Competitive inhibition of protein-protein interactions (PPI) is challenging due to their large and often flat binding interfaces that cannot easily be disrupted by a small molecule. In contrast, peptide-based inhibitors of PPIs has become far more accessible with the emergence of cyclic peptide screening platforms such as mRNA and phage display. Cyclic peptides provide numerous advantages over their linear counterparts due to improved conformational rigidity, proteolytic stability, and membrane permeability with bicyclic peptides being more superior than their monocyclic counterparts.
A commonly used linker for producing bicyclic peptide is the 1,3,5-trisbromomethyl benzene (TBMB) linker which utilises a SN2 reaction between bromine with cysteine thiols1. However, this linker is symmetrical and thus, leads to a globular conformation with a benzene hydrophobic core. Some PPIs, however, have more shallow and extended ridges where the protein partners bind2. In these instances, the conformation of peptide produced by the 1,3,5-TBMB linker may not be as suitable. This led us to design a variation of the TBMB linker that had a 1,2,3-bromomethyl substitution pattern where the bromines are positioned asymmetrically on a single face of the ring to bias the peptide towards more extended conformation.
In this work, we synthesised the 1,2,3-TBMB linker and found the reaction to be compatible across 96 different peptide sequences tested with high efficiency of cyclisation and gives rise to unique peptide conformations by circular dichroism. We envision this linker methodology will be applicable towards a variety of protein target interfaces with irregular extended conformations.