Structural characterization of a peptoid with lysine-like side chains and biological activity using NMR and computational methods

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.

Strategies to Control the Cis‐Trans Isomerization of Peptoid Amide Bonds

“…Sternberg et al designed a Rhodamin B labelled peptoid [RhoB spiro -Ahx]-[But] 6A NH 2 49 having a lysine side chain on the nitrogen atom, which showed very good cellular uptake similar to conventional cell-penetrating peptides (Figure 11C). [54] Interestingly, conformational analysis on the peptoid [RhoB spiro -Ahx]-[But] 6A NH 2 by 2D-NMR spectroscopy as well as QM/MM force field COSMOS-NMR calculations indicated that the amide bonds in 49 preferentially adopted cis conformation in solution. However, a detailed investigation on the role of various molecular interactions in the lysine-like side chain containing peptoids have not been carried out yet.…”

Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα‐amino acids

“…The preferred conformations adopted by peptoids in solution were analyzed in detail in a large variety of NMR and CD studies. Curiously, the first 1 H NMR spectra recorded for poly‐peptoids based on higher ( N ‐ethyl, N‐n ‐propyl, and N‐n ‐butyl) homologues of N ‐methyl‐glycine (Sar) were published as early as in 1972 .…”

“…All of the peptoids examined by NMR with sterically hindered N ‐( t Bu) side chains show a single set of signals indicative of an all‐ cis amide arrangement . A water‐soluble hexamer peptoid with all N ‐(4‐aminobutyl)glycine residues adopts a pseudo‐helical structure with all‐ cis amide bonds according to a combined quantum mechanics/molecular mechanics (QM/MM) force field NMR strategy . The protonated ammonium side chains are extended, a prerequisite for efficient cell‐penetrating compounds.…”

Cyclic Peptoid-Peptide Hybrids as Versatile Molecular Transporters

“…So far, mainly positively charged CPPos have been synthesized with cellular uptake specificity for endosomes, the cytosol, or the nucleus. (Murphy et al, 1998;Wender et al, 2000;Wright et al, 2003;Schröder et al, 2007;Schröder et al, 2008;Eggenberger et al, 2009;Unciti-Broceta et al, 2009;Huang et al, 2012;Kölmel et al, 2012;Sternberg et al, 2013;Kölmel et al, 2014;Marouseau et al, 2017) The incorporation of a critical amount of lipophilic side chains led to a specific accumulation in mitochondria. (Kölmel et al, 2012;Nam et al, 2018) It was stated, that a cationic charge may be a prerequisite for interaction with the negatively charged head groups of the phospholipid bilayer and subsequent cellular uptake through the plasma membrane.…”