bims-cepepe 2025-04-20 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–04–20
thirteen papers selected by
Henry Lamb, Queensland University of Technology

De Novo Design of Cyclic Peptide Binders Based on Fragment Docking and Assembling.
Novel Cyclic Peptides as Interleukin-23 Inhibitor for Treating Inflammatory Disorders.
Membrane Permeability of Cyclic and Linear Peptides, a Halogenated Antisickling Molecule, and Water Across a Red Blood Cell Bilayer Model.
Probing Thrombosis Initiation with Lasso Peptide Variants as Inhibitors to the von Willebrand Protein-Collagen interaction.
End-to-End Backbone Cyclization Enhances Passive Permeability of bRo5 Oligomeric Depsipeptides with Nonlinear Size Dependence.
Employing Broad Substrate Specificity of Omniligase to Generate Phage-Encoded Bicyclic Peptide Libraries for Ligand Discovery.
The Potential of Peptide-Based Inhibitors in Disrupting Protein-Protein Interactions for Targeted Cancer Therapy.
Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability.
Selective targeting of oncogenic KRAS G12D using peptide nucleic acid oligomers attached to cell-penetrating peptides.
De Novo Design of Parallel and Antiparallel A3B3 Heterohexameric α-Helical Barrels.
Peptide Therapeutics: Current Status and Future Opportunity with Focus on Nose-to-Brain Delivery.
The emergence and loss of cyclic peptides in Nicotiana illuminate dynamics and mechanisms of plant metabolic evolution.
Rat Sarcoma (RAS)-Protein-Targeting Synthetic Cell-Penetrating Peptide as an Anticancer Biomaterial.

J Chem Inf Model. 2025 Apr 14.

De Novo Design of Cyclic Peptide Binders Based on Fragment Docking and Assembling.

Changsheng Zhang, Fanhao Wang, Tiantian Zhang, Yang Yang, Liying Wang, Xiaoling Zhang, Luhua Lai.

Cyclic peptides offer distinct advantages in modulating protein-protein interactions (PPIs), including enhanced target specificity, structural stability, reduced toxicity, and minimal immunogenicity. However, most cyclic peptide therapeutics currently in clinical development are derived from natural products or the cyclization of protein loops, with few methodologies available for de novo cyclic peptide design based on target protein structures. To fill this gap, we introduce CycDockAssem, an integrative computational platform that facilitates the systematic generation of head-to-tail cyclic peptides made entirely of natural - or -amino acid residues. The cyclic peptide binders are constructed from oligopeptide fragments containing 3-5 amino acids. A fragment library comprising 15 million fragments was created from the Protein Data Bank. The assembly workflow involves dividing the targeted protein surface into two docking boxes; the updated protein-protein docking program SDOCK2.0 is then utilized to identify the best binding fragments for these boxes. The fragments binding in different boxes are concatenated into a ring using two additional peptide fragments as linkers. A ROSETTA script is employed for sequence redesign, while molecular dynamics simulations and MM-PBSA calculations assess the conformational stability and binding free energy. To enhance docking performance, cation-π interactions, backbone hydrogen bonding potential, and explicit water exclusion energy were incorporated into the docking score function of SDOCK2.0, resulting in a significantly improved performance on the updated test set. A mirror design strategy was developed for cyclic peptides composed of -amino acids, where natural amino acid cyclic peptide binders are first designed for the mirror image of the target protein and the resulting complexes are then mirrored back. CycDockAssem was experimentally validated using tumor necrosis factor α (TNFα) as the target. Surface plasmon resonance experiments demonstrated that six of the seven designed cyclic peptides bind TNFα with micromolar affinity, two of which significantly inhibit TNFα downstream gene expression. Overall, CycDockAssem provides a robust strategy for targeted de novo cyclic peptide drug discovery.

DOI: https://doi.org/10.1021/acs.jcim.5c00088
ACS Med Chem Lett. 2025 Apr 10. 16(4): 532-533

Novel Cyclic Peptides as Interleukin-23 Inhibitor for Treating Inflammatory Disorders.

Qi-Long Hu, Steven H Liang.

This patent application illustrates a series of cyclic peptides inhibiting Interleukin-23 (IL-23), as represented by Formula I. These cyclic peptides exhibit significant therapeutic potential for treating diseases and disorders associated with IL-23 imbalance, with a particular focus on inflammatory bowel disease (IBD).

DOI: https://doi.org/10.1021/acsmedchemlett.5c00135
J Phys Chem Lett. 2025 Apr 14. 4021-4030

Membrane Permeability of Cyclic and Linear Peptides, a Halogenated Antisickling Molecule, and Water Across a Red Blood Cell Bilayer Model.

N Galamba.

We studied through molecular dynamics and inhomogeneous solubility-diffusion theory the permeability of several cyclic peptides (CPs) recently proposed as potential antisickling drugs, across a red blood cell (RBC) membrane model. The permeability of the CPs is compared to that of a linear precursor, a highly charged CP, a high permeability halogenated antisickling molecule (PD150606), and water. The influence of cholesterol (45% of the membrane) is assessed through comparison with the permeability across a homogeneous lipid bilayer. The most promising CPs concerning their potential antisickling activity depict the highest permeabilities, only exceeded by PD150606. The permeability of a hydrophobic CP is four decades higher than its linear precursor despite noncovalent cyclization in the interior of the membrane. Further, cholesterol is found to significantly reduce the permeability of water and a model CP, while not influencing that of PD150606. The influence of the water model is also investigated.

DOI: https://doi.org/10.1021/acs.jpclett.4c03339
Chembiochem. 2025 Apr 15. e202500188

Probing Thrombosis Initiation with Lasso Peptide Variants as Inhibitors to the von Willebrand Protein-Collagen interaction.

Danielle Amalie Guarracino, Drew V Carson, Toby G Johnson, A James Link.

  Currently, there are no peptide-based therapeutics that safely target thrombosis initiation. Anti-clot medications are mostly focused on platelet interactions, leading to side-effects and complications. Herein we describe the utilization of known peptide natural products, lasso peptides, as scaffolds for the development of new inhibitors to the protein-protein interaction between von Willebrand factor (vWF) and collagen, paramount to clot initiation. The microcin J25 lasso peptides tolerated substitution of four contiguous amino acids within its loop, leading to two variants with LWEQ and FRSH sequences grafted within the loop. Each variant showed low micromolar activity in a fluorescently-linked immunosorbent assay (FLISA), an in vitro test for inhibition of the collagen-vWF interaction. In addition, the lasso peptides were treated with a panel of proteases and showed exceptional stability. These peptides launch a new class of potential anti-thrombosis agents and also help probe the connection between peptide structure and its inhibitory, drug-like characteristics.

Keywords:  Inhibition; Peptides; natural products; therapeutics; thrombosis

DOI:  https://doi.org/10.1002/cbic.202500188
ACS Med Chem Lett. 2025 Apr 10. 16(4): 638-645

End-to-End Backbone Cyclization Enhances Passive Permeability of bRo5 Oligomeric Depsipeptides with Nonlinear Size Dependence.

Madelaine P Thorpe, Corey R Hopkins, Jeffrey N Johnston.

A majority of drugs are small molecules that satisfy Lipinski's Rule-of-Five (Ro5), but efforts to target topologically complex biomolecular interactions have reignited interest in nonconforming molecular therapeutics, dubbed "beyond Ro5 (bRo5)". Broadly useful design principles for bRo5 molecules are few in number, although several studies have highlighted the benefit to bioavailability and proteolytic stability that can result from the introduction of a constraining ring into conformationally mobile peptides. Here we show that a linear oligomeric depsipeptide (OD) template can be leveraged to link size to permeability, while the corresponding cyclic oligomeric depsipeptide (COD) series is used to determine the impact of cyclization as an added conformational constraint. Unexpectedly, certain macrocycle sizes confer a greater benefit to permeability than others.

DOI: https://doi.org/10.1021/acsmedchemlett.5c00037
Org Lett. 2025 Apr 17.

Employing Broad Substrate Specificity of Omniligase to Generate Phage-Encoded Bicyclic Peptide Libraries for Ligand Discovery.

Xiao-Cui Wan, Wen-Jing Zhu, Hui-Min Wei, Yan-Ni Zhang, Feng-Hao Zheng, Hua Zhang, Ying Chen, Jun-Hao Xue, Yu-Xuan Wang, Ge-Min Fang.

We report an enzymatic cyclization strategy termed omniligase-mediated peptide bicyclization. An electrophilic group was introduced into the recognition sequence of omniligase to achieve intramolecular bicyclization with Cys residues. In combination with phage display, we identified a bicyclic peptide ligand targeting TEAD4 with a KD value of 1.5 μM, 100-fold lower than its linear version, demonstrating the utility of this platform for discovering bicyclic peptide ligands.

DOI: https://doi.org/10.1021/acs.orglett.5c01205
Int J Mol Sci. 2025 Mar 28. pii: 3117. [Epub ahead of print]26(7):

The Potential of Peptide-Based Inhibitors in Disrupting Protein-Protein Interactions for Targeted Cancer Therapy.

Alexandra L Afonso, Catarina T Cavaleiro, Miguel A R B Castanho, Vera Neves, Marco Cavaco.

  Protein-protein interactions (PPIs) form an intricate cellular network known as the interactome, which is essential for various cellular processes, such as gene regulation, signal transduction, and metabolic pathways. The dysregulation of this network has been closely linked to various disease states. In cancer, these aberrant PPIs, termed oncogenic PPIs (OncoPPIs), are involved in tumour formation and proliferation. Therefore, the inhibition of OncoPPIs becomes a strategy for targeted cancer therapy. Small molecule inhibitors have been the dominant strategy for PPI inhibition owing to their small size and ability to cross cell membranes. However, peptide-based inhibitors have emerged as compelling alternatives, offering distinct advantages over small molecule inhibitors. Peptides, with their larger size and flexible backbones, can effectively engage with the broad interfaces of PPIs. Their high specificity, lower toxicity, and ease of modification make them promising candidates for targeted cancer therapy. Over the past decade, significant advancements have been made in developing peptide-based inhibitors. This review discusses the critical aspects of targeting PPIs, emphasizes the significance of OncoPPIs in cancer therapy, and explores the advantages of using peptide-based inhibitors as therapeutic agents. It also highlights recent progress in peptide design aimed at overcoming the limitations of peptide therapeutics, offering a comprehensive overview of the current landscape and potential of peptide-based inhibitors in cancer treatment.

Keywords:  OncoPPIs; peptide-based inhibitors; peptides; protein–protein interactions (PPIs); targeted cancer therapy

DOI:  https://doi.org/10.3390/ijms26073117
ACS Med Chem Lett. 2025 Apr 10. 16(4): 681-687

Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability.

Vasanthanathan Poongavanam, Stefan Peintner, Yordanos Abeje, Florian Kölling, Daniel Meibom, Mate Erdelyi, Jan Kihlberg.

The ability to adopt folded conformations that have a low solvent-accessible 3D polar surface area has been found to be important for PROTACs to display a high passive cell permeability. We have studied two VHL PROTACs that differ only by the replacement of two methylene groups in the linker by oxygen atoms but that displayed vast differences in their cell permeability. MD simulations and NMR spectroscopy revealed an unexpected, environment-dependent conformational behavior for the low-permeability PROTAC that has an alkyl linker. Hydrophobic interactions enforced extended and polar conformations for this PROTAC in nonpolar media, explaining its low cell permeability. In water, hydrophobic collapse around the linker led to folded and less polar conformations. In contrast, the highly permeable PROTAC having a PEG linker adopted conformations of similar shapes and polarities in polar and nonpolar environments.

DOI: https://doi.org/10.1021/acsmedchemlett.5c00068
bioRxiv. 2025 Apr 02. pii: 2025.03.28.645837. [Epub ahead of print]

Selective targeting of oncogenic KRAS G12D using peptide nucleic acid oligomers attached to cell-penetrating peptides.

Jayati Mondal, Dennis Lam, Mary E Gerritsen, Tilmann M Brotz, Jodi G Kennedy, Bruce Rehlaender, Arthur J Ross, Daniel E Levy, Christopher A Bonagura, William N Lanzilotta, Frank McCormick, Jeffrey H Rothman, Andrew L Wolfe.

KRAS is a proto-oncogene that contains activating mutations in up to 30% of tumors. Many conventional therapies inhibit both cancerous and normal cells, which may cause toxicity. Thus, programmable mutant-selective targeted inhibitors are needed. Peptide nucleic acids (PNAs) incorporate base sequences analogous to DNA, with modified peptide backbones instead of ribose-phosphate backbones, allowing PNAs to hybridize with DNA with high avidity to suppress transcription. Here, we developed KRAS G12D-selective PNA oligomers with novel cell-penetrating flanking regions. Fluorescein-labeled PNA oligomers displayed high uptake rates in cells and nuclei. Exposure to PNA-delivery peptide conjugates resulted in repression of KRAS G12D mRNA and protein expression within 2 hours and lasting up to 48 hours. Varying cell-penetrating peptide (CPP) compositions and lengths of complementary KRAS sequences were tested using dose-response cell viability assays. These experiments identified configurations that were effective at selectively preventing growth of on-target KRAS G12D cells, while relatively sparing off-target KRAS G12C cells. Electrophoretic mobility shift assays demonstrated in vitro binding and selectivity for KRAS G12D DNA sequences. CPP-PNA-G12D-1 was effective against a panel of pancreatic ductal adenocarcinoma cell lines and patient-derived xenografts in vivo . These results show promise for an enhanced PNA-delivery peptide conjugate strategy as both a tool for studying tumors driven by oncogenic point mutations and as a potential therapeutic strategy to selectively target mutant cancer cells.

DOI: https://doi.org/10.1101/2025.03.28.645837
Biochemistry. 2025 Apr 14.

De Novo Design of Parallel and Antiparallel A3B3 Heterohexameric α-Helical Barrels.

Joel J Chubb, Katherine I Albanese, Alison Rodger, Derek N Woolfson.

The de novo design of α-helical coiled-coil peptides is advanced. Using established sequence-to-structure relationships, it is possible to generate various coiled-coil assemblies with predictable numbers and orientations of helices. Here, we target new assemblies, namely, A3B3 heterohexamer α-helical barrels. These designs are based on pairs of sequences with three heptad repeats (abcdefg), programmed with a = Leu, d = Ile, e = Ala, and g = Ser, and b = c = Glu to make the acidic (A) chains and b = c = Lys in the basic (B) chains. These design rules ensure that the desired oligomeric state and stoichiometry are readily achieved. However, controlling the orientation of neighboring helices (parallel or antiparallel) is less straightforward. Surprisingly, we find that assembly and helix orientation are sensitive to the length of the overhang between helices. To study this, cyclically permutated peptide sequences with three heptad repeats (the register) in the peptide sequences were analyzed. Peptides starting at g (g-register) form a parallel 6-helix barrel in solution and in an X-ray crystal structure, whereas the b- and c-register peptides form an antiparallel complex. In lieu of experimental X-ray structures for b- and c-register peptides, AlphaFold-Multimer is used to predict atomistic models. However, considerably more sampling than the default value is required to match the models and the experimental data, as many confidently predicted and plausible models are generated with incorrect helix orientations. This work reveals the previously unknown influence of the heptad register on helical overhang and the orientation of α-helical coiled-coil peptides and provides insights for the modeling of oligopeptide coiled-coil complexes with AlphaFold.

DOI: https://doi.org/10.1021/acs.biochem.4c00584
Peptides. 2025 Apr 11. pii: S0196-9781(25)00065-8. [Epub ahead of print] 171404

Peptide Therapeutics: Current Status and Future Opportunity with Focus on Nose-to-Brain Delivery.

Eva-Maria Jülke, Annette G Beck-Sickinger.

  Peptide drugs are a highly diverse group of therapeutic agents. Over the last decade, more than 40 peptides have been approved for clinical use. They target different structures, ranging from G protein-coupled receptors (GPCRs) to pathogens and are used to treat a variety of indications, including metabolic disorders, genetic diseases, acute illnesses and more. Structurally, peptide therapeutics are a heterogeneous class. This diversity allows them to bridge the gap between small molecules and biologics. However, limited metabolic stability and bioavailability must be addressed. Strategies to improve the half-life include backbone and sequence modification, cyclization and the addition of stabilizing moieties. Great strides have been made in recent years towards achieving sufficient drug uptake for oral application have been achieved within recent years. However, these methods require specialized peptide design or involve permeabilization of the gastrointestinal tract. Consequently, other routes of administration are being explored. One promising approach is the nasal application of peptides. This method can be used for systemic uptake, but also allows for direct nose-to-brain delivery of compounds. While successful nose-to-brain delivery is already used in the clinic, the underlining mechanisms are poorly understood. Strategies for rational optimization are needed to make this method more applicable to a wider range of compounds. Overall, approved peptide therapeutics cover a wide range of applications and have demonstrated a growing and novel potential in recent drug discovery.

Keywords:  Nose-to-brain delivery; Peptide stability; Peptide therapeutics

DOI:  https://doi.org/10.1016/j.peptides.2025.171404
Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2425055122

The emergence and loss of cyclic peptides in Nicotiana illuminate dynamics and mechanisms of plant metabolic evolution.

Elliot M Suh, Jakob K Reinhardt, Jing-Ke Weng.

  Specialized metabolism plays a central role in how plants cope with both biotic and abiotic stresses in order to survive and reproduce within dynamic and challenging environments. One recently described class of plant-specific, ribosomally synthesized, and posttranslationally modified peptides are the burpitides, which are characterized by the installation of distinct sidechain macrocycles by enzymes known as burpitide cyclases. While they are found across many plant families and exhibit diverse bioactivities, little is known about their evolution or how new variants arise. Here, we present the identification of a burpitide cyclase, resurrected from a defunct pseudogene from the model organism Nicotiana attenuata, the coyote tobacco. By repairing the pseudogene ΨNatBURP2 and expressing it heterologously in Nicotiana benthamiana, we successfully reconstituted its original enzymatic activity. As an autocatalytic peptide cyclase, it installs a unique C-C bond between the tyrosine side chain and a specific backbone α-carbon of a heptapeptide core motif, resulting in burpitides dubbed "nanamins." Despite its pseudogenization in N. attenuata, we found that the closely related species, Nicotiana clevelandii, retains the wild-type gene and produces nanamins. Phylogenetic analyses and targeted mutagenesis experiments reveal that this chemotype must have evolved from the duplication and neofunctionalization of a more promiscuous ancestral gene. This work highlights how novel peptide chemotypes may rapidly emerge and disappear in plants, while expanding the molecular toolkit for engineering novel peptides with applications in agriculture and drug discovery.

Keywords:  RiPPs; cyclic peptides; metabolic evolution

DOI:  https://doi.org/10.1073/pnas.2425055122
Biomater Res. 2025 ;29 0175

Rat Sarcoma (RAS)-Protein-Targeting Synthetic Cell-Penetrating Peptide as an Anticancer Biomaterial.

Gookjin Yoon, Jinsook Suh, Beom Soo Jo, Dong Woo Lee, Deogil Kim, Moonsil Choi, Eui Kyun Jeong, Hoo Cheol Lee, Hye Min Shin, Yu-Bin Kim, Sanghui Seok, Yoon Shin Park, Chong Pyung Chung, Jue-Yeon Lee, Yoon Jeong Park.

Various bioactive materials, including peptides, have become potential candidates for slowing cancer growth and metastasis. Among bioactive peptides, a synthetic cell-penetrating peptide referred to as rat sarcoma (RAS)-binding peptide (RBP) was suggested as a potential entity that targets RAS with high affinity in MDA-MB-231 cancer cells. This RAS binding further inhibits the RAS-rapidly accelerated fibrosarcoma (RAF) protein-protein interaction. The current study revealed that RBP effectively suppresses proliferation and extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation by disrupting the RAS-RAF interaction. This intervention not only inhibits cell migration and invasion but also has substantial potential for preventing metastasis. The RAS-RAF-ERK1/2 pathway is a key target for anticancer drug development because of frequent ERK and mitogen-activated protein kinase activation in human cancers. MDA-MB-231, a triple-negative breast cancer cell line, harbors a G13D Kirsten rat sarcoma viral oncogene homolog mutation, making it resistant to many drugs. In addition to its in vitro antitumor activity, RBP was identified as a potent antagonist that substantially arrests tumor growth and invasiveness in in vivo chicken egg and mouse xenograft tumor models. Notably, histopathological analyses revealed increased immune cell infiltration and decreased Ki-67 expression, confirming the ability of RBP to inhibit tumor cell proliferation. Taken together, these findings highlight RBP as a therapeutic anticancer biomaterial capable of impeding the progression and metastasis of RAS-mutated cancers.

DOI: https://doi.org/10.34133/bmr.0175