bims-cepepe 2025-03-02 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2025–03–02
twelve papers selected by
Henry Lamb, Queensland University of Technology

MultiCycPermea: accurate and interpretable prediction of cyclic peptide permeability using a multimodal image-sequence model.
Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display.
Tumor Microenvironment pH-Sensitive Peptidomimetics for Targeted Anticancer Drug Delivery.
Role of sequence length and functionalization in interactions of bioconjugated peptides with mitomembranes.
Synthesis and Evaluation of 68Ga- and 177Lu-Labeled [diF-Pro14]Bombesin(6-14) Analogs for Detection and Radioligand Therapy of Gastrin-Releasing Peptide Receptor-Expressing Cancer.
Recent Chemical Biology Insights Towards Reversible Stapled Peptides.
Twisted Amide-Mediated Synthesis and Rapid Structure-Activity Relationship Study of Medium-Sized Cyclic Peptides.
Structure-guided development of chemically tailored peptide binders of RNF43/ZNRF3 to enable versatile design of membrane protein-targeting PROTACs.
Head-to-Tail Cyclization Enhances Ice-Growth Inhibition by Linear Threonine Oligomers.
Development and Evaluation of 68Ga-Labeled TMTP1-Based Cyclic Peptide Probes for Targeting Hepatocellular Carcinoma.
Transmembrane clustering of short amyloid peptide fragments: A coarse grained molecular dynamics study.
Peptide classification landscape: An in-depth systematic literature review on peptide types, databases, datasets, predictors architectures and performance.

BMC Biol. 2025 Feb 27. 23(1): 63

MultiCycPermea: accurate and interpretable prediction of cyclic peptide permeability using a multimodal image-sequence model.

Zixu Wang, Yangyang Chen, Yifan Shang, Xiulong Yang, Wenqiong Pan, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng.

   BACKGROUND: Cyclic peptides, known for their high binding affinity and low toxicity, show potential as innovative drugs for targeting "undruggable" proteins. However, their therapeutic efficacy is often hindered by poor membrane permeability. Over the past decade, the FDA has approved an average of one macrocyclic peptide drug per year, with romidepsin being the only one targeting an intracellular site. Biological experiments to measure permeability are time-consuming and labor-intensive. Rapid assessment of cyclic peptide permeability is crucial for their development.
RESULTS: In this work, we proposed a novel deep learning model, dubbed as MultiCycPermea, for predicting cyclic peptide permeability. MultiCycPermea extracts features from both the image information (2D structural information) and sequence information (1D structural information) of cyclic peptides. Additionally, we proposed a substructure-constrained feature alignment module to align the two types of features. MultiCycPermea has made a leap in predictive accuracy. In the in-distribution setting of the CycPeptMPDB dataset, MultiCycPermea reduced the mean squared error (MSE) by approximately 44.83% compared to the latest model Multi_CycGT (0.29 vs 0.16). By leveraging visual analysis tools, MultiCycPermea can reveal the relationship between peptide modification structures and membrane permeability, providing insights to improve the membrane permeability of cyclic peptides.
CONCLUSIONS: MultiCycPermea provides an effective tool that accurately predicts the permeability of cyclic peptides, offering valuable insights for improving the membrane permeability of cyclic peptides. This work paves a new path for the application of artificial intelligence in assisting the design of membrane-permeable cyclic peptides.

Keywords:  Cyclic peptide; Deep learning; Interpretable model; Peptide membrane permeability

DOI:  https://doi.org/10.1186/s12915-025-02166-2
J Am Chem Soc. 2025 Feb 24.

Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display.

Sijie Wang, Franco F Faucher, Matilde Bertolini, Heeyoung Kim, Bingchen Yu, Li Cao, Katharina Roeltgen, Scott Lovell, Varun Shanker, Scott D Boyd, Lei Wang, Ralf Bartenschlager, Matthew Bogyo.

Peptide macrocycles are promising therapeutics for a variety of disease indications due to their overall metabolic stability and potential to make highly selective binding interactions with targets. Recent advances in covalent macrocycle peptide discovery, driven by phage and mRNA display methods, have enabled the rapid identification of highly potent and selective molecules from large libraires of diverse macrocycles. However, there are currently limited examples of macrocycles that can be used to disrupt protein-protein interactions and even fewer examples that function by formation of a covalent bond to a target protein. In this work, we describe a directed counter-selection method that enables identification of covalent macrocyclic ligands targeting a protein-protein interaction using a phage display screening platform. This method utilizes binary and ternary screenings of a chemically modified phage display library, employing the stable and weakly reactive aryl fluorosulfate electrophile. We demonstrate the utility of this approach using the SARS-CoV-2 spike-ACE2 protein-protein interaction and identify multiple covalent macrocyclic inhibitors that disrupt this interaction. The resulting compounds displayed antiviral activity against live virus that was irreversible after washout due to the covalent binding mechanism. These results highlight the potential of this screening platform for developing covalent macrocyclic drugs that disrupt protein-protein interactions with long lasting effects.

DOI: https://doi.org/10.1021/jacs.4c15843
Biochemistry. 2025 Feb 27.

Tumor Microenvironment pH-Sensitive Peptidomimetics for Targeted Anticancer Drug Delivery.

Biswanath Maity, Hariharan Moorthy, Thimmaiah Govindaraju.

Cell-penetrating peptides (CPPs) are known for their effective intracellular transport of bioactives such as therapeutic proteins, peptides, nucleic acid, and small molecule drugs. However, the excessive cationic charges that promote their membrane permeability result in nonselective delivery and cellular toxicity. In this study, we report a decamer cell-penetrating peptidomimetic, Hkd, designed to selectively deliver anticancer drugs into tumor cells in response to the acidic microenvironment. The pH-sensitive histidine (H) imidazole side chain undergoes protonation in acidic environments, facilitating membrane permeability. The rigid cyclic dipeptide (CDP) core (kd) of Hkd has multiple hydrogen bond donor and acceptor sites, enabling selective interaction-driven cellular uptake. Pharmacokinetic studies revealed the excellent serum stability of Hkd. Cellular uptake studies of Hkd showed improved uptake at a lower pH than physiological pH. Conjugation of Hkd to the anticancer drug camptothecin (Cpt) reduced nonselective drug transport to normal cells while effectively delivering the drug into cancerous cells at the tumor microenvironment pH and retaining the therapeutic potential of the drug. The systematic design of pH-sensitive peptidomimetics offers a viable method to overcome the challenges of stability and selectivity faced by traditional highly cationic CPPs, potentially expanding the application range of this delivery system.

DOI: https://doi.org/10.1021/acs.biochem.4c00657
Biointerphases. 2025 Jan 01. pii: 011006. [Epub ahead of print]20(1):

Role of sequence length and functionalization in interactions of bioconjugated peptides with mitomembranes.

Son V Nguyen, Roy P Planalp, Harish Vashisth.

Cell-penetrating peptides are efficient tools for intracellular delivery of a variety of cargoes. In this study, we explored the effect of chain length, side chain chemistry, and the locations of conjugated molecules on the interaction between iron-chelating peptides and a mitochondrial-mimicking membrane. We report that a longer chain length enhanced peptide/membrane interactions, and conjugation at the N-terminus lowered the free-energy barrier for peptide translocation across the membrane. Peptides containing Phe side chains and those containing modified Phe (cyclohexane) side chains showed comparable peptide/membrane energetics and translocation energy barriers. Using steered molecular dynamics (SMD) simulations, we further probed the mechanistic details of translocation of each N-terminated peptide across the membrane and compared their metastable states. At a higher steering velocity, the peptide adopted a compact structure due to frequent π-π interactions among conjugated molecules, but at lower steering velocities, each N-terminated peptide adopted an extended structure. This structure allowed cationic residues to maximize their interactions with phosphate headgroups in the mitomembrane. The hydrophobic residues also formed interactions with the lipid acyl tails, facilitating the passage of peptides across the membrane with decreased free energy barriers. Our results highlight the significance of peptide chain length and conjugation in facilitating peptide transport across the membrane.

DOI: https://doi.org/10.1116/6.0004197
Pharmaceuticals (Basel). 2025 Feb 08. pii: 234. [Epub ahead of print]18(2):

Synthesis and Evaluation of 68Ga- and 177Lu-Labeled [diF-Pro14]Bombesin(6-14) Analogs for Detection and Radioligand Therapy of Gastrin-Releasing Peptide Receptor-Expressing Cancer.

Lei Wang, Chao-Cheng Chen, Devon Chapple, Antonio A W L Wong, Sara Kurkowska, Wing Sum Lau, Carlos F Uribe, François Bénard, Kuo-Shyan Lin.

  Background/Objectives: Overexpressed in various solid tumors, the gastrin-releasing peptide receptor (GRPR) is a promising target for cancer diagnosis and therapy. However, the high pancreas uptake of the current clinically evaluated GRPR-targeted radiopharmaceuticals limits their applications. In this study, we replaced the Pro14 residue in our previously reported GRPR-targeted LW02056 and ProBOMB5 with 4,4-difluoroproline (diF-Pro) to obtain an agonist LW02060 (DOTA-Pip-[D-Phe6,Tle10,NMe-His12,diF-Pro14]Bombesin(6-14)) and an antagonist LW02080 (DOTA-Pip-[D-Phe6,NMe-Gly11,Leu13(ψ)diF-Pro14]Bombesin(6-14)), respectively. Methods/Results: The binding affinities (Ki) of Ga-LW02060, Ga-LW02080, Lu-LW02060, and Lu-LW02080 were measured by in vitro competition binding assays using PC-3 cells and were found to be 5.57 ± 2.47, 21.7 ± 6.69, 8.00 ± 2.61, and 32.1 ± 8.14 nM, respectively. The 68Ga- and 177Lu-labeled ligands were obtained in 36-75% decay-corrected radiochemical yields with >95% radiochemical purity. PET imaging, SPECT imaging, and ex vivo biodistribution studies were conducted in PC-3 tumor-bearing mice. Both [68Ga]Ga-LW02060 and [68Ga]Ga-LW02080 enabled clear tumor visualization in PET images at 1 h post-injection (pi). Tumor uptake values of [68Ga]Ga-LW02060 and [68Ga]Ga-LW02080 at 1 h pi were 16.8 ± 2.70 and 7.36 ± 1.33 %ID/g, respectively, while their pancreas uptake values were 3.12 ± 0.89 and 0.38 ± 0.04 %ID/g, respectively. Compared to [177Lu]Lu-LW02080, [177Lu]Lu-LW02060 showed higher tumor uptake at all time points (1, 4, 24, 72, and 120 h pi). However, fast tumor clearance was observed for both [177Lu]Lu-LW02060 and [177Lu]Lu-LW02080. Conclusions: Our data demonstrate that [68Ga]Ga-LW02060 is promising for clinical translation for the detection of GRPR-expressing tumor lesions. However, further optimizations are needed for [177Lu]Lu-LW02060 and [177Lu]Lu-LW02080 to prolong tumor retention for therapeutic applications.

Keywords:  4,4-difluoroproline; gallium-68; gastrin-releasing peptide receptor; lutetium-177; pancreas uptake

DOI:  https://doi.org/10.3390/ph18020234
Chembiochem. 2025 Feb 26. e202500052

Recent Chemical Biology Insights Towards Reversible Stapled Peptides.

Ying Chen, Chuan Dai, Jinyan Han, Yun Xing, Feng Yin, Zigang Li.

  Peptides are increasingly recognized for their advantages over small molecules in the modulation of protein-protein interactions (PPIs), particularly in terms of potency and selectivity. "Staples" can be coupled to the amino acid residues of linear peptides to limit their conformation, improving the stability, membrane permeability, and resistance to proteolysis of peptides. However, the addition of staples can sometimes lead to the complete inactivation of the original peptide or result in extensive interactions that complicate biophysical analysis. Besides, reversible peptide probes are also indispensable tools for thoroughly investigating PPIs. Consequently, the development of diverse reversible stapling techniques for stapled peptides is crucial for broadening the applications of peptide molecules in drug discovery, drug delivery, and as tools in chemical biology research. This review aims to summarize representative chemical design strategies for reversible stapled peptides, focusing on reversible chemical stapling methods involving sulfhydryl, amino, and methylthio groups, as well as reversible modulation of the conformational states of stapled peptides. Additionally, we demonstrate some intriguing biological applications of stapled peptides and, finally, suggest future research directions in the field that will serve as references for related researchers.

Keywords:  Reversible stapled peptide * Linear peptide * Stapling methodology * Reversible conformation * Biological application

DOI:  https://doi.org/10.1002/cbic.202500052
Chemistry. 2025 Feb 25. e202500331

Twisted Amide-Mediated Synthesis and Rapid Structure-Activity Relationship Study of Medium-Sized Cyclic Peptides.

Takefumi Kuranaga, Ai Koyama, Junta Asano, Takumi Matsumoto, Hideaki Kakeya.

  Medium-sized cyclic peptides are expected to be ideal drug leads because these peptides combine the advantages, while compensating for the disadvantages, of small molecules and antibodies. Although medium-sized peptides can be produced by chemical synthesis, two major problems, namely (i) Cα-epimerization during C-terminal modification and (ii) side reactions in the cyclization, remain to be solved. These issues have hampered the synthesis of pure materials for bioassays, making it difficult to accomplish accurate structure-activity relationship (SAR) studies. Herein, we report an efficient synthesis of medium-sized cyclic peptides based on the twisted amide-mediated amidation strategy. First, a variety of linear peptides were synthesized by the "inverse" peptide synthesis and fragment coupling. Second, the C-terminus of the linear peptides were converted to twisted amides, which were then reacted with a variety of α-amino acyl sulfonamides, realizing the rapid C-terminal diversification of peptides. Finally, the resulting linear peptides were cyclized by the intramolecular twisted amide-mediated amidation to afford stereochemically pure cyclic peptides. Using this strategy, total synthesis of acyl-surugamide A, the stereoselective synthesis of 13 non-natural analogs, and the discovery of potent antimicrobial/antifungal peptides beyond the natural product were also achieved.

Keywords:  SAR studies; amide bond formation; peptide synthesis; peptides; surugamides

DOI:  https://doi.org/10.1002/chem.202500331
Angew Chem Int Ed Engl. 2025 Feb 25. e202501488

Structure-guided development of chemically tailored peptide binders of RNF43/ZNRF3 to enable versatile design of membrane protein-targeting PROTACs.

Man Pan, Jibin Cui, Qingyun Zheng, Yicheng Weng, Xiaoguo Zhai, Zhen Su, YunXiang Du, Xiaoxiong Wei, Yuanyuan Yu, Qian Qu.

  Targeted membrane protein degradation using cell surface E3 ligases RNF43/ZNRF3 via proteolysis targeting chimeras (PROTACs) represents an effective strategy for treating membrane drug targets that cannot be fully inhibited using traditional inhibitors. Several ingenious chimeras have been developed to tether RNF43/ZNRF3 to target membrane proteins, resulting in the degradation of targets at sub-nanomolar concentrations both in vitro and in vivo. However, currently available RNF43/ZNRF3 binders are genetically encoded and have poor plasticity, which limits the design and promotion of such PROTACs. Here, we exploited the alphafold predicted complex structures of ligand-bound RNF43/ZNRF3 and developed a class of chemically tailored peptide binders for ZNRF3/RNF43. With these peptide binders that can be conveniently prepared by de novo peptide synthesis, we established a new membrane protein degradation platform that allows versatile modular design and targeted degradation of clinically relevant membrane proteins, i.e. PD-L1 and EGFR. This study presents a new subtype within the PROTAC field to develop therapeutic peptides targeting membrane proteins.

Keywords:  Targeted membrane protein degradation * Cell-surface E3 ligases * Peptide binders * Chemically tailored degraders * Synthesis and refolding of disulfide-rich peptide

DOI:  https://doi.org/10.1002/anie.202501488
J Chem Inf Model. 2025 Feb 24.

Head-to-Tail Cyclization Enhances Ice-Growth Inhibition by Linear Threonine Oligomers.

Haipeng Wang, Xuyang Liu, Wensheng Cai, Xueguang Shao.

Developing short antifreeze peptides with low immunogenicity is considered to be a promising strategy for improving cryopreservation. Inspired by the design principles of cyclic peptide drugs characterized by high stability and strong affinity, we propose to use the cyclization strategy as a principle for the design of antifreeze peptides, aiming to enhance their structural stability and ice-binding ability, thereby significantly improving their antifreeze activity. In this study, we choose linear threonine oligomers (L-(Thr)n), composed of common and biocompatible threonine residues, to investigate the mechanism and efficacy of cyclization. Molecular dynamics (MD) simulations are used to compare the ice-growth inhibition ability of a series of linear oligomers and their corresponding cyclic counterparts (49 molecular systems) on different ice planes, resulting in 80.8 μs MD trajectories. A detailed analysis of conformational changes during inhibition and their correlation with inhibitory efficiency reveals that conformational variability is detrimental to the binding of L-(Thr)n to ice, while β-sheet-like conformation has a significant advantage in inhibiting ice growth and is identified as a key factor for the superior performance of cyclized oligomers (C-(Thr)n) over their linear counterparts. Encouragingly, we find that C-(Thr)12 exhibits the most prominent performance, surpassing previously reported cyclic peptides of similar size due to its enhanced structural stability, superior ice binding, coverage, and antiengulfment capabilities. This study provides valuable insights into the design of small-sized ice-growth inhibitors through head-to-tail cyclization of linear oligomers. However, it should be noted that our findings are based purely on computational simulations, and experimental validation in actual cryopreservation conditions remains necessary.

DOI: https://doi.org/10.1021/acs.jcim.4c02418
Mol Pharm. 2025 Feb 24.

Development and Evaluation of 68Ga-Labeled TMTP1-Based Cyclic Peptide Probes for Targeting Hepatocellular Carcinoma.

Yesen Li, Yanjie Wang, Yaoxuan Wang, Jinxiong Huang, Zhide Guo.

  This study focused on the development and evaluation of four [68Ga]-labeled cyclic TMTP1 peptide-based probes for targeting highly metastatic hepatocellular carcinoma (HCC). The probes─[68Ga]Ga-N-G-NVvRQ, [68Ga]Ga-c[K(N)NVvRQ], [68Ga]Ga-c[K(N)NVVRQ], and [68Ga]Ga-c[K(N)NVvRQ]2─were designed using a head-to-tail cyclization strategy to enhance their stability, improve tumor targeting, and reduce uptake in nontarget organs. The microPET imaging results showed that although tumor uptake for all four probes was similar at each time point, renal evaluation revealed that [68Ga]Ga-c[K(N)NVvRQ] had the lowest value at 15 min (1.90 ± 0.87%ID/g), significantly outperforming linear analog [68Ga]Ga-N-G-NVvRQ (2.87 ± 0.86%ID/g) and dimeric peptide, [68Ga]Ga-c[K(N)NVvRQ]2 (3.92 ± 0.68%ID/g), and the probe exhibited the lowest physiological uptake across major organs. At 30 min, the liver uptake of [68Ga]Ga-c[K(N)NVvRQ] was 0.29 ± 0.08%ID/g, with a tumor-to-liver (T/L) ratio of 2.45 ± 0.03. This low nonspecific uptake in normal organs contributed to high-contrast PET imaging, facilitating the diagnosis of small tumor lesions. In addition, the probe demonstrated sustained low renal radioactivity retention, which may offer potential benefits for minimizing additional radioactive damage to the kidneys. Overall, [68Ga]Ga-c[K(N)NVvRQ] achieved a good balance between strong tumor uptake and low nonspecific uptake in organs (especially in kidneys), making it an ideal candidate for further investigation in HCC imaging applications.

Keywords:  PET imaging; TMTP1; cyclic peptide; dimerization; hepatocellular carcinoma

DOI:  https://doi.org/10.1021/acs.molpharmaceut.4c01123
Biophys Chem. 2025 Feb 20. pii: S0301-4622(25)00030-4. [Epub ahead of print]320-321 107418

Transmembrane clustering of short amyloid peptide fragments: A coarse grained molecular dynamics study.

Aleksandra Drajkowska, Andrzej Molski.

  Toxicity of amyloid peptides has been linked to peptide aggregation and interactions with lipid bilayers. In this work we use coarse-grained molecular dynamics simulations to study aggregation and transmembrane clustering of short amyloid peptide fragments, Aβ(25-35) and Aβ(29-42), in the presence of dipalmitoylphosphatidylcholine (DPPC) and palmitoylolyoilphosphatidylcholine (POPC) bilayers. First, we explored peptide aggregation starting from free monomers placed at the interface of preformed lipid membranes. At low peptide concentrations, no transmembrane clusters were formed in DPPC or POPC membranes. At high peptide concentration, the longer fragment, Aβ(29-42), showed strong peptide-peptide interactions that led to spontaneous formation of transmembrane clusters in POPC and DPPC. However, the shorter fragment, Aβ(25-35), did not form transmembrane clusters within the simulation time in either bilayer. To overcome the free-energy barriers to transmembrane clustering, we changed the simulation protocol and started simulations from random mixtures of peptides, lipids, and solvent. Using this system self-assembly approach, we found that both Aβ(25-35) and Aβ(29-42) can form stable transmembrane clusters in DPPC and POPC bilayers. Our study suggests that the cooperative effects induced by a localized increase in peptide density may be a mechanism of membrane disruption by short amyloid peptide fragments.

Keywords:  Amyloid peptides; Cooperative effects; Lipid membranes; Transmembrane clustering

DOI:  https://doi.org/10.1016/j.bpc.2025.107418
Comput Biol Med. 2025 Feb 22. pii: S0010-4825(25)00171-4. [Epub ahead of print]188 109821

Peptide classification landscape: An in-depth systematic literature review on peptide types, databases, datasets, predictors architectures and performance.

Muhammad Nabeel Asim, Tayyaba Asif, Faiza Mehmood, Andreas Dengel.

  Peptides are gaining significant attention in diverse fields such as the pharmaceutical market has seen a steady rise in peptide-based therapeutics over the past six decades. Peptides have been utilized in the development of distinct applications including inhibitors of SARS-COV-2 and treatments for conditions like cancer and diabetes. Distinct types of peptides possess unique characteristics, and development of peptide-specific applications require the discrimination of one peptide type from others. To the best of our knowledge, approximately 230 Artificial Intelligence (AI) driven applications have been developed for 22 distinct types of peptides, yet there remains significant room for development of new predictors. A Comprehensive review addresses the critical gap by providing a consolidated platform for the development of AI-driven peptide classification applications. This paper offers several key contributions, including presenting the biological foundations of 22 unique peptide types and categorizes them into four main classes: Regulatory, Therapeutic, Nutritional, and Delivery Peptides. It offers an in-depth overview of 47 databases that have been used to develop peptide classification benchmark datasets. It summarizes details of 288 benchmark datasets that are used in development of diverse types AI-driven peptide classification applications. It provides a detailed summary of 197 sequence representation learning methods and 94 classifiers that have been used to develop 230 distinct AI-driven peptide classification applications. Across 22 distinct types peptide classification tasks related to 288 benchmark datasets, it demonstrates performance values of 230 AI-driven peptide classification applications. It summarizes experimental settings and various evaluation measures that have been employed to assess the performance of AI-driven peptide classification applications. The primary focus of this manuscript is to consolidate scattered information into a single comprehensive platform. This resource will greatly assist researchers who are interested in developing new AI-driven peptide classification applications.

Keywords:  Artificial intelligence based peptide classification; Benchmark peptides classification datasets; Delivery peptides; Nutritional peptides; Peptide classification tasks; Peptides classification; Peptides databases; Peptidomics; Predictive pipelines; Regulatory peptides; Sensory peptides; Signaling peptides; State-of-the-art peptides classification predictor; Therapeutic peptides

DOI:  https://doi.org/10.1016/j.compbiomed.2025.109821