molecular forces driving cooperative helix formation. Analysis of simulation data by Lifson-Roig helix-coil theory show that the modified potential predicts much more cooperative folding for Nspe helices. Unlike peptides, per-residue entropy changes for helix nucleation and extension are mostly positive, suggesting that steric bulk provides the main driving force for folding. We expect these results to inform future work aimed at predicting and designing peptoid peptidomimetics and tertiary assemblies of peptoid helices.
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Affiliation(s)
- Sudipto Mukherjee
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Guangfeng Zhou
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Chris Michel
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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29
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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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30
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Proulx C, Yoo S, Connolly MD, Zuckermann RN. Accelerated Submonomer Solid-Phase Synthesis of Peptoids Incorporating Multiple Substituted N-Aryl Glycine Monomers. J Org Chem 2015; 80:10490-7. [DOI: 10.1021/acs.joc.5b01449] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Caroline Proulx
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Stan Yoo
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Michael D. Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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31
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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32
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Nandel FS, Jaswal RR, Saini A, Nandel V, Shafique M. Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures. J Mol Model 2014; 20:2429. [DOI: 10.1007/s00894-014-2429-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/07/2014] [Indexed: 12/29/2022]
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33
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Kölmel DK, Hörner A, Rönicke F, Nieger M, Schepers U, Bräse S. Cell-penetrating peptoids: introduction of novel cationic side chains. Eur J Med Chem 2014; 79:231-43. [PMID: 24739871 DOI: 10.1016/j.ejmech.2014.03.078] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/17/2022]
Abstract
During the last decade peptoid-based molecular transporters have been broadly applied. They are highly valued for their easy synthesis and their superior stability against enzymatic degradation. The special structure of peptoids generally allows introducing a variety of different side chains. Yet, the cationic side chains of cell-penetrating peptoids displayed solely lysine- or arginine-like structures. Thus this report is intended to extend the spectrum of cationic peptoid side chains. Herein, we present novel functional groups, like polyamines, aza-crown ethers, or triphenylphosphonium ions that are introduced into peptoids for the first time. In addition, the obtained peptoids were tested for their cell-penetrating properties.
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Affiliation(s)
- Dominik K Kölmel
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Anna Hörner
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Light Technology Institute, Engesserstraße 13, D-76131 Karlsruhe, Germany
| | - Franziska Rönicke
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Martin Nieger
- University of Helsinki, Laboratory of Inorganic Chemistry, PO Box 55, FIN-00014, Finland
| | - Ute Schepers
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany.
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34
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Shin HM, Kang CM, Yoon MH, Seo J. Peptoid helicity modulation: precise control of peptoid secondary structures via position-specific placement of chiral monomers. Chem Commun (Camb) 2014; 50:4465-8. [DOI: 10.1039/c3cc49373c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of position-specific placement of structure-inducing monomer(s) on the peptoid secondary structure was investigated.
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Affiliation(s)
- Hye-Min Shin
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology
- Gwangju, Republic of Korea
| | - Chang-Muk Kang
- Department of Chemistry
- Gwangju Institute of Science and Technology
- Gwangju, Republic of Korea
| | - Myung-Han Yoon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology
- Gwangju, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry
- Gwangju Institute of Science and Technology
- Gwangju, Republic of Korea
- Division of Liberal Art and Sciences
- Gwangju Institute of Science and Technology
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35
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Mirijanian DT, Mannige RV, Zuckermann RN, Whitelam S. Development and use of an atomistic CHARMM-based forcefield for peptoid simulation. J Comput Chem 2013; 35:360-70. [DOI: 10.1002/jcc.23478] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/06/2013] [Indexed: 01/31/2023]
Affiliation(s)
- Dina T. Mirijanian
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
| | - Ranjan V. Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
| | - Ronald N. Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
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36
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Gorske BC, Nelson RC, Bowden ZS, Kufe TA, Childs AM. “Bridged” n→π* Interactions Can Stabilize Peptoid Helices. J Org Chem 2013; 78:11172-83. [DOI: 10.1021/jo4014113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Benjamin C. Gorske
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Ryan C. Nelson
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Zara S. Bowden
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Turner A. Kufe
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Adam M. Childs
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
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37
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Fuller AA, Yurash BA, Schaumann EN, Seidl FJ. Self-Association of Water-Soluble Peptoids Comprising (S)-N-1-(Naphthylethyl)glycine Residues. Org Lett 2013; 15:5118-21. [DOI: 10.1021/ol4025502] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
| | - Brett A. Yurash
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
| | - Erik N. Schaumann
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
| | - Frederick J. Seidl
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
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38
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Sun J, Zuckermann RN. Peptoid polymers: a highly designable bioinspired material. ACS NANO 2013; 7:4715-32. [PMID: 23721608 DOI: 10.1021/nn4015714] [Citation(s) in RCA: 307] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.
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Affiliation(s)
- Jing Sun
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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39
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Kalia D, Merey G, Guo M, Sintim HO. N–O Tethered Carbenoid Cyclopropanation Facilitates the Synthesis of a Functionalized Cyclopropyl-Fused Pyrrolidine. J Org Chem 2013; 78:6131-42. [DOI: 10.1021/jo400788a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dimpy Kalia
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - Gökce Merey
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
- Chemical Engineering Department, Hitit University, Corum, Turkey
| | - Min Guo
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - Herman O. Sintim
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
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40
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Crapster JA, Guzei IA, Blackwell HE. A peptoid ribbon secondary structure. Angew Chem Int Ed Engl 2013; 52:5079-84. [PMID: 23576308 DOI: 10.1002/anie.201208630] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/02/2013] [Indexed: 01/02/2023]
Affiliation(s)
- J Aaron Crapster
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
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42
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Szekely T, Caumes C, Roy O, Faure S, Taillefumier C. α-Peptoïdes et composés apparentés : synthèse et contrôle de la conformation. CR CHIM 2013. [DOI: 10.1016/j.crci.2012.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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Gangloff N, Luxenhofer R. Peptoids for Biomimetic Hierarchical Structures. HIERARCHICAL MACROMOLECULAR STRUCTURES: 60 YEARS AFTER THE STAUDINGER NOBEL PRIZE II 2013. [DOI: 10.1007/12_2013_237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sternberg U, Birtalan E, Jakovkin I, Luy B, Schepers U, Bräse S, Muhle-Goll C. Structural characterization of a peptoid with lysine-like side chains and biological activity using NMR and computational methods. Org Biomol Chem 2012; 11:640-7. [PMID: 23223799 DOI: 10.1039/c2ob27039k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
N-substituted glycine oligomers or peptoids with charged side chains are a novel class of cell penetrating peptide mimetics and have been shown to serve as drug delivery agents. Here, we investigated by NMR spectroscopy and quantum chemical calculations whether a Rhodamine B labelled peptoid [RhoB(Spiro)-Ahx]-[But](6A)NH(2) with lysine-like side chains adopts structural motifs similar to regular peptides. Due to a low chemical shift dispersion, high resolution structure determination with conventional NMR-derived distance restraints and J-couplings was not possible. Instead, a combined assignment and structure refinement strategy using the QM/MM force field COSMOS-NMR was developed to interpret the highly ambiguous chemical shift and distance constraints and obtain a medium resolution three-dimensional structural model. This allowed us to select for the all cis-amide conformation of the peptide with a pseudo-helical arrangement of extended side chains as a faithful representative structure of [RhoB(Spiro)-Ahx]-[But](6A)NH(2). We tested the biological activity of the peptoid by live-cell imaging, which showed that the cellular uptake of the peptoid was comparable to conventional cell-penetrating peptides.
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Affiliation(s)
- Ulrich Sternberg
- Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
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Jordan PA, Paul B, Butterfoss GL, Renfrew PD, Bonneau R, Kirshenbaum K. Oligo(N-alkoxy glycines): trans substantiating peptoid conformations. Biopolymers 2012; 96:617-26. [PMID: 22180909 DOI: 10.1002/bip.21675] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Peptoid oligomers possess many desirable attributes bioactive peptidomimetic agents, including their ease of synthesis, chemical diversity, and capability for molecular recognition. Ongoing efforts to develop functional peptoids will necessitate improved capability for control of peptoid structure, particularly of the backbone amide conformation. We introduce alkoxyamines as a new reagent for solid phase peptoid synthesis. Herein, we describe the synthesis of N-alkoxy peptoids, and present NMR data indicating that the oligomers adopt a single stable conformation featuring trans amide bonds. These findings, combined with results from computational modeling, suggest that N-alkoxy peptoid oligomers have a strong propensity to adopt a polyproline II type secondary structure.
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Affiliation(s)
- Peter A Jordan
- Department of Chemistry, New York University, NY 10003, USA
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