bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2025–06–15
eight papers selected by
Henry Lamb, Queensland University of Technology
  1. CycleDesigner: Leveraging CycRFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets.
  2. Enhancing cyclic peptide functionality with hydrophilic diamino acids for improved APC-Asef interaction inhibition.
  3. Asparaginyl Ligases with Engineered Substrate Specificity for Controlled, Sequential Transpeptidation Reactions.
  4. The Different Cellular Entry Routes for Drug Delivery Using Cell Penetrating Peptides.
  5. Profiling Cytosolic Drug Delivery in Mammalian Cells: A Generalizable Assay for Intracellular Accumulation.
  6. Insights into platelet factor 4-derived peptide macrocycles; the mechanistic basis of their rapid and selective antiplasmodial actions.
  7. High-throughput enrichment of functional disulfide-rich peptides by droplet microfluidics.
  8. Design and discovery of novel cyclic peptides as TSP1-CD36 interaction inhibitors for intestinal fibrosis treatment.
  1. J Chem Inf Model. 2025 Jun 10.
    CycleDesigner: Leveraging CycRFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets.
    Chenhao Zhang, Zhenyu Xu, Kang Lin, Ning Zhu, Chengyun Zhang, Wen Xu, Jingjing Guo, An Su, Chengxi Li, Hongliang Duan.
      Cyclic peptides are potentially therapeutic in clinical applications, due to their great stability and activity. Yet, designing and identifying potential cyclic peptide binders targeting specific targets remains a formidable challenge, entailing significant time and resources. In this study, we modified the powerful RFdiffusion model to allow the cyclic peptide structure identification (CycRFdiffusion) and integrated it with ProteinMPNN and HighFold to design binders for specific targets. This innovative approach, termed CycleDesigner, was followed by a series of scoring functions for efficient filtering. With the combination of effective cyclic peptide design and filtering, our study aims to further broaden the scope of cyclic peptide binder design.
    DOI:  https://doi.org/10.1021/acs.jcim.5c00227
  2. Bioorg Med Chem. 2025 Jun 08. pii: S0968-0896(25)00218-4. [Epub ahead of print]128 118277
    Enhancing cyclic peptide functionality with hydrophilic diamino acids for improved APC-Asef interaction inhibition.
    Shipeng He, Jie Zhong, Ziqiang Yu, Haohao Bai, Ping Zheng, Donald Bierer, Xiuyan Yang, Jian Zhang, Hong-Gang Hu.
      Cyclic peptides inherently possess advantages in inhibiting protein-protein interactions (PPIs). However, those constructed using traditional disulfide bonds are susceptible to cleavage by disulfide isomerase or reducing environments, leading to diminished biological activity. To address this challenge, our study employed novel hydrophilic diamino acids with enhanced electronegativity to construct cyclic peptides, effectively resolving issues related to stability and aqueous solubility, thereby overcoming the limitations associated with disulfide bond-based cyclic peptides. Furthermore, we applied this diamino acid strategy to the APC-Asef PPI peptide inhibitor MAI-516. Compared to cyclic peptides constructed using traditional disulfide bonds, those generated using the diamino acid strategy exhibited enhanced aqueous solubility, stability, and inhibitory activity. This study provides an application example for the modification of novel hydrophilic diamino acids in peptide cyclization and offers an effective strategy for the development of therapeutic agents for metastatic colorectal cancer.
    Keywords:  APC-Asef interaction; Cyclic peptides; Hydrophilic diamino acids; Protein-protein interaction inhibition
    DOI:  https://doi.org/10.1016/j.bmc.2025.118277
  3. J Am Chem Soc. 2025 Jun 11.
    Asparaginyl Ligases with Engineered Substrate Specificity for Controlled, Sequential Transpeptidation Reactions.
    Yan Zhou, Simon J de Veer, Tristan J Tyler, Yufei Chen, Thomas Durek, David J Craik, Fabian B H Rehm.
      Transpeptidases are valuable enzymes for peptide and protein engineering due to their ease of use and highly defined substrate specificities. Asparaginyl ligases are a class of highly efficient transpeptidases. Engineered asparaginyl ligases with orthogonal substrate specificities would provide access to new types of sequential transpeptidation regimes, but no such engineered variants have been reported thus far. Here, we engineer the widely used asparaginyl ligase OaAEP1 for altered substrate specificity. We find that a single amino acid substitution, Y188A, facilitates the recognition of a substrate sequence that is essentially unmodified by the parent enzyme or an alternative Y188W mutant. This orthogonality enables controlled sequential reactions for the generation of a dual N- and C-terminally labeled protein and the one-pot synthesis of two distinct cyclic peptides from a single linear synthetic peptide precursor. Introducing the equivalent mutation in a consensus-designed asparaginyl ligase facilitates similarly altered substrate specificity, suggesting that the Tyr188 residue is a general determinant of the asparaginyl ligase substrate specificity.
    DOI:  https://doi.org/10.1021/jacs.5c04693
  4. Biol Cell. 2025 Jun;117(6): e70012
    The Different Cellular Entry Routes for Drug Delivery Using Cell Penetrating Peptides.
    Michael Okafor, David Schmitt, Stéphane Ory, Stéphane Gasman, Christelle Hureau, Peter Faller, Nicolas Vitale.
      The cell plasma membrane acts as a semi-permeable barrier essential for cellular protection and function, posing a challenge for therapeutic molecule delivery. Conventional techniques for crossing this barrier, including biophysical and biochemical methods, often exhibit limitations such as cytotoxicity and the risk of genomic integration when viral vectors are involved. In contrast, cell-penetrating peptides (CPPs) offer a promising non-invasive means to deliver a broad range of molecular cargoes, including proteins, nucleic acids and small molecules, into cells. CPPs, typically 5 to 30 amino acids long and rich in basic or non-polar residues, interact favourably with different cell membranes. These peptides have evolved since the discovery of the HIV-1 TAT peptide in the 1980s, expanding into various CPP families with diverse therapeutic applications. CPPs can form covalent or non-covalent complexes with their cargo, influencing their stability and efficacy. Based on their sequence properties and interactions, CPPs can be amphipathic or non-amphipathic, with distinct mechanisms of membrane penetration, such as direct penetration and endocytosis. While their uptake mechanisms are complex and not fully elucidated, ongoing optimization aims to enhance CPP specificity and efficacy. CPPs have demonstrated potential in drug delivery, gene therapy, cancer treatment and vaccine development, addressing key safety and efficiency concerns associated with viral vectors. This review explores the classification, mechanisms of action and therapeutic potential. It focuses on the intracellular vesicular trafficking of CPPs, highlighting their role as transformative tools in advancing cellular therapies and medical treatments.
    Keywords:  cell penetrating peptides; endocytosis; endosomes; macropinocytosis; membrane penetration
    DOI:  https://doi.org/10.1111/boc.70012
  5. bioRxiv. 2025 Jun 06. pii: 2025.06.03.656700. [Epub ahead of print]
    Profiling Cytosolic Drug Delivery in Mammalian Cells: A Generalizable Assay for Intracellular Accumulation.
    Sobika Bhandari, George M Ongwae, Rachita Dash, Zichen Liu, Mahendra D Chordia, Yuchen He, Marcos M Pires.
      The ability of biologically active molecules to access intracellular targets remains a critical barrier in drug development. While assays for measuring cellular uptake exist, they often fail to distinguish between membrane-associated or endosomal trapped compounds and those that successfully reach the cytosol. Here, we present the Chloroalkane HaloTag Azide-based Membrane Penetration (CHAMP) Assay, a novel high-throughput method that employs a minimally disruptive azide tag to report the cytosolic accumulation of diverse molecules in mammalian cells. The CHAMP assay utilizes HaloTag-expressing cells and strain-promoted azide-alkyne cycloaddition (SPAAC) chemistry to quantify the presence of azide-tagged test compounds in the cytosol. We demonstrate the versatility of this approach by evaluating the accumulation profiles of small molecules, peptides, and proteins, revealing how structural variations and stereochemical differences influence cytosolic penetration. Our findings with cell-penetrating peptides confirm established structure-activity relationships, with longer polyarginine sequences showing enhanced accumulation. Additionally, we observed that C -terminal amidation and D-amino acid substitutions significantly impact cellular penetration. When applied to supercharged proteins and antibiotics, CHAMP successfully discriminates between compounds with varying accumulation capabilities. This method provides a robust platform for screening cytosolic accumulation while minimizing the confounding effects of large tags on molecular permeability, potentially accelerating the development of therapeutics targeting intracellular pathways.
    DOI:  https://doi.org/10.1101/2025.06.03.656700
  6. Cell Mol Life Sci. 2025 Jun 09. 82(1): 228
    Insights into platelet factor 4-derived peptide macrocycles; the mechanistic basis of their rapid and selective antiplasmodial actions.
    Dianne W Xu, Karoline Raven, Sarah R Woodcock, Bruce Munro, Isabella R Palombi, Caitlin L Gare, Andrew M White, Lara R Malins, Nicole Lawrence, Brendan J McMorran.
      The malarial parasite Plasmodium can acquire resistance to most mainstay antimalarial drugs, necessitating the development of new antiplasmodial agents with different modes of action. The innate defense protein, human platelet factor 4 (PF4), has a unique antiplasmodial action that involves selective entry into Plasmodium-infected red blood cells (RBC) and subsequent destruction of the parasite's digestive vacuole (DV). This activity is recapitulated in PF4-derived internalization peptides (PDIPs). Here, we characterized the actions of PDIP analogs and PF4 in live P. falciparum-infected human RBC to understand their kinetics, effects on cell and parasite viability, and molecular requirements for antiplasmodial activity. The entry and accumulation of PDIP, and peptide-induced DV destruction, were distinguishable as ordered and rapidly occurring events that were equivalent to PF4. Both host cell and parasite plasma membranes remained intact and undamaged following destruction of the DV, although modest changes in phosphatidylserine (PS) exposure on the surface of the host cells (indicative of changes to its phospholipid organization) and swelling (but not lysis) of the intracellular parasite were observed. PDIP retained its macrocyclic structure, and its activity depended on elevated levels of PS on the surface of infected versus uninfected cells. Neither the intramolecular disulfide bond of PDIP, nor the parasite's nutrient and ion transporter functions were required. These actions on the parasite DV were not detected for other antiplasmodial drugs and compounds. In conclusion, this study reveals the unique, rapid, and distinct antiplasmodial actions of PDIP, highlighting its potential for future antimalarial development.
    Keywords:  Antiplasmodial peptide; Cell internalization; Host defense peptide; Membrane-active peptide; Microbe-host cell selectivity
    DOI:  https://doi.org/10.1007/s00018-025-05757-y
  7. Lab Chip. 2025 Jun 10.
    High-throughput enrichment of functional disulfide-rich peptides by droplet microfluidics.
    Jing Xie, Kuok Yap, Simon J de Veer, Selvakumar Edwardraja, Thomas Durek, Matt Trau, David J Craik, Conan K Wang.
      Disulfide-rich peptides (DRPs) have evolved intricate topologies to carry out a wide range of bioactivities throughout nature, e.g., in fungi, insects, plants and animals, and have proven applications in medicine and agriculture. To discover novel DRPs, it is now routine to screen DRP libraries for target affinity, but target binding does not necessarily correlate with function. This study reports an innovative platform for screening of DRP libraries based on the functional endpoint of biochemical reactions within picoliter-sized water-in-oil droplets. We leveraged yeast secretory expression to ensure proper assembly of disulfide connectivity, and thus peptide shape, and engineered customizable strains for facile detection of function (i.e., protease inhibitory activity) for libraries of DRPs. Rapid enrichment of a potent trypsin inhibitor (MCoTI-II) from a >100 000 pool of randomized variants across four rounds of selection was achieved, far exceeding the library sizes explored previously for peptide systems in droplet microfluidics. This developed platform provides a foundation to explore the functional engineering of DRPs.
    DOI:  https://doi.org/10.1039/d5lc00261c
  8. Bioorg Chem. 2025 Jun 04. pii: S0045-2068(25)00547-4. [Epub ahead of print]163 108667
    Design and discovery of novel cyclic peptides as TSP1-CD36 interaction inhibitors for intestinal fibrosis treatment.
    Wen Zhang, Liang Qi, Wei Cheng, Xianggui Wang, Yujie Hong, Rui Dong, Weiqi Yuan, Dekui Zhang.
      Intestinal fibrosis is a refractory complication of inflammatory bowel disease (IBD), arising from recurrent intestinal inflammation and excessive wound healing. Repeated strictures can lead to intestinal obstruction, with three-quarters of patients with strictures eventually requiring surgery, which severely impacts their quality of life. Thrombospondin-1 (TSP1) is a matricellular protein that regulates tissue fibrosis by binding to its cell membrane receptor, CD36, and activating transforming growth factor β (TGF-β). In this study, based on molecular docking simulations, overlapping peptide libraries, and introducing non-natural amino acid modifications, we designed a cyclic peptide derived from the structure of CD36 (93-110), 19A8.8, which potently inhibited the epithelial-mesenchymal transition (EMT) of IEC-6 cells and reduced extracellular matrix protein deposition by disrupting the TSP1-CD36 interaction. In both in vitro and in vivo intestinal fibrosis models, 19A8.8 was shown to alleviate intestinal fibrosis by suppressing Smad3 phosphorylation and blocking the TGF-β/Smad3 signaling pathway. This study is the first to identify a novel therapeutic target for intestinal fibrosis and proposes the cyclic peptide 19A8.8 as a potential candidate drug for its treatment.
    Keywords:  Cyclic peptide; Inflammatory bowel disease; Intestinal fibrosis; Smad3
    DOI:  https://doi.org/10.1016/j.bioorg.2025.108667
This page is being maintained by Thomas Krichel. It was last updated on 2025‒06‒29 at 7:48.