Targeting RNA with cysteine-constrained peptides

Abstract

A combined approach for targeting RNA with novel, biologically active ligands has been developed using a cyclic peptide library and in silico modeling. This approach has successfully identified novel cyclic peptide constructs that can target bTAR RNA. Subsequently, RNA/peptide interactions were effectively modeled using the HADDOCK docking program.

Cysteinoyl‐ and Cysteine‐containing Dipeptidoylbenzotriazoles with Free Sulfhydryl Groups: Easy Access to N‐terminal and Internal Cysteine Peptides

“…The filtrate was evaporated under reduced pressure to give a crude product, which was washed with diethyl ether and recrystallized from CH 2 Cl 2 -hexanes to afford N-Fmoc-1H-benzotriazole. White microcrystals, yield 88%, mp 90-91°C; 1 13 Synthesis of N-(N¢-Cbz-and N¢-Fmoc-L-Cys)-1Hbenzotriazoles 7a,c Thionyl chloride (1 mmol) was added to a solution of 1H-benzotriazole (4 mmol) in anhydrous THF (30 mL) at 25°C, and the reaction mixture was stirred for 20 min. N-Cbz-and N-Fmoc-L-cysteines 4ac (1 mmol) were added to the reaction mixture, which was stirred for 2 h at 0-5°C.…”

“…Evaporation of the solvent gave the desired products, which were recrystallized from chloroform-hexanes or ethyl acetate-hexanes. 13 Synthesis of N-(N¢-Cbz-and N¢-Fmoc-adipeptidoyl)-1H-benzotriazoles 10a,b Thionyl chloride (1 mmol) was added to a solution of 1H-benzotriazole (4 mmol) in anhydrous THF (30 mL) at 20°C, and the reaction mixture was stirred for 20 min. N-Cbz-and N-Fmoc-L-cysteine dipeptides 9a,b (1 mmol) were added to the reaction mixture at )30°C, which was stirred for 4 h at )30°C.…”

“…The residue was dissolved in ethyl acetate, and the organic layer was washed with 6 N HCl solution, sat. NaCl solution, and dried over anhydrous 02 (m, 5H), 0.86 (d, J = 6.9 Hz, 6H); 13 General procedure for disulfide-bridged cysteine peptides 14a,b N-(N¢-Cbz-L-Cys)-1H-benzotriazole 7a (0.712 g, 2 mmol) was added at room temperature to a solution of [1,4-butanediamine (0.088 g, 1 mmol) or 1,6-hexanediamine (0.116 g, 1 mmol)] in a solution of THF in the presence of triethylamine (0.2 mL). The reaction mixture was then stirred at room temperature until the starting material was completely consumed, as observed by TLC using hexanes-ethyl acetate (2:1) as development solvent.…”

“…This procedure allowed the synthesis of dipeptides 8d (yield 77%) and 8c (yield 73%) containing tryptophan and serine residues and possessing intact free indole N-H and hydroxyl groups, respectively (Scheme 2, Table 2). Novel N-Cbz, N-Boc-, and N-Fmoc-L-cysteine dipeptides 8a-e and tripeptides 8f-h were characterized by 1 H, 13 C NMR spectroscopy and elemental analysis. Dipeptides 8a (8a + 8a¢) retained diastereomeric purity, which was evidenced by Chiral HPLC analysis using a Chirobiotic T column (detection at 254 nm, flow rate 0.5 mL ⁄ min, and MeOH-H 2 O (98:2) as eluent.…”

CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids

“…4 The advantages that constrained peptides display over linear peptides have led to their use as potential protein binding compounds in phage-display libraries, 5 as mimics of protein turn structure in virtual libraries, 6 and as binding ligands of RNA in virtual libraries. 7 To generate virtual libraries of constrained peptides, it is necessary to use chemoinformatics techniques to assemble the amino acid building blocks into a linear peptide. The SMILES 8 (Simplified Molecular Input Line Entry System) chemical notation system may be used to computationally assemble constrained peptides as a string of text, unambiguously describing each atom and bond in the molecule in a manner amenable to machine processing.…”