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. 2009 Nov 18;131(45):16555-67.
doi: 10.1021/ja907184g.

New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems

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New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems

Benjamin C Gorske et al. J Am Chem Soc. .

Abstract

Controlling the equilibria between backbone cis- and trans-amides in peptoids, or N-substituted glycine oligomers, constitutes a significant challenge in the construction of discretely folded peptoid structures. Through the analysis of a set of monomeric peptoid model systems, we have developed new and general strategies for controlling peptoid conformation that utilize local noncovalent interactions to regulate backbone amide rotameric equilibria, including n-->pi*, steric, and hydrogen bonding interactions. The chemical functionalities required to implement these strategies are typically confined to the peptoid side chains, preserve chirality at the side chain N-alpha-carbon known to engender peptoid structure, and are fully compatible with standard peptoid synthesis techniques. Our examinations of peptoid model systems have also elucidated how solvents affect various side chain-backbone interactions, revealing fundamental aspects of these noncovalent interactions in peptoids that were largely uncharacterized previously. As validation of our monomeric model systems, we extended the scope of this study to include peptoid oligomers and have now demonstrated the importance of local steric and n-->pi* interactions in dictating the structures of larger, folded peptoids. This new, modular design strategy has guided the construction of peptoids containing 1-naphthylethyl side chains, which we show can be utilized to effectively eliminate trans-amide rotamers from the peptoid backbone, yielding the most conformationally homogeneous class of peptoid structures yet reported in terms of amide rotamerism. Overall, this research has afforded a valuable and expansive set of design tools for the construction of both discretely folded peptoids and structurally biased peptoid libraries and should shape our understanding of peptoid folding.

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Figures

Figure 1
Figure 1
Comparison of the peptoid and α-peptide primary structures.
Figure 2
Figure 2
Left: The n→π*Ar interaction (indicated by the red arrow) proposed to increase Kcis/trans for peptoid backbone amides. Right: Newman projection depicting the n→π*Ar interaction.
Figure 3
Figure 3
Structures of the peptoid model systems (115) designed to probe n→π* interactions.
Figure 4
Figure 4
Left: Structures of model compounds 6 and 8. Right: Newman projections depicting the most populated conformations for cis-6 and cis-8, as indicated by the NOEs shown: red=stronger for 8 v. 6, black=identical for 6 and 8.
Figure 5
Figure 5
Left: The n→π*C=O interaction (indicated by the red arrow) proposed to reduce Kcis/trans for the donating amide in peptoids. Right: Newman projection depicting the n→π*C=O interaction
Figure 6
Figure 6
Structures of the peptoid model systems (1626) designed to probe steric interactions.
Figure 7
Figure 7
Structures of the peptoid model systems (2732) designed to probe hydrogen bonding interactions.
Figure 8
Figure 8
Possible noncovalent interactions affecting Kcis/trans for 27. A) Direct hydrogen bond (red dashes) stabilizing the cis-acetamide. B) Backbone-side chain n→π*C=O interaction (green arrow) stabilizing the cis-acetamide. C) Backbone-backbone n→π*C=O interaction (blue arrow) stabilizing the trans-acetamide.
Figure 9
Figure 9
Structures of the polypeptoids (3337) designed to examine noncovalent interactions in peptoid oligomers.
Figure 10
Figure 10
CD spectra of Ac-s1npe-Pip (S-26), Ac-(s1npe)2-CONH2 (37), and Ac-(s1npe)3-CONH2 (38) at 60 μM concentration in acetonitrile. Spectra were collected at 25 °C.
Scheme 1
Scheme 1
The generic synthetic routes (eqs 1 and 2) used in the construction of the peptoid model systems. Reagents and conditions: a. 0.9 equiv. R1NH2, 1 equiv. triethylamine, CH2Cl2, 0 °C, 60 min. b. 0.85 equiv. R2NH2, DMF, 0–24 °C, 12 h. c. 4 equiv. (CH3CO)2O, 2.1 equiv. (i-Pr)2EtN, CH2Cl2, 25 °C, 30 min. d. 2.1 equiv. (CH3CO)2O, CH2Cl2, 25 °C, 30 min. e. 2 equiv. NaH, 1.2 equiv. CH3I, DMF, 0 °C, 5 min. Details of representative syntheses of these compound classes have been reported previously.

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References

    1. Simon RJ, et al. Proc Natl Acad Sci U S A. 1992;89:9367–9371. - PMC - PubMed
    1. Figliozzi GM, Goldsmith R, Ng SC, Banville SC, Zuckermann RN. Methods Enzymol. 1996;267:437–447. - PubMed
    1. Zuckermann RN, Kerr JM, Kent SBH, Moos WH. J Am Chem Soc. 1992;114:10646–10647.
    1. Miller SM, Simon RJ, Ng S, Zuckermann RN, Kerr JM, Moos WH. Bioorg Med Chem Lett. 1994;4:2657–2662.
    1. Kwon YU, Kodadek T. J Am Chem Soc. 2007;129:1508–1509. - PMC - PubMed

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