Recent advances in the synthesis of cyclic pseudopeptides

Overcoming the shortcomings of peptide-based therapeutics

Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.

Hierarchical self-assembly of aromatic peptide conjugates into supramolecular polymers: it takes two to tango

Supramolecular polymers are self-assembled materials displaying adaptive and responsive "life-like" behaviour which are often made of aromatic compounds capable of engaging in π-π interactions to form larger assemblies. Major advances have been made recently in controlling their mode of self-assembly, from thermodynamically-controlled isodesmic to kinetically-controlled living polymerization. Dynamic covalent chemistry has been recently implemented to generate dynamic covalent polymers which can be seen as dynamic analogues of biomacromolecules. On the other hand, peptides are readily-available and structurally-rich building blocks that can lead to secondary structures or specific functions. In this context, the past decade has seen intense research activity in studying the behaviour of aromatic-peptide conjugates through supramolecular and/or dynamic covalent chemistries. Herein, we review those impressive key achievements showcasing how aromatic- and peptide-based self-assemblies can be combined using dynamic covalent and/or supramolecular chemistry, and what it brings in terms of the structure, self-assembly pathways, and function of supramolecular and dynamic covalent polymers.

3-Substituted 2-isocyanopyridines as versatile convertible isocyanides for peptidomimetic design

We report the use of 3-substituted 2-isocyanopyridines as convertible isocyanides in Ugi four-component reactions. The N-(3-substituted pyridin-2-yl)amide Ugi products can be cleaved by amines, alcohols, and water with Zn(OAc)2 as a catalyst. In addition, the applicability of the method was demonstrated in constrained di-/tripeptides bearing acid and base sensitive protective groups obtained via Ugi-4CR post-condensation modifications.

Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins

Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.

Heteroaryl Rings in Peptide Macrocycles

This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.

Synthesis of thioureido peptidomimetics employing alkyl azides and dithiocarbamates

An unprecedented approach for the assembly of thioureido peptidomimetics is developed employing alkyl azides and dithiocarbamates. Dithiocarbamates react with alkyl azides with the liberation of N2 and elemental sulfur thereby leading to thiourea in a traceless manner. Thioureido peptidomimetics are thus furnished in good yields with no epimerization. This process is mild, free from the use of a base, scalable and step economic. The practicability of this methodology has been highlighted by the synthesis of N,N'-orthogonally protected thioureido peptidomimetics.

The Pseudoproline Approach to Peptide Cyclization

The development of efficient methods for the synthesis of cyclic peptides is of interest because of the many potential applications of this class of molecule. Pseudoprolines are derived from serine, threonine, and cysteine and can be used as traceless turn-inducers to facilitate the cyclization of a wide range of linear peptide precursors. The incorporation of a pseudoproline into the peptide to be cyclized generally results in a cyclization reaction that proceeds more quickly and with higher yield than that of an analogous sequence without the pseudoproline. Installation of a pseudoproline at the C-terminal position of a linear peptide sequence has also been shown to eliminate any epimerization of this residue during the reaction. Following pseudoproline-mediated cyclization, these turn-inducers can be removed on treatment with acid in a similar manner to other protecting groups to provide the native peptide sequence, and in the case of cysteine-derived pseudoprolines, the resulting cysteine can be readily converted into alanine through desulfurization. These traceless turn-inducers have been successfully used in the synthesis of cyclic peptides containing either serine, threonine, cysteine or alanine residues.