Carbopeptides: carbohydrates as potential templates for de novo design of protein models

Abstract

De novo design of proteins has evolved into a powerful approach for studying the factors governing protein folding and stability. Among the families of structures frequently studied is the 'four-helix bundle' in which four alpha-helical peptide strands, linked by loops, form a hydrophobic core. Assembly of protein models on a template has been suggested as a way to reduce the entropy of folding. Here we describe the potential use of a carbohydrate as such a template. The monosaccharide D-galactose was per-O-acylated with (Nbeta-Fmoc-betaAla)2O to give a penta-substituted derivative, which was converted to the corresponding glycosyl bromide and used for the glycosylation of 4-hydroxymethylbenzoic acid pentafluorophenyl ester (HMBA-OPfp). The beta-glycosidic carbohydrate template (Nbeta-Fmoc-3Ala)4-beta-D-Galp-(1-O)-MBA-OPfp thus obtained was coupled to a PAL-PEG-PS resin and simultaneously extended at the four arms to yield, after cleavage from the solid support, a carbopeptide with four identical peptide strands. Extension of this concept to, for example, synthesis of novel multiple antigenic peptides (MAPs) and synthesis of carbohydrate clusters can be easily envisioned. The ability to efficiently synthesize such structures sets the stage for further studies to test whether the carbohydrate templates do indeed nucleate folding.

Peptide-Based Polymer Therapeutics

“…Amino acid based dendrimers can be described as molecules based on branched amino acids (i.e., lysine, glutamic acid, aspartic acid, cis-4-amino-L-proline [207][208][209][210][211][212]) or other building blocks, such as cyclic peptides, poly(amido amines) (PAMAM) [213], polypropylene imines (PPI) [214], poly(aryl ethers) [215,216] and a large variety of other branched moieties including carbohydrates [217,218]. In this review, we will focus on examples coming from amino acid based dendrimers exclusively composed of amide bonds.…”

Amino Acid‐Based Dendrimers

“…Peptide dendrimers constructed by coupling peptide segments onto polyphenylene scaffolds have been synthesized, affording shape-persistent, MAP candidates [45]. Examples of the use of carbohydrates as potential templates for multivalent peptide assembly have also been reported [12,13]. A novel amino acidbased dendrimer was prepared from 3,5-bis(2-tert-butyloxycarbonyl aminoethoxy) benzoic acid methyl ester [46,47].…”

“…The dendrimer generation is defined as the number of branching points from the core to the surface of the dendrimer. Here, amino acid-based dendrimers, or peptide dendrimers, are loosely defined as molecules formed from amino acids emanating from a branched template or scaffold, in which branched templates can be branched amino acids such as lysine [3][4][5], glutamic and aspartic acid [6,7], cis-4-amino-Lproline [8], or other building blocks, including cyclic peptides, poly(amido amines) (PAMAM) [9], polypropylene imines (PPI) [1], poly(aryl ethers) [10,11], and a variety of other organic branched motifs such as carbohydrates [12,13]. In this chapter we focus mainly on peptide dendrimers that are branched with amino acids (natural or unnatural) and exclusively composed of amide bonds.…”

Carbohydrates in peptide and protein design

“…In this strategy, the monosaccharide was per-O-acylated with four Fmoc--Ala-OH moieties and linked through the anomeric center to a solid support, following which the peptides were assembled on all four ''arms'' simultaneously ( Figure 14). 95 The carbopeptide concept was next extended to carboproteins in a second-generation approach with the goal to prepare protein-sized structures, starting with the relatively well-understood 4--helix bundles. Inspired by the progress in chemoselective ligation chemistry, a convergent modular synthesis strategy was adopted to increase the freedom of the design.…”

“…Peptide: H-Ala-Leu-Ala-LysLeu-Gly-. 95 ( Figure 15, with R: -C 6 H 4 -NHCO-CH 2 SH). Also, for this study, the largest carboprotein was assembled, a 4--helix bundle dimer with a disulfide bridge connecting the two templates through the anomeric center.…”