bims-cepepe 2025-02-16 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–02–16
fourteen papers selected by
Henry Lamb, Queensland University of Technology

Development of selective nanomolar cyclic peptide ligands as GBA1 enzyme stabilisers.
Boronic Acid-Linked Apo-Zinc Finger Protein for Ubiquitin Delivery in Live Cells.
Dual-Functional Synthetic Linear and Cyclic Peptides with Anti-Amyloid and Antimicrobial Activities for Alzheimer's disease.
Advances of deep Neural Networks (DNNs) in the development of peptide drugs.
Isolation of Peptide Ligands for the HIV Capsid Protein p24 by Phage-Display.
Screening of homing and tissue-penetrating peptides by microdialysis and in vivo phage display.
A Site-Specific MiniAp4-Trastuzumab Conjugate Prevents Brain Metastasis.
Peptide‑based therapeutic strategies for glioma: Current state and prospects.
An optimised Bcl-3 inhibitor for melanoma treatment.
Look Beyond Plasma Membrane Biophysics: Revealing Considerable Variability of the Dipole Potential Between Plasma and Organelle Membranes of Living Cells.
Preliminary Study of a Novel 68Ga-Labeled Probe Targeting Neuropilin-1 for Tumor Diagnosis.
Host Defense Peptide Mimics Synergize with Pt(IV) Prodrugs for Surmounting Cisplatin Resistance via Selective Cancer Membrane Disruption.
Masked Graph Transformer for Blood-Brain Barrier Permeability Prediction.
Cyclic Peptide Natural Product Inspired Inhibitors of the Free-Living Amoeba Balamuthia mandrillaris.

RSC Chem Biol. 2025 Jan 31.

Development of selective nanomolar cyclic peptide ligands as GBA1 enzyme stabilisers.

Rebecca E Katzy, Renier H P van Neer, Maria J Ferraz, Kim Nicolai, Toby Passioura, Hiroaki Suga, Seino A K Jongkees, Marta Artola.

The stabilisation of recombinant glycosidases by exogenous ligands, known as pharmacological chaperones or enzyme stabilisers, has recently garnered great clinical interest. This strategy can prevent enzyme degradation in the blood, reducing required dosages of recombinant enzyme and extending IV injection intervals, thereby reducing side effects, improving patient lifestyles and treatment costs. While this therapeutic approach has been successfully implemented for treating Pompe and Fabry diseases, clinical studies for Gaucher disease using chaperones alone or in combination with enzyme replacement therapy (ERT) have been limited, and no small molecule chaperones have yet been approved for this condition. Developing such therapies requires selective and effective reversible GBA1 ligands. Here, we describe the development of a new class of selective macrocyclic peptide GBA1 ligands using random nonstandard peptides integrated discovery (RaPID) technology, and demonstrate their ability to bind and stabilise rhGBA1 in plasma at nanomolar concentrations. These cyclic peptides do not inhibit endogenous GBA1 in cells due to poor cell permeability but can stabilise extracellular rhGBA1 in plasma, presenting significant potential as a combinatorial ERT-pharmacological chaperone therapy for Gaucher disease.

DOI: https://doi.org/10.1039/d4cb00218k
Chembiochem. 2025 Feb 11. e202401040

Boronic Acid-Linked Apo-Zinc Finger Protein for Ubiquitin Delivery in Live Cells.

Pritam Ghosh, Oliver Seitz.

  Delivering cargo into living cells has extensive applications in chemistry, biology, and medicine. Cell-penetrating peptides (CPPs) provide an ideal solution for cellular delivery. Enhancing CPPs with additional functional units can improve delivery efficiency. We investigate the conjugation of boronic acid modules to enhance internalization through interactions with cell surface glycans. The aim of this study is to determine whether adding boronic acid can transform a peptide that typically lacks CPP properties into one that functions as a CPP, enabling the delivery of crucial biological cargo like ubiquitin. The zinc finger protein in its apo state was selected as a "boronate-enabled" CPP. Results indicate that skeletal point mutations and post-synthetic modifications, combined with conjugated benzoboroxole derivatives, enable the apo-ZFP the ability to transport ubiquitin within A549 cells, confirmed through microscopy and flow cytometry. This effective internalization of cargo offers valuable insights for advancing the development of boronic acid-mediated cell-penetrating peptides.

Keywords:  Boronic Acid * Ubiquitin * Live Cells * Cell Penetrating Peptide *

DOI:  https://doi.org/10.1002/cbic.202401040
Chemistry. 2025 Feb 11. e202404349

Dual-Functional Synthetic Linear and Cyclic Peptides with Anti-Amyloid and Antimicrobial Activities for Alzheimer's disease.

Lujuan Yang, Yao Wang, Peng Shang, Gang Ma.

  Dual-functional peptides exhibiting both anti-amyloid and antimicrobial activities have attracted attention as promising candidates for Alzheimer's disease treatment. The advantage of these peptides lies in their ability to simultaneously target both the amyloid cascade hypothesis and the microbial infection hypothesis, in contrast to single-function inhibitors. However, most of the reported dual-functional peptides to date are natural peptides, and the development of synthetic peptides in this area remains limited. In this study, we propose two strategies to aid in the discovery of synthetic dual-functional peptides. We then report four distinct synthetic dual-functional peptides identified using these strategies, with the Aβ1-40/Aβ1-42 fibrillation system and common bacterial strains serving as a proof-of-concept platform. One strategy involves repurposing existing knowledge, while the other breaks from established conventions. Using the first strategy, we discovered a very short dual-functional linear peptide. With the second strategy, we identified a simple dual-functional cyclic peptide. Furthermore, by combining these two strategies, we developed a hybrid dual-functional peptide incorporating both linear and cyclic structures. We hope that our findings will contribute to the future discovery of more synthetic dual-functional peptides for treating Alzheimer's disease.

Keywords:  Amyloid; Aβ; amyloid fibrillation; amyloid inhibitor

DOI:  https://doi.org/10.1002/chem.202404349
Future Med Chem. 2025 Feb 12. 1-15

Advances of deep Neural Networks (DNNs) in the development of peptide drugs.

Yuzhen Niu, Pingyang Qin, Ping Lin.

  Peptides are able to bind to difficult disease targets with high potency and specificity, providing great opportunities to meet unmet medical requirements. Nevertheless, the unique features of peptides, such as their small size, high structural flexibility, and scarce data availability, bring extra challenges to the design process. Firstly, this review sums up the application of peptide drugs in treating diseases. Then, the review probes into the advantages of Deep Neural Networks (DNNs) in predicting and designing peptide structures. DNNs have demonstrated remarkable capabilities in structural prediction, enabling accurate three-dimensional modeling of peptide drugs through models like AlphaFold and its successors. Finally, the review deliberates on the challenges and coping strategies of DNNs in the development of peptide drugs, along with future research directions. Future research directions focus on further improving the accuracy and efficiency of DNN-based peptide drug design, exploring novel applications of peptide drugs, and accelerating their clinical translation. With continuous advancements in technology and data accumulation, DNNs are poised to play an increasingly crucial role in the field of peptide drug development.

Keywords:  Deep Neural Networks (DNNs); de novo design; optimizing model architectures; peptide drug; target-based design

DOI:  https://doi.org/10.1080/17568919.2025.2463319
Int J Pept Res Ther. 2025 ;31(2): 32

Isolation of Peptide Ligands for the HIV Capsid Protein p24 by Phage-Display.

Jerry Woo, Emily Orozco, Srinivas S Thota, Maede Chabi, Katerina Kourentzi, Richard Willson, Brian K Kay.

   Purpose: Isolate renewable and cost-efficient affinity reagents that will facilitate the detection of p24, the capsid protein of Human Immunodeficiency Virus (HIV), by screening phage-displayed combinatorial peptide libraries and identifying peptide ligands.
Method: Four in-house combinatorial peptide libraries were screened for binders in three progressive rounds against monomeric p24 protein. Peptide binders were characterized by ELISA and Surface Plasmon Resonance (SPR) and one peptide sequence was evaluated in a lateral flow assay (LFA).
Result: We identified 26 unique peptide sequences that exhibit varying phage ELISA signals above background for p24. We subsequently validated the binding of one linear and two cyclized peptide sequences with synthetic peptides. Alanine-scanning identified several residues critical to binding in the linear peptide. The linear peptide could be used for p24 detection in ELISA and LFAs.
Conclusion: Phage-displayed combinatorial peptide libraries are suitable for isolation of binders against p24 and potentially other targets. Upon identification of a minimal binding sequence, the subsequent characterization and future optimization of it can lead to a variety of diagnostic assays.

Keywords:  Combinatorial peptides; HIV; Phage display; p24 capsid protein

DOI:  https://doi.org/10.1007/s10989-025-10696-0
Life Sci Alliance. 2025 May;pii: e202201490. [Epub ahead of print]8(5):

Screening of homing and tissue-penetrating peptides by microdialysis and in vivo phage display.

Toini Pemmari, Stuart Prince, Niklas Wiss, Kuldar Kõiv, Ulrike May, Tarmo Mölder, Aleksander Sudakov, Fernanda Munoz Caro, Soili Lehtonen, Hannele Uusitalo-Järvinen, Tambet Teesalu, Tero Ah Järvinen.

In vivo phage display is a method used for identification of organ- or disease-specific vascular homing peptides for targeted delivery of pharmaceutics. It is agnostic as to the nature and identity of the target molecules. The current in vivo biopanning lacks inbuilt mechanisms to select for peptides capable of vascular homing that would also be capable of tissue penetration to reach therapeutically relevant cells in the tissue parenchyma. Here, we combined in vivo phage display with microdialysis-based parenchymal recovery and high-throughput sequencing to select for peptides that, besides vascular homing, facilitate extravasation and tissue penetration. We first demonstrated in skin wounds that the method can selectively separate known homing peptides from those with additional tissue-penetrating ability. Screening of a naïve peptide library identifies peptides that home and extravasate to extravascular granulation tissue in vascularized and diabetic wounds and cross blood-retina barrier in retinopathy. Our work suggests that in vivo phage display combined with microdialysis can be used for the discovery of vascular homing peptides capable of extravasation and tissue penetration.

DOI: https://doi.org/10.26508/lsa.202201490
Mol Pharm. 2025 Feb 10.

A Site-Specific MiniAp4-Trastuzumab Conjugate Prevents Brain Metastasis.

Mariam Masmudi-Martín, Benjamí Oller-Salvia, María Perea, Meritxell Teixidó, Manuel Valiente, Ernest Giralt, Macarena Sánchez-Navarro.

  Monoclonal antibodies (mAbs) are changing cancer treatments. However, the presence of the blood-brain barrier (BBB) and the blood-tumor barrier (BTB) limits the use of mAbs to treat brain cancer or brain metastasis. Molecules that hijack endogenous transport mechanisms on the brain endothelium (brain shuttles) have been shown to increase the transport of large molecules and nanoparticles across the BBB. Among these shuttles, protease-resistant peptides such as MiniAp-4 are particularly efficient. Here, we report the synthesis, characterization, and evaluation of site-specific mAb-brainshuttle antibody conjugates (ASC) based on the anti-HER2 mAb trastuzumab (Tz) and four molecules of MiniAp-4. The ASCs preserve the binding and cell cycle arrest capacity of Tz. MiniAp-4 ASC displays enhanced transport across an in vitro BBB cellular model with respect to Tz and Tz conjugated to Angiopep-2, the brain shuttle that has advanced the most in clinical trials. More importantly, evaluation of Tz-MiniAp4 in a murine brain metastasis model demonstrated that the protease-resistant peptide showed preferential transport across the BBB/BTB, displaying a marked therapeutic effect and protecting against metastasis development. The technology described herein could be applied to any antibody of interest to treat central nervous system-related diseases. MiniAp-4 enhances the brain transport of the monoclonal antibody trastuzumab, preventing brain metastasis.

Keywords:  brain metastasis; brain shuttle peptide; trastuzumab

DOI:  https://doi.org/10.1021/acs.molpharmaceut.4c01091
Peptides. 2025 Feb 06. pii: S0196-9781(25)00015-4. [Epub ahead of print]185 171354

Peptide‑based therapeutic strategies for glioma: Current state and prospects.

Yajing Mi, Pengtao Jiang, Jing Luan, Lin Feng, Dian Zhang, Xingchun Gao.

  Glioma is a prevalent form of primary malignant central nervous system tumor, characterized by its cellular invasiveness, rapid growth, and the presence of the blood-brain barrier (BBB)/blood-brain tumor barrier (BBTB). Current therapeutic approaches, such as chemotherapy and radiotherapy, have shown limited efficacy in achieving significant antitumor effects. Therefore, there is an urgent demand for new treatments. Therapeutic peptides represent an innovative class of pharmaceutical agents with lower immunogenicity and toxicity. They are easily modifiable via chemical means and possess deep tissue penetration capabilities which reduce side effects and drug resistance. These unique pharmacokinetic characteristics make peptides a rapidly growing class of new therapeutics that have demonstrated significant progress in glioma treatment. This review outlines the efforts and accomplishments in peptide-based therapeutic strategies for glioma. These therapeutic peptides can be classified into four types based on their anti-tumor function: tumor-homing peptides, inhibitor/antagonist peptides targeting cell surface receptors, interference peptides, and peptide vaccines. Furthermore, we briefly summarize the results from clinical trials of therapeutic peptides in glioma, which shows that peptide-based therapeutic strategies exhibit great potential as multifunctional players in glioma therapy.

Keywords:  Blood-brain barrier; Glioma; Peptide vaccines; Peptide-based targeting therapy; Tumor-homing peptides

DOI:  https://doi.org/10.1016/j.peptides.2025.171354
Br J Pharmacol. 2025 Feb 12.

An optimised Bcl-3 inhibitor for melanoma treatment.

Karunakar Saamarthy, Renée Daams, Wondossen Sime, Cecilia Persson, Eduard Chygorin, Kristofer Ahlqvist, Susan Evans-Axelsson, Daniel Strand, Ramin Massoumi.

   BACKGROUND AND PURPOSE: Malignant melanoma is the most lethal form of skin cancer, characterised by a poor survival rate. One of the key factors driving the aggressive growth of melanoma cells is the elevated expression of the proto-oncogene Bcl-3. This study aims to optimise, evaluate and characterise a second-generation Bcl-3 inhibitor, using melanoma as a model to demonstrate its potential therapeutic efficacy.
EXPERIMENTAL APPROACH: We synthesised and screened a series of structural analogues and selected A27, the most promising candidate for further investigation. We assessed whether A27 disrupted the interaction between Bcl-3 and its binding partner, p50, and examined the subsequent effects on cyclin D1 expression. Additionally, we evaluated the impact of A27 on melanoma cell proliferation and migration in vitro, as well as its therapeutic efficacy in various in vivo melanoma models.
KEY RESULTS: Nuclear magnetic resonance (NMR) confirmed that A27 directly binds to Bcl-3, effectively inhibiting its function. By disrupting the Bcl-3/p50 interaction, A27 led to a significant down-regulation of cyclin D1 expression. In cellular assays, A27 markedly reduced proliferation and migration of melanoma cells. In vivo, treatment with A27 resulted in a substantial reduction in melanoma tumour growth, with no observed toxicity in treated animals.
CONCLUSIONS AND IMPLICATIONS: At present, no other Bcl-3 inhibitors exist for clinical application in the field of oncology, and as a result, our novel findings provide a unique opportunity to develop a highly specific drug against malignant melanoma to meet an urgent clinical need.

Keywords:  Bcl‐3; cell proliferation; cyclin D1; melanoma; metastasis

DOI:  https://doi.org/10.1111/bph.17467
Int J Mol Sci. 2025 Jan 22. pii: 889. [Epub ahead of print]26(3):

Look Beyond Plasma Membrane Biophysics: Revealing Considerable Variability of the Dipole Potential Between Plasma and Organelle Membranes of Living Cells.

Mate Szabo, Bence Cs Szabo, Kitti Kurtan, Zoltan Varga, Gyorgy Panyi, Peter Nagy, Florina Zakany, Tamas Kovacs.

  Due to the lack of measurement techniques suitable for examining compartments of intact, living cells, membrane biophysics is almost exclusively investigated in the plasma membrane despite the fact that its alterations in intracellular organelles may also contribute to disease pathogenesis. Here, we employ a novel, easy-to-use, confocal microscopy-based approach utilizing F66, an environment-sensitive fluorophore in combination with fluorescent organelle markers and quantitative image analysis to determine the magnitude of the molecular order-related dipole potential in the plasma membrane and intracellular organelles of various tumor and neural cell lines. Our comparative analysis demonstrates considerable intracellular variations of the dipole potential that may be large enough to modulate protein functions, with an inward decreasing gradient on the route of the secretory/endocytic pathway (plasma membrane >> lysosome > Golgi > endoplasmic reticulum), whereas mitochondrial membranes are characterized by a dipole potential slightly larger than that of lysosomes. Our approach is suitable and sensitive enough to quantify membrane biophysical properties selectively in intracellular compartments and their comparative analysis in intact, living cells, and, therefore, to identify the affected organelles and potential therapeutic targets in diseases associated with alterations in membrane lipid composition and thus biophysics such as tumors, metabolic, neurodegenerative, or lysosomal storage disorders.

Keywords:  Golgi; endoplasmic reticulum; fluorescence microscopy; intracellular organelles; lysosome; membrane biophysics; membrane dipole potential; mitochondrion

DOI:  https://doi.org/10.3390/ijms26030889
Mol Pharm. 2025 Feb 11.

Preliminary Study of a Novel 68Ga-Labeled Probe Targeting Neuropilin-1 for Tumor Diagnosis.

Shuyue Cai, Rui Tang, Jichen Yang, Manxuan Ge, Yuxuan Zhou, Quan Xie, Qingzhu Liu, Ling Qiu, Jianguo Lin.

  Neuropilin-1 (NRP-1), a transmembrane protein related to tumor progression and invasion, presents potential as a prospective biomarker for tumor diagnosis and therapy. Positron emission tomography (PET) is acknowledged as an ideal modality for accurately monitoring NRP-1 expression in vivo due to its superior sensitivity and resolution. In this study, a novel peptide-based PET imaging probe, [68Ga]Ga-DOTA-NEP, was successfully developed for specifically visualizing NRP-1 expression in tumors. The probe was prepared with a radiochemical yield (RCY) and radiochemical purity (RCP) greater than 95%, a molar activity of 13.28 ± 0.97 GBq/μmol, and a lipid-water partition coefficient (log P) of -2.20 ± 0.13. In vitro stability assay showed that the probe possessed sufficient stability for biological evaluation. The cellular uptake of the probe in U87 and A549 cells (4.91 ± 0.14 and 4.58 ± 0.40%AD) with high expression of NRP-1 was higher than that observed in NRP-1 negative cells HCT116 and NCI-H1299 (2.84 ± 0.23 and 1.76 ± 0.25%AD) at 1 h. In vivo PET imaging revealed that the maximum tumor uptake of the probe in U87 (7.20 ± 1.03%ID/mL) and A549 (5.90 ± 0.57%ID/mL) tumor-bearing mice was also markedly higher compared to that in HCT116 (3.09 ± 0.43%ID/mL) and NCI-H1299 (2.90 ± 0.70%ID/mL) tumor-bearing mice. Ex vivo analysis further confirmed the targeting specificity of the probe [68Ga]Ga-DOTA-NEP for NRP-1. These results suggest that [68Ga]Ga-DOTA-NEP could serve as a promising PET imaging probe for the diagnosis of NRP-1 positive tumors.

Keywords:  NRP-1; imaging probe; positron emission tomography (PET); tumor diagnosis

DOI:  https://doi.org/10.1021/acs.molpharmaceut.4c01406
ACS Appl Mater Interfaces. 2025 Feb 13.

Host Defense Peptide Mimics Synergize with Pt(IV) Prodrugs for Surmounting Cisplatin Resistance via Selective Cancer Membrane Disruption.

Anqi Shen, Xiangyong He, Shuo Tang, Yu Tao, Yuge Jiang, Song Gao, Linliang Deng, Taotian Wei, Miao Zhang, Rongfeng Hu, Yong-Ling Wang, Shengqi Chen.

  Drug resistance has emerged as a great challenge for achieving satisfactory therapeutic efficacy in platinum-based chemotherapy. Specifically, we synthesized a series of host defense peptide mimics with different degrees of polymerization (DP), i.e., poly(ethylene glycol)-poly(2-azepane ethyl methacrylate) (PEG45-PAEMAn, n = 8, 20, 43, 87, and 183), which displayed DP- and pH-dependent plasma membrane-disruptive capability and antitumor activity. Among these, PEG45-PAEMA43 exhibited the highest cytotoxicity at tumor acidity (pH 6.7), selectivity index, and in vivo antitumor activity, and was selected to encapsulate the hydrophobic Pt(IV) prodrug to form the PEG-PAEMA-Pt(IV) nanoprodrug. The nanoprodrug boosted the membrane-disruptive capability and antitumor activity of A549 and cisplatin-resistant A549/DDP cells at tumor acidity. Notably, it exhibited a much higher cellular uptake for A549/DDP cells and in vivo antitumor activity than PEG-PAEMA or cisplatin alone. This indicated that the PEG-PAEMA-Pt(IV) nanoprodrug could break the drug diffusion barrier posed by the cell membrane and disable even reverse efflux resistance.

Keywords:  Pt(IV) nanoprodrug; cisplatin resistance; host defense peptide mimics; stimuli responsiveness; transmembrane diffusion barrier

DOI:  https://doi.org/10.1021/acsami.4c21448
J Mol Biol. 2025 Feb 08. pii: S0022-2836(25)00049-X. [Epub ahead of print] 168983

Masked Graph Transformer for Blood-Brain Barrier Permeability Prediction.

Tuan Vinh, Phuc H Le, Binh P Nguyen, Thanh-Hoang Nguyen-Vo.

  The blood-brain barrier (BBB) is a highly protective structure that strictly regulates the passage of molecules, ensuring the central nervous system remains free from harmful chemicals and maintains brain homeostasis. Since most compounds cannot easily cross the BBB, assessing the blood-brain barrier permeability (BBBP) of drug candidates is critical in drug discovery. While several computational methods have been developed to screen BBBP with promising results, these approaches have limitations that affect their predictive power. In this study, we constructed classification models for screening the BBBP of molecules. Our models were trained with chemical data featurized by a Masked Graph Transformer-based Pretrained (MGTP) encoder. The molecular encoder was designed to generate molecular features for various downstream tasks. The training of the MGTP encoder was guided by masked attention-based learning, improving the model's generalization in encoding molecular structures. The results showed that classification models developed using MGTP features had outperformed those using other representations in 6 out of 8 cases, demonstrating the effectiveness of the proposed encoder. Also, chemical diversity analysis confirmed the encoder's ability to effectively distinguish between different classes of molecules.

Keywords:  attention; blood-brain barrier; deep learning; masked graph; molecular encoder; transformer

DOI:  https://doi.org/10.1016/j.jmb.2025.168983
J Nat Prod. 2025 Feb 13.

Cyclic Peptide Natural Product Inspired Inhibitors of the Free-Living Amoeba Balamuthia mandrillaris.

Chenyang Lu, Samantha Nelson, Gabriela Coy, Chris Neumann, Elizabeth I Parkinson, Christopher A Rice.

Balamuthia mandrillaris is a pathogenic free-living amoeba (pFLA) that can cause infection of the central nervous system (CNS), called Balamuthia amoebic encephalitis (BAE), as well as cutaneous and systemic diseases. Patients infected with B. mandrillaris have a high mortality rate due to a lack of effective treatments. A nonoptimized antimicrobial drug regimen is typically recommended; however, it has poor antiparasitic activity and can cause various and severe side effects. Cyclic peptides exhibit a broad spectrum of antimicrobial activities but are underexplored for their antiamoebic activity. In this study, we evaluated the anti-B. mandrillaris effect of Synthetic Natural Product Inspired Cyclic Peptides (SNaPP) mined from ∼500 biosynthetic gene clusters of various bacterial species. The predicted natural product-43 (pNP-43; BICyP1), identified from the SNaPP library, and its derivates displayed a significant inhibition against B. mandrillaris trophozoites, with five pNPs having IC50s ≤ 5 μM. Furthermore, all hit natural product inspired peptides demonstrated minimal to no hemolytic and cytotoxic effects on human red blood cells (RBCs) and immortalized human carcinoma cells, respectfully. Our study is the first to demonstrate the anti-B. mandrillaris effects of cyclic peptides, offering a promising new direction for drug development.

DOI: https://doi.org/10.1021/acs.jnatprod.4c00834