bims-cepepe 2025-04-27 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–04–27
eleven papers selected by
Henry Lamb, Queensland University of Technology

Macrocyclic Peptide Probes for Immunomodulatory Protein CD59: Potent Modulators of Bacterial Toxin Activity and Antibody-Dependent Cytotoxicity.
NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation.
Heterophyllin B: Combining Isotropic and Anisotropic NMR for the Conformational Analysis of a Natural Occurring Cyclic Peptide.
Cyclization of the Analgesic α-Conotoxin Vc1.1 With a Non-Natural Linker: Effects on Structure, Stability, and Bioactivity.
Structure of a lasso peptide bound ETB receptor provides insights into the mechanism of GPCR inverse agonism.
Current progress and remaining challenges of peptide-drug conjugates (PDCs): next generation of antibody-drug conjugates (ADCs)?
An Orthogonal Protection Strategy for the Synthesis of Conotoxins Containing Three Disulfide Bonds.
Structural characterisation of a cysteine-rich conotoxin, sigma(σ)S-GVIIIA, extracted from the defensive venom of the marine cone snail Conus geographus.
Computer aided design of CGA-N9 derived peptides based on oligopeptide transporters and their antifungal evaluations.
Microstructure of Sea Cucumber Parastichopus tremulus Peptide Hydrogels and Bioactivity in Caco-2 Cell Culture Model.
A rationale approach in developing proline based small peptide as U-shaped analogues of arachidonic acid: Dual inhibitors of cyclooxygenase-2 and 5-lipoxygenase for developing anti-inflammatory agents.

Angew Chem Int Ed Engl. 2025 Apr 24. e202422673

Macrocyclic Peptide Probes for Immunomodulatory Protein CD59: Potent Modulators of Bacterial Toxin Activity and Antibody-Dependent Cytotoxicity.

Edward William Tate, Jasmine K Bickel, Ammar I S Ahmed, Aidan B Pidd, Rhodri M Morgan, Tom E McAllister, Sam M Horrell, Emma C Couves, Hemavathi Nagaraj, Edward J Bartlett, Kamel El Omari, Akane Kawamura, Doryen Bubeck.

  CD59 is an immunomodulatory cell surface receptor associated with human disease. Despite its importance in complement regulation and bacterial pathogenesis, CD59 remains a challenging therapeutic target. Research to date has focused on antibody or protein-based strategies. Here we present a new approach to target CD59 using macrocyclic peptides with low nanomolar affinity for CD59. Through X-ray crystallographic studies and structure-activity relationship studies we identify key interactions which are essential for binding and activity. We find that the macrocyclic peptide CP-06 adopts a beta-hairpin structure and binds CD59 through an intermolecular beta-sheet, mimicking protein-protein interactions of biologically relevant CD59 interaction partners. We create dimeric and lipidated macrocyclic peptide conjugates as enhanced cell-active CD59 inhibitors and show that these probes can be used to modulate both complement-mediated killing of human cells and lytic activity of bacterial virulence factors. Together, our data provide a starting point for future development of macrocyclic peptides to target CD59 activity in diverse cellular contexts.

Keywords:  cell-surface receptors; macrocyclic peptides; membrane attack complex; protein-protein interaction inhibitors; structure-guided design

DOI:  https://doi.org/10.1002/anie.202422673
J Chem Theory Comput. 2025 Apr 21.

NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation.

Qingyi Mao, Tianfeng Shang, Wen Xu, Silong Zhai, Chengyun Zhang, Jingjing Guo, An Su, Chengxi Li, Hongliang Duan.

Artificial intelligence-based peptide structure prediction methods have revolutionized biomolecular science. However, restricting predictions to peptides composed solely of 20 natural amino acids significantly limits their practical application; as such, peptides often demonstrate poor stability under physiological conditions. Here, we present NCPepFold, a computational approach that can utilize a specific cyclic position matrix to directly predict the structure of cyclic peptides with noncanonical amino acids. By integrating multigranularity information at the residual and atomic level, along with fine-tuning techniques, NCPepFold significantly improves prediction accuracy, with the average peptide root-mean-square deviation (RMSD) for cyclic peptides being 1.640 Å. In summary, this is a novel deep learning model designed specifically for cyclic peptides with noncanonical amino acids, offering great potential for peptide drug design and advancing biomedical research.

DOI: https://doi.org/10.1021/acs.jctc.5c00139
Magn Reson Chem. 2025 Apr 20.

Heterophyllin B: Combining Isotropic and Anisotropic NMR for the Conformational Analysis of a Natural Occurring Cyclic Peptide.

Anton F Ketzel, Yang Hu, Xiao-Lu Li, Jiaqian Li, Xinxiang Lei, Han Sun.

  Heterophyllin B is a natural occurring cyclic peptide with diverse attributed bioactivities. NMR-based conformational analysis of cyclic peptides often poses a challenge due to limited isotropic solution-state NMR data. In this study, we combined isotropic and anisotropic NMR observables including J-coupling, NOEs, amide proton temperature coefficients, and residual dipolar couplings (RDCs), which enabled the determination of a minimal conformational ensemble of heterophyllin B in methanol at density functional theory (DFT) accuracy. For conformational sampling of a cyclic peptide with a high degree of conformational freedom, we proposed a computational strategy that combines the Conformer-Rotamer Ensemble Sampling Tool (CREST) with the Commandline Energetic SOrting (CENSO). This combined computational and NMR-based approach offers a robust framework for the conformational analysis of cyclic peptides.

Keywords:  CENSO; CREST; DFT; NMR; RCSA; RDC; anisotropic NMR; conformational analysis; cyclic peptide

DOI:  https://doi.org/10.1002/mrc.5523
J Pept Sci. 2025 Jun;31(6): e70017

Cyclization of the Analgesic α-Conotoxin Vc1.1 With a Non-Natural Linker: Effects on Structure, Stability, and Bioactivity.

Yuhui Zhang, Han Shen Tae, David J Adams, Thomas Durek, David J Craik.

  α-Conotoxin Vc1.1 is a disulfide-rich peptide and a promising drug candidate for treating neuropathic and chronic pain. Backbone cyclization was applied to enhance its drug-like properties, resulting in improved serum stability and oral bioavailability. However, this modification also adversely affected its stability and activity in simulated intestinal fluid (SIF). To address these adverse effects, we explored the use of polyethylene glycol (PEG) linkers as substitutes for peptide backbone cyclization linkers. PEG linkers are smaller, more flexible, and more stable than peptide linkers. Furthermore, previous studies have demonstrated that PEG backbone linkers can enhance the activity of conotoxins. In this study, we synthesized four PEG-backboned cyclic Vc1.1 (cVc1.1) analogues with varying lengths of PEG linkers and used a chemo-enzymatic method to cyclize these analogues. Their structure, stability, and activity were subsequently evaluated. Although the results revealed that PEG linkers preserved the SIF stability and activity of cVc1.1, they highlighted the crucial role of the peptide's helical structure in maintaining its stability and activity. Additionally, this work introduces a novel approach for synthesizing cyclic conotoxins.

Keywords:  PEG linker; conotoxin; helicity; nicotinic acetylcholine receptor

DOI:  https://doi.org/10.1002/psc.70017
Nat Commun. 2025 Apr 22. 16(1): 3446

Structure of a lasso peptide bound ETB receptor provides insights into the mechanism of GPCR inverse agonism.

Wataru Shihoya, Hiroaki Akasaka, Peter A Jordan, Anna Lechner, Bethany K Okada, Gabriella Costa Machado da Cruz, Fumiya K Sano, Tatsuki Tanaka, Ryo Kawahara, Rajan Chaudhari, Hiroko Masamune, Mark J Burk, Osamu Nureki.

Lasso peptides exhibit a unique lariat-like knotted structure imparting exceptional stability and thus show promise as therapeutic agents that target cell-surface receptors. One such receptor is the human endothelin type B receptor (ETB), which is implicated in challenging cancers with poor immunotherapy responsiveness. The Streptomyces-derived lasso peptide, RES-701-3, is a selective inhibitor for ETB and a compelling candidate for therapeutic development. However, meager production from a genetically recalcitrant host has limited further structure-activity relationship studies of this potent inhibitor. Here, we report cryo-electron microscopy structures of ETB receptor in both its apo form and complex with RES-701-3, facilitated by a calcineurin-fusion strategy. Hydrophobic interactions between RES-701-3 and the transmembrane region of the receptor, especially involving two tryptophan residues, play a crucial role in RES-701-3 binding. Furthermore, RES-701-3 prevents conformational changes associated with G-protein coupling, explaining its inverse agonist activity. A comparative analysis with other lasso peptides and their target proteins highlights the potential of lasso peptides as precise drug candidates for G-protein-coupled receptors. This structural insight into RES-701-3 binding to ETB receptor offers valuable information for the development of novel therapeutics targeting this receptor and provides a broader understanding of lasso peptide interactions with human cell-surface receptors.

DOI: https://doi.org/10.1038/s41467-025-57960-x
J Nanobiotechnology. 2025 Apr 22. 23(1): 305

Current progress and remaining challenges of peptide-drug conjugates (PDCs): next generation of antibody-drug conjugates (ADCs)?

Dongyuan Wang, Feng Yin, Zigang Li, Yu Zhang, Chen Shi.

  Drug conjugates have emerged as a promising alternative delivery system designed to deliver an ultra-toxic payload directly to the target cancer cells, maximizing therapeutic efficacy while minimizing toxicity. Among these, antibody-drug conjugates (ADCs) have garnered significant attention from both academia and industry due to their great potential for cancer therapy. However, peptide-drug conjugates (PDCs) offer several advantages over ADCs, including more accessible industrial synthesis, versatile functionalization, high tissue penetration, and rapid clearance with low immunotoxicity. These factors position PDCs as up-and-coming drug candidates for future cancer therapy. Despite their potential, PDCs face challenges such as poor pharmacokinetic properties and low bioactivity, which hinder their clinical development. How to design PDCs to meet clinical needs is a big challenge and urgent to resolve. In this review, we first carefully analyzed the general consideration of successful PDC design learning from ADCs. Then, we summarised the basic functions of each component of a PDC construct, comprising of peptides, linkers and payloads. The peptides in PDCs were categorized into three types: tumor targeting peptides, cell penetrating peptide and self-assembling peptide. We then analyzed the potential of these peptides for drug delivery, such as overcoming drug resistance, controlling drug release and improving therapeutic efficacy with reduced non-specific toxicity. To better understand the potential druggability of PDCs, we discussed the pharmacokinetics of PDCs and also briefly introduced the current PDCs in clinical trials. Lastly, we discussed the future perspectives for the successful development of an oncology PDC. This review aimed to provide useful information for better construction of PDCs in future clinical applications.

Keywords:  Antibody drug conjugate; Clinical trials; Peptide drug conjugate; Pharmacokinetics; Targeted drug delivery

DOI:  https://doi.org/10.1186/s12951-025-03277-2
Mar Drugs. 2025 Apr 14. pii: 168. [Epub ahead of print]23(4):

An Orthogonal Protection Strategy for the Synthesis of Conotoxins Containing Three Disulfide Bonds.

Hengyu Zhang, Lai Yue Chan, Huanhuan Zhang, Tao Jiang, David J Craik, Wenqing Cai, Rilei Yu.

  Disulfide bonds are crucial for stabilizing bioactive peptides such as conotoxins. We have developed a method for synthesizing conotoxins with three disulfide bonds using Mob, Trt, and Acm protection groups for regionally selective synthesis. This approach enabled the efficient synthesis of peptides with the desired disulfide bond connectivities independent of their sequences. Using our strategy, we synthesized five conotoxins, achieving yields of 20-30%. The results demonstrate the potential of our method for synthesizing complex peptides with multiple disulfide bonds.

Keywords:  conotoxins; orthogonal oxidation method; three disulfide bonds

DOI:  https://doi.org/10.3390/md23040168
Biochem J. 2025 Apr 23. pii: BCJ20240753. [Epub ahead of print]

Structural characterisation of a cysteine-rich conotoxin, sigma(σ)S-GVIIIA, extracted from the defensive venom of the marine cone snail Conus geographus.

Yoshimi Peck, David Wilson, Danica Lennox-Bulow, Julien Giribaldi, Jamie Seymour, Sebastien Dutertre, K Rosengren, Michael Liddell, Norelle Daly.

  The activity of the serotonin type 3 (5-HT3) receptor is associated with neurodegenerative, inflammatory and metabolic diseases, neuropsychiatric disorders, and cancer. Structural analysis of modulators of this receptor is likely to aid in future medicinal chemistry studies aimed at developing lead molecules targeting this receptor. Here we report the structure of a cone snail venom peptide that was purified from the crude venom of Conus geographus and shown to be an antagonist of the 5-HT3 receptor more than 25 years ago, sigma(σ)GVIIIA. This lag in structural characterisation studies is likely due to challenges in isolating the native peptide and difficulties in producing synthetic peptide due to the presence of ten cysteine residues involved in five disulfide bonds. Using NMR spectroscopy, we show that σS-GVIIIA adopts a growth factor cystine knot (GFCK) fold. This is the first example of a cone snail venom peptide experimentally determined to contain the GFCK structural motif, and the first example of a 5-HT3 receptor antagonist containing this motif. Our study also highlights complexities in the use of artificial intelligence-based structure prediction models. Peptide structure predictions using AlphaFold 3 were consistent with our NMR structure when the input sequence contained the well-conserved precursor sequence, but inconsistent when the precursor sequence was excluded. AI-based structure prediction of proteins is a rapidly advancing field, but this inconsistency emphasises the need for more experimental structural training data when novel structures are involved, as was the case here for a cysteine-rich peptide.

Keywords:  AlphaFold; NMR spectroscopy; Nuclear Magnetic Resonance (NMR) spectroscopy; conotoxin; cysteine-rich peptide; growth factor cystine knot; growth factor cystine knot (GFCK)

DOI:  https://doi.org/10.1042/BCJ20240753
Bioorg Chem. 2025 Apr 16. pii: S0045-2068(25)00365-7. [Epub ahead of print]160 108485

Computer aided design of CGA-N9 derived peptides based on oligopeptide transporters and their antifungal evaluations.

Fu Yan, Yiqing Sun, Shaojie Zhang, Yifan Jia, Jinhua Zhang, Liang Huang, Qiang Xu, Yinzhi Zhang, Shihua Chen, Xingquan Wu, Ruifang Li.

  CGA-N9 is an antifungal peptide that primarily targets Candida spp. with a mild activity. Our preceding research confirmed that the CGA-N9 crosses cell membrane with the assistance of C. tropicalis oligopeptide transporter (CtOPT) -1 and - 9. In this study, CGA-N9-derived peptides were designed following the molecular docking results with CtOPT-1 and -9. Compared with CGAN9, they exhibit higher transmembrane efficiency with the assistance of CtOPT-1 during the early phase of transmembrane processes and CtOPT-9 in the late phase. And they displayed significantly enhanced antifungal activity, with lower minimum inhibitory concentrations (MICs) against C. tropicalis, C. albicans, and C. parapsilosis, as well as improved biosafety. Among them, CGAN93 was the most optimizing, with a therapeutic index of 145.33. Furthermore, in a mouse model of systemic candidiasis, CGAN93 demonstrated a therapeutic effect comparable to fluconazole, significantly improving the survival rate of mice, attenuating organ damage, and enhancing the immune organ index. In conclusion, OPTs-based computer aided design is an effective strategy for enhancing the activities of antimicrobial peptides (AMPs) by improving transmembrane transport efficiency. CGAN93 is a promising drug candidate for treating Candidiasis.

Keywords:  Antimicrobial activity; Antimicrobial peptide; Candida tropicalis oligopeptide transporter; Drug design; Molecular docking

DOI:  https://doi.org/10.1016/j.bioorg.2025.108485
Gels. 2025 Apr 08. pii: 280. [Epub ahead of print]11(4):

Microstructure of Sea Cucumber Parastichopus tremulus Peptide Hydrogels and Bioactivity in Caco-2 Cell Culture Model.

Miroslava Rossenova Atanassova, Jennifer Mildenberger, Marianne Doré Hansen, Tarmo Tamm.

  Wider availability of marine proteins for the development of food and biomedical applications has a high importance. Sea cucumber body wall proteins have specific functional properties that could be very promising for such product development. However, protein extraction from whole animals is costly and complex, whereas peptide hydrogel production using biotechnological methods can be considered an economically viable approach. Body-wall derived peptides from sea cucumber Parastichopus tremulus have been suggested as a nontraditional source of potentially edible hydrocolloids. In the current work, four peptides were produced through custom synthesis. Scanning electron microscopy (SEM) of the combined mix of the four peptides (1:1 ratio; 15 mM concentration) in a calcium ion-containing buffer confirmed untargeted self-assembly with long, thick fibrillar formations at a microscale (measured mean cross-section 2.78 µm and length sizes of 26.95 µm). The antioxidant activity of the peptides separately, and in combination (1:1 molar ratio), was studied in vitro through ORAC (values in the range from 279 to 543 µmol TE/g peptide), ABTS (from 80.4 to 1215 µmol TE/g peptide), and DPPH (from 5.2 to 19.9 µmol TE/g) assays, and confirmed for protection against oxidation in a Caco-2 cell culture model. Angiotensin-I converting enzyme inhibitory activity was also confirmed for two of the four peptides, with the highest IC 50 of 7.11 ± 0.84 mg/mL.

Keywords:  Caco-2; angiotensin-I converting enzyme inhibitory activity; antioxidant activity; de novo peptides; electron microscopy; hydrogel formation; microstructure; protection against oxidation in cell culture; sea cucumbers

DOI:  https://doi.org/10.3390/gels11040280
Bioorg Chem. 2025 Apr 12. pii: S0045-2068(25)00332-3. [Epub ahead of print]160 108452

A rationale approach in developing proline based small peptide as U-shaped analogues of arachidonic acid: Dual inhibitors of cyclooxygenase-2 and 5-lipoxygenase for developing anti-inflammatory agents.

Vivesh Vivesh, Priya Kumari, Palwinder Singh.

  Guided by the molecular modelling studies, here, we report the development of small molecules containing Pro-Pro, Gly-Pro-Pro ester motifs as dual inhibitors of COX-2 and 5-LOX enzymes. The synthesized compounds exhibited potent inhibitory activities against COX-2 and 5-LOX, with IC50 values in nanomolar range. Lineweaver-Burk plot analysis revealed that these molecules act as competitive inhibitors of COX-2 and 5-LOX. In vivo studies using the HET-CAM assay indicated that the compounds exhibit moderate to good anti-inflammatory effects. Hence, taking into account the physicochemical properties, including aqueous solubility, binding affinity to HSA and stability in blood plasma and liver microsomes, anti-inflammatory agents targeting dual pathways of arachidonic acid metabolism are identified.

Keywords:  Anti-inflammatory; Arachidonic acid pathway; Inflammation; Small peptides

DOI:  https://doi.org/10.1016/j.bioorg.2025.108452