bims-cepepe 2025-04-06 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–04–06
eleven papers selected by
Henry Lamb, Queensland University of Technology

Diversity Scale of Library Matters: Impact of mRNA Library Diversity Scales on the Discovery of Macrocyclic Peptides Targeting a Protein by the RaPID System.
Peptide-functionalized nanoparticles for brain-targeted therapeutics.
In Silico Design of Foldable Lasso Peptides.
Design, synthesis, and antitumor activity of stapled peptide inhibitors targeting the RAS-RAF interactions.
Refining the NaV1.7 pharmacophore of a class of venom-derived peptide inhibitors via a combination of in silico screening and rational engineering.
PepH3-modified nanocarriers for delivery of therapeutics across the blood-brain barrier.
Antibody-Free Immunopeptide Nano-Conjugates for Brain-Targeted Drug Delivery in Glioblastoma Multiforme.
Selection of MDM2-binding peptides in Escherichia coli using an engineered split intein and aminoglycoside phosphotransferase.
Precision peptide disruptors: The next generation of targeted therapeutics in oncology.
Devices to overcome the buccal mucosal barrier to administer Therapeutic Peptides.
Broadening the Therapeutic Window of ADCs Using Site-Specific Bioconjugation Showcased by an MMAE-Containing Peptide Linker in a CD79b-Targeting ADC.

ACS Cent Sci. 2025 Mar 26. 11(3): 431-440

Diversity Scale of Library Matters: Impact of mRNA Library Diversity Scales on the Discovery of Macrocyclic Peptides Targeting a Protein by the RaPID System.

Jinxuan Zhao, Yi Li, Naohiro Terasaka, Haruo Aikawa, Hiroaki Suga.

Macrocyclic peptides make up a unique class of modalities known for their high affinity, specificity, and ability to modulate protein-protein interactions, including receptor activation. Messenger RNA display, including the Random Nonstandard Peptides Integrated Discovery (RaPID) system, stands out in identifying target-specific macrocyclic peptides, producing potent binders with low to subnanomolar dissociation constants against diverse targets. It has often been discussed that this success is partly attributed to the vast library of over a trillion different peptide sequences expressed from the corresponding mRNA sequences. However, the impact of library scales on the identification of various binders has not been experimentally validated. Here, we report the RaPID selections against an ectodomain of a receptor tyrosine kinase MET using peptide libraries ranging from 106 to 1014 unique members of mRNAs. We thoroughly analyzed the outcomes, including the binding kinetic properties, of the enriched peptide families. This study provides valuable guidelines for designing libraries with various numbers of sequences and selection conditions to enrich macrocyclic peptides with the desired characteristics.

DOI: https://doi.org/10.1021/acscentsci.4c01021
Drug Deliv Transl Res. 2025 Mar 31.

Peptide-functionalized nanoparticles for brain-targeted therapeutics.

Sophia Tang, Emily L Han, Michael J Mitchell.

  Despite the rapid development of nanoparticle (NP)-based drug delivery systems, intravenous delivery of drugs to the brain remains a major challenge due to various biological barriers. To achieve therapeutic effects, NP-encapsulated drugs must avoid accumulation in off-target organs and selectively deliver to the brain, successfully cross the blood-brain barrier (BBB), and reach the target cells in the brain. Conjugating receptor-specific ligands to the surface of NPs is a promising technique for engineering NPs to overcome these barriers. Specifically, peptides as brain-targeting ligands have been of increasing interest given their ease of synthesis, low cytotoxicity, and strong affinity to target proteins. The success of peptides as targeting ligands is largely due to the diverse strategies of designing and modifying peptides with favorable properties, including membrane permeability and multi-receptor targeting. Here, we review the design and implementation of peptide-functionalized NP systems for neurological disease applications. We also explore advances in rational peptide design strategies for brain targeting, including using generative deep-learning models to computationally design new peptides.

Keywords:  Blood–Brain Barrier; Drug Delivery; Nanoparticles; Peptides

DOI:  https://doi.org/10.1007/s13346-025-01840-w
Biophys J. 2025 Apr 03. pii: S0006-3495(25)00210-3. [Epub ahead of print]

In Silico Design of Foldable Lasso Peptides.

John D M Nguyen, Gabriel C A da Hora, Marcus C Mifflin, Andrew G Roberts, Jessica M J Swanson.

Lasso peptides are a unique class of natural products with distinctively threaded structures, conferring exceptional stability against thermal and proteolytic degradation. Despite their promising biotechnological and pharmaceutical applications, reported attempts to prepare them by chemical synthesis result in forming the nonthreaded branched-cyclic isomer, rather than the desired lassoed structure. This is likely due to the entropic challenge of folding a short, threaded motif prior to chemically mediated cyclization. Accordingly, this study aims to better understand and enhance the relative stability of pre-lasso conformations-the essential precursor to lasso peptide formation-through sequence optimization, chemical modification, and disulfide incorporation. Using Rosetta fixed backbone design, optimal sequences for several class II lasso peptides are identified. Enhanced sampling with well-tempered metadynamics confirmed that designed sequences derived from the lasso structures of rubrivinodin and microcin J25 exhibit a notable improvement in pre-lasso stability relative to the competing nonthreaded conformations. Chemical modifications to the isopeptide bond-forming residues of microcin J25 further increase the probability of pre-lasso formation, highlighting the beneficial role of non-canonical amino acid residues. Counterintuitively, the introduction of a disulfide cross-link decreased pre-lasso stability. Although cross-linking inherently constrains the peptide structure, decreasing the entropic dominance of unfolded phase space, it hinders the requisite wrapping of the N-terminal end around the tail to adopt the pre-lasso conformation. However, combining chemical modifications with the disulfide cross-link results in further pre-lasso stabilization, indicating that the ring modifications counteract the constraints and provide a cooperative benefit with cross-linking. These findings lay the groundwork for further design efforts to enable synthetic access to the lasso peptide scaffold.

DOI: https://doi.org/10.1016/j.bpj.2025.03.036
Eur J Med Chem. 2025 Mar 24. pii: S0223-5234(25)00333-2. [Epub ahead of print]290 117568

Design, synthesis, and antitumor activity of stapled peptide inhibitors targeting the RAS-RAF interactions.

Dan Han, Zhou Yu, Kai Zhang, Conghao Gai, Peichao Zhang, Xiaoyun Chai, Xiaobing Zhuo, Qingjie Zhao, Yan Zou, Lie Zhu.

  RAS-RAF interactions play a vital role in the RAS-RAF-MEK-ERK signaling pathway, significantly regulating cell proliferation, differentiation, and survival. Some small molecule inhibitors targeting various components of this pathway, such as MRTX849 and AMG 510, have been introduced for clinical application. However, peptide-based drugs encounter several challenges, such as poor cell permeability, low biological stability, and rapid in vivo clearance, which hinder their application. Herein, based on co-crystal complex structures and RAS-RAF interaction hotspots, we identified four linear peptides-Raf-0 to Raf-2 and CRD-0-derived from the α-helical regions of the RAS-binding domain (RBD) and the cysteine-rich domain (CRD) of CRAF. Raf-1 was selected for further modification using a hydrocarbon stapling strategy, capping it with stearic acid at the N-terminal due to its highest binding affinity in the SPR assay. As a result, Sraf-2-1 and Sraf-7-1 bound to KRASG12C with Kd values of 3.56 μM and 2.62 μM, respectively, demonstrating robust anticancer activity in the CCK8 assay. Additionally, Sraf-2-1 and Sraf-7-1 reduced AKT phosphorylation, induced cancer cell apoptosis in a concentration-dependent manner, and effectively inhibited cancer cell migration, showing improved α-helix stability and cell permeability. In summary, our findings indicate that the hydrocarbon stapling strategy and stearic acid tagging enhanced the therapeutic potential of peptide inhibitors, offering methods for targeting RAS in cancer therapy.

Keywords:  AKT; Antitumor; RAS-RAF interactions; Stapled peptides

DOI:  https://doi.org/10.1016/j.ejmech.2025.117568
FEBS Lett. 2025 Mar 29.

Refining the NaV1.7 pharmacophore of a class of venom-derived peptide inhibitors via a combination of in silico screening and rational engineering.

Gagan Sharma, Jennifer R Deuis, Xinying Jia, Theo Crawford, Sassan Rahnama, Eivind A B Undheim, Irina Vetter, Yanni K-Y Chin, Mehdi Mobli.

  Ion channels are among the main targets of venom peptides. Extensive functional screening has identified a number of these peptides as modulators of the voltage-gated sodium channel subtype NaV1.7, a potential target for the treatment of chronic pain. In this study, we used a bioinformatic approach that can automatically identify NaV1.7 gating modifier toxins from sequence information alone. The method further enables the incorporation of evolutionarily accessible sequence space in structure-activity relationship studies. The in silico method identified a putative NaV1.7 inhibitor, μ-theraphotoxin Cg4a, which we produced recombinantly and confirmed as a NaV1.7 inhibitor. Using structural and mutagenesis studies, we propose an improved definition of the pharmacophore of this class of NaV1.7 inhibitors, aiding future in silico screening and classification of NaV1.7 inhibitors.

Keywords:  NaV1.7; pain; peptide structure; venom peptides; voltage‐gated sodium channels

DOI:  https://doi.org/10.1002/1873-3468.70036
Fluids Barriers CNS. 2025 Apr 01. 22(1): 31

PepH3-modified nanocarriers for delivery of therapeutics across the blood-brain barrier.

Anikó Szecskó, Mária Mészáros, Beatriz Simões, Marco Cavaco, Catarina Chaparro, Gergő Porkoláb, Miguel A R B Castanho, Mária A Deli, Vera Neves, Szilvia Veszelka.

   BACKGROUND: Nanocarriers targeting the blood-brain barrier (BBB) are promising drug delivery systems to enhance the penetration of therapeutic molecules into the brain. Immunotherapy, particularly monoclonal antibodies designed to bind amyloid-beta peptides have become a promising strategy for Alzheimer's disease, but ensuring efficacy and safety is challenging and crucial for these therapies. Our aim was to develop an innovative nanocarriers conjugated with PepH3, a cationic peptide derived from Dengue virus type-2 capsid protein that crosses the BBB and acts as a shuttle peptide for the encapsulated single domain antibody (sdAb) recognizing Aβ oligomers.
RESULTS: PepH3 peptide enhanced the uptake of the nanoparticles (NPs) into brain endothelial cells, and transcytosis of sdAb, as a potential therapeutic molecule, across both rat and human BBB culture models. The cargo uptake was a temperature dependent active process that was reduced by metabolic and endocytosis inhibitors. The cellular uptake of the cationic PepH3-tagged NPs decreased when the negative surface charge of brain endothelial cells became more positive after treatments with a cationic lipid or with neuraminidase by digesting the glycocalyx. The NPs colocalized mostly with endoplasmic reticulum and Golgi apparatus and not with lysosomes, indicating the cargo may avoid cellular degradation.
CONCLUSIONS: Our results support that combination of NPs with a potential brain shuttle peptide such as PepH3 peptide can improve the delivery of antibody fragments across the BBB.

Keywords:  Blood-brain barrier; Brain delivery; Nanoparticle; PepH3; Single domain antibody

DOI:  https://doi.org/10.1186/s12987-025-00641-0
bioRxiv. 2025 Mar 12. pii: 2025.03.07.641755. [Epub ahead of print]

Antibody-Free Immunopeptide Nano-Conjugates for Brain-Targeted Drug Delivery in Glioblastoma Multiforme.

Saurabh Sharma, David Lee, Surjendu Maity, Prabhjeet Singh, Jay Chadokiya, Neda Mohaghegh, Alireza Hassani, Hanjun Kim, Ankit Gangarade, Julia Y Ljubimova, Amanda Kirane, Eggehard Holler.

  Glioblastoma Multiforme (GBM) represents a significant clinical challenge amongst central nervous system (CNS) tumors, with a dismal mean survival rate of less than 8 months, a statistic that has remained largely unchanged for decades (National Brain Society, 2022). The specialized intricate anatomical features of the brain, notably the blood-brain barrier (BBB), pose significant challenges to effective therapeutic interventions, limiting the potential reach of modern advancements in immunotherapy to impact these types of tumors. This study introduces an innovative, actively targeted immunotherapeutic nanoconjugate (P12/AP-2/NCs) designed to serve as an immunotherapeutic agent capable of traversing the BBB via LRP-1 receptor-mediated transcytosis. P12/AP-2/NCs exert its immune-modulating effects by inhibiting the PD-1/PD-L1 axis through a small-size PD-L1/PD-L2 antagonist peptide Aurigene NP-12 (P12). P12/AP-2/NCs are synthesized from completely biodegradable, functionalized high molecular weight β-poly(L-malic acid) (PMLA) polymer, conjugated with P12 and Angiopep-2 (AP2) to yield P12/AP-2/NCs. Evaluating nanoconjugates for BBB permeability and 3-D tumor model efficacy using an in vitro BBB-Transwell spheroid based model demonstrating successful crossing of the BBB and internalization in brain 3D tumor environments. In addition, the nanoconjugate mediated T cell's cytotoxicity on 3D tumor region death in a U87 GBM 3-D spheroid model. AP2/P12/NCs is selectively inhibited in PD1/PDL1 interaction on T cells and tumor site, increasing inflammatory cytokine secretion and T cell proliferation. In an in-vivo murine brain environment, rhodamine fluorophore-labeled AP2/P12/NCs displayed significantly increased accumulation in the brain during 2-6 h time intervals post-injection with a prolonged bioavailability over unconjugated peptides. AP2/P12/NCs demonstrated a safety profile at both low and high doses based on major organ histopathology evaluations. Our findings introduce a novel, programmable nanoconjugate platform capable of penetrating the BBB for directed delivery of small peptides and significant immune environment modulation without utilizing antibodies, offering promise for treating challenging brain diseases like glioblastoma multiforme and beyond.

Keywords:  3D Tumor-BBB Model; Biodistribution; Immunotherapy; Nanoconjugate

DOI:  https://doi.org/10.1101/2025.03.07.641755
Chem Commun (Camb). 2025 Apr 01.

Selection of MDM2-binding peptides in Escherichia coli using an engineered split intein and aminoglycoside phosphotransferase.

Yutaro Watanabe, Chiori Tezuka, Kana Nobusawa, Tsuyoshi Takahashi.

A protein trans-splicing (PTS)-based method for screening the peptides capable of binding to a target protein was developed using an engineered split intein and an aminoglycoside phosphotransferase. Two peptides selected against MDM2 bind to MDM2 with high affinity and a peptide can induce apoptosis in SJSA-1 cells.

DOI: https://doi.org/10.1039/d4cc06138a
Cell Signal. 2025 Apr 01. pii: S0898-6568(25)00196-2. [Epub ahead of print]132 111783

Precision peptide disruptors: The next generation of targeted therapeutics in oncology.

Bria O'Gorman, Sean F Cooke, Connor M Blair.

  Therapeutically targeting the pathologically remodelled protein-protein interaction network in cancer with peptide disruptors increasingly represents a clinically attractive approach to treating recalcitrant cancers. In this review, we map the pre-clinical and clinical-stage peptide disruptor landscape within an oncology-specific context and discuss key clinical examples that are making significant impact to patients; demonstrating a key role for peptide disruptors in precision medicine as a next-generation targeted therapeutic.

Keywords:  Oncology; Peptide disruptors; Precision medicine; Protein-protein interactions

DOI:  https://doi.org/10.1016/j.cellsig.2025.111783
Adv Drug Deliv Rev. 2025 Mar 31. pii: S0169-409X(25)00057-2. [Epub ahead of print] 115572

Devices to overcome the buccal mucosal barrier to administer Therapeutic Peptides.

Sahil Malhotra, Thomas Lijnse, Eoin O' Cearbhaill, David J Brayden.

  Peptide therapeutics are important in healthcare owing to their high target specificity, therapeutic efficacy, and relatively low side effect profile. Injections of these agents have improved thetreatment of chronic diseases including autoimmune, metabolic disorders, and cancer. However, their administration via injections can prove a barrier to patient acceptability of treatments. While oral delivery of these molecules is preferable, oral peptide formulations are associated with limited bioavailability due to degradation in the intestine and low epithelial permeability. Buccal administration of peptides is a potential alternative to injections and oral formulations. Similar to the oral route, the buccal route can promote better patient adherence to dosing regimens, along with the added advantages of not requiring restriction on food or drink consumption before and after administration, as well as avoidance of the liver first-pass metabolism. However, like oral, effective buccal absorption of peptides is still challenging due to the high epithelial permeability barrier. We present a multidisciplinary approach to understanding the buccal physiological barrier to macromolecule permeation and discuss how engineered devices may overcome it. Selected examples of buccal devices can facilitate fast and efficient macromolecule absorption through multiple mechanisms including physical disruption of epithelia, convection-based mass transfer, and a combination of physicochemical strategies. Importantly, minimally invasive devices can be self-applied and are associated with the maintenance of the barrier after exposure. We analysed the critical attributes that are required forthe clinical translation of buccal peptide administration devices. These include performance-driven device development, manufacturing features, patient acceptability, and commercial viability.

Keywords:  Bioinspired suction patch; Buccal peptide delivery; Buccal peptide permeability; Microneedles; Needle-free jet injectors; Oromucosal drug administration

DOI:  https://doi.org/10.1016/j.addr.2025.115572
Mol Cancer Ther. 2025 Apr 03. OF1-OF13

Broadening the Therapeutic Window of ADCs Using Site-Specific Bioconjugation Showcased by an MMAE-Containing Peptide Linker in a CD79b-Targeting ADC.

Philipp Probst, Isabella Attinger-Toller, Romain Bertrand, Ramona Stark, Roger Santimaria, Bernd Schlereth, Dragan Grabulovski, Philipp René Spycher.

The limitations of first-generation antibody-drug conjugate (ADC) technologies include suboptimal stability and efficacy, poor safety profiles, and challenging manufacturing processes. In this study, we describe an anti-CD79b-monomethyl auristatin E (MMAE) ADC generated using a novel peptide-based linker technology that allows for site-specific linker-payload conjugation to native antibodies in only one step. The ADC comprises native polatuzumab as the targeting antibody and a linker-payload consisting of a RKAA-peptide linker and MMAE. We compared our anti-CD79b-RKAA-MMAE ADC with polatuzumab vedotin (PV), the FDA-approved ADC for diffuse large B-cell lymphoma. In the clinic, PV shows significant instability in circulation, leading to strong and dose-limiting side effects, including neutropenia and peripheral neuropathy. The anti-CD79b-RKAA-MMAE ADC showed optimal biophysical properties with a well-defined drug-to-antibody ratio of 2. It demonstrated potent cytotoxicity in multiple cancer cell lines and was very stable in mouse, cynomolgus monkey, and human sera. The anti-CD79b-RKAA-MMAE conjugate showed equal antitumor efficacy at half the payload dose compared with PV in different xenograft models. At equal MMAE concentrations, greater tumor growth inhibition and a considerably longer duration of response were observed. Ultimately, the highest nonseverely toxic dose of 30 mg/kg was determined in a 4-week repeat-dose toxicology study in rats, which is a 3-fold higher ADC dose than reported for PV. In summary, the data show that our novel site-specific bioconjugation technology enabled the generation of an anti-CD79b-RKAA-MMAE ADC with highly favorable biophysical properties and a greatly improved therapeutic index by a factor of 4 to 6 compared with PV. The ADC may therefore represent a safe and efficacious alternative for patients with diffuse large B-cell lymphoma.

DOI: https://doi.org/10.1158/1535-7163.MCT-24-0983