Cyclic α,β-Tetrapeptoids: Sequence-Dependent Cyclization and Conformational Preference

Caumes, Cécile; Fernandes, Carlos; Roy, Olivier; Hjelmgaard, Thomas; Wenger, Emmanuel; Didierjean, Claude; Taillefumier, Claude; Faure, Sophie

doi:10.1021/ol401478j

Cited by 26 publications

(26 citation statements)

References 43 publications

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“…An analysis of the ϕ and ψ angles present in published peptoid structures (41 crystal structures, 5 NMR structures, 132 total dihedral combinations, Supporting Information Table S1) reveal that trans‐ and cis ‐amides show similar preferences for ϕ and ψ combinations, with trans ‐amide and cis ‐amide residues primarily occupying two main regions that span across the bottom and top edges of the Ramachandran plot (ϕ ≈ 70° and −70° and ψ ≈ 180° and −180°, Figure ). Replotting these data to represent ϕ and ψ from 0° to 360° (adding 360° to ϕ and ψ values below 0°, Figure C,F) shows that the preferred dihedrals lay in the same low‐energy regions for trans and cis disarcosine calculatations, with regions centered around (70°, 180°) and (290°,180°) (Figure C,F).…”

Section: The Ramachandran Plotmentioning

confidence: 99%

Stereochemistry of polypeptoid chain configurations

et al. 2019

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Like polypeptides, peptoids, or N‐substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N‐substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. One hundred thirty‐two monomer dihedral angle pairs were compared to the calculated energy landscape for the peptoid Ramachandran plot, and were found to fall within the expected minima. Interestingly, only two regions of the backbone dihedral angles ϕ and ψ were found to be populated that are mirror images of each other. Furthermore, these two conformers are present in both cis and trans forms. Thus, there are four primary conformers that are sufficient to describe almost all known backbone conformations for peptoid oligomers, despite conformational constraints imposed by a variety of side chains, macrocyclization, or crystal packing forces. Because these conformers are predominant in peptoid structure, and are distinct from those found in protein secondary structures, we propose a simple naming system to aid in the description and classification of peptoid structure.

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Section: The Ramachandran Plotmentioning

confidence: 99%

Stereochemistry of polypeptoid chain configurations

et al. 2019

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“…19 We accomplished a comparable 71% yield of 6, a 15-atom cyclopenta-α-peptoid (entry 13). Swapping out the HOBt coreagent for the 7-aza analogue, 1-hydroxy-7-azabenzotriazole (HOAt), 20 we attained an astonishing increase in isolated yield to 97% of 6, with 90% for 4 but a disappointing 38% for 5 (entries 3, 6, and 15).…”

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confidence: 99%

Small Head-to-Tail Macrocyclic α-Peptoids

et al. 2014

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Access and use of this website and the material on it are subject to the Terms and Conditions set forth at Small head-to-tail macrocyclic α-peptoids Culf, Adrian S.; Čuperlović-Culf, Miroslava; Léger, Daniel A.; Decken, Andreas http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=fr L'accès à ce site Web et l'utilisation de son contenu sont assujettis aux conditions présentées dans le site LISEZ CES CONDITIONS ATTENTIVEMENT AVANT D'UTILISER CE SITE WEB. NRC Publications Record / Notice d'Archives des publications de CNRC:http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=21272916&lang=en http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=21272916&lang=fr READ THESE TERMS AND CONDITIONS CAREFULLY BEFORE USING THIS WEBSITE.http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=en Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. For the publisher's version, please access the DOI link below./ Pour consulter la version de l'éditeur, utilisez le lien DOI ci-dessous.http://doi.org/10.1021/ol501102bOrganic Letters, 16, 10, pp. 2780Letters, 16, 10, pp. -2783Letters, 16, 10, pp. , 2014 Small Head-to-Tail Macrocyclic α-Peptoids ABSTRACT: A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.

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“…The crystal structure showed that the peptoid adopted a β cis ‐α trans ‐β cis ‐α‐ trans configuration (Figure 4). 37 …”

Section: Head‐to‐tail Cyclisationmentioning

confidence: 99%

Recent Advances in the Synthesis of Peptoid Macrocycles

Webster

Cobb

2018

Chemistry A European J

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Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide‐based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide‐based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide‐based therapeutics, namely peptides are readily metabolised in vivo. Peptoids are an emerging class of peptidomimetic and they offer an alternative to peptides. Peptoids are comprised of N‐substituted glycines where side‐chains are located on the nitrogen atom of the amide backbone rather than the α‐carbon as is the case in peptides. This change in structure confers a high degree of resistance to proteolytic degradation but the absence of any backbone hydrogen bonding means that peptoids exhibit a high degree of conformational flexibility. Cyclisation has been explored as one possible route to rigidify peptoid structures, making them more selective, and, therefore more desirable as potential therapeutics. This review outlines the various strategies that have been developed over the last decade to access new types of macrocyclic peptoids.

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Cyclic α,β-Tetrapeptoids: Sequence-Dependent Cyclization and Conformational Preference

Cited by 26 publications

References 43 publications

Stereochemistry of polypeptoid chain configurations

Stereochemistry of polypeptoid chain configurations

Small Head-to-Tail Macrocyclic α-Peptoids

Recent Advances in the Synthesis of Peptoid Macrocycles

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