Next Generation Bicycle Scaffolds: Phage Selection With Added Functionality

BicycleTx Ltd is a biotech company founded to develop a new therapeutic modality based on thioether bridged bicyclic peptides (Bicycles). Their technology is based on screening synthetically constrained phage encoded combinatorial peptide libraries.1 M13 phage displaying short peptide libraries (9 - 20 residues) including three Cys residues are cross-linked through reaction of the Cys-SH with reactive functional groups on a C3-symmetrical small molecule scaffold to give conformationally constrained bicyclic peptides expressed on the pIII coat protein. These Bicycle libraries are then screened against a range of biological targets to identify peptide sequences with high affinity and selectivity. This powerful technology enables BicycleTx to develop novel leads to tackle intractable diseases and undruggable targets in oncology, immunoncology and antimicrobial therapeutics.2
A critical limitation is that it is not currently possible to screen Bicycle libraries with additional functionality, such as cell penetrating peptides, lipids to anchor the Bicycles to membranes, or siderophores for active uptake to Gram -ve bacteria. This would make it possible to screen the resulting Bicycle-conjugated libraries for binding to their targets, where the selection process would inherently include cell penetration, membrane surface localisation, or uptake to Gram -ve bacteria.
In this project, the student will design and synthesise novel bifunctional, C3-symmetric scaffolds bearing (i) three identical groups for covalent attachment to the three phage Cys-SH and (ii) one or three "click" handles to attach additional functionality. These Next Generation C3-symmetric Bicycle scaffolds will be designed with alkylating groups that can be reacted with the phage peptide under mild aqueous conditions; the click handles will allow biorthogonal attachment of lipids, peptides and siderophores. Structurally simple scaffolds will be used to avoid side-reactions with other regions of the phage peptide. Two types of scaffolds will be synthesised and tested: rigid scaffolds based on an adamantane core, which will have three symmetrical alkylating groups and a fourth point of attachment for bioconjugation of the additional functionality; and symmetrical cycle hexapeptide-based scaffolds with three groups that can be conjugated to the Cys-SH and three for attachment of the additional groups. The student will then test these scaffolds with phage libraries to optimise the efficiency of conjugation to the scaffolds, and may then screen a library containing one of these scaffolds for binding to a therapeutically relevant target. NMR/X-ray studies of high-affinity Bicycles will be carried out to determine the effects of the new scaffolds on the conformation of the constrained peptides.
These next generation Bicycles will combine the pharmacological properties of a biologic with the pharmacokinetic and synthetic advantages of a small molecule, enabling a range of therapeutically relevant targets to be tackled, including many that have so far been undruggable with small molecules. The proposed work is a clear fit to the BBSRC Advancing the frontiers of bioscience discovery objective (in particular the transformative technologies priority). It is aligned to the Pharmaceuticals and Technology Development research areas, and has potential impact relating to the combatting antimicrobial resistance priority area.
1. Nature Chem Biol 5, 502 (2009) 2. J Med Chem 63, 4107 (2020)