Constrained Peptides in Drug Discovery and Development

Abstract

Constrained peptides represent a new class of peptide molecules whose supramolecular structure is controlled via intramolecular covalent bonds, generally to confer upon them biochemical and/or physicochemical properties superior to those of ordinary peptides. Both academia and industry are showing increasing interest in constrained peptides, due to their promise as medicines and tools for drug discovery. The major categories of constrained peptides are macrocyclic peptides 1 and stapled peptides, 2 as illustrated in Figure 1. The related eld of foldamers, which can be thought of as conformationally constrained peptides, has been recently reviewed and will not be discussed here.3 This paper will present an overview of ongoing research and development efforts in this eld, with particular focus on our approach toward constrained peptide research and development. Why Study Constrained Peptides? PPI Drug TargetsMost investigational and approved drugs to date fall into the broad categories of small molecules or macromolecular biologics, with antibodies, proteins and vaccines representing the predominant forms of approved biologic therapies. Until recently, aside from a small number of natural products, there has been much less progress in designing drugs for the intervening space of medium sized molecules, de ned here as molecules with molecular weights ranging from 500 to 6000 Daltons.From the perspective of small molecule drug discovery, the FDA approval of Bcl 2 inhibitor venetoclax (Figure 2) in 2016, after nearly 30 years of research and development, dem- Abstract: Constrained peptides, namely macrocyclic and stapled peptides, are receiving increasing attention as a promising class of compounds for the inhibition of protein protein interactions (PPI). The current state of peptide therapeutics is discussed, including their merits and challenges, as well as recent technological developments that have enabled a new era in peptide research and development. The technology behind PeptiDream s Peptide Discovery Platform System (PDPS) is described, showing how it can be used to rapidly generate libraries of constrained peptides and obtain detailed SAR information. This technology can provide, with a high rate of success, potent peptide ligands that may be developed as drug candidates themselves, utilized in peptide drug conjugates (PDC), or converted into small molecule drug leads. The outlook for the eld of constrained peptides and their use in the clinic is also described.

Macrocyclization of an all-D linear peptide improves target affinity and imparts cellular activity: A novel stapled α-helical peptide modality

“…adenine [65]. Consistent with our observations in mammalian cells, the linear d PMI-δ peptide and the double stapled d PMI-δ (1)(2)(3)(4)(5)(9)(10)(11)(12) peptide had no effect on p53-Mdm2 interaction ( Figure 9A-B). In contrast, the d PMI-δ (1,5,12) peptide completely prevented the growth of yeast cells expressing p53/Mdm2 at 12.5 µM ( Figure 9C, left panel).…”

“…We also tested the ability of d PMI-δ, d PMI-δ (1)(2)(3)(4)(5)(9)(10)(11)(12), d PMI-δ (1,5,12) and scrambled d PMIδ (1,5,12) peptides to inhibit the p53 (1-52)-Mdm2 interaction in a Yeast 2-hybrid (Y2H) assay optimized for detecting small-molecule inhibitors [65]. In this assay, inactivation of p53(1-…”

“…We tried to obtain crystal structures of the stitched peptide d PMI-δ (1,5,12) in complex with Mdm2 (6-125) and of the double stapled peptide d PMI-δ (1)(2)(3)(4)(5)(9)(10)(11)(12) in complex with Mdm2 (6-125). We could only obtain crystals for the latter and were able to resolve its structure ( Figures 11 A, B).…”

“…The elucidated structure possessed only a single copy of the Mdm2 -d PMI-δ(1-5, 9-12) complex in the asymmetric unit. The p53 peptide binding groove on Mdm2 was occupied by a single molecule of d PMI-δ (1)(2)(3)(4)(5)(9)(10)(11)(12), which interacted with Mdm2 by projecting the following three residues 6-F-d Trp3, p-CF3-d Phe7 and d Leu11 deep into the hydrophobic peptide binding site on Mdm2. The Mdm2 -d PMI-δ (1)(2)(3)(4)(5)(9)(10)(11)(12) complex was overlaid with the Mdm2 -d PMI-δ structure (PDB: ID 3TPX), which demonstrated that the double stapling maintained the overall fold of the bound peptide and its critical interactions with Mdm2 [ Figure 11 C].…”

“…When taken out of the protein ligand context and synthesized, such peptides may often be unstructured and intrinsically disordered, yet able to achieve their biologically-relevant conformation upon protein target binding [4]. However, for intracellular targets, the peptide modality may be challenging due to proteolytic sensitivity, low conformational stability (yielding weak affinities and off-target effects), and poor cell permeability (further limiting engagement of intracellular targets and/or oral bioavailability) [5][6][7][8][9][10][11]. To address these issues, several strategies have been pursued, including macrocyclization and modifications of the peptide backbone to yield molecules with improved biological activities and pharmacokinetic properties as well as constraining the peptide into its biologically-relevant conformation that binds its target [5][6][7][8][9][10][11][12][13].…”