Cell-permeable chameleonic peptides: Exploiting conformational dynamics in de novo cyclic peptide design.

Curr Opin Struct Biol

Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA. Electronic address:

Published: June 2023

Membrane-traversing peptides offer opportunities for targeting intracellular proteins and oral delivery. Despite progress in understanding the mechanisms underlying membrane traversal in natural cell-permeable peptides, there are still several challenges to designing membrane-traversing peptides with diverse shapes and sizes. Conformational flexibility appears to be a key determinant of membrane permeability of large macrocycles. We review recent developments in the design and validation of chameleonic cyclic peptides, which can switch between alternative conformations to enable improved permeability through cell membranes, while still maintaining reasonable solubility and exposed polar functional groups for target protein binding. Finally, we discuss the principles, strategies, and practical considerations for rational design, discovery, and validation of permeable chameleonic peptides.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10923192PMC
http://dx.doi.org/10.1016/j.sbi.2023.102603DOI Listing

Publication Analysis

Top Keywords

chameleonic peptides
8
membrane-traversing peptides
8
peptides
6
cell-permeable chameleonic
4
peptides exploiting
4
exploiting conformational
4
conformational dynamics
4
dynamics novo
4
novo cyclic
4
cyclic peptide
4

Similar Publications

Article Synopsis
  • CycloAnt is an opioid peptide effective in pain relief (antinociception) with fewer side effects when tested systemically in mice.
  • It shows stability against degradation in mouse serum and is resistant to metabolism in the liver, indicating a long-lasting effect in the body.
  • CycloAnt successfully crosses the blood-brain barrier, aided by its flexible structure that changes shape depending on its environment, enhancing its ability to penetrate the brain.
View Article and Find Full Text PDF

IMHB-Mediated Chameleonicity in Drug Design: A Focus on Structurally Related PROTACs.

J Med Chem

July 2024

Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy.

Molecular chameleonicity may enable compounds to compensate for the unfavorable ADME properties typically associated with complex molecules, such as PROTACs. Here we present a few strategies to implement chameleonicity considerations in drug design. Initially, we identified six structurally related CRBN-based PROTACs targeting BET proteins and experimentally verified whether chameleonicity is needed to obtain an acceptable physicochemical profile.

View Article and Find Full Text PDF

The discovery of safe platforms that can circumvent the endocytic pathway is of great significance for biological therapeutics that are usually degraded during endocytosis. Here we show that a self-assembled and dynamic macrocycle can passively diffuse through the cell membrane and deliver a broad range of biologics, including proteins, CRISPR Cas9, and ssDNA, directly to the cytosol while retaining their bioactivity. Cell-penetrating macrocycle CPM can be easily prepared from the room temperature condensation of diketopyrrolopyrrole lactams with diamines.

View Article and Find Full Text PDF

We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide.

View Article and Find Full Text PDF

Some macrocycles exhibit enhanced membrane permeability through conformational switching in different environmental polarities, a trait known as chameleonic behavior. In this study, we demonstrate specific backbone and side chain modifications that can control chameleonic behavior and passive membrane permeability using a cyclosporin O (CsO) scaffold. To quantify chameleonic behavior, we used a ratio of the population of the closed conformation obtained in polar solvent and nonpolar solvent for each CsO derivative.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!