bims-cepepe 2025-08-10 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–08–10
ten papers selected by
Henry Lamb, Queensland University of Technology

Ai-driven de novo design of customizable membrane permeable cyclic peptides.
Modular platform for therapeutic drug delivery using trifunctional bio-orthogonal macromolecular conjugates.
Using muscle homing peptide CyPep10 to deliver phosphorodiamidate morpholino oligomers in the mdx mouse.
De Novo Design of Multiple Microplastic-Binding Peptides with a Protein Language Model-Guided Generative Adversarial Network.
Intrastrand Peptide Staples That Promote β-Sheet Folding, Self-Assembly, and Amyloid Seeding.
Enzyme-free biochemical production of seamlessly N-to-C cyclized peptides from natural or recombinant proteins.
Direct Editing of Cysteine to Electrophilic Alkyl Halides in Peptides.
Crown Ether-Peptide Rotaxanes.
Structural insights of the complex formed by KRAS G12V and a novel TIG3 peptide.
Case Report: Personalized peptide-based immunization in an advanced-stage prostate cancer patient with bone metastasis.

J Comput Aided Mol Des. 2025 Aug 09. 39(1): 63

Ai-driven de novo design of customizable membrane permeable cyclic peptides.

Yu Yunxiang, Zhang Zhou, Guo Hai, Ren Xinlu, Zhang Yuting, Meng Jianna, Zhou Yi, Han Jian, Tian Jinhui, Yan Wenjin, Huang Jinqi.

  Cyclic peptides, prized for their remarkable bioactivity and stability, hold great promise across various fields. Yet, designing membrane-penetrating bioactive cyclic peptides via traditional methods is complex and resource-intensive. To address this, we introduce CCPep, an AI-driven de novo design framework that combines reinforcement and contrastive learning for efficient, customizable membrane-penetrating cyclic peptide design. It assesses peptide membrane penetration with scoring models and optimizes transmembrane ability through reinforcement learning. Customization of peptides with specific properties is achieved via custom functions, while contrastive learning incorporates molecular dynamics simulation time series to capture dynamic penetration features, enhancing model performance. Result shows that CCPep generated cyclic peptide sequences have a promising membrane penetration rate, with customizable chain length, natural amino acid ratio, and target segments. This framework offers an efficient tool for cyclic peptide drug design and paves the way for AI-driven multi-objective molecule design.

Keywords:  Cyclic peptide; Molecular Dynamic; Permeability; Reinforcement Learning

DOI:  https://doi.org/10.1007/s10822-025-00639-8
bioRxiv. 2025 Jul 26. pii: 2025.07.24.666613. [Epub ahead of print]

Modular platform for therapeutic drug delivery using trifunctional bio-orthogonal macromolecular conjugates.

Danmeng Luo, Ning Wang, Hannah Major-Monfried, John Ralls, Sophia Rha, Stacy A Maitland, Karthikeyan Ponnienselvan, Makiko Yamada, Daniel E Bauer, Scot A Wolfe, Alex Kentsis.

Targeted delivery of macromolecular therapeutics holds great promise for overcoming the limitations of conventional small molecules, enabling modulation of protein-protein interactions and precise genome editing. However, efficient, safe, and cell type-specific delivery remains a major challenge. To address this, we developed a modular platform for synthesizing heterotrifunctional bio-orthogonal macromolecular conjugates (BMCs) by engineering diverse combinations of targeting ligands, cell-penetrating peptides (CPPs), and bioactive cargos. We optimized facile bioconjugation chemistries to generate BMCs with improved yields, structural integrity, and activity. Modular BMCs accommodate diverse components, including antibodies and receptor ligands for targeting, CPPs for intracellular trafficking, and optical probes, therapeutic peptidomimetics, and CRISPR-Cas9 nuclease as cargos to confer specific biological activities. We assayed their utility across multiple applications: BMCs with fluorescently labeled cargo revealed endosomal escape and intracellular accumulation; peptidomimetic MYB transcription factor inhibitor BMCs exhibited potent anti-leukemic activity against acute myeloid leukemia cells; and Cas9 BMCs achieved rapid delivery and cell type-specific gene editing in human cells. The BMC approach enables customizable delivery of functional macromolecules, nominating BMCs as a broadly applicable platform for biomedical applications.
One-Sentence Summary: The establishment of modular platform for synthesizing bio-orthogonal macromolecular conjugates (BMC) enabled fast and targeted delivery of membrane-impermeant macromolecular drugs.

DOI: https://doi.org/10.1101/2025.07.24.666613
Mol Ther Nucleic Acids. 2025 Sep 09. 36(3): 102625

Using muscle homing peptide CyPep10 to deliver phosphorodiamidate morpholino oligomers in the mdx mouse.

Anne-Fleur E Schneider, Christa L Tanganyika-de Winter, Silvana M G Jirka, Xuyu Tan, Emily G Thompson, Kristen Ha, Anindita Mitra, Stephanie Garcia, Marleen Luimes, Ryan A Oliver, Vincent Guerlavais, Annemieke Aartsma-Rus.

  The severe muscle wasting disorder Duchenne muscular dystrophy (DMD) is characterized by the absence of dystrophin, a protein that is essential for muscle stability. Restoring this protein has therapeutic potential. Antisense oligonucleotides (ASOs), designed to target and skip exons, can restore the reading frame that is disrupted in these patients, enabling the production of partially functional dystrophin. Achieving optimal dystrophin restoration remains challenging due to limited delivery and cellular uptake. Muscle homing peptides conjugated to ASOs are a way to achieve this. Previously, CyPep10 (CP10) has been used to significantly increase exon skipping efficiency for the 2'-O-methyl phosphorothioate chemistry in the mdx mouse model for DMD. Here, we explore the effect of using peptide CP10 as a conjugate to phosphorodiamidate morpholino oligomers (PMOs) ASOs to improve muscle delivery, thereby hoping to achieve increased treatment efficiency. Overall, we confirmed the homing ability of CP10 and observed significantly increased muscle tissue concentration levels of PMO when CP10 was conjugated. This did not lead to increased levels of exon skipping or dystrophin restoration. Conjugating both a cell-penetrating peptide (CPP) and CP10 to a PMO showed that increased exon skipping efficiency can be achieved to a slightly greater extent than with CPP-PMO treatment.

Keywords:  Duchenne muscular dystrophy; MT: Delivery Strategies; PMO; antisense oligonucleotide; cell-penetrating peptide; cyclic peptide; muscle uptake

DOI:  https://doi.org/10.1016/j.omtn.2025.102625
J Chem Inf Model. 2025 Aug 06.

De Novo Design of Multiple Microplastic-Binding Peptides with a Protein Language Model-Guided Generative Adversarial Network.

Siyuan Wang, Michael T Bergman, Carol K Hall, Fengqi You.

Microplastics are heterogeneous pollutants that pose significant risks to ecosystems and human health. Innovative mitigation strategies are urgently needed. Plastic-binding peptides represent a promising eco-friendly approach for detecting or capturing microplastic pollution. Since real-world microplastic pollution consists of multiple types of plastic, it would be particularly useful to have peptides that bind to multiple plastics. However, there are no known peptides with this property. We present a generalizable AI-driven framework for the de novo design of plastic-binding peptides with a high affinity for multiple plastics. The framework integrates a pretrained protein language model (PLM), fine-tuned on biophysical modeling data of peptide adsorption to plastics generated by the PepBD algorithm, that guides peptide design with a generative adversarial network (GAN). The PLM provides appropriate embeddings of peptide physicochemical features that lead to accurate predictions of peptide affinity for a given plastic. The GAN model is trained via a modular split-training strategy to ensure stability, sequence diversity, and the ability to optimize peptide affinity to any desired combination of plastics. We use this framework to design peptides with high affinity for polyethylene, polypropylene, and poly(ethylene terephthalate). Molecular dynamics simulations confirm that the generated peptides exhibit strong multiplastic binding, having average adsorption free energies to the three plastics that are ∼30% more favorable than those of peptides previously designed using biophysical methods. Steered molecular dynamics simulations reveal that one peptide has an exceptionally high affinity for both polyethylene and polypropylene. These findings highlight the potential of AI-driven peptide design for addressing microplastic pollution and broader applications in peptide engineering.

DOI: https://doi.org/10.1021/acs.jcim.5c01401
J Am Chem Soc. 2025 Aug 08.

Intrastrand Peptide Staples That Promote β-Sheet Folding, Self-Assembly, and Amyloid Seeding.

Abha Dangi, Isaac J Angera, Juan R Del Valle.

Side chain stapling of cysteine (Cys) residues offers convenient entry into constrained peptides with enhanced bioactivity and bioavailability. Despite its widespread application in the constraint of α-helical, PPII, and loop conformations, the stabilization of β-sheet folds via intrastrand side chain Cys stapling remains largely unexplored. Here, we demonstrate that i→i+2 stapling with E-butenyl, butynyl, and m-xylyl linkers significantly enhances the folded population of two distinct β-hairpin model peptides. High-resolution NMR structures reveal that these staples support canonical β-sheet backbone torsions and stabilize cross-strand interactions. Leveraging the maintenance of intact backbone hydrogen-bonding edges, we employed i→i+2 side chain macrocyclization in the design of constrained β-arch peptides derived from the tau protein. We show that intrastrand stapling of a nonaggregation-prone segment promotes self-assembly into β-sheet-like filaments. The resulting filaments also seed the aggregation of endogenous tau in a cell-based assay in a macrocycle- and sequence-dependent manner. These findings establish di-Cys i→i+2 stapling as a versatile and synthetically accessible method to stabilize β-sheet structure and modulate the self-assembly of seed-competent amyloidogenic peptides.

DOI: https://doi.org/10.1021/jacs.5c06944
bioRxiv. 2025 Aug 02. pii: 2025.07.31.667801. [Epub ahead of print]

Enzyme-free biochemical production of seamlessly N-to-C cyclized peptides from natural or recombinant proteins.

Ali Behboodian, Eugene Serebryany.

  Many naturally occurring or synthetic cyclic peptides are valuable as pharmaceuticals, but this stable and versatile class of molecules has not yet found applications beyond medicine. The main reason is the high cost of developing, producing, and altering these molecules via the gold-standard solid-phase synthesis methods. We focus on a class of cyclic peptides that have no disulfides, only canonical amino acids, and seamless peptide backbones. Known as orbitides or circular bacteriocins, such compounds are ribosomally synthesized and enzymatically cyclized by plants and bacteria. We report a simple method for producing them from naturally abundant proteins or from recombinantly expressed precursor polypeptides. The reaction proceeds under mild aqueous conditions, without the need for enzymes, and using only one chemical reagent, which is readily available. We demonstrate production of a 17-mer cyclic peptide from a wild-type human eye lens γ-crystallin and of a set of 10-residue cyclic peptides from recombinantly expressed polypeptide precursors. We investigate the effects of reaction conditions and sequence changes on reaction efficiency, identify the products by their complex mass spectrometry fragmentation patterns, and chromatographically separate linear and cyclic peptide forms. Our methodology opens the way to large-scale, cost-effective production of stable yet biodegradable, easily designable cyclic peptides for applications not only in medicine, but in areas like biotechnology, materials, agriculture, and pest control. It may also enable production of diverse cyclic peptide libraries from arbitrarily chosen natural protein sources.

Keywords:  Cyclic peptides; aminolysis; cyanylation; cyclization; orbitides; peptide macrocycles

DOI:  https://doi.org/10.1101/2025.07.31.667801
J Am Chem Soc. 2025 Aug 05.

Direct Editing of Cysteine to Electrophilic Alkyl Halides in Peptides.

Daniel S Honeycutt, Waldo Salgado-Bello, Harlan S Greenberg, William K McCarthy, Jason M Mrosla, Brian Pallares, Jacob M Goldberg, Fang Wang.

Functional group conversion is a cornerstone of modern synthetic chemistry. Many strategies routinely employed for small-molecule transformations are unsuitable for modifying biomacromolecules, including peptides. Here, we describe a simple but chemoselective approach that directly converts the nucleophilic cysteine carbon-thiol side chain into an electrophilic carbon-halogen bond under mild conditions, compatible with diverse peptides. The incorporation of this versatile synthetic handle facilitates a range of subsequent transformations that are rarely, if ever, applied to complicated peptides. We envision that this side-chain editing methodology will open a broad expanse of unexplored peptide chemical space, which will concomitantly unlock applications for an entire class of new biomacromolecules.

DOI: https://doi.org/10.1021/jacs.5c06200
Angew Chem Int Ed Engl. 2025 Aug 06. e202513115

Crown Ether-Peptide Rotaxanes.

Peng-Lai Wang, Peng Chen, Raorao Yang, Daniel J Tetlow, Zhi-Hui Zhang, Jing Han, Stephen D P Fielden, Prodip Howlader, Liang Zhang, David A Leigh.

  We report on the metal-free active template synthesis of crown ether-peptide rotaxanes. A 24-crown-8 ring is sufficiently small that the side chains of canonical branched amino acids act as barriers that trap the macrocycle on the particular glycine residue used to assemble the rotaxane. The resulting crown ether-tripeptide rotaxane can subsequently be extended from either or both N- and C-termini of the axle. Three distinct positional isomers of a heptapeptide [2]rotaxane containing three glycine units were selectively synthesized, and in each case the unique position of the crown ether on the peptide axle was confirmed by 1H nuclear magnetic resonance spectroscopy and tandem mass spectrometry. The three positional isomers adopt different conformations in the region adjacent to the trapped macrocycle, and have different chemical stabilities and secondary interactions in comparison to the unthreaded peptide axle. The crown ether does not inhibit enzymatic proteolysis over the entire length of the heptapeptide-axle rotaxanes, but rather provides significant protection from degradation for the three to four residues local to the encapsulated region. The strategy opens a pathway to new analogs of naturally occurring mechanically interlocked peptides.

Keywords:  Active template synthesis; Lasso peptides; Mechanically interlocked molecules; Rotaxanes

DOI:  https://doi.org/10.1002/anie.202513115
Biochim Biophys Acta Proteins Proteom. 2025 Jul 31. pii: S1570-9639(25)00029-9. [Epub ahead of print] 141091

Structural insights of the complex formed by KRAS G12V and a novel TIG3 peptide.

Min Seon Ha, Chang Woo Han, Mi Suk Jeong, Se Bok Jang.

  Pancreatic cancer remains a severe malignancy with a dismal 5-year survival rate, and most pancreatic cancer patients harbor KRAS mutations, which are critical targets for anti-cancer drug development. However, the structural characteristics of KRAS present challenges for therapeutic targeting. In this study, we developed a novel peptide derived from TIG3 protein, a type II tumor suppressor, and confirmed its moderate affinity binding to KRAS G12V. X-ray crystallography revealed that this peptide binds near the Switch II domain of KRAS G12V, causing conformational changes likely to affect its activity. Furthermore, the peptide reduced the viability of cancer cell lines harboring the KRAS G12V mutation, thus demonstrating its potential as a KRAS G12V inhibitor. Our results indicate that the developed novel TIG3 peptide is a promising candidate for KRAS-targeted therapy and provide structural insights useful for the development of pancreatic ductal adenocarcinoma therapeutics.

Keywords:  KRAS G12V mutant; Peptides; TIG3; X-ray crystallography

DOI:  https://doi.org/10.1016/j.bbapap.2025.141091
Front Oncol. 2025 ;15 1596315

Case Report: Personalized peptide-based immunization in an advanced-stage prostate cancer patient with bone metastasis.

Nils Heinrich Thoennissen, Mari Carmen Martos-Contreras, Mehdi Manoochehri, Mauro Nogueira, Franziska Bremm, Jan Dörrie, Jan Christoph, Meik Kunz, Wolfgang Schönharting.

  Neoantigens, which are recognized as non-self and trigger an immune response, are novel antigens generated by tumor cells. Here, we report a de novo metastatic hormone-sensitive prostate cancer (mHSPC) case, which benefited from our personalized peptide immunization named BioInformatic Tumor Address Peptides (BITAP) in a monotherapeutic setting. Our in-house bioinformatics pipeline involved identifying somatic variations, analyzing their expression, and computationally predicting novel epitopes from both metastatic and primary tumors, separately. As stand-alone therapy, the patient has been administered multiple injections of two peptide pools (BITAP-1 and BITAP-2). Several months following immunizations, a significant regression of both metastatic and primary tumor lesions was recorded along with low-level of prostate-specific antigen (PSA). Besides mild and short-lasting local and systemic reactions, no serious treatment-related adverse effects were reported by the patient. In conclusion, this case suggests that BITAP immunization is feasible and safe, and may present an immunotherapeutic approach inducing sustainable tumor regressions in mHSPC patients.

Keywords:  case report; immunotherapy; neoantigen; peptide; prostate cancer

DOI:  https://doi.org/10.3389/fonc.2025.1596315