bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2025–06–08
eight papers selected by
Henry Lamb, Queensland University of Technology



  1. J Med Chem. 2025 Jun 04.
      Cyclic peptides have emerged as promising modulators of protein-protein interactions due to their unique pharmacological properties and ability to target extensive flat binding interfaces. However, traditional strategies for developing cyclic peptides are often hindered by significant resource constraints. Recent advancements in computational techniques and artificial intelligence-driven methodologies have significantly enhanced the cyclic peptide drug discovery pipeline, while breakthroughs in automated synthesis platforms have accelerated experimental validation, presenting transformative potential for pharmaceutical innovation. In this review, we examine state-of-the-art computational and artificial intelligence-driven strategies that address challenges such as peptide flexibility, limited data availability, and complex conformational landscapes. We discuss how the integration of physics-based simulations with deep learning techniques is redefining the design and optimization of cyclic peptide therapeutics and propose future perspectives to advance the precision and efficiency of cyclic peptide drug development, ultimately offering innovative solutions to unmet medical needs.
    DOI:  https://doi.org/10.1021/acs.jmedchem.5c00712
  2. J Med Chem. 2025 Jun 06.
      FANCM-RMI is a protein-protein interaction that maintains genome stability during DNA repair events in cancers that rely on the Alternative Lengthening of Telomeres (ALT) pathway for survival. We report the first valid chemical inhibitors of the FANCM-RMI interaction discovered by screening cyclic peptides via mRNA display. These inhibitors engage the FANCM-binding pocket of RMI1/2 with nanomolar affinity (KD = 2-10 nM) and are potent disruptors of the FANCM-RMI interaction (IC50 = 54-104 nM). X-ray crystallography and alanine scanning reveal novel binding modes and interactions between the cyclic peptides and RMI1/2 that drive high-potency inhibition. Co-immunoprecipitation studies confirm the complete disruption of the native interaction in whole osteosarcoma cell lysates. These inhibitors represent the first validated RMI binders toward developing chemical tools for interrogating the mechanistic roles of FANCM-RMI in mediating genome stability and provide a much-anticipated starting point to accelerate the development of FANCM-RMI inhibitors for intervention against ALT-driven cancers.
    DOI:  https://doi.org/10.1021/acs.jmedchem.5c00365
  3. Chembiochem. 2025 Jun 04. e202500375
      Cyclic peptides offer several advantages over their linear counterparts, including enhanced structural stability due to their rigid conformation and increased resistance to enzymatic proteolysis. Additionally, their ring structure and constrained conformation reduce the entropic cost upon binding to receptors and other biological targets, leading to higher binding affinity and specificity. However, peptide macrocyclization is often synthetically challenging due to reduced entropy, oligomer formation, and C-terminal epimerization. The conventional approach for synthesizing cyclic peptides involves the direct coupling of amine and carboxyl termini in solution phase, using protected side-chain peptides and coupling reagents. Despite this, improving the efficiency of head-to-tail cyclization remains a key challenge. In this study, we optimized the cyclization of a de novo octapeptide composed of alternating l- and d-amino acids. The impact of various factors on the cyclization was examined, including coupling reagents, temperature, heating, chaotropic agents, solvent and concentration. This investigation has not only led to the identification of efficient cyclization conditions, but it also provides a valuable framework for the cyclization of challenging peptide sequences. The insights gained in this study contribute to the field of peptide chemistry, expanding the understanding of peptide cyclization reactions, which could accelerate the development of cyclic peptide-based therapeutics.
    Keywords:  Amidation; Cyclic peptides; Head-to-tail cyclization; Macrocyclization
    DOI:  https://doi.org/10.1002/cbic.202500375
  4. Microb Biotechnol. 2025 Jun;18(6): e70158
      New therapeutics are urgently needed to curb the spread of drug-resistant diseases. Bioactive peptides (BAPs), including antimicrobial peptides, are emerging as an exciting new class of compounds with advantages over current drug modalities, especially small molecule drugs that are prone to resistance development. Here, we evaluated a bacteriophage P22 virus-like particle (VLP) system where BAPs are encapsulated as fusion proteins with the P22 scaffold protein (SP) within self-assembling protein cages in Escherichia coli. Representative peptides from three structurally distinct classes of BAPs were successfully encapsulated into P22 VLPs at high cargo to VLP coat protein (CP) ratios that corresponded to interactions between the compact electropositive structures of the SP-BAPs and electronegative regions on the inward facing surface of CP subunits. However, high loading densities did not correspond to improved SP-BAP yields. An unexpected finding of this study was that while encapsulation alleviated negative effects of SP-BAPs on E. coli growth, the P22 scaffold protein acted as a sufficient fusion partner for accumulating BAPs, and co-expression of the CP did not further improve SP-BAP yields. Nevertheless, encapsulation in VLPs provided a useful first step in the purification pipeline for producing both linear and cyclic recombinant (r)BAPs that were functionally equivalent to their synthetic counterparts. Further efforts to optimise expression ratios of CP to SP-BAP fusions will be required to realise the full potential of encapsulation for protecting expression hosts and maximising rBAP yields.
    Keywords:  bacteriophage P22; bioactive peptide; protein encapsulation; recombinant expression; virus‐like particle
    DOI:  https://doi.org/10.1111/1751-7915.70158
  5. Angew Chem Int Ed Engl. 2025 Jun 02. e202506802
      Protein-based tools are emerging as innovative solutions to interfere with biological pathways in molecular biology and medicine. They offer advantages over traditional small molecules due to their adaptable structural diversity and their ability to engage previously inaccessible cellular targets. However, most proteins do not penetrate the lipid bilayer of mammalian cells and are therefore restricted to extracellular targets. Despite recent advances, a general method for the delivery of functional proteins into human cells remains a significant challenge. In this study, we present a bioreversible protein modification strategy of amines using short arginine-containing peptides (termed BioRAM), that enables cytosolic delivery starting from genetically non-engineered proteins. We optimized the bioconjugation-strategy to achieve fast intracellular cleavage and complete recovery of the native protein. In combination with our previously established cell-penetrating peptide (CPP)-additive protocol, we show superior delivery of fluorescent protein and functional RNase A into the cytosol, achieving physiological response. Moreover, we are able to demonstrate the excellent performance of BioRAM in the presence of serum, thereby broadening the scope for intracellular applications of functional proteins.
    Keywords:  Intracellular protein delivery Bioconjugation Cell-penetrating peptide Bioreversible modification RNase A
    DOI:  https://doi.org/10.1002/anie.202506802
  6. Chem Commun (Camb). 2025 Jun 02.
      Recurrent neural networks underwent reinforcement procedures for de novo generation of peptide binders with desired properties. Docking and scoring of peptides from these models allowed enrichment of focused sets with validated sequences for iterative fine-tuning, leading to reinforcement of those models. They enabled de novo generation of peptide sequences with high binding affinity to the target and possibly additional properties.
    DOI:  https://doi.org/10.1039/d5cc02530c
  7. bioRxiv. 2025 May 23. pii: 2025.05.19.654863. [Epub ahead of print]
      Protein-peptide interactions underlie key biological processes and are commonly utilized in biomedical research and therapeutic discovery. It is often desirable to identify peptide sequence properties that confer high-affinity binding to a target protein. However, common approaches to such characterization are typically low throughput and only sample regions of sequence space near an initial hit. To overcome these challenges, we built a yeast surface displayed library representing ∼6.1 × 109 unique peptides. We then performed screens against diverse protein targets, including two antibodies, an E3 ubiquitin ligase, and an essential membrane-bound bacterial enzyme. In each case, we observed motifs that appear to drive peptide binding and we identified multiple novel, high-affinity clones. These results highlight the library's utility as a robust and versatile tool for discovering peptide ligands and for characterizing protein-peptide binding interactions more generally. To enable further studies, we will make the library freely available upon request.
    DOI:  https://doi.org/10.1101/2025.05.19.654863
  8. J Am Chem Soc. 2025 Jun 04.
      Peptides and proteins are invaluable therapeutics and biological tools, where stimuli-responsive and fully reversible conjugation chemistry is essential to advances in drug delivery systems and chemical biology. However, methods that allow precise conjugation, efficient regulation of biochemical functions, and customized recovery of parent peptides remain underdeveloped. Here, we introduce a straightforward yet powerful reversible chemical strategy targeting methionine (Met), a widespread yet low abundance amino acid in peptides and proteins. By selectively alkylating Met-containing peptides under weakly acidic conditions, we form a stable C-S+ bond, which can be cleaved rapidly via 1,6-benzyl elimination upon stimulus. This versatile chemistry is demonstrated in diverse applications: (i) PEGylated prodrugs of antimicrobial peptides with reduced toxicity and enhanced enzymatic stability, (ii) esterase-responsive peptide-peptide inhibitor conjugates (PPICs) with improved cell membrane permeability and therapeutic effects, (iii) reversibly stapled peptides with switchable conformations for targeting both intra- and extracellular sites, and (iv) bioorthogonal control of C-terminal Met-caged neuropeptides. Overall, this work describes, for the first time, a valuable traceless modification strategy that promises to greatly benefit the peptide community and advance the field of chemical biology.
    DOI:  https://doi.org/10.1021/jacs.5c04329