Crystal Structures of Protein-Bound Cyclic Peptides

Abstract

Cyclization is an important post-translational modification of peptides and proteins that confers key advantages such as protection from proteolytic degradation, altered solubility, membrane permeability, bioavailability, and especially restricted conformational freedom in water that allows the peptide backbone to adopt the major secondary structure elements found in proteins. Non-ribosomal synthesis in bacteria, fungi, and plants or synthetic chemistry can introduce unnatural amino acids and non-peptidic constraints that modify peptide backbones and side chains to fine-tune cyclic peptide structure. Structures can be potentially altered further upon binding to a protein in biological environments. Here we analyze three-dimensional crystal structures for 211 bioactive cyclic peptides bound to 65 different proteins. The protein-bound cyclic peptides were examined for similarities and differences in bonding modes, for main-chain and side-chain structure, and for the importance of polarity, hydrogen bonds, hydrophobic effects, and water molecules in interactions with proteins. Many protein-bound cyclic peptides show backbone structures like those (strands, sheets, turns, helices, loops, or distorted variations) found at protein−protein binding interfaces. However, the notion of macrocycles simply as privileged scaffolds that primarily project side-chain substituents for complementary interactions with proteins is dispelled here. Unlike small-molecule drugs, the cyclic peptides do not rely mainly upon hydrophobic and van der Waals interactions for protein binding; they also use their main chain and side chains to form polar contacts and hydrogen bonds with proteins. Compared to small-molecule ligands, cyclic peptides can bind across larger, polar, and water-exposed protein surface areas, making many more contacts that can increase affinity, selectivity, biological activity, and ligand−receptor residence time. Cyclic peptides have a greater capacity than small-molecule drugs to modulate protein−protein interfaces that involve large, shallow, dynamic, polar, and water-exposed protein surfaces.

Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2

“…To obtain robust crystallization conditions for hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) in complex with inhibitors and substrates, we explored all of the aforementioned approaches, but none has been efficient to date. As an alternative, we explored the use of cyclic peptides (CPs), which we identified via application of mRNA display technology [8][9][10] ; this led to a CP that binds tightly to the catalytic domain of PHD2 (K D value of 270 pM) 8 at a site away from the active site in a manner that efficiently enables efficient crystallization in previously unobserved forms.…”

Bent into shape: Folded peptides to mimic protein structure and modulate protein function

“…Because the catch‐all definition of a loop precludes categorization by structure, we will discuss peptides based on the chemistries used for peptide cyclization. Recent reviews by Fairlie, Hutton, and coworkers highlight many natural and synthetic peptides that bind to proteins, including several that competitively inhibit PPIs . We will also mention novel chemical approaches that have been applied with the intent of stabilizing non‐regular structures, even in the absence of structures.…”

“…Aside from lactam, disulfide, and thioether cyclization, various other linkages have been used for peptide cyclization, including ether, triazole, biaryl, olefin, and lactone bonds . Some of these cyclic peptides have been structurally characterized but the dataset is generally too sparse to draw significant conclusions relating crosslinking strategy to specific structure(s) …”

Expanded toolbox for directing the biosynthesis of macrocyclic peptides in bacterial cells

“…Macrocyclic peptides have emerged as an attractive class of bioactive molecules and therapeutic agents, in particular because of their potential ability to interact with extended and shallow protein surfaces 1,2 and thus provide a means to address notoriously challenging targets such as protein-protein interactions. [3][4][5][6][7] Conformational restriction through backbone and/or side-chain cyclization 8 has been shown to impart peptides with several advantageous features such as increased specicity and affinity toward the target protein, [9][10][11] enhanced proteolytic resistance [12][13][14][15] and/or improved cell permeability.…”