Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries

DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.

An Electrochemical Beckmann Rearrangement: Traditional Reaction via Modern Radical Mechanism

Electrosynthesis as a potential means of introducing heteroatoms into the carbon framework is rarely studied. Herein, the electrochemical Beckmann rearrangement, i. e. the direct electrolysis of ketoximes to amides, is presented for the first time. Using a constant current as the driving force, the reaction can be easily carried out under neutral conditions at room temperature. Based on a series of mechanistic studies, a novel radical Beckmann rearrangement mechanism is proposed. This electrochemical Beckmann rearrangement does not follow the trans-migration rule of the classical Beckmann rearrangement.

Ligation Technologies for the Synthesis of Cyclic Peptides

Cyclic peptides have been attracting a lot of attention in recent decades, especially in the area of drug discovery, as more and more naturally occurring cyclic peptides with diverse biological activities have been discovered. Chemical synthesis of cyclic peptides is essential when studying their structure-activity relationships. Conventional peptide cyclization methods via direct coupling have inherent limitations, like the susceptibility to epimerization at the C-terminus, poor solubility of fully protected peptide precursors, and low yield caused by oligomerization. In this regard, chemoselective ligation-mediated cyclization methods have emerged as effective strategies for cyclic peptide synthesis. The toolbox for cyclic peptide synthesis has been expanded substantially in the past two decades, allowing more efficient synthesis of cyclic peptides with various scaffolds and modifications. This Review will explore different chemoselective ligation technologies used for cyclic peptide synthesis that generate both native and unnatural peptide linkages. The practical issues and limitations of different methods will be discussed. The advance in cyclic peptide synthesis will benefit the biological and medicinal study of cyclic peptides, an important class of macrocycles with potentials in numerous fields, notably in therapeutics.

Sterically Demanding Oxidative Amidation of α-Substituted Malononitriles with Amines Using O2

An efficient amidation method between readily available 1,1‐dicyanoalkanes and either chiral or nonchiral amines was realized simply with molecular oxygen and a carbonate base. This oxidative protocol can be applied to both sterically and electronically challenging substrates in a highly chemoselective, practical, and rapid manner. The use of cyclopropyl and thioether substrates support the radical formation of α‐peroxy malononitrile species, which can cyclize to dioxiranes that can monooxygenate malononitrile α‐carbanions to afford activated acyl cyanides capable of reacting with amine nucleophiles.

KAHA Ligation at Serine

Oxazetidine assisted KAHA ligation was developed by the Bode group as an efficient peptide segment ligation strategy at native serine residues. This milestone achievement should enable the chemical synthesis of difficult-to-prepare proteins for biological studies.

Chemical Protein Synthesis with the KAHA Ligation

Since the first report of the chemoselective amide bond forming reaction between α-ketoacids and hydroxylamines in 2006, the KAHA (α-ketoacid-hydroxylamine) ligation has advanced to a useful tool for the routine synthesis of small to medium sized proteins and cyclic peptides. In this chapter we introduce the concept of KAHA ligation starting with the synthesis and properties of hydroxylamines and α-ketoacids, methods for their incorporation into peptides, and give an insight into the mechanism of the KAHA ligation. We cover important improvements including sequential ligations with 5-oxaproline, traceless synthesis of peptide α-ketoacids and show their application in chemical protein synthesis and cyclic peptide synthesis. Recent developments of the KAT (potassium acyl trifluoroborate) ligation and its application as fast and chemoselective bioconjugation method are described and an outlook on ongoing work and possible future developments is given at the end of the chapter.