1
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Belletto D, Vigna V, Barretta P, Ponte F, Mazzone G, Scoditti S, Sicilia E. Computational assessment of the use of graphene-based nanosheets as Pt II chemotherapeutics delivery systems. J Comput Chem 2024. [PMID: 38741357 DOI: 10.1002/jcc.27394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/05/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Graphene is the newest form of elemental carbon and it is becoming rapidly a potential candidate in the framework of nano-bio research. Many reports confirm the successful use of graphene-based materials as carriers of anticancer drugs having relatively high loading capacities compared with other nanocarriers. Here, the outcomes of a systematic study of the adsorption behavior of FDA approved PtII drugs cisplatin, oxaliplatin, and carboplatin on surface models of pristine, holey, and nitrogen-doped holey graphene are reported. DFT investigations in water solvent have been carried out considering several initial orientations of the drugs with respect to the surfaces. Adsorption free energies, calculated including basis set superposition error (BSSE) corrections, result to be significantly negative for many of the drug@carrier adducts indicating that tested layers could be used as potential carriers for the delivery of anticancer PtII drugs. The reduced density gradient (RDG) analysis allows to show that many kinds of non-covalent interactions, including canonical H-bond, are responsible for the stabilization of the formed adducts.
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Affiliation(s)
- Daniele Belletto
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
| | - Vincenzo Vigna
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
| | - Pierraffaele Barretta
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
| | - Fortuna Ponte
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
| | - Gloria Mazzone
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
| | - Stefano Scoditti
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
| | - Emilia Sicilia
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende, Italy
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2
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Abstract
Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. Equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.
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Affiliation(s)
- Bradley S Harris
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Karteek K Bejagam
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Liu B, Xing P. Hydrogen Bonded Foldamers with Axial Chirality: Chiroptical Properties and Applications. Chemistry 2023; 29:e202202665. [PMID: 36281580 DOI: 10.1002/chem.202202665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Folding phenomenon refers to the formation of a specific conformation widely featured by the intramolecular interactions, which broadly exist in biomacromolecules, and are closely related to their structures and functions. A variety of oligomeric folded molecules have been designed and synthesized, namely "foldamer", exhibiting potentials in pharmaceutical and catalysis. Molecular folding is a promising strategy to transfer chirality from substituents to the whole skeleton, when chirality transfer, amplification, evolution, and other behaviors could be achieved. Investigating chirality using foldamer model deepens the understanding of the structure-function correlation in biomacromolecules and expands the molecular toolbox towards chiroptical and asymmetrical chemistry. Substitutes with abundant hydrogen bonding sites conjugated to a rotatable aryl group afford a parallel β-sheet-like conformation, which enables the emergence and manipulation of axial chirality. This concept aims to give a brief introduction and summary of the hydrogen bonded foldamers with anchored axial chirality, by taking some recent cases as examples. Design principles, control over axial chirality and applications are also reviewed.
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Affiliation(s)
- Bingyu Liu
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Pengyao Xing
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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5
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Pollastrini M, Pasquinelli L, Górecki M, Balzano F, Cupellini L, Lipparini F, Uccello Barretta G, Marchetti F, Pescitelli G, Angelici G. A Unique and Stable Polyproline I Helix Sorted out from Conformational Equilibrium by Solvent Polarity. J Org Chem 2022; 87:13715-13725. [PMID: 36242553 PMCID: PMC9639007 DOI: 10.1021/acs.joc.2c01377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Polyproline I helical structures are often considered as the hidden face of their most famous geminal sibling, Polyproline II, as PPI is generally spotted only within a conformational equilibrium. We designed and synthesized a stable Polyproline I structure exploiting the striking tendency of (S)-indoline-2-carboxylic acid to drive the peptide bond conformation toward the cis amide isomer, when dissolved in polar solvents. The cooperative effect of only four amino acidic units is sufficient to form a preferential structure in solution. We shed light on this rare secondary structure with a thorough analysis of the spectroscopic and chiroptical properties of the tetramer, supported by X-ray crystallography and computational studies.
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Affiliation(s)
- Matteo Pollastrini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Luca Pasquinelli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Marcin Górecki
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy,Institute
of Organic Chemistry, Polish Academy of
Sciences, ul. Kasprzaka
44/52, Warsaw 01-224, Poland
| | - Federica Balzano
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Gloria Uccello Barretta
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Fabio Marchetti
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy,
| | - Gaetano Angelici
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy,
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6
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Thurston R, Zantop V, Park KS, Maid H, Seitz A, Heinrich MR. pH-Dependent Conformational Switching of Amide Bonds─from Full trans to Full cis and Vice Versa. Org Lett 2022; 24:3488-3492. [PMID: 35544347 DOI: 10.1021/acs.orglett.2c00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Strategies enabling the pH-dependent conformational switching of amide bonds from trans to cis, and vice versa, are yet limited in the sense that, in a suitable pH range, one rotamer may be stabilized to a large extent while the complementary pH range only leads to a mixture of isomers. By exploiting the effects of steric demand and the interaction of the amide carbonyl with a positive charge, we herein present the first examples for reversible pH-dependent switching from full trans to full cis.
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Affiliation(s)
- Ryan Thurston
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Viviane Zantop
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Kristen Sodam Park
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Harald Maid
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Organic Chemistry II, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Anke Seitz
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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8
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Pierri G, Schettini R, Summa FF, De Riccardis F, Monaco G, Izzo I, Tedesco C. Right- and left-handed PPI helices in cyclic dodecapeptoids. Chem Commun (Camb) 2022; 58:5253-5256. [PMID: 35388839 DOI: 10.1039/d2cc00682k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enantiomorphic right- and left-handed polyproline type I helices in four cyclic dodecapeptoids with methoxyethyl and propargyl side chains are observed for the first time by single crystal X-ray diffraction. The peculiar absence of NH⋯OC hydrogen bonds in peptoids unveils the role of intramolecular backbone-to-backbone CO⋯CO interactions and CH⋯OC hydrogen bonds in the stabilization of the macrocycle conformation. Moreover, intramolecular backbone-side chain C5 CH⋯OC hydrogen bonds emerge as a stabilizing factor.
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Affiliation(s)
- Giovanni Pierri
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Rosaria Schettini
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Francesco F Summa
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Guglielmo Monaco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Consiglia Tedesco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
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9
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Purushotham M, Paul B, Gajula SNR, Sahariah B, Sonti R. Deciphering C–H⋯O/X weak hydrogen bonding and halogen bonding interactions in aromatic peptoids. NEW J CHEM 2022. [DOI: 10.1039/d2nj02616c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We deciphered weak interactions in aromatic peptoids, such as C–H⋯O/X, and simultaneously identified strong interactions, including N–H⋯N and N–H⋯O, in this class of foldamer.
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Affiliation(s)
- Manasa Purushotham
- Department of Chemistry, Jnana Bharathi Campus, Bangalore University, Bangalore 560056, India
| | - Bishwajit Paul
- Department of Chemistry, Jnana Bharathi Campus, Bangalore University, Bangalore 560056, India
| | - Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
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11
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Shyam R, Forestier C, Charbonnel N, Roy O, Taillefumier C, Faure S. Solution‐Phase Synthesis of Backbone‐Constrained Cationic Peptoid Hexamers with Antibacterial and Anti‐Biofilm Activities. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Radhe Shyam
- 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
| | - Claude Taillefumier
- Université Clermont Auvergne, Clermont Auvergne INP CNRS, ICCF F-63000 Clermont-Ferrand France
| | - Sophie Faure
- Université Clermont Auvergne, Clermont Auvergne INP CNRS, ICCF F-63000 Clermont-Ferrand France
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12
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Rajale T, Miner JC, Michalczyk R, Phipps ML, Schmidt JG, Gilbertson RD, Williams RF, Strauss CEM, Martinez JS. Conformational control via sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling. Chem Commun (Camb) 2021; 57:9922-9925. [PMID: 34498621 DOI: 10.1039/d1cc01992a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis. Their sequence-structure propensity is confirmed by circular dichroism, and conformer subtypes are enumerated by NMR. Biasing the ψ-angle backbone to trans (180°) in Monte Carlo modelling favors i to i + 3 naphthyl-naphthyl stacking, and matches experimental ensemble distributions. Taken together, high-yield synthesis of heterooligomers and NMR with structure prediction enables rapid determination of sequences that induce secondary structural propensities for predictive design of hydrophilic peptidomimetic foldamers and their future libraries.
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Affiliation(s)
- Trideep Rajale
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jacob C Miner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ryszard Michalczyk
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - M Lisa Phipps
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert D Gilbertson
- Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert F Williams
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Charlie E M Strauss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jennifer S Martinez
- Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, Arizona 86011, USA. .,Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, Arizona 86011, USA
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13
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Abstract
In nature, the self-assembly of sequence-specific biopolymers into hierarchical structures plays an essential role in the construction of functional biomaterials. To develop synthetic materials that can mimic and surpass the function of these natural counterparts, various sequence-defined bio- and biomimetic polymers have been developed and exploited as building blocks for hierarchical self-assembly. This review summarizes the recent advances in the molecular self-assembly of hierarchical nanomaterials based on peptoids (or poly-N-substituted glycines) and other sequence-defined synthetic polymers. Modern techniques to monitor the assembly mechanisms and characterize the physicochemical properties of these self-assembly systems are highlighted. In addition, discussions about their potential applications in biomedical sciences and renewable energy are also included. This review aims to highlight essential features of sequence-defined synthetic polymers (e.g., high stability and protein-like high-information content) and how these unique features enable the construction of robust biomimetic functional materials with high programmability and predictability, with an emphasis on peptoids and their self-assembled nanomaterials.
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Affiliation(s)
- Zhiliang Li
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Bin Cai
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemistry and Chemical Engineering, Shandong University, Shandong 250100, China
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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14
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Pollastrini M, Lipparini F, Pasquinelli L, Balzano F, Barretta GU, Pescitelli G, Angelici G. A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of ( S)-Indoline-2-carboxylic Acid Derivatives. J Org Chem 2021; 86:7946-7954. [PMID: 34080867 PMCID: PMC8456495 DOI: 10.1021/acs.joc.1c00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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A thorough experimental and computational study on the conformational properties of
(S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl
(S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and
phenylalanine, shows a remarkable tendency toward the cis amide isomer
when dissolved in polar solvents. This behavior is opposite to the general preference of
proline for the trans isomer, making indoline-2-carboxylic acid a good
candidate for the design of different secondary structures and new materials.
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Affiliation(s)
- Matteo Pollastrini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Luca Pasquinelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Federica Balzano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gloria Uccello Barretta
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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15
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Affiliation(s)
- Francesco De Riccardis
- Department of Chemistry and Biology “A. Zambelli”; University of Salerno; Via Giovani Paolo II, 132 84084 Fisciano SA Italy
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16
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Webber AL, Yates JR, Zilka M, Sturniolo S, Uldry AC, Corlett EK, Pickard CJ, Pérez-Torralba M, Angeles Garcia M, Santa Maria D, Claramunt RM, Brown SP. Weak Intermolecular CH···N Hydrogen Bonding: Determination of 13CH- 15N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations. J Phys Chem A 2020; 124:560-572. [PMID: 31880451 DOI: 10.1021/acs.jpca.9b10726] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Weak hydrogen bonds are increasingly hypothesized to play key roles in a wide range of chemistry from catalysis to gelation to polymer structure. Here, 15N/13C spin-echo magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) experiments are applied to "view" intermolecular CH···N hydrogen bonding in two selectively labeled organic compounds, 4-[15N] cyano-4'-[13C2] ethynylbiphenyl (1) and [15N3,13C6]-2,4,6-triethynyl-1,3,5-triazine (2). The synthesis of 2-15N3,13C6 is reported here for the first time via a multistep procedure, where the key element is the reaction of [15N3]-2,4,6-trichloro-1,3,5-triazine (5) with [13C2]-[(trimethylsilyl)ethynyl]zinc chloride (8) to afford its immediate precursor [15N3,13C6]-2,4,6-tris[(trimethylsilyl)ethynyl]-1,3,5-triazine (9). Experimentally determined hydrogen-bond-mediated 2hJCN couplings (4.7 ± 0.4 Hz (1) and 4.1 ± 0.3 Hz (2)) are compared with density functional theory (DFT) gauge-including projector augmented wave (GIPAW) calculations, whereby species-independent coupling values 2hKCN (29.0 × 1019 kg m-2 s-2 A-2 (1) and 27.9 × 1019 kg m-2 s-2 A-2 (2)) quantitatively demonstrate the J couplings for these "weak" CH···N hydrogen bonds to be of a similar magnitude to those for conventionally observed NH···O hydrogen-bonding interactions in uracil (2hKNO: 28.1 and 36.8 × 1019 kg m-2 s-2 A-2). Moreover, the GIPAW calculations show a clear correlation between increasing 2hJCN (and 3hJCN) coupling and reducing C(H)···N and H···N hydrogen-bonding distances, with the Fermi contact term accounting for at least 98% of the isotropic 2hJCN coupling.
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Affiliation(s)
- Amy L Webber
- Department of Physics , University of Warwick , Coventry CV4 7AL , U.K
| | - Jonathan R Yates
- Department of Materials , University of Oxford , Parks Road , Oxford OX1 3PH , U.K
| | - Miri Zilka
- Department of Physics , University of Warwick , Coventry CV4 7AL , U.K
| | - Simone Sturniolo
- Scientific Computing Department , Rutherford Appleton Laboratory , Chilton, Didcot , Oxfordshire OX11 0QX , U.K
| | - Anne-Christine Uldry
- Department for Biomedical Research , University of Bern , Freiburgstrasse 15 , Bern 3010 , Switzerland
| | - Emily K Corlett
- Department of Physics , University of Warwick , Coventry CV4 7AL , U.K
| | - Chris J Pickard
- Department of Materials Science and Metallurgy , University of Cambridge , 27 Charles Babbage Road , Cambridge CB3 0FS , U.K.,Advanced Institute for Materials Research , Tohoku University 2-1-1 Katahira , Aoba, Sendai 980-8577 , Japan
| | - Marta Pérez-Torralba
- Departamento de Química Orgánica y Bio-Orgánica , Facultad de Ciencias, UNED , Senda del Rey 9 , Madrid E-28040 , Spain
| | - M Angeles Garcia
- Departamento de Química Orgánica y Bio-Orgánica , Facultad de Ciencias, UNED , Senda del Rey 9 , Madrid E-28040 , Spain
| | - Dolores Santa Maria
- Departamento de Química Orgánica y Bio-Orgánica , Facultad de Ciencias, UNED , Senda del Rey 9 , Madrid E-28040 , Spain
| | - Rosa M Claramunt
- Departamento de Química Orgánica y Bio-Orgánica , Facultad de Ciencias, UNED , Senda del Rey 9 , Madrid E-28040 , Spain
| | - Steven P Brown
- Department of Physics , University of Warwick , Coventry CV4 7AL , U.K
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pierri G, Schettini R, Nuss J, Dinnebier RE, De Riccardis F, Izzo I, Tedesco C. Cyclic hexapeptoids with N-alkyl side chains: solid-state assembly and thermal behaviour. CrystEngComm 2020. [DOI: 10.1039/d0ce01136c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The solid state assembly of two cyclic hexapeptoids decorated respectively with five and six carbon N-alkyl side chains is analyzed by X-ray diffraction, intermolecular energies and lattice energy calculations.
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Affiliation(s)
- Giovanni Pierri
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- 84084 Fisciano (SA)
- Italy
| | - Rosaria Schettini
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- 84084 Fisciano (SA)
- Italy
| | - Jürgen Nuss
- Max Planck Institute for Solid State Research
- Stuttgart
- Germany
| | | | - Francesco De Riccardis
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- 84084 Fisciano (SA)
- Italy
| | - Irene Izzo
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- 84084 Fisciano (SA)
- Italy
| | - Consiglia Tedesco
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- 84084 Fisciano (SA)
- Italy
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19
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Bhattacharjee N, Perrin L, Jolibois F. Relating circular dichroism to atomic structure by means of MD simulations and computed CD spectra with α-peptoids as an example. Phys Chem Chem Phys 2020; 22:13192-13200. [DOI: 10.1039/d0cp01336f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate TD-DFT calculations of electronic circular dichroism have been performed to characterise the 3D structure of α-peptoids.
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Affiliation(s)
| | - Lionel Perrin
- Université de Lyon
- Université Claude Bernard Lyon 1
- CPE Lyon
- INSA Lyon
- ICBMS
| | - Franck Jolibois
- Université de Toulouse-INSA-UPS
- LPCNO
- CNRS UMR 5215
- 135 av. Rangueil
- Toulouse
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20
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Shyam R, Nauton L, Angelici G, Roy O, Taillefumier C, Faure S. NCα-gem-dimethylated peptoid side chains: A novel approach for structural control and peptide sequence mimetics. Biopolymers 2019; 110:e23273. [PMID: 30897209 DOI: 10.1002/bip.23273] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/05/2023]
Abstract
The design of linear peptoid oligomers adopting well-defined secondary structures while mimicking defined peptide primary sequences is a major challenge in the context of drug discovery. To this end, chemists have developed cis-inducing peptoid side chains to build robust polyproline type I helices. However, the number of efficient examples remains scarce and chemical diversity accessible through the use of these side chains is limited. Herein, we introduce an array of NCα-gem-dimethylated peptoid residues mimicking proteinogenic amino acids. Submonomer synthesis and block-coupling approaches were explored to access heterooligomers incorporating these novel types of side chains. NMR studies of monomer and trimer models showed that the NCα-gem-dimethylated groups exert complete cis control on the backbone amide conformation. Lastly, a preliminary molecular modeling study gave an insight into the preferred orientation of the substituents of the NCα-gem-dimethyl side chains relative to the peptoid backbone.
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Affiliation(s)
- Radhe Shyam
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Lionel Nauton
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Gaetano Angelici
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - 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
| | - Sophie Faure
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
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21
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Spencer RK, Butterfoss GL, Edison JR, Eastwood JR, Whitelam S, Kirshenbaum K, Zuckermann RN. Stereochemistry of polypeptoid chain configurations. Biopolymers 2019; 110:e23266. [DOI: 10.1002/bip.23266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry University of California Irvine California
- Department of Chemical Engineering & Materials Science University of California Irvine California
| | - Glenn L. Butterfoss
- Center for Genomics and Systems Biology New York University Abu Dhabi Abu Dhabi United Arab Emirates
| | - John R. Edison
- Martin A Fisher School of Physics Brandeis University Waltham Massachusetts
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California
| | | | - Stephen Whitelam
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California
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22
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Lim D, Kim H, Gong J, Eom JH, Yoon E, Driver RW, Baik MH, Lee HS. Directing Foldamer Self-Assembly with a Cyclopropanoyl Cap. Chemistry 2019; 25:2226-2233. [PMID: 30600849 DOI: 10.1002/chem.201805783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/22/2018] [Indexed: 11/07/2022]
Abstract
The rational design of self-assembling organic materials is extremely challenging due to the difficulty in precisely predicting solid-state architectures from first principles, especially if synthons are conformationally flexible. A tractable model system to study self-assembly was constructed by appending cyclopropanoyl caps to the N termini of helical α/β-peptide foldamers, designed to form both N-H⋅⋅⋅O and Cα -H⋅⋅⋅O hydrogen bonds, which then rapidly self-assembled to form foldectures (foldamer architectures). Through a combined analytical and computational investigation, cyclopropanoyl capping was observed to markedly enhance self-assembly in recalcitrant substrates and direct the formation of a single intermolecular N-H⋅⋅⋅O/Cα -H⋅⋅⋅O bonding motif in single crystals, regardless of peptide sequence or foldamer conformation. In contrast to previous studies, foldamer constituents of single crystals and foldectures assumed different secondary structures and different molecular packing modes, despite a conserved N-H⋅⋅⋅O/Cα -H⋅⋅⋅O bonding motif. DFT calculations validated the experimental results by showing that the N-H⋅⋅⋅O/Cα -H⋅⋅⋅O interaction created by the cap was sufficiently attractive to influence self-assembly. This versatile strategy to harness secondary noncovalent interactions in the rational design of self-assembling organic materials will allow for the exploration of new substrates and speed up the development of novel applications within this increasingly important class of materials.
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Affiliation(s)
- Danim Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Multiscale Chiral Architectures (CMCA), Daejeon, 34141, Republic of Korea
| | - Hyunjoong Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jintaek Gong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Multiscale Chiral Architectures (CMCA), Daejeon, 34141, Republic of Korea
| | - Jae-Hoon Eom
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Multiscale Chiral Architectures (CMCA), Daejeon, 34141, Republic of Korea
| | - Eunyoung Yoon
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Russell W Driver
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Department of Chemistry and Physics, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hee-Seung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Multiscale Chiral Architectures (CMCA), Daejeon, 34141, Republic of Korea
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23
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Szekely T, Roy O, Dériaud E, Job A, Lo-Man R, Leclerc C, Taillefumier C. Design, Synthesis, and Immunological Evaluation of a Multicomponent Construct Based on a Glycotripeptoid Core Comprising B and T Cell Epitopes and a Toll-like Receptor 7 Agonist That Elicits Potent Immune Responses. J Med Chem 2018; 61:9568-9582. [PMID: 30351939 DOI: 10.1021/acs.jmedchem.8b00960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present here for the first time the synthesis and immunological evaluation of a fully synthetic three-component anticancer vaccine candidate that consists of a β-glycotripeptoid core mimicking a cluster of Tn at the surface of tumor cells (B epitope), conjugated to the OVA 323-339 peptide (T-cell epitope) and a Toll-like receptor 7 (TLR7) agonist for potent adjuvanticity. The immunological evaluation of this construct and of precursor components demonstrated the synergistic activity of the components within the conjugate to stimulate innate and adaptive immune cells (DCs, T-helper, and B-cells). Surprisingly, immunization of mice with the tricomponent GalNAc-based construct elicited a low level of anti-Tn IgG but elicited a very high level of antibodies that recognize the TLR7 agonist. This finding could represent a potential vaccine therapeutic approach for the treatment of some autoimmune diseases such as lupus.
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Affiliation(s)
- Thomas Szekely
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF , F-63000 Clermont-Ferrand , France
| | - Olivier Roy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF , F-63000 Clermont-Ferrand , France
| | - Edith Dériaud
- Unité Régulation Immunitaire et Vaccinologie, Equipe Labellisée Ligue Contre le Cancer , Institut Pasteur , 75015 Paris , France.,INSERM U1041 , 75724 Paris Cedex 15, France
| | - Aurélie Job
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF , F-63000 Clermont-Ferrand , France
| | - Richard Lo-Man
- Unité Régulation Immunitaire et Vaccinologie, Equipe Labellisée Ligue Contre le Cancer , Institut Pasteur , 75015 Paris , France.,INSERM U1041 , 75724 Paris Cedex 15, France
| | - Claude Leclerc
- Unité Régulation Immunitaire et Vaccinologie, Equipe Labellisée Ligue Contre le Cancer , Institut Pasteur , 75015 Paris , France.,INSERM U1041 , 75724 Paris Cedex 15, France
| | - Claude Taillefumier
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF , F-63000 Clermont-Ferrand , France
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24
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Dumonteil G, Bhattacharjee N, Angelici G, Roy O, Faure S, Jouffret L, Jolibois F, Perrin L, Taillefumier C. Exploring the Conformation of Mixed Cis–Trans α,β-Oligopeptoids: A Joint Experimental and Computational Study. J Org Chem 2018; 83:6382-6396. [DOI: 10.1021/acs.joc.8b00606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Geoffrey Dumonteil
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Nicholus Bhattacharjee
- Université de Toulouse-INSA-UPS, LPCNO, CNRS UMR 5215, 135 av Rangueil, F-31077, Toulouse, France
- Université de Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INSA Lyon, ICBMS, CNRS UMR 5246, Equipe ITEMM, Bât Curien, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Gaetano Angelici
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Olivier Roy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Sophie Faure
- 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
| | - 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 1, CPE Lyon, INSA Lyon, ICBMS, CNRS UMR 5246, Equipe ITEMM, Bât Curien, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claude Taillefumier
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
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25
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Greer DR, Stolberg MA, Kundu J, Spencer RK, Pascal T, Prendergast D, Balsara NP, Zuckermann RN. Universal Relationship between Molecular Structure and Crystal Structure in Peptoid Polymers and Prevalence of the cis Backbone Conformation. J Am Chem Soc 2018; 140:827-833. [DOI: 10.1021/jacs.7b11891] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Douglas R. Greer
- Materials
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- College
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Michael A. Stolberg
- Materials
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joyjit Kundu
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ryan K. Spencer
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697, United States
| | - Tod Pascal
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- College
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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26
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Roy O, Dumonteil G, Faure S, Jouffret L, Kriznik A, Taillefumier C. Homogeneous and Robust Polyproline Type I Helices from Peptoids with Nonaromatic α-Chiral Side Chains. J Am Chem Soc 2017; 139:13533-13540. [PMID: 28837348 DOI: 10.1021/jacs.7b07475] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptoids that are oligomers of N-substituted glycines represent a class of peptide mimics with great potential in areas ranging from medicinal chemistry to biomaterial science. Controlling the equilibria between the cis and trans conformations of their backbone amides is the major hurdle to overcome for the construction of discrete folded structures, particularly for the development of all-cis polyproline type I (PPI) helices, as tools for modulating biological functions. The prominent role of backbone to side chain electronic interactions (n → π*) and side chains bulkiness in promoting cis-amides was essentially investigated with peptoid aromatic side chains, among which the chiral 1-naphthylethyl (1npe) group yielded the best results. We have explored for the first time the possibility to achieve similar performances with a sterically hindered α-chiral aliphatic side chain. Herein, we report on the synthesis and detailed conformational analysis of a series of (S)-N-(1-tert-butylethyl)glycine (Ns1tbe) peptoid homo-oligomers. The X-ray crystal structure of an Ns1tbe pentamer revealed an all-cis PPI helix, and the CD curves of the Ns1tbe oligomers also resemble those of PPI peptide helices. Interestingly, the CD data reported here are the first for any conformationally homogeneous helical peptoids containing only α-chiral aliphatic side chains. Finally we also synthesized and analyzed two mixed oligomers composed of NtBu and Ns1tbe monomers. Strikingly, the solid state structure of the mixed oligomer Ac-(tBu)2-(s1tbe)4-(tBu)2-COOtBu, the longest to be solved for any linear peptoid, revealed a PPI helix of great regularity despite the presence of only 50% of chiral side chain in the sequence.
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Affiliation(s)
- Olivier Roy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand, France
| | - Geoffrey Dumonteil
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand, France
| | - Sophie Faure
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand, France
| | - Laurent Jouffret
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand, France
| | - Alexandre Kriznik
- Université de Lorraine , Fédération de Recherche CNRS 3209, Service Commun de Biophysique Interactions Moléculaires, and Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, CNRS, UMR 7365, BP 20199, F-54505 Vandoeuvre les Nancy, France
| | - Claude Taillefumier
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand, France
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27
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Abstract
The cis-directing effect of the 1,2,3-triazolium-type side chain was studied on dimeric peptoid models with various patterns: αα, αβ, βα and ββ. Low influences of the sequence and of the solvent were observed, the cis conformation of the amide carrying the triazolium ranging from 83 to 94% in proportion. The synthesis of peptoid homooligomers with four or eight pendant 1,2,3-triazolium side chains is described. α-, β- and α,β-peptoids carrying propargyl groups were subjected to CuAAC reaction using alkyl azides, and the resulting triazoles were quaternized providing well-defined multitriazolium platforms. The influence of the counteranion (PF6-, BF4- or I-) on the conformation was also studied.
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Affiliation(s)
- Hafida Aliouat
- Université Clermont Auvergne , CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.,Laboratoire de Chimie Physique Moléculaire et Macromoléculaire, Département de Chimie, Faculté des Sciences, Université de Blida , I.B.P 270 Route de Soumaa, Blida, Algeria
| | - Cécile Caumes
- Université Clermont Auvergne , CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Olivier Roy
- Université Clermont Auvergne , CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Mohamed Zouikri
- Laboratoire de Chimie Physique Moléculaire et Macromoléculaire, Département de Chimie, Faculté des Sciences, Université de Blida , I.B.P 270 Route de Soumaa, Blida, Algeria
| | - Claude Taillefumier
- Université Clermont Auvergne , CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Sophie Faure
- Université Clermont Auvergne , CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
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28
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Abstract
The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.
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Affiliation(s)
- Russell W Driver
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA.
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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29
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Tedesco C, Meli A, Macedi E, Iuliano V, Ricciardulli AG, De Riccardis F, Vaughan GBM, Smith VJ, Barbour LJ, Izzo I. Ring size effect on the solid state assembly of propargyl substituted hexa- and octacyclic peptoids. CrystEngComm 2016. [DOI: 10.1039/c6ce01800a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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