Cell-Permeable Cyclic Peptides from Synthetic Libraries Inspired by Natural Products

Abstract

Drug design efforts are turning to a new generation of therapeutic targets, such as protein-protein interactions (PPIs), that had previously been considered "undruggable" by typical small molecules. There is an emerging view that accessing these targets will require molecules that are larger and more complex than typical small molecule drugs. Here, we present a methodology for the discovery of geometrically diverse, membrane permeable cyclic peptide scaffolds based on the synthesis and permeability screening of a combinatorial library, followed by deconvolution of membrane-permeable scaffolds to identify cyclic peptides with good to excellent passive cell permeabilities. We use a combination of experimental and computational approaches to investigate structure-permeability relationships in one of these scaffolds, and uncover structural and conformational factors that govern passive membrane diffusion in a related set of cyclic peptide diastereomers. Further, we investigate the dependency of permeability on side-chain identity of one of these scaffolds through single-point diversifications to show the adaptability of these scaffolds toward development of permeability-biased libraries suitable for bioactivity screens. Overall, our results demonstrate that many novel, cell permeable scaffolds exist beyond those found in extant natural products, and that such scaffolds can be rapidly identified using a combination of synthesis and deconvolution which can, in principle, be applied to any type of macrocyclic template.

Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products

“…Nonetheless, the solution structures reveal that, in general, the NH hydrogen bond counts for cyclic peptides 1, 4, 5, 6, and 14 correlate well with cell permeability and EPSA, while hydrogen bonding among the −OH groups is prevalent throughout most of the structures and does not appear to correlate with permeability. These observations are consistent with other studies that challenge overall hydrogen bond count as a useful predictor of permeabilty, 2,4,22,44 especially when other factors are at play (such as flexibility and steric occlusion of polar groups).…”

Anthranilic acid-containing cyclic tetrapeptides: at the crossroads of conformational rigidity and synthetic accessibility

“…80 In fact, making cyclic peptides cell permeable by inclusion of N -methyl groups is an area of interest in the contemporary literature. 81–83 Molecules 1 show promise as cell permeable molecules, even though they do not have tertiary amide N -methyl groups. We suggest this is because the favored conformers of 1 in solution orient their N-H vectors towards a central point, ie relatively insulated from the medium around the mimic.…”

Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability

“…Specifically, structural studies of cell-permeable peptides have suggested that steric occlusion of polar groups and internal hydrogen bonding can lead to increased permeability [39,40]. Recognizing that hydrogen bonding potential is heavily dependent on conformation, we explored whether structural tools that can experimentally probe the hydrogen bond network can also be used as biomarkers of peptide permeability.…”