One-Pot Photochemical Ring-Opening/Cleavage Approach for the Synthesis and Decoding of Cyclic Peptide Libraries

Abstract

ABSTRACT:A novel dual ring-opening/cleavage strategy to determine the sequence of cyclic peptides from one-bead-onecompound libraries is described. The approach uses a photolabile residue within the macrocycle and as a linker to allow a simultaneous ring-opening and cleavage from the beads upon UV irradiation and provide linearized molecules. Cyclic peptides of 5 to 9 residues were synthesized and the generated linear peptides successfully sequenced by tandem mass spectrometry.Peptide macrocycles are useful tools in chemical biology and medicinal chemistry to study and modulate proteins functions. 1 With great potential as therapeutic agents, they have gained a lot of interest in drug discovery. 2 Compared to their linear counterparts, cyclic peptides are more resistant to proteases and their increased conformational rigidity lowers the entropic cost of binding, making them tighter-binding to a given macromolecule. 3 The great degree of molecular diversity and complexity that can be accessed by simple changes in their sequence has prompted the use of cyclic peptides in combinatorial chemistry. The one-bead-one-compound (OBOC) approach, in which each bead carries many copies of a unique compound, has become a powerful tool in the drug discovery process. 4 However, the use of cyclic peptides in combinatorial OBOC libraries has been limited by difficulties in sequencing hit compounds after the screening. Lacking a free N-terminal amine, Edman degradation sequencing cannot be used on cyclic peptides and complicated fragmentation patterns are obtained by tandem mass spectrometry (MS/MS). 5 In this regard, a one-bead-two-compound approach on topologically segregated bilayer beads has been developed. 6 Initially introduced with an enzymatic shaving strategy 7 and later via chemical approaches, 8 topological bilayer segregation offers the opportunity to synthesize two compounds per bead, namely one which is exposed on the bead surface for screening (cyclic peptide) and the other found inside as a tag for sequencing and compound identification (linear peptide). More recently, Lim and co-workers reported a ring-opening strategy on cyclic peptoids to eliminate the need for encoding. 9 The approach involved the introduction of a cleavable alkylthioaryl bridge in the cycle to allow linearization of the molecule after the screening by thioether oxidation followed by nucleophilic displacement of the sulfone to generate a linear peptoid which can be sequenced by MS/MS. An attractive advantage of the ring-opening strategy over encoding methods is the absence of interference by the coding tag during screening since the same molecules are displayed inside and on the surface of the beads. Based on this strategy, we and other groups placed a methionine or a thioether bridge in cyclic peptides or peptoids and as a linker to allow a simultaneous linearization and compound release from the bead upon treatment with cyanogen bromide. 10 A similar approach was applied to cyclic depsipeptides where an aminolysis with NH 3 or hydrolysi...

Ultra-large chemical libraries for the discovery of high-affinity peptide binders

“…Interfacing non-canonical amino acid incorporation with the macrocyclic architectures that have been rendered accessible to phage 56 and mRNA display 57 would further expand the breadth of chemical space amenable to exploration by AS-MS. In our case, performing selections on libraries of macrocycles would require an additional, postenrichment linearization step for reliable MS/MS-based sequencing 58,59 . We envision that progress in these areas, along with improved mass spectral methods to enable investigation of libraries of even greater diversities, may ultimately facilitate discovery of fully non-natural peptide binders to historically undruggable targets.…”

ADAMTS4-specific MR probe to assess aortic aneurysms in vivo using synthetic peptide libraries

“…To identify peptides with higher binding affinities, we expanded this technique to cyclic peptides. Sequencing of cyclic peptides can be difficult 42 and often requires special reagents, like photochemical linkers 43 or special protection group strategy, to form cleavable cycles 44 , 45 . In our study, we used a disulfide for ring closure.…”

Radiometallation and photo-triggered release of ready-to-inject radiopharmaceuticals from the solid phase

“…29 Here, we report the development, optimization, and validation of Solid Phase Radiometallation and Photorelease (SPRP), a modular radiosynthesis approach of radiometal-based radiopharmaceuticals. The already broadly applied, photochemically triggered release of peptides from solid support using 3-amino-3-(2-nitrophenyl)propionic acid (Anp) [30][31][32] has been extensively validated for applications ranging from on-bead analysis of peptide sequences using MALDI to the selective capture of Cr 6+ ions in drinking water. 33 Other accounts report successful implementation of the photochemical cleavage of linkers and core peptides for concerted synthesis applications.…”