bims-cepepe 2024-12-29 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2024–12–29
seven papers selected by
Henry Lamb, Queensland University of Technology

Facile preparation of sulfonium peptide and protein probes for selective crosslinking of methyllysine readers.
Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions.
Highly Efficient Transpeptidase-Catalyzed Isopeptide Ligation.
Cell-Permeable Peptide Inhibitors of the p53-hDM2 Interaction via Foldamer Helix Mimicry and Bis-Thioether Stapling.
vCPP2319 interacts with metastatic breast cancer extracellular vesicles (EVs) and transposes a human blood-brain barrier model.
Development of a Peptide-Based Tumor-Activated Checkpoint Inhibitor for Cancer Immunotherapy.
Generating a Peptide Library Using the Repeats of Amino Acid Scaffolds Created by Sliding the Framework of a 7-mer Human Chemerin Segment and Discovery of Potent Antibacterial and Antimycobacterial Peptides.

Chem Sci. 2024 Dec 12.

Facile preparation of sulfonium peptide and protein probes for selective crosslinking of methyllysine readers.

Kun Zou, Jinyu Yang, Yingxiao Gao, Feng Feng, Mingxuan Wu.

Sulfonium is an electrophilic and biocompatible group that is widely applied in synthetic chemistry on small molecules. However, there have been few developments of peptide or protein-based sulfonium tools. We recently reported sulfonium-mediated tryptophan crosslinking and developed NleS+me2 (norleucine-dimethylsulfonium) peptides as dimethyllysine mimics that crosslink site-specific methyllysine readers. Therefore, sulfonium probes show great potential for investigating methyllysine readers and other aromatic cage-containing proteins. However, the current synthesis is not very efficient and is limited to peptide probes that, in many cases, cannot mimic protein-protein interactions. In addition to peptidyl conjugates that are valuable for reader identification, there are unavoidable methyl conjugates as side products. As a result, a robust method to prepare peptide and protein sulfonium tools with great crosslinking reactivity and selectivity is highly desirable. Here, we report a cysteine alkylation method to introduce site-specific sulfonium at protein level with excellent yield. In addition to dimethylsulfonium, we also developed cyclic sulfonium warheads that enhanced peptidyl conjugate selectivity. The method thus made it possible to prepare nucleosome probes in which LEDGF and NSD2, as H3K36 methylation readers were readily crosslinked. We thus believe this method will accelerate the development of sulfonium peptide and protein tool sets for broad applications in chemical biology studies.

DOI: https://doi.org/10.1039/d4sc05886k
Angew Chem Int Ed Engl. 2024 Dec 23. e202416348

Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions.

Camille Perdriau, Anaïs Luton, Katharina Zimmeter, Maxime Neuville, Claire Saragaglia, Carole Peluso-Iltis, Judit Osz, Brice Kauffmann, Gavin W Collie, Natacha Rochel, Gilles Guichard, Morgane Pasco.

  Peptide stapling has emerged as a versatile approach in drug discovery to reinforce secondary structure elements especially α-helices and improve properties of linear bioactive peptides. Inspired by the prevalence of arginine in protein-protein and protein-DNA interfaces, we investigated guanidinium-stapling as a means to constrain helical peptides. Guanidinium stapling was readily achieved on solid support, utilizing two orthogonally protected lysine or unatural α-amino acid residues with an amino function. This method allows for easy modulation of the nature and size of the staple as well as helix propensity. Evaluating a set of guanidinium-stapled peptides for their interaction with different protein targets identified several binders with increased target affinity. X-ray structure determination of four complexes revealed that all stapled peptides adopt a helical conformation upon protein binding. Notably, the disubstituted guanidinium generally exhibits a distinct cis/trans conformation and, in one instance, retains a conserved hydrogen bond with the protein surface. By identifying, for the first time, the guanidinium moiety as an effective helical peptide stapling group, this research significantly expands the repertoire of α-helix stapling techniques for the creation of useful protein mimics.

Keywords:  Guanidinium; Helix; Protein-protein interaction; Stapled peptide; solid-phase synthesis

DOI:  https://doi.org/10.1002/anie.202416348
J Am Chem Soc. 2024 Dec 23.

Highly Efficient Transpeptidase-Catalyzed Isopeptide Ligation.

Simon J de Veer, David J Craik, Fabian B H Rehm.

Transpeptidases are specialized enzymes that have evolved for site-selective modification of peptides and proteins at their backbone termini. Approaches for adapting transpeptidases to catalyze side chain modifications are substantially more restricted, and typically rely on large recognition tags or require specific reaction conditions that are not easily compatible with broader applications. Here we show that the engineered asparaginyl ligase OaAEP1 catalyzes direct isopeptide ligation by accepting an internal 2,3-diaminopropionic acid (Dap) residue adjacent to Leu, a motif that mimics the canonical N-terminal Gly-Leu substrate. These reactions proceed efficiently at near-neutral pH without any required additives, enabling straightforward formation of diverse isopeptide-linked products under simple reaction conditions. We demonstrate that OaAEP1-catalyzed isopeptide ligation can be utilized for site-selective side chain labeling at an introduced Dap residue with minimal off-target labeling of Lys residues. Additionally, we generate engineered peptide topologies via intramolecular side chain-to-tail cross-links and produce direct protein-cyclic peptide fusions via efficient intermolecular ligation. We also show that OaAEP1-catalyzed isopeptide ligation extends to d-peptide acceptors containing a retro-inverso d-Leu-d-Dap motif. This capability further expands the range and complexity of isopeptide-linked products that can be accessed with OaAEP1, which we exemplify by forming a hybrid d-/l- bicyclic peptide topology where both termini are linked to internal side chains.

DOI: https://doi.org/10.1021/jacs.4c11964
J Med Chem. 2024 Dec 24.

Cell-Permeable Peptide Inhibitors of the p53-hDM2 Interaction via Foldamer Helix Mimicry and Bis-Thioether Stapling.

Maxime Neuville, Mathieu Bourgeais, Bo Li, Laetitia Varajao, François Hallé, Sébastien R Goudreau, Emmanuelle Thinon, Morgane Pasco, Abdel-Majid Khatib, Gilles Guichard.

Combining helical foldamers with α-peptides can produce α-helix mimetics with a reduced peptide character and enhanced resistance to proteolysis. Previously, we engineered a hybrid peptide-oligourea sequence replicating the N-terminal α-helical domain of p53 to achieve high affinity binding to hDM2. Here, we further advance this strategy by combining the foldamer approach with side chain cross-linking to create more constrained cell-permeable inhibitors capable of effectively engaging the target within cells. Starting from the crystal structure of the foldamer-hDM2 complex, we identified specific sites suitable for stapling, and generated a small library of macrocyclic foldamer-peptide hybrids. The most promising binders were subsequently optimized for cellular uptake and tested in a cellular assay. We observed that the introduction of a short segment of positively charged residues at the N-terminus of the sequence led to inhibitors that exhibited cytotoxic activity independently of p53. In contrast, neutral acetylated peptide-foldamer macrocycles demonstrated activity in a p53-dependent manner.

DOI: https://doi.org/10.1021/acs.jmedchem.4c01762
Heliyon. 2024 Dec 15. 10(23): e40907

vCPP2319 interacts with metastatic breast cancer extracellular vesicles (EVs) and transposes a human blood-brain barrier model.

Filipa D Oliveira, Marco Cavaco, Tiago N Figueira, Patrícia Napoleão, Javier Valle, Vera Neves, David Andreu, Miguel A R B Castanho.

  Brain metastases (BM) are frequently found in cancer patients and, though their precise incidence is difficult to estimate, there is evidence for a correlation between BM and specific primary cancers, such as lung, breast, and skin (melanoma). Among all these, breast cancer is the most frequently diagnosed among women and, in this case, BM cause a critical reduction of the overall survival (OS), especially in triple negative breast cancer (TNBC) patients. The main challenge of BM treatment is the impermeable nature of the blood-brain barrier (BBB), which shields the central nervous systems (CNS) from chemotherapeutic drugs. Extracellular vesicles (EVs) have been proposed as ideal natural drug carriers and these may exhibit some advantages over synthetic nanoparticles (NPs). In this work, we isolate breast cancer-derived EVs and study their ability to carry vCPP2319, a peptide with dual cell-penetration and anticancer activities. The selective cytotoxicity of anticancer peptide-loaded EVs towards breast cancer cells and their ability to translocate an in vitro BBB model are also addressed. Overall, it was possible to conclude that vCPP2319 naturally interacts with breast cancer-derived EVs, being retained at the surface of these vesicles. Moreover, the results revealed a cytotoxic activity for peptide-loaded EVs similar to that obtained with the peptide alone and the ability of peptide-loaded EVs to translocate an in vitro BBB model, which contrasts with the results obtained with the peptide alone. In conclusion, this work supports the use of EVs in the development of biological drug-delivery systems (DDS) capable of translocating the BBB.

Keywords:  Anticancer peptide; Blood-brain barrier; Brain metastases; Drug-delivery systems; Extracellular vesicles; Metastatic breast cancer

DOI:  https://doi.org/10.1016/j.heliyon.2024.e40907
Acta Biomater. 2024 Dec 21. pii: S1742-7061(24)00769-4. [Epub ahead of print]

Development of a Peptide-Based Tumor-Activated Checkpoint Inhibitor for Cancer Immunotherapy.

Zhen Zhao, John Fetse, Umar-Farouk Mamani, Yuhan Guo, Yuanke Li, Pratikkumar Patel, Yanli Liu, Chien-Yu Lin, Yongren Li, Bahaa Mustafa, Kun Cheng.

  Antibody-based checkpoint inhibitors have achieved great success in cancer immunotherapy, but their uncontrollable immune-related adverse events remain a major challenge. In this study, we developed a tumor-activated nanoparticle that is specifically active in tumors but not in normal tissues. We discovered a short anti-PD-L1 peptide that blocks the PD-1/PD-L1 interaction. The peptide was modified with a PEG chain through a novel matrix metalloproteinase-2 (MMP-2)-specific cleavage linker. The modified TR3 peptide self-assembles into a micelle-like nanoparticle (TR3-M-NP), which remains inactive and unable to block the PD-1/PD-L1 interaction in its native form. However, upon cleavage by MMP-2 in tumors, it releases the active peptide. The TR3-M-NP5k nanoparticle was specifically activated in tumors through enzyme-mediated cleavage, leading to the inhibition of tumor growth and extended survival compared to control groups. In summary, TR3-M-NP shows great potential as a tumor-responsive immunotherapy agent with reduced toxicities. STATEMENT OF SIGNIFICANCE: : In this study, we developed a bioactive peptide-based checkpoint inhibitor that is active only in tumors and not in normal tissues, thereby potentially avoiding immune-related adverse effects. We discovered a short anti-PD-L1 peptide, TR3, that blocks the PD-1/PD-L1 interaction. We chemically modified the TR3 peptide to self-assemble into a micelle-like nanoparticle (TR3-M-NP), which itself cannot block the PD-1/PD-L1 interaction but releases the active TR3 peptide in tumors upon cleavage by MMP-2. In contrast, the nanoparticle is randomly degraded in normal tissues into peptides fragments that cannot block the PD-1/PD-L1 interaction. Upon intraperitoneal injection, TR3-M-NP5k was activated specifically in tumors through enzyme cleavage, leading to the inhibition of tumor growth and extended survival compared to the control groups. In summary, TR3-M-NP holds significant promise as a tumor-responsive immunotherapy agent with reduced toxicities. The bioactive platform has the potential to be used for other types of checkpoint inhibitor.

Keywords:  Peptide; anti-PD-L1; self-assembly nanoparticle; tumor-activated immunotherapy

DOI:  https://doi.org/10.1016/j.actbio.2024.12.051
J Med Chem. 2024 Dec 24.

Generating a Peptide Library Using the Repeats of Amino Acid Scaffolds Created by Sliding the Framework of a 7-mer Human Chemerin Segment and Discovery of Potent Antibacterial and Antimycobacterial Peptides.

Sariyah Akhtar, Mohd Mustkim Ansari, Rahul Dev Verma, Juhi Sharma, Arvind Gupta, Rajendra Kumar Dhuriya, Devesh Pratap Verma, Jyotshana Saroj, Mehmood Ali, Neeraj Kumar Verma, Kalyan Mitra, Bhupendra Narain Singh, Jimut Kanti Ghosh.

The quest for new approaches for generating novel bioactive designer proteins/peptides has continued with their success in various biomedical applications. Previously, we designed a 14-mer α-helical peptide with antimicrobial and antimycobacterial activities by employing a tandem repeat of the 7-mer, "KVLGRLV" human chemerin segment. Herein, we devised a new method of "sliding framework" with this segment to create amino acid scaffolds of varying sizes and sequences and explored the design of a peptide library with antibacterial and antimycobacterial activities. By utilizing 2 to 7 repeats of these 2 to 6-residue scaffolds, we designed and synthesized 30 peptides of 10-16 residue lengths. Thus, we identified novel AMPs with α-helical, β-sheet, and random coil structures, membrane-destabilizing, and intracellular modes of action, and 9 of them showed therapeutic indices between 100 and 750. Three and two of these nine peptides showed in vivo antibacterial and antitubercular efficacies against Escherichia coli ATCC 25922 and Mycobacterium bovis BCG infections, respectively, in a mouse model.

DOI: https://doi.org/10.1021/acs.jmedchem.4c02351