Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery

Abstract

A surprisingly high number of drug discovery projects begin with a peptide as the initial hit.1-4 These starting molecules typically need significant chemical development as linear peptides have poor pharmacokinetic properties (e.g., oral bioavailability and stability to peptidases). 5,6 Cyclic peptides, however, are far less susceptible to proteolysis 7 and often have increased biological activity because of their conformational rigidity, which decreases entropic loss upon binding. 8,9 In contrast to (and possibly as a result of) their relative underutilization in industry, cyclic peptide libraries have been extensively employed in academia, with multiple approaches developed for their generation. Such work has demonstrated the suitability of the cyclic peptide scaffold for the identification of inhibitors against some of the most challenging targets, including protein-protein interactions (PPIs).10 Macrocyclic peptide scaffolds appear to be optimal for this purpose, and with genetically encoded cyclic peptide libraries in particular, 11,12 there is potential for the straightforward creation of large sequence diversity (e.g., 6.4 × 10 7 members for six randomized amino acids). For synthetic cyclic peptide libraries, there are several approaches for identification of hits, including mass spectrometry, or by sequencing an associated genetic tag (incorporated during library synthesis). 13For the purpose of this review, we have divided cyclic peptide libraries into three main categories: biologic, semisynthetic, and fully synthetic. Some of these libraries are constrained to the canonical peptidogenic amino acids, whereas others are able to include nonpeptidogenic amino acids such as β-or γ-amino acids, D-amino acids, or nonnatural amino acids. 14-16The majority of biologically produced cyclic peptide libraries are formed using phage/phagemid display 8,17 or by splitintein cyclisation of peptides and proteins (SICLOPPS). 11,18,19 The latter uses a selectively randomized library of splitinteins for the production of genetically encoded, backbone cyclized peptide libraries. Semisynthetic libraries are able to incorporate nonpeptidogenic amino acids while retaining ribosomal synthesis and an associated genetic tag. The most frequently used method for semisynthetic library production is mRNA display 7,20 ; novel variants thereof include random nonstandard peptide integrated discovery (RaPID) 14 or protein synthesis using recombinant elements (PURE).15 Both methods use promiscuous enzymes to expand the amino acid library encoded into peptides by reprogramming codons. 16Another semisynthetic technique has been used for the creation of macrocyclic organic-peptide hybrids (MOrPHs) 21,22 and bicyclic organo-peptide hybrids (BOrPHs), 23 which produce geometrically constrained peptide libraries. Fully AbstractThe identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for s...

In VitroSelection of Cancer Cell-Specific Molecular Recognition Elements from Amino Acid Libraries

“…Ribosome display links the amino acid library directly to the ribosome and the encoding mRNA. Alternatively, in mRNA display, translated mRNA is covalently linked to the protein through an adaptor molecule [ 65 ]. These techniques have each been used to display and select peptides and antibody fragments [ 64 , 66 , 67 ].…”

Anti-amyloidogenic Heterocyclic Peptides

“…There are many methods to create libraries of cyclic peptides (reviewed in [50]), some of which have been implemented in the search for anti-amyloidogenic agents. As mentioned before, heterocyclic peptides have been studied in many antiamyloidogenic therapeutic approaches.…”

Targeting intracellular protein–protein interactions with cell-permeable cyclic peptides

“…Since these methodologies have been the subject of several recent, exhaustive reviews [6–10], we will provide here only a brief overview of them. The proper method of choice depends on the nature of the PPI in question and the expertise available within a research laboratory.…”