bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2023–12–31
nine papers selected by
Henry Lamb, Queensland University of Technology
  1. Intrinsically Disordered Ku Protein-Derived Cell-Penetrating Peptides.
  2. Development of cyclic peptides that can be administered orally to inhibit disease targets.
  3. Cell-Penetrating Peptide Delivery of Nucleic Acid Cargo to Emiliania huxleyi, a Calcifying Marine Coccolithophore.
  4. De novo development of small cyclic peptides that are orally bioavailable.
  5. Development of stapled NONO-associated peptides reveals unexpected cell permeability and nuclear localisation.
  6. Immune Checkpoint-Blocking Nanocages Cross the Blood-Brain Barrier and Impede Brain Tumor Growth.
  7. Big peptide drugs in a small molecule world.
  8. Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes.
  9. Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins.
  1. ACS Bio Med Chem Au. 2023 Dec 20. 3(6): 471-479
    Intrinsically Disordered Ku Protein-Derived Cell-Penetrating Peptides.
    Biswanath Maity, Hariharan Moorthy, Thimmaiah Govindaraju.
      Efficient delivery of bioactive ingredients into cells is a major challenge. Cell-penetrating peptides (CPPs) have emerged as promising vehicles for this purpose. We have developed novel CPPs derived from the flexible and disordered tail extensions of DNA-binding Ku proteins. Ku-P4, the lead CPP identified in this study, is biocompatible and displays high internalization efficacy. Biophysical studies show that the proline residue is crucial for preserving the intrinsically disordered state and biocompatibility. DNA binding studies showed effective DNA condensation to form a positively charged polyplex. The polyplex exhibited effective penetration through the cell membrane and delivered the plasmid DNA inside the cell. These novel CPPs have the potential to enhance the cellular uptake and therapeutic efficacy of peptide-drug or gene conjugates.
    DOI:  https://doi.org/10.1021/acsbiomedchemau.3c00032
  2. Nat Chem Biol. 2023 Dec 28.
    Development of cyclic peptides that can be administered orally to inhibit disease targets.
      
    DOI:  https://doi.org/10.1038/s41589-023-01505-0
  3. ACS Synth Biol. 2023 Dec 26.
    Cell-Penetrating Peptide Delivery of Nucleic Acid Cargo to Emiliania huxleyi, a Calcifying Marine Coccolithophore.
    Cory Flavin, Anushree Chatterjee.
      Coccolithophores are a group of unicellular marine phytoplankton that exhibit a prolific capacity for carbon conversion and are critical to ocean biogeochemistry. A fundamental understanding of coccolithophore biomineralization has been limited, in part, by the lack of genetic and molecular tools to investigate the organisms. In particular, it has proven to be difficult to deliver macromolecules across the coccosphere-membrane complex. To overcome this barrier, we employed cell-penetrating peptides (CPP) in the Emiliania huxleyi coccolithophores. We evaluated three established CPPs (TAT, R9, and KFF) and designed a CPP that incorporates a high proline content identified in the protein transduction domain of EhV060, an E. huxleyi virus lectin protein. To measure the delivery performance, we covalently linked CPPs to synthetic peptide nucleic acids (PNA) and attached a fluorescein marker. CPP-PNA-FITC complexes were efficiently delivered across the coccosphere-membrane complex to the cytoplasm of E. huxleyi cells. Characterization of E. huxleyi demonstrates that CPP-PNA are nontoxic and reveals specific effects of CPP-PNA on cell biology and calcification. Direct delivery and characterization of synthetic nucleic acids represent a step forward in synthetic biology to explore coccolithophore biomineralization.
    Keywords:  Biomineralization; Carbon Capture and Storage; Cell-Penetrating Peptide; Coccolithophore; Genetic Engineering
    DOI:  https://doi.org/10.1021/acssynbio.3c00670
  4. Nat Chem Biol. 2023 Dec 28.
    De novo development of small cyclic peptides that are orally bioavailable.
    Manuel L Merz, Sevan Habeshian, Bo Li, Jean-Alexandre G L David, Alexander L Nielsen, Xinjian Ji, Khaled Il Khwildy, Maury M Duany Benitez, Phoukham Phothirath, Christian Heinis.
      Cyclic peptides can bind challenging disease targets with high affinity and specificity, offering enormous opportunities for addressing unmet medical needs. However, as with biological drugs, most cyclic peptides cannot be applied orally because they are rapidly digested and/or display low absorption in the gastrointestinal tract, hampering their development as therapeutics. In this study, we developed a combinatorial synthesis and screening approach based on sequential cyclization and one-pot peptide acylation and screening, with the possibility of simultaneously interrogating activity and permeability. In a proof of concept, we synthesized a library of 8,448 cyclic peptides and screened them against the disease target thrombin. Our workflow allowed multiple iterative cycles of library synthesis and yielded cyclic peptides with nanomolar affinities, high stabilities and an oral bioavailability (%F) as high as 18% in rats. This method for generating orally available peptides is general and provides a promising push toward unlocking the full potential of peptides as therapeutics.
    DOI:  https://doi.org/10.1038/s41589-023-01496-y
  5. J Pept Sci. 2023 Dec 26. e3562
    Development of stapled NONO-associated peptides reveals unexpected cell permeability and nuclear localisation.
    Reginald Young, Tiancheng Huang, Zijie Luo, Yaw Sing Tan, Amandeep Kaur, Yu Heng Lau.
      The non-POU domain-containing octamer-binding protein (NONO) is a nucleic acid-binding protein with diverse functions that has been identified as a potential cancer target in cell biology studies. Little is known about structural motifs that mediate binding to NONO apart from its ability to form homodimers, as well as heterodimers and oligomers with related homologues. We report a stapling approach to macrocyclise helical peptides derived from the insulin-like growth factor binding protein (IGFBP-3) that NONO interacts with, and also from the dimerisation domain of NONO itself. Using a range of chemistries including Pd-catalysed cross-coupling, cysteine arylation and cysteine alkylation, we successfully improved the helicity and observed modest peptide binding to the NONO dimer, although binding could not be saturated at micromolar concentrations. Unexpectedly, we observed cell permeability and preferential nuclear localisation of various dye-labelled peptides in live confocal microscopy, indicating the potential for developing peptide-based tools to study NONO in a cellular context.
    Keywords:  DBHS proteins; NONO; alpha helix; cell permeability; cyclic peptide; stapling
    DOI:  https://doi.org/10.1002/psc.3562
  6. ACS Biomater Sci Eng. 2023 Dec 27.
    Immune Checkpoint-Blocking Nanocages Cross the Blood-Brain Barrier and Impede Brain Tumor Growth.
    Minseong Kim, Hee Jung Yoon, Chanju Lee, Minah Lee, Rang-Woon Park, Byungheon Lee, Eun Jung Park, Soyoun Kim.
      Glioblastoma (GBM) is the deadliest tumor of the central nervous system, with a median survival of less than 15 months. Despite many trials, immune checkpoint-blocking (ICB) therapies using monoclonal antibodies against the PD-1/PD-L1 axis have demonstrated only limited benefits for GBM patients. Currently, the main hurdles in brain tumor therapy include limited drug delivery across the blood-brain barrier (BBB) and the profoundly immune-suppressive microenvironment of GBM. Thus, there is an urgent need for new therapeutics that can cross the BBB and target brain tumors to modulate the immune microenvironment. To this end, we developed an ICB strategy based on the BBB-permeable, 24-subunit human ferritin heavy chain, modifying the ferritin surface with 24 copies of PD-L1-blocking peptides to create ferritin-based ICB nanocages. The PD-L1pep ferritin nanocages first demonstrated their tumor-targeting and antitumor activities in an allograft colon cancer model. Next, we found that these PD-L1pep ferritin nanocages efficiently penetrated the BBB and targeted brain tumors through specific interactions with PD-L1, significantly inhibiting tumor growth in an orthotopic intracranial tumor model. The addition of PD-L1pep ferritin nanocages to triple in vitro cocultures of T cells, GBM cells, and glial cells significantly inhibited PD-1/PD-L1 interactions and restored T-cell activity. Collectively, these findings indicate that ferritin nanocages displaying PD-L1-blocking peptides can overcome the primary hurdle of brain tumor therapy and are, therefore, promising candidates for treating GBM.
    Keywords:  PD-L1 binding peptide; blood brain barrier; ferritin; glioblastoma; immune checkpoint; nanocage
    DOI:  https://doi.org/10.1021/acsbiomaterials.3c01200
  7. Front Chem. 2023 ;11 1302169
    Big peptide drugs in a small molecule world.
    Laszlo Otvos, John D Wade.
      A quarter of a century ago, designer peptide drugs finally broke through the glass ceiling. Despite the resistance by big pharma, biotechnology companies managed to develop injectable peptide-based drugs, first against orphan or other small volume diseases, and later for conditions affecting large patient populations such as type 2 diabetes. Even their lack of gastrointestinal absorption could be utilized to enable successful oral dosing against chronic constipation. The preference of peptide therapeutics over small molecule competitors against identical medical conditions can be achieved by careful target selection, intrachain and terminal amino acid modifications, appropriate conjugation to stability enhancers and chemical space expansion, innovative delivery and administration techniques and patient-focused marketing strategies. Unfortunately, however, pharmacoeconomical considerations, including the strength of big pharma to develop competing small molecule drugs, have somewhat limited the success of otherwise smart peptide-based therapeutics. Yet, with increasing improvement in peptide drug modification and formulation, these are continuing to gain significant, and growing, acceptance as desirable alternatives to small molecule compounds.
    Keywords:  peptide drug design and development; peptide drugs; peptide pharmaceuticals; pharma; small molecules
    DOI:  https://doi.org/10.3389/fchem.2023.1302169
  8. J Phys Chem Lett. 2023 Dec 28. 175-179
    Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes.
    Peter Pajtinka, Robert Vácha.
      Curvature sensing is an essential ability of biomolecules to preferentially localize to membrane regions of a specific curvature. It has been shown that amphipathic helices (AHs), helical peptides with both hydrophilic and hydrophobic regions, could sense a positive membrane curvature. The origin of this AH sensing has been attributed to their ability to exploit lipid-packing defects that are enhanced in regions of positive curvature. In this study, we revisit an alternative framework where AHs act as sensors of local internal stress within the membrane, suggesting the possibility of an AH sensing a negative membrane curvature. Using molecular dynamics simulations, we gradually tuned the hydrophobicity of AHs, thereby adjusting their insertion depth so that the curvature preference of AHs is switched from positive to negative. This study suggests that highly hydrophobic AHs could preferentially localize proteins to regions of a negative membrane curvature.
    DOI:  https://doi.org/10.1021/acs.jpclett.3c02785
  9. JACS Au. 2023 Dec 25. 3(12): 3290-3296
    Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins.
    T M Simon Tang, Jody M Mason.
      Peptide backbone cyclization is commonly observed in nature and is increasingly applied to proteins and peptides to improve thermal and chemical stability and resistance to proteolytic enzymes and enhance biological activity. However, chemical synthesis of head-to-tail cyclic peptides and proteins is challenging, is often low yielding, and employs toxic and unsustainable reagents. Plant derived asparaginyl endopeptidases such as OaAEP1 have been employed to catalyze the head-to-tail cyclization of peptides in vitro, offering a safer and more sustainable alternative to chemical methods. However, while asparaginyl endopeptidases have been used in vitro and in native and transgenic plant species, they have never been used to generate recombinant cyclic proteins in live recombinant organisms outside of plants. Using dihydrofolate reductase as a proof of concept, we show that a truncated OaAEP1 variant C247A is functional in the Escherichia coli physiological environment and can therefore be coexpressed with a substrate protein to enable concomitant in situ cyclization. The bacterial system is ideal for cyclic protein production owing to the fast growth rate, durability, ease of use, and low cost. This streamlines cyclic protein production via a biocatalytic process with fast kinetics and minimal ligation scarring, while negating the need to purify the enzyme, substrate, and reaction mixtures individually. The resulting cyclic protein was characterized in vitro, demonstrating enhanced thermal stability compared to the corresponding linear protein without impacting enzyme activity. We anticipate this convenient method for generating cyclic peptides will have broad utility in a range of biochemical and chemical applications.
    DOI:  https://doi.org/10.1021/jacsau.3c00591
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