A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake

Abstract

While peptides are promising as probes and therapeutics, targeting intracellular proteins will require greater understanding of highly structured, cell-internalized scaffolds. We recently reported BC1, an 11-residue bicyclic peptide that inhibits the Src homology 2 (SH2) domain of growth factor receptor-bound protein 2 (Grb2). In this work, we describe the unique structural and cell uptake properties of BC1 and similar cyclic and bicyclic scaffolds. These constrained scaffolds are taken up by mammalian cells despite their net neutral or negative charges, while unconstrained analogs are not. The mechanism of uptake is shown to be energy-dependent and endocytic, but distinct from that of Tat. The solution structure of BC1 was investigated by NMR and MD simulations, which revealed discrete water-binding sites on BC1 that reduce exposure of backbone amides to bulk water. This represents an original and potentially general strategy for promoting cell uptake.

Bicyclic Peptides as Next‐Generation Therapeutics

“…Quartararo et al designed a bicyclic peptide inhibitor of the Grb2 SH2 domain. [58] They found that conversion of a monocyclic undecapeptide, G1, into a bicyclic peptide, BC1 ( 22 , Figure 9), resulted in 60-fold higher potency and 200-fold improved selectivity for the Grb2 SH2 domain. In another application, dimerization of a potent monocyclic peptide inhibitor produced an effective bicyclic peptide therapeutic against vascular endothelial growth factor (VEGF).…”

Understanding and designing head‐to‐tail cyclic peptides

“…Several challenges are associated with using MD simulations to accurately and efficiently predict CP structures (Figure ). (1) Both experimental and computational studies have shown that solvent plays a significant role in the structure a CP adopts . Therefore, to accurately account for direct CP–solvent interactions, explicit solvent simulations are necessary.…”

“…In a recent study, Quartararo and co‐workers found that water was key to the structure of a bicyclic peptide . Using MD simulations, several water molecules with long‐lived hydrogen bonds to the CP backbone atoms were identified.…”

“…Recently, ring expansion has been shown as a promising alternative to head‐to‐tail cyclization, mitigating the entropic barriers of cyclization using the more traditional method . Multiple cyclizations can also be incorporated to generate bicyclic peptides, tricyclic peptides, etc., where these additional cyclizations can provide further restraints to rigidify the peptides and afford an even greater complexity of design space . In this review we will focus on head‐to‐tail cyclized peptides.…”

Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display

“…6 Cyclization 7 has also been shown to lead to improved target affinity, 8, 9, 10, 11 specificity, 12, 13 and cell permeability. 14, 15, 16, 17 Introduction of a second macrocycle into a peptide is particularly advantageous and has been shown to further increase both target affinity 18, 19 and bio-stability 11, 20 and cell permeability 21, 22, 23 relative to the linear and monocyclic versions. Highly-constrained bicyclic peptides are similar to the highly potent knotted peptide natural products, an attractive and emerging class of therapeutics with enhanced stability and bioavailability derived from their knotted structures.…”