Constructing Head-to-Tail Cyclic Peptide DNA-Encoded Libraries Using Two-Directional Synthesis Strategy

Abstract

Macrocyclic peptides are an important class of therapeutic agents for the biological targets that are difficult to modulate by small-molecule compounds. Meanwhile, DNA-encoded library technology (DELT) provides a powerful platform for hits discovery. The unity of both fields has proven highly productive in finding cyclic peptide hits against diverse pharmaceutical proteins. Many researchers have extended the chemical toolbox for constructing head-to-tail macrocyclic DNA-encoded libraries with various ring sizes. However, the linear peptides of different lengths necessitate tuning the distance between closing sites and DNAlinked sites to perform the macrocyclization process, presumably due to the constrained conformation of linear precursors. To tackle this issue and streamline the synthetic workflow, we report a two-directional synthesis strategy. This method starts from a trifunctional reagent and prepares DNA-linked macrocyclic peptides of ring size between 15 (5-mer) and 24 (8-mer) via amide bond formation reaction, a common method to create macrocyclic peptides.

DNA-Compatible Conditions for the Formation of N-Methyl Peptide Bonds

“…HATU in the cosolvent system has been successfully applied for constructing DEL peptides. 25 Our data further confirmed that HATU is an efficient coupling reagent for the acylation of primary amines. However, we were not able to observe acylation to the DNA-conjugated secondary amine ( Table 3 ).…”

“…We repeated the coupling between Fmoc-Leu-OH and the four DNA conjugates ( 1–4 ) in mixed solvents containing water and an organic cosolvent (Table ). HATU in the cosolvent system has been successfully applied for constructing DEL peptides . Our data further confirmed that HATU is an efficient coupling reagent for the acylation of primary amines.…”

Synthesis of DNA-Encoded Macrocyclic Peptides via Nitrile-Aminothiol Click Reaction

“…In the following years, additional on-DNA cyclization methods were explored, including amide coupling, S-arylation, Ru catalyzed ring closing metathesis, thioether, 2-substituted isoindole, dihydroquinazolinone and benzimidazole formation (Figure ). − Despite these efforts, methodologies for on-DNA macrocyclization are still limited in diversity. Some of the reported reactions also suffer from incomplete cyclization and unwanted side reactions that complicate hit validation.…”