Light-responsive bicyclic peptides

Abstract

In this paper, we describe a method for the synthesis of light-responsive (LR) bicyclic macrocycles from linear peptides composed of 20 natural amino acids. Small molecules, peptide macrocycles, and protein conjugates that reversibly turn their function on and off in response to visible light enabled the fields of photopharmacology and optochemical genetics. Bioactive LR molecules could be produced by grafting azobenzene or other LR-structures onto molecules with known biological functions (e.g., alpha-helical peptides). It is also possible to discover such LR ligands de novo by selecting compounds with a desired function-such as binding to a target-from a library of LR-compounds or a genetically-encoded (GE) library of LR-macrocycles. The bicyclic topology of ligands offers added value such as improved binding and stability when compared to monocyclic peptides, but approaches for the design of bicyclic light-responsive architectures are limited. To address this need, we developed a tridentate C2-symmetric hydroxyl amine and di-chlorobenzene containing azobenzene (HADCAz) LR-linker with two orthogonally reactive functionalities (chlorobenzyl and hydroxylamine) to convert a linear unprotected peptide into a bicyclic peptide in a one-pot, two-step reaction. This linker reversibly isomerizes from the trans to cis form upon irradiation with blue light (365 nm). The resulting bicyclic peptide contains two loops of amino acids, one of which is constrained with an azobenzene moiety that can change the conformation in response to visible light. A scalable synthetic route to the HADCAz linker allowed us to demonstrate its application in multiple synthetic bicyclic peptides with loops that contain 2-5 amino acids.

Genetically-Encoded Discovery of Proteolytically Stable Bicyclic Inhibitors of Morphogen NODAL

“…Such libraries can be used to discover pro- 78 Finally, the lower symmetry of the TSL-style linkers allows their diversification with any chemotype of C2-symmetry. 71 It offers a significant expansion of the bicyclization repertoire beyond traditional architectures produced from three-fold symmetric cross-linkers.…”

“…We note that aniline can catalyze oxime reactions 51,70 ; however, we avoided aniline and other nucleophilic catalysts to prevent the formation of byproducts with TSL-6. 71 The addition of 1 mM TCEP to the ligated product reduced the disulfide linkage. Raising the pH to 10 led to bicyclization of peptides in 3 hours.…”

A phage display approach to identify highly selective covalent binders

“…We chose to focus on cyclic peptides based on the fact that both cyclic and bicyclic structures can be generated directly from peptide sequences on an expressed phage coat protein [21,31,54].…”

Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties

“…This allowed simple immobilization of conformationally constrained bicycles on solid matrices. In addition, Jafari et al [46] have designed a scaffold that undergoes geometric isomerization when irradiated with UV light, leading to a conformational shift in one of the peptide loops (Figure 6). This feature might be harnessed for development of peptides with tunable binding affinity.…”