Encoded macrocycles

Encoded chemical libraries can be used to screen a vast array of compounds against a protein target to identify potent binders. A collection of articles in this issue discuss different methods to increase the chemical space sampled by encoded macrocycle libraries and the advantages that such libraries offer for discovering new drug leads.

Ghotas Evindar, Chemistry Group Leader at GlaxoSmithKline, talks with Nature Chemistry about the advantages of using encoded libraries in drug discovery and the challenges these technologies present.

Certain drug targets have been deemed undruggable because of the difficulty in finding pharmacologically useful inhibitors. Now, two teams have developed exciting technologies for the creation of diverse collections of macrocyclic molecules and have demonstrated their usefulness for discovering macrocyclic inhibitors.

A second-generation DNA-templated library of 256,000 small-molecule macrocycles has been developed. The improved method was created by streamlining and integrating multiple aspects of DNA-encoded and DNA-templated library synthesis methodology. In vitro selection of the macrocycle library against insulin-degrading enzyme enabled the discovery of potent inhibitors.

Crosslinking within peptides containing two pairs of cysteines to form chemical bridges has now been shown to provide rapid access to thousands of different macrocyclic scaffolds in libraries that are easy to synthesize, screen and decode. Applying this strategy to phage-encoded libraries yielded binders with remarkable affinities despite the small molecular mass.

The extent to which peptide synthesis by the ribosome can tolerate the inclusion of non-peptidic components is not clear. Yet such hybrids would expand the range of ribosomally synthesized structures. Now it has been shown that tRNAs acylated by aromatic foldamers can initiate the ribosomal synthesis of non-cyclic and cyclic foldamer–peptide hybrid molecules. The oligo-aryl segments contain folding information that can control peptide conformation in the hybrids.

Encoded display of multiple chemical elements on a constant macrocyclic scaffold could mimick antibody–antigen recognition. A chemical library constructed using this approach enabled the identification of specific binders against a variety of protein targets, including difficult targets, such as TNF.

Controlling macrocycle conformation represents a powerful tool for the construction of new bioactive molecules. Now, peptide-based macrocycles bearing a 1,3,4-oxadiazole moiety grafted into their backbone have been synthesized via a new cyclization approach. The resulting cyclic products exhibit conformationally rigid turn structures (stabilized through intramolecular hydrogen bonding) that can display passive membrane permeability.

Macrocyclic oligomers are a unique structural class of compounds in which the ring size and structure can be tuned through the precise control of the primary sequence. Now, it has been shown that oligothioetheramide (oligoTEA) macrocycles can be synthesized using a one-pot acid-catalysed cascade reaction. Preliminary results indicate that cationic oligoTEAs are promising bactericidal agents.

The repertoire of amino acids available for ribosomal peptide synthesis is limited by the genetic code. Now, a method to reduce the redundancy of codons has been developed based on the artificial division of codon boxes. This method enables non-proteinogenic amino acids to be included in peptides without sacrificing proteinogenic ones.

A method to identify pairs of ligands that simultaneously bind to a target protein has been developed. The method uses two DNA-encoded chemical sub-libraries that self-assemble to form stable dual-display structures, and an encoding system that can be decoded by DNA sequencing and enables both ligands to be identified.

Life-science research and biomedical diagnostics call for robust fluorescence barcodes of compact size and high multiplexing capability. Here DNA-origami technology was used to construct a new kind of geometrically encoded barcode with excellent structural stiffness. They hold promise for both in situ and ex situ imaging of diverse biologically relevant entities.

A DNA-encoded reaction discovery system has revealed reactivity that led to the development of a visible-light-induced, biomolecule-compatible azide reduction. This reaction exhibits remarkable chemoselectivity and can be performed on oligonucleotide and oligosaccharide substrates, and in the presence of a protein enzyme, without undesired side reactions or loss of enzyme activity.