Constrained peptides mimic a viral suppressor of RNA silencing

Abstract

The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.

pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides

“…Bioactive peptides originate from various natural sources (e.g., endogenous hormones, toxins, etc. ), hit-finding approaches (e.g., phage display), , and rational design (e.g., epitope mimetics). , Peptide starting points are often modified with nCAAs to modulate the interaction with the target surface and improve in vivo stability and oral bioavailability. − Short cross-linked peptides mimicking interaction epitopes are often designed for the inhibition of protein–protein interactions (PPIs). ,,,, Peptides chemically linked with a cargo molecule can serve as targeted delivery vehicles to the tissues of interest . In addition to these applications, medicinal chemists are also constantly searching for noncanonical peptide mimetics and peptide-hybrids, such as peptoids, peptidomimetics, foldamers, and peptide-natural product combinations for their use as therapeutics .…”

“… 11 − 13 Short cross-linked peptides mimicking interaction epitopes are often designed for the inhibition of protein–protein interactions (PPIs). 7 , 8 , 10 , 14 , 15 Peptides chemically linked with a cargo molecule can serve as targeted delivery vehicles to the tissues of interest. 16 In addition to these applications, medicinal chemists are also constantly searching for noncanonical peptide mimetics and peptide-hybrids, such as peptoids, 17 peptidomimetics, 18 foldamers, 19 and peptide-natural product combinations for their use as therapeutics.…”

Bicyclic Engineered Sortase A Performs Transpeptidation under Denaturing Conditions

“…Biotinylated thiol biotin-PEG 3 -Cys was synthesized using Fmoc-based solid-phase peptide synthesis. , In brief, the H-Rink amide resin was used for the synthesis and all couplings were performed in an orthogonal manner. Removal of the Fmoc-group was performed with 25% piperidine in DMF for 10 min.…”

Peptide‐based covalent inhibitors of protein–protein interactions

“… 91 , 92 , 93 , 94 Based on the crystal structure of a FtsB fragment bound to the periplasmic domain of FtsQ, 91 proteomimetic ligands were designed (Figure 13A ). Notably, the stabilization of a tertiary motif 95 , 96 , 97 was necessary to achieve meaningful binding. 98 Here, an essential intramolecular salt bridge between FtsB R72 and E82 was replaced by a covalent crosslink providing 24‐mer cyclic peptide 24f (Figure 13B ).…”