Crystal and NMR Structures of a Peptidomimetic β‐Turn That Provides Facile Synthesis of 13‐Membered Cyclic Tetrapeptides

Abstract

Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.

Acyclic peptides incorporating the d‐Phe‐2‐Abz turn motif: Investigations on antimicrobial activity and propensity to adopt β‐hairpin conformations

“…This hydrophobic β‐hairpin served as a proof of principle for the turn design. It is to be noted that, compared with the parent peptide, incorporation of this turn results in a significantly altered turn geometry, as we recently reported, due to the presence of the β‐amino acid, 2‐Abz.…”

“…While 2‐Abz containing peptides have been designed to adopt unique turn conformations in model peptides, biological activities were not intended, other than our own recently reported tyrocidine A analogues . Having established that d ‐Phe‐2‐Abz is a promising motif for a designed β‐hairpin, both in this work and our previous reports, we decided to use this motif to design acyclic cationic AMPs with potential β‐hairpin structure . The choice of the strand residues was based upon their β‐sheet forming propensity and their likelihood for bioactivity .…”

“…To further aid in nucleating a tighter turn, the first residue of each strand was chosen to be the d ‐configuration. Thus, the four residue β‐turn we have previously documented in both crystal and solution state was maintained and evaluated in bioactive β‐hairpin design . The peptides were designed so as to create an amphipathic structure with hydrophobic residues such as Val and Trp, which possess high intrinsic β‐sheet forming properties, on one face and cationic residues on the other.…”

“…22,[32][33][34][35] Having established that D-Phe-2-Abz is a promising motif for a designed β-hairpin, both in this work and our previous reports, we decided to use this motif to design acyclic cationic AMPs with potential β-hairpin structure. 21,22 The choice of the strand residues was based upon their β-sheet forming propensity and their likelihood for bioactivity. 35,36 For simplicity and cost, L-amino acids were used for all but one of the residues in each strand.…”

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

“…Figure 3 illustrates the distribution of Molecular Weight (MW) in the Asymmetric Unit of PDB MX structures (Data Citation 1). PDB structures span an extremely wide range of MW, from the lowest value of 468 Dalton (Da) for a small D-peptide (6 anm) 42 to the current maximum value of 97,730,800 Da for an Adenovirus capsid (4cwu) 43 . Like 4cwu, many of the PDR outliers greater than 1,000,000 are virus structures or other large macromolecular assemblies falling into particular subsets.…”