Ring size effect on the solid state assembly of propargyl substituted hexa- and octacyclic peptoids

Tedesco, Consiglia; Meli, Alessandra; Macedi, Eleonora; Iuliano, Veronica; Ricciardulli, Antonio Gaetano; Riccardis, Francesco De; Vaughan, Gavin; Smith, Vincent J.; Barbour, Leonard J.; Izzo, Irene

doi:10.1039/c6ce01800a

Cited by 15 publications

(14 citation statements)

References 54 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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“…Izzo and coworkers studied the crystal structures of hexameric and octameric propargylated cyclic polypeptoids, that is, cyclo‐(Npa) 6 and cyclo‐(Npa) 8 , and the impact of ring size on the crystallization of cyclic polypeptoids with guest molecules . For cyclo‐(Npa) 6 , the guest molecules such as acetonitrile, water and DMSO molecules intercalate between layered crystal structure.…”

Section: Crystallization and Self‐assembly Of Polypeptoid Polymersmentioning

confidence: 99%

Recent advances in crystallization and self‐assembly of polypeptoid polymers

Zeng

Qiu

Wen

2019

Polymer Crystallization

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Poly(N‐substituted glycine)s, or polypeptoids, have attracted great interest from researchers due to their structural similarity to polypeptides. By taking advantage of relative ease of synthesis and good solubility in common solvents, polypeptoid polymers provide a versatile platform to generate peptide mimics with well‐defined chemical structures and architectures. As a class of peptidomimetic polymers, a deep understanding on the impact of side‐chain structures, main‐chain topologies, and backbone conformations with respect to the aggregation behaviors is the prerequisite for developing peptidomimetic polymers toward macromolecular and supramolecular engineering. This mini‐review highlights recent developments in the crystallization and self‐assembly of homopolymers, block copolymers, and macrocycles of polypeptoids.

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“…This molecular assembly represents the peptoid counterpart of -sheet secondary structures in proteins. It can be related to a general feature of the solid-state assembly of cyclic peptoids: CH 2 groups in peptoids replace NH groups in peptides to form backbone-to-backbone hydrogen bonds (Tedesco et al, 2014(Tedesco et al, , 2016Meli et al, 2016).…”

Section: Figure 14mentioning

confidence: 99%

“…We also concluded that methoxyethyl and propargyl side chains are the most effective in inducing a columnar arrangement of peptoid macrocycles. In fact, they act as pillars and extend vertically with respect to the macrocycle plane interacting with the backbone atoms of the macrocycles below and above (Maulucci et al, 2008;Izzo et al, 2013;Meli et al, 2016;Tedesco et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Synthesis, crystallization, X-ray structural characterization and solid-state assembly of a cyclic hexapeptoid with propargyl and methoxyethyl side chains

Tedesco

Macedi

Meli

et al. 2017

Acta Crystallogr Sect B

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The synthesis and the structural characterization of a cyclic hexapeptoid with four methoxyethyl and two propargyl side chains have disclosed the presence of a hydrate crystal form [form (I)] and an anhydrous crystal form [form (II)]. The relative amounts of form (I) and form (II) in the as-purified product were determined by Rietveld refinement and depend on the purification procedures. In crystal form (I), peptoid molecules assemble in a columnar arrangement by means of side-chain-to-backbone C=CH...OC hydrogen bonds. In the anhydrous crystal form (II), cyclopeptoid molecules form ribbons by means of backbone-to-backbone CH...OC hydrogen bonds, thus mimicking β-sheet secondary structures in proteins. In both crystal forms side chains act as joints among the columns or the ribbons and contribute to the stability of the whole solid-state assembly. Water molecules in the hydrate crystal form (I) bridge columns of cyclic peptoid molecules, providing a more efficient packing.

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Ring size effect on the solid state assembly of propargyl substituted hexa- and octacyclic peptoids

Cited by 15 publications

References 54 publications

Stereochemistry of polypeptoid chain configurations

Stereochemistry of polypeptoid chain configurations

Recent advances in crystallization and self‐assembly of polypeptoid polymers

Synthesis, crystallization, X-ray structural characterization and solid-state assembly of a cyclic hexapeptoid with propargyl and methoxyethyl side chains

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