bims-cepepe 2025-05-11 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–05–11
ten papers selected by
Henry Lamb, Queensland University of Technology

Regioselective and Efficient Synthesis of Nonsymmetric Cyclic Peptides via a Stapling Reaction of 2-Acetyl-thiophene-3-carboxaldehyde with Primary Amine and Thiol.
Computational Design of a Bicyclic Peptide Inhibitor Targeting the ICOS/ICOS-L Protein-Protein Interaction.
A novel 68Ga-labeled cyclic peptide: A potential radiotracer for PET imaging of CD36-positive cancers.
A convergent approach to resorcinolic macrolides to expand structural diversity.
Exploration of Bicyclic Peptide Ligands for Immune-Specific PET Imaging: Targeting Tumor PD-L1 with [18F]AlF-BCY10959.
Plasmid DNA delivery using arginine-rich cell-penetrating L/D-peptides containing α-aminoisobutyric acids.
Late-Stage Amination of Peptides on the Solid Phase.
Therapeutic peptides: chemical strategies fortify peptides for enhanced disease treatment efficacy.
Dissecting oxidative folding of conotoxins using 3D structures of cysteine mutants predicted by AlphaFold 3: A case study of α-conotoxin RgIA, χ-conotoxin CMrVIA and ω-conotoxin MVIIA-Gly.
Discovery of Novel Cyclic Peptides as SMAD2-SMAD4 Interaction Inhibitors for the Treatment of Hepatic Fibrosis.

Chem Asian J. 2025 May 06. e202500534

Regioselective and Efficient Synthesis of Nonsymmetric Cyclic Peptides via a Stapling Reaction of 2-Acetyl-thiophene-3-carboxaldehyde with Primary Amine and Thiol.

Tianyu Bo, Jiawei Wang, Ruotong Liang, Meiqi Wu, Shigang Shen, Shuying Huo.

  In this work, 13 nonsymmetric cyclic peptides with a thieno[2,3-c]pyrrole bridge were efficiently and regioselectively synthesized by a stapling reaction of the primary amine (from lysine (Lys) side chain and peptide N-terminus), thiol (from cysteine (Cys) side chain), and 2-acetyl-thiophene-3-carboxaldehyde (ATA). A single regioisomeric thieno[2,3-c]pyrrole staple was formed, generating the thieno[2,3-c]pyrrole-bridged peptide. The stapling reaction can be carried out in various solvents. Moreover, the obtained nonsymmetric cyclic peptides were stable in PBS solution. Furthermore, three bicyclic peptides containing both an acetone-like bridge and the thieno[2,3-c]pyrrole bridge were synthesized via two stapling strategies: (1) a symmetric stapling reaction of 1,3-dichloroacetone (DCA) with two Cys residues, and (2) a nonsymmetric stapling reaction of ATA with Lys and Cys residues. Satisfied yields of the bicyclic peptides were achieved. The positions of the two bridges determined the synthetic accessiblity of the bicyclic peptides. Certainly, a wide variety of thieno[2,3-c]pyrrole-bridged nonsymmetric cyclic peptides can be designed, thus entrenching the methodologies in peptide cyclization. The strategy is applied conveniently to the synthesis of nonsymmetric cyclic peptides with a large structural diversity.

Keywords:  Nonsymmetric cyclic peptide; Regioselective synthesis; Stapling reaction; Thieno[2,3‐c]pyrrole bridge

DOI:  https://doi.org/10.1002/asia.202500534
Chem Biol Drug Des. 2025 May;105(5): e70117

Computational Design of a Bicyclic Peptide Inhibitor Targeting the ICOS/ICOS-L Protein-Protein Interaction.

Laura Calvo-Barreiro, Maxim Secor, Jovan Damjanovic, Somaya A Abdel-Rahman, Yu-Shan Lin, Moustafa Gabr.

  The interaction between the inducible T-cell costimulatory molecule (ICOS) and its ligand (ICOS-L) is a critical pathway in T-cell activation and immune regulation. We computationally designed a bicyclic peptide (CP5) that inhibits the ICOS/ICOS-L protein-protein interaction (PPI). Using the structural insights derived from the ICOS/ICOS-L co-crystal structure (PDB: 6X4G) and bias-exchange metadynamics simulations (BE-META), we first designed monocyclic peptide candidates containing the β-strand (residues 51-55 51YVYWQ55) of ICOS-L that interact with ICOS. Using Rosetta's flex ddG calculations and further disulfide-bond restraint, we arrived at CP5 (cyclo-RVY[CQPGWC]WVLpG) as a potential ICOS/ICOS-L inhibitor. Using dynamic light scattering (DLS), we examined the interaction between CP5 and ICOS. Importantly, we validated the ICOS/ICOS-L inhibitory activity of CP5 using both TR-FRET assay and ELISA. Notably, CP5 demonstrated satisfactory in vitro pharmacokinetic properties, such as metabolic stability and lipophilicity, positioning it as a promising candidate for further drug development. Our findings provide a foundation for future drug discovery efforts aiming to develop cyclic peptides that specifically target the ICOS/ICOS-L interaction.

Keywords:  ICOS; cyclic peptides; immune checkpoints; in silico design; protein–protein interactions

DOI:  https://doi.org/10.1111/cbdd.70117
Bioorg Chem. 2025 May 01. pii: S0045-2068(25)00395-5. [Epub ahead of print]161 108515

A novel 68Ga-labeled cyclic peptide: A potential radiotracer for PET imaging of CD36-positive cancers.

Bo Zhou, Yicong Wang, Can Diao, Jingyue Gao, Ting Liang, Chao Zhang, Shuyong Liu, Chun Guo, Feng Gao.

   PURPOSE: CD36, a transmembrane glycoprotein, which is involved in various cellular functions, including lipid metabolism, inflammation, and tumor initiation and progression, has been considered as an important therapeutic target of tumors. However, the lack of effective imaging methods for non-invasive monitoring of CD36 expression and assessing the efficacy of CD36-targeted therapies limits the clinical application of CD36-targeted therapeutic drugs. To address this issue, we designed and synthesized two novel CD36-targeted radiotracers, and evaluated their biological properties and imaging performance, in order to select the more effective candidate for potential application in monitoring the CD36 expression and assessing the therapeutic efficacy.
METHODS: The chelator NOTA was conjugated to both linear and cyclic peptides via a bioconjugation approach, yielding the linear peptide conjugate ZL01 and the cyclic peptide conjugate ZL02. Their structures were confirmed using HRMS. The solutions of peptide conjugates (ZL01 and ZL02) were mixed with a [68Ga]GaCl₃ solution to obtain the radiotracers, and the radiochemical purity of both radiotracers was determined by radio-HPLC. Non-radioactive [natGa]Ga-ZL01 and [natGa]Ga-ZL02 were used to confirm [68Ga]Ga-ZL01 and [68Ga]Ga-ZL02. The radiochemical and biological properties were evaluated, including in vitro stability, hydrophilicity, binding affinity, pharmacokinetics, micro PET/CT imaging, and biodistribution.
RESULTS: [68Ga]Ga-ZL01 and [68Ga]Ga-ZL02 were obtained with radiochemical purity over 95 %. Both radiotracers demonstrated hydrophilic character, and good stability in PBS and human serum. The blood clearance of [68Ga]Ga-ZL01 and [68Ga]Ga-ZL02 (half-life) was measured at 17.8 min and 21.6 min, respectively. [natGa]Ga-ZL01 and [natGa]Ga-ZL02 exhibited high binding affinities to U87MG cells, with inhibition constant (Ki) of 1.59 ± 0.35 nM for [natGa]Ga-ZL01 and 1.12 ± 0.44 nM for [natGa]Ga-ZL02, respectively. Micro PET/CT imaging and biodistribution study revealed [68Ga]Ga-ZL02 had superior tumor-to-background ratio and prolonged tumor retention, highlighting its potential as a promising candidate for clinical translation.
CONCLUSIONS: In this study, two CD36-targeted radiotracers ([68Ga]Ga-ZL01 and [68Ga]Ga-ZL02) were developed and evaluated. 68Ga-labeled cyclic peptide [68Ga]Ga-ZL02 demonstrated superior tumor-to-background ratio and prolonged tumor retention time, making it a promising radiotracer for monitoring the CD36 expression and assessing the therapeutical efficacy.

Keywords:  (68)Ga; CD36; Labeling; Positron emission tomography (PET); Radiotracer

DOI:  https://doi.org/10.1016/j.bioorg.2025.108515
Chemistry. 2025 May 07. e202501509

A convergent approach to resorcinolic macrolides to expand structural diversity.

Jesus M Madrigal Lombera, Xi Feng, Xiaokun Shu, Ian B Seiple.

  The resorcinolic macrolide (RM) family comprises over 50 natural products with diverse biological activities, including the potent natural Hsp90 inhibitor radicicol. Here, we report a modular and enantioselective synthetic strategy featuring a biomimetic macrocyclization-aromatization cascade that enables rapid access to natural and unnatural RMs. Using this route, we generated a small panel of minimal RMs, introducing covalent warheads, double bonds for macrocycle rigidification, and modifications at the C15 position, a position that has not been modified before. We also synthesized macrocyclic peptide-RM hybrids, offering a platform for rapid diversification. We evaluated all analogs for inhibitory activity against Hsp90α and Hsp90β and for disruption of the KRasG12C-CRAF protein-protein interaction (PPI). We found that introduction of polar groups at C15 improved Hsp90 activity relative to the representative RM de-O-methyllasiodiplodin, dependent on stereochemistry, whereas introduction of larger groups at C15 or introduction of a trans double bond into the macrocycle reduced activity. Two analogs with poor Hsp90 inhibitory activity exhibited dose-dependent inhibition of the KRasG12C-CRAF PPI. This work demonstrates that strategic modifications of a minimal RM scaffold through modular chemical insight can provide foundational structure-activity relationships for the class.

Keywords:  Cyclic peptides; Hsp90 Inhibitors; Macronalactonizations; Resorcinolic macrolides; natural products

DOI:  https://doi.org/10.1002/chem.202501509
Mol Pharm. 2025 May 08.

Exploration of Bicyclic Peptide Ligands for Immune-Specific PET Imaging: Targeting Tumor PD-L1 with [18F]AlF-BCY10959.

Xiaobo Wang, Jianyang Fang, Fei Kang, Jia Wang, Meng Niu, Hengyi Ou, Jiajun Ye, Mingru Zhang, Jie Dong, Guiyu Li, Zhiguo Liu, Wenbin Zeng, Jing Wang.

  As a new modality of ligands, bicyclic peptides hold great promise in the discovery of novel programmed death ligand 1 (PD-L1) targeted radiotracers, which have not yet been reported. In this study, first-in-class bicyclic peptide-based radiotracers [18F]AlF-BCY509 and [18F]AlF-BCY10959 were developed and evaluated for PET imaging of tumor PD-L1 expression. The automatic radiosynthesis was achieved with robust radiochemical yields (55.1-90.2%) and high molar activity (42.5-90.8 GBq/μmol). Cell-based assays demonstrated high specificity and affinity of [18F]AlF-BCY509 and [18F]AlF-BCY10959 with IC50 values of 9.36 ± 1.35 and 7.12 ± 1.24 nM and KD values of 11.41 ± 1.04 and 8.09 ± 0.85 nM. In PET imaging, the accumulation of [18F]AlF-BCY10959 in PD-L1-positive tumors with moderate retention over 120 min was discovered, with the tumor uptake of 14.74 ± 1.67%ID/cc and tumor-to-muscle ratio of 12.41 ± 1.07 at 30 min. The in vivo specificity was strictly verified by PD-L1-knockout and PD-L1-positive tumors with blocking. The biodistribution manifested a rapid distribution and fast clearance from the body, supporting the favorable pharmacokinetics of [18F]AlF-BCY10959. [18F]AlF-BCY10959 was excreted through the urinary and hepatobiliary systems, indicating the doomed radiation exposure organs. The effective doses of [18F]AlF-BCY10959 and [18F]-FDG were comparable, highlighting its safety for human use. In conclusion, [18F]AlF-BCY10959 provides an attractive option to detect PD-L1 expression and lays the groundwork to further develop promising bicyclic peptide tracers for clinical use.

Keywords:  PD-L1 expression; bicyclic peptides; immunotherapy; positron emission tomography; radiotracers

DOI:  https://doi.org/10.1021/acs.molpharmaceut.5c00442
Org Biomol Chem. 2025 May 06.

Plasmid DNA delivery using arginine-rich cell-penetrating L/D-peptides containing α-aminoisobutyric acids.

Tomohiro Umeno, Hiroyasu Takemoto, Makoto Oba.

The relationship between intracellular uptake efficacy and the folding behavior of arginine-rich cell-penetrating L/D-peptides with α,α-disubstituted α-amino acids in plasmid DNA (pDNA) delivery was examined. Nano-sized complexes formed from pDNA and L/D-peptides efficiently traversed the cell membrane regardless of the peptide conformation. This finding represents a significant deviation from previously reported covalent cargo delivery methods using cell penetrating peptides with L- and D-amino acids.

DOI: https://doi.org/10.1039/d5ob00627a
Chemistry. 2025 May 05. e202501229

Late-Stage Amination of Peptides on the Solid Phase.

Franziska Thomas, Julian Brinkhofer, Marius Werner, Agon Kokollari, Shih-Yu Pan, Christian Klein, Truc Lam Pham.

  Late-stage peptide modification is a powerful tool for rapidly generating a library of peptide mimetics e.g. for drug discovery or catalyst development. While late-stage modifications exist for many types of structural features, methods for introducing amines into peptides via a late-stage approach are rare, despite their enormous potential for the development of peptide therapeutics. Here we present a protocol for introducing amines into peptides by our established on-resin iodination-substitution approach. Our method is compatible with a wide variety of amines, including primary and secondary amines, anilines and other heteroaromatic N-nucleophiles mostly giving good to excellent yields. We introduce amines that are pharmacologically relevant as well as those that can impart catalytic or metal binding properties into the peptide of interest. As a proof-of-concept study, we introduce the metal ligand tris(2-aminoethyl)amine (tren) into a tryptophan zipper scaffold using our late-stage amination approach to explore metal-induced stapling. Indeed, metal complexation via the tren ligand resulted in a thermal stabilization of more than 30 K in one of our tryptophan zipper designs.

Keywords:  Late-stage functionalization; amines; peptides; solid-phase synthesis; tryptophan zippers

DOI:  https://doi.org/10.1002/chem.202501229
Amino Acids. 2025 May 08. 57(1): 25

Therapeutic peptides: chemical strategies fortify peptides for enhanced disease treatment efficacy.

Qingmei Li, Wen Chao, Lijuan Qiu.

  Therapeutic peptides, as a unique form of medication composed of orderly arranged sequences of amino acids, are valued for their high affinity, specificity, low immunogenicity, and economical production costs. Currently, more than 100 peptides have already secured market approval. Over 150 are actively undergoing clinical trials, while an additional 400-600 are in the preclinical research stage. Despite this, their clinical application is limited by factors such as salt sensitivity, brief residence in the bloodstream, inadequate cellular uptake, and high structural flexibility. By employing suitable chemical methods to modify peptides, it is possible to regulate important physicochemical factors such as charge, hydrophobicity, conformation, amphiphilicity, and sequence that affect the physicochemical properties and biological activity of peptides. This can overcome the inherent deficiencies of peptides, enhance their pharmacokinetic properties and biological activity, and promote continuous progress in the field of research. A diverse array of modified peptides is currently being developed and investigated across numerous therapeutic fields. Drawing on the latest research, this review encapsulates the essential physicochemical factors and significant chemical modification strategies that influence the properties and biological activity of peptides as pharmaceuticals. It also assesses how physicochemical factors affect the application of peptide drugs in disease treatment and the effectiveness of chemical strategies in disease therapy. Concurrently, this review discusses the prospective advancements in therapeutic peptide development, with the goal of offering guidance for designing and optimizing therapeutic peptides and to delve deeper into the therapeutic potential of peptides for disease intervention.

Keywords:  Chemical strategies; Disease treatment strategies; Druggability; Physicochemical factors; Therapeutic peptides

DOI:  https://doi.org/10.1007/s00726-025-03454-5
Toxicon. 2025 May 07. pii: S0041-0101(25)00176-X. [Epub ahead of print] 108402

Dissecting oxidative folding of conotoxins using 3D structures of cysteine mutants predicted by AlphaFold 3: A case study of α-conotoxin RgIA, χ-conotoxin CMrVIA and ω-conotoxin MVIIA-Gly.

K Radhakrishna, Patil Kanchan Rajshekhar, R Arshitha, Kashibai Patil, Shweta Dhannura, Konkallu Hanumae Gowd.

The ability of AlphaFold 3 to accurately predict the 3D structure of polypeptides has been explored to investigate the oxidative folding steps of conotoxins. The peptides α-conotoxin RgIA (α-RgIA) and χ-conotoxin CMrVIA (χ-CMrVIA) share a similar cysteine pattern but differ in their native disulfide connectivity. These short peptides, containing two intramolecular disulfides, may undergo sequential steps of disulfide formation during the oxidative folding process. The current report computed all six possible single disulfide alanine mutants of the peptides and predicted their 3D structures using the AlphaFold 3 server. The potential energy of the conformers derived from the five predicted model structures of the peptides was calculated using the OPLS4 force field in Schrödinger's MacroModel software. The relative potential energy of the single disulfide mutant peptides was computed using the Boltzmann-weighted average energy of the conformers of the corresponding peptides. [C2A,C8A]α-RgIA and [C2A,C11A]χ-CMrVIA are the most stable forms, corresponding to the native single disulfide intermediate analogues. Accordingly, the folding events for α-RgIA are C3-C12 followed by C2-C8, while for χ-CMrVIA, they are C3-C8 followed by C2-C11 connectivity. The current report also explored the native folding steps of an Inhibitory Cystine Knot (ICK) motif peptide ω-conotoxin-MVIIA-Gly using one/two cysteine disulfide alanine mutants. The computation of relative potential energy of the mutant peptides indicates the formation of C15-C25 followed by C8-C20 and C1-C16 disulfide bonds. The newly proposed technique that combines AlphaFold 3 with MacroModel conformational sampling tool is allowing to identify the oxidative folding steps of disulfide-rich peptides.

DOI: https://doi.org/10.1016/j.toxicon.2025.108402
J Med Chem. 2025 May 04.

Discovery of Novel Cyclic Peptides as SMAD2-SMAD4 Interaction Inhibitors for the Treatment of Hepatic Fibrosis.

Wei Cheng, Yawen Zheng, Qinglin Tang, Liang Qi, Zihan Shi, Qihong Yu, Mingmin Li, Xianzhi Wei, Yifeng Zhou, Xianxing Jiang.

Hepatic fibrosis, characterized by the excessive deposition of the extracellular matrix, represents a common consequence of various chronic liver disorders. However, no specific drugs are available for antifibrotic therapy to date. SMAD2 is phosphorylated by transforming growth factor-β and subsequently binds to SMAD4 to generate a heteromeric complex, which then translocates into the nucleus and aggravates liver fibrosis. Herein, based on molecular docking simulation and structure-activity relationship study, we report the discovery of a novel cyclic peptide CMF9 that targets SMAD2 and potently interferes with the SMAD2-SMAD4 interaction. The subsequent in vivo and in vitro pharmacological studies demonstrated that CMF9 dramatically suppressed hepatic stellate cells activation and collagen synthesis, alleviating CCl4-induced hepatic inflammation and fibrosis. Overall, we first demonstrated that the novel cyclic peptide CMF9 could efficiently block the SMAD2-SMAD4 interaction via selectively inhibiting SMAD2 phosphorylation, providing a promising therapeutic strategy for targeting SMAD2 and an alternative candidate for the treatment of liver fibrosis.

DOI: https://doi.org/10.1021/acs.jmedchem.4c02938