Synthesis of a Novel Macrocyclic Library: Discovery of an IGF-1R Inhibitor

Abstract

We present a new approach for the conversion of active sequences of proteins and peptides into small molecules. A library of macrocyclic disulfide molecules was made, in which the active pharmacophores of the parent peptide are preserved while the size of the macromolecular scaffold on which the pharmacophores are arranged is varied. This enables a systematic search for macromolecules in which the pharmacophores are in an appropriate conformation for biological activity. We developed two procedures for the synthesis of such libraries from building blocks that include commercial amino acids and functionalized aldehydes. Chemical synthesis using the "tea-bag" method gave a library with higher diversity, but low yields, compared to the manual synthesis of the library, in which the compounds were synthesized in individual vessels and the yield and purity improved dramatically. As a proof of concept, we synthesized a 34-member library derived from the sequence of the activation loop of insulin-like growth factor-1 receptor. Selected compounds were screened, and one was found to be biologically active in the low micromolar range. The concept presented here may prove particularly useful in cases where the pharmacophores are known but need to be systematically screened for a spatial arrangement that will enable biological activity.

Insulin-like Growth Factor-1 Receptor (IGF-1R) Kinase Inhibitors in Cancer Therapy: Advances and Perspectives

“…Interestingly, Qvit et al synthesized a novel macrocyclic combinatorial library based on pharmacophores derived from the sequence of the activation loop of IGF-1R to inhibit the activation of it [68]. Members of these compounds combined the advantages of peptide-based drugs with those of constrained macrocyclic scaffold, and retained the flexibility to induce fitting upon binding to the receptor.…”

Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design

“…29,36,37 Inhibiting kinase-substrate interactions by mimicking the sequence of known substrate peptides is an approach that is being actively pursued by several labs. 22,35,[38][39][40] For example, the sequence of the activation loop of insulin-like growth factor-1 receptor, which undergoes autophosphorylation, was used as a pharmacophore template to be mimicked by novel macrocyclic molecules.…”

“…Combinatorial approaches to peptides as protein-site mimetics have been discussed in a recent review. 56 Such screens of either random [57][58][59][60][61] or biased peptide libraries 22,38,62 of peptides of up to 20 amino acids in length, 63 may identify potent peptidic inhibitors that are not necessarily similar to native ligands of the protein, but nevertheless efficiently inhibit the proteinprotein interaction of interest. Lead inhibitory peptides, whether based on a known binding partner or obtained from a library screen, often serve as merely the first step in developing an inhibitor.…”

“…17 It has become clear that proteinpeptide interactions are very abundant in the cell and estimates suggest they represent 15-40% of all interactions, 18 making peptide discovery and development of wide applicability and interest. Cyclic peptides [19][20][21][22] and other modified peptides 23,24 can be highly potent as well as selective, providing a compromise between structural preorganization and sufficient flexibility to mold to a target surface and maximize binding interactions. There is much evidence that despite having molecular masses well above Lipinski's rule constraints, cyclic peptides and other macrocycles can possess drug-like physicochemical and pharmacokinetic properties such as good solubility, lipophilicity, metabolic stability and bioavailability.…”

“…For example, cyclic peptides [19][20][21][22]110 and peptides that include non-native residues such as N-methylated 111,112 or D-amino acids, 42 may improve stability, cell permeability and efficacy of natural peptide leads. Sequence-based tools or knowledgebased protein force fields cannot be applied to these compounds, which are no longer merely short proteins.…”