bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2024–10–13
eight papers selected by
Henry Lamb, Queensland University of Technology
  1. Exploring the Utility of Cell-Penetrating Peptides as Vehicles for the Delivery of Distinct Antimalarial Drug Cargoes.
  2. Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers.
  3. Chemically Stable Diazo Peptides as Selective Probes of Cysteine Proteases in Living Cells.
  4. Structural basis of μ-opioid receptor targeting by a nanobody antagonist.
  5. Beyond chloroquine: Cationic amphiphilic drugs as endosomal escape enhancers for nucleic acid therapeutics.
  6. Enhanced Delivery of Biomolecules into Caco2 Cells Based on the Cell-Penetrating Ability of Keratin Peptides.
  7. Enhancing De Novo Protein Sequencing through the C-Terminal Labeling Strategy: Resolving Isobaric Ambiguities by Electron-Transfer/Higher Energy Collision Dissociation (EThcD).
  8. A Novel Bifunctional Chelating Agent for Tyrosine-Specific Radiolabeling of Peptides and Proteins.
  1. ChemMedChem. 2024 Oct 08. e202400637
    Exploring the Utility of Cell-Penetrating Peptides as Vehicles for the Delivery of Distinct Antimalarial Drug Cargoes.
    Caitlin L Gare, Isabella R Palombi, Andrew M White, Marina Chavchich, Michael D Edstein, Aaron Lock, Vicky M Avery, David J Craik, Brendan J McMorran, Nicole Lawrence, Lara Rebecca Malins.
      The devastating impact of malaria includes significant mortality and illness worldwide. Increasing resistance of the causative parasite, Plasmodium, to existing antimalarial drugs underscores a need for additional compounds with distinct modes of action in the therapeutic development pipeline. Here we showcase peptide-drug conjugates (PDCs) as an attractive compound class, in which therapeutic or lead antimalarials are chemically conjugated to cell-penetrating peptides. This approach aims to enhance selective uptake into Plasmodium-infected red blood cells and impart additional cytotoxic actions on the intraerythrocytic parasite, thereby enabling targeted drug delivery and dual modes of action. We describe the development of PDCs featuring four compounds with antimalarial activity - primaquine, artesunate, tafenoquine and methotrexate - conjugated to three cell-penetrating peptide scaffolds with varied antiplasmodial activity, including active and inactive analogs of platelet factor 4 derived internalization peptide (PDIP), and a cyclic polyarginine peptide. Development of this diverse set of PDCs featured distinct and adaptable conjugation strategies, to produce conjugates with in vitro antiplasmodial activities ranging from low nanomolar to low micromolar potencies according to the drug cargo and bioactivity of the partner peptide. Overall, this study establishes a strategic and methodological framework for the further development of dual mode of action peptide-drug antimalarial therapeutics.
    Keywords:  bioconjugation; cell-penetrating peptide; click chemistry; malaria; peptide-drug conjugate
    DOI:  https://doi.org/10.1002/cmdc.202400637
  2. Mol Inform. 2024 Oct 10. e202400186
    Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers.
    Markus Orsi, Jean-Louis Reymond.
      Herein we report a virtual library of 1E+60 members, a common estimate for the size of the drug-like chemical space. The library consists of linear or cyclic oligomers forming molecules within the size range of peptide drugs. We demonstrate ligand-based virtual screening using a genetic algorithm.
    Keywords:  chemical space; cheminformatics; genetic algorithm; therapeutic peptides
    DOI:  https://doi.org/10.1002/minf.202400186
  3. Angew Chem Int Ed Engl. 2024 Oct 09. e202411006
    Chemically Stable Diazo Peptides as Selective Probes of Cysteine Proteases in Living Cells.
    Juliane Wahl, Ahsanullah Ahsanullah, Hana Zupan, Franziska Gottschalk, Andreas Nerlich, Christoph Arkona, Andreas C Hocke, Bettina G Keller, Jörg Rademann.
      Diazo peptides have been described earlier, however, due to their high reactivity have not been broadly used until today. Here, we report the preparation, properties, and applications of chemically stable internal diazo peptides. Peptidyl phosphoranylidene-esters and amides were found to react with triflyl azide primarily to novel 3,4-disubstituted triazolyl-peptides. Nonaflyl azide instead furnished diazo peptides, which are chemically stable from pH 1-14 as amides and from pH 1-8 as esters. Thus, diazo peptides prepared by solid phase peptide synthesis were stable to final deprotection with 95% trifluoroacetic acid. Diazo peptides with the recognition sequence of caspase-3 were identified as specific, covalent, and irreversible inhibitors of this enzyme at low nanomolar concentrations. A fluorescent diazo peptide entered living cells enabling microscopic imaging and quantification of apoptotic cells via flow cytometry. Thus, internal diazo peptides constitute a novel class of activity-based probes and enzyme inhibitors useful in chemical biology and medicinal chemistry.
    Keywords:  Diazo compounds; activity-based probes; apoptosis; diazo peptides; irreversible protease inhibitors
    DOI:  https://doi.org/10.1002/anie.202411006
  4. Nat Commun. 2024 Oct 09. 15(1): 8687
    Structural basis of μ-opioid receptor targeting by a nanobody antagonist.
    Jun Yu, Amit Kumar, Xuefeng Zhang, Charlotte Martin, Kevin Van Holsbeeck, Pierre Raia, Antoine Koehl, Toon Laeremans, Jan Steyaert, Aashish Manglik, Steven Ballet, Andreas Boland, Miriam Stoeber.
      The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbE's antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments.
    DOI:  https://doi.org/10.1038/s41467-024-52947-6
  5. Curr Opin Chem Biol. 2024 Oct 05. pii: S1367-5931(24)00107-8. [Epub ahead of print]83 102531
    Beyond chloroquine: Cationic amphiphilic drugs as endosomal escape enhancers for nucleic acid therapeutics.
    Aliona Debisschop, Bram Bogaert, Cristina Muntean, Stefaan C De Smedt, Koen Raemdonck.
      Nucleic acid (NA) therapeutics have the potential to treat or prevent a myriad of diseases but generally require cytosolic delivery to be functional. NA drugs are therefore often encapsulated into delivery systems that mediate effective endocytic uptake by target cells, but unfortunately often display limited endosomal escape efficiency. This review will focus on the potential of repurposing cationic amphiphilic drugs (CADs) to enhance endosomal escape. In general terms, CADs are small molecules with one or more hydrophobic groups and a polar domain containing a basic amine. CADs have been reported to accumulate in acidified intracellular compartments (e.g., endosomes and lysosomes), integrate in cellular membranes and alter endosomal trafficking pathways, ultimately resulting in improved cytosolic release of the endocytosed cargo. As many CADs are widely used drugs, their repurposing offers opportunities for combination therapies with NAs.
    Keywords:  Cationic amphiphilic drugs; Drug repurposing; Endosomal escape; Functional inhibitors of acid sphingomyelinase; Lysosomal membrane permeabilization; Nucleic acid therapeutics
    DOI:  https://doi.org/10.1016/j.cbpa.2024.102531
  6. ACS Appl Mater Interfaces. 2024 Oct 09.
    Enhanced Delivery of Biomolecules into Caco2 Cells Based on the Cell-Penetrating Ability of Keratin Peptides.
    Xiaojie Qin, Yujie Guo, Ruilin Li, Johannes H Bitter, Elinor L Scott, Chunhui Zhang.
      Keratin, as a promising bioresource, possesses significant potential for diverse biological applications due to its favorable biocompatibility, low toxicity, biodegradability, and cell adhesion ability. However, there are few studies on the cell-penetrating ability of keratin peptides (KEPs) for biomolecule delivery. Therefore, this study explored the cell-penetrating ability of KEPs with different molecular weights (Mw) on Caco2 cells using fluorescein-labeled insulin (FITC-INS) as the target intracellular biomolecule. The potential cell-penetrating mechanism was elaborated by combining cellular investigation with the physicochemical characterization of KEPs. The result shows that the KEPs <3 kDa (KEP1) exhibited the highest cell-penetrating ability at 2 mg/mL, allowing efficient delivery of FITC-INS into Caco2 cells without covalent bonding. The cellular uptake mechanism was energy-dependent, mainly involving macropinocytosis. The further fractionation of KEP1 reveals that the most effective components consisted of 8-19 amino acids, including specific hydrophobic peptides (e.g., RVVIEPSPVVV and IIIQPSPVVV), PPII amphipathic peptides (e.g., PPPVVVTFP and FIQPPPVVV), and Cys-rich peptides (e.g., LCAPTPCGPTPL and CLPCRPCGPTPL). Additionally, analysis of the secondary and tertiary structure and amino acid composition illustrated that KEP1 exhibited rich hydrophobic residues and disulfide bonds, which probably contributed to its cell-penetrating ability, as opposed to its small particle size and electrostatic interactions. This study reveals the cell-penetrating ability of KEPs, thus highlighting their potential as biomaterials for noncovalently delivering biomolecules.
    Keywords:  biomolecules delivery; cell-penetrating ability; cellular uptake; keratin peptides; noncovalent bonding
    DOI:  https://doi.org/10.1021/acsami.4c13236
  7. Anal Chem. 2024 Oct 10.
    Enhancing De Novo Protein Sequencing through the C-Terminal Labeling Strategy: Resolving Isobaric Ambiguities by Electron-Transfer/Higher Energy Collision Dissociation (EThcD).
    Thierry Le Bihan, Zac McDonald, Konrad R Celejewski, Qixin Liu, Bin Ma.
      De novo protein sequencing via a bottom-up approach requires various proteases to produce overlapping peptides. However, peptides generated by proteases other than trypsin, LysC, and ArgC often yield C-terminal fragments with suboptimal ionization in positive mode mass spectrometry (MS). This study introduces a novel peptide labeling strategy that involves modifying peptides at the C-terminal and at the carboxyl groups of Aspartic and Glutamic acid with arginine methyl ester (R-met) to improve peptide fragmentation and resolve isobaric ambiguities encountered during sequencing. An amidation reaction is used with coupling reagents to conjugate R-met to the peptide's C-terminal end, introducing a functional group that enhances the detectability of C-terminal peptide fragment ions by mass spectrometry. Subsequently, selecting a charge state of +2 or higher can facilitate optimal fragmentation of the derivatized peptides using electron-transfer/higher energy collision dissociation (EThcD), thereby generating essential w-ions to resolve common isobaric ambiguities. Demonstrating this strategy across diverse protein types, including albumin and antibodies and using different proteases for digestion, highlights the unique characteristics of combining the proposed amidation reaction with the specific proteases tested.
    DOI:  https://doi.org/10.1021/acs.analchem.4c03459
  8. Bioconjug Chem. 2024 Oct 07.
    A Novel Bifunctional Chelating Agent for Tyrosine-Specific Radiolabeling of Peptides and Proteins.
    Daiki Nakano, Hiroyuki Watanabe, Saito Kosuke, Masahiro Ono.
      Site-specific radiolabeling is utilized for the development of antibody- or peptide-based radiotheranostic agents. Although tyrosine can be exploited as one of the target residues for site-specific radiolabeling of peptides and proteins, a tyrosine-specific radiolabeling method has not been established. In this study, we newly designed and synthesized a novel bifunctional chelating agent, TBD-DO3A, consisting of a triazabutadiene (TBD) scaffold and metal chelator, 1,4,7,10-tetraazacyclododecane 1,4,7-triacetic acid (DO3A). Conjugation of TBD-DO3A with Ac-Tyr-NHMe followed by 111In-labeling afforded [111In]In-Tyr-DO3A, which showed high-level stability in mouse plasma. Then, we selected the tyrosine-containing cyclic peptide c(RGDyK) as a model ligand and synthesized [111In]In-RYD. [111/natIn]In-RYD showed in vitro binding properties for integrin αvβ3 equivalent to those of [111/natIn]In-RKD, a lysine residue-labeled control compound. In in vivo biodistribution and SPECT/CT imaging studies using U87MG/PC-3 tumor-bearing mice, [111In]In-RYD and [111In]In-RKD were selectively accumulated and facilitated U87MG tumor visualization at 24 h postinjection. These results indicate that TBD-DO3A has fundamental properties as a bifunctional chelator for tyrosine-specific radiolabeling of peptides and proteins.
    DOI:  https://doi.org/10.1021/acs.bioconjchem.4c00363
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