bims-cepepe 2024-07-28 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2024–07–28
thirteen papers selected by
Henry Lamb, Queensland University of Technology

Cyclic tachyplesin I kills proliferative, non-proliferative and drug-resistant melanoma cells without inducing resistance.
Small Natural Cyclic Peptides from DBAASP Database.
Cell-Penetrating Peptide-Mediated Biomolecule Transportation in Artificial Lipid Vesicles and Living Cells.
An approach for the intracellular delivery of IgG via enzymatic ligation with a cell-permeable attenuated cationic amphiphilic lytic peptide.
Predicting Peptide Permeability Across Diverse Barriers: A Systematic Investigation.
Development and biological evaluation of 68Ga-labeled peptides for potential application in HER2-positive colorectal cancer.
Macrophage-engaging peptidic bispecific antibodies (pBsAbs) for immunotherapy via a facile bioconjugation strategy.
Structure of Designer Antibody-like Peptides Binding to the Human C5a with Potential to Modulate the C5a Receptor Signaling.
Disulfide bond replacement with non-reducible side chain to tail macrolactamization for the development of potent and selective CXCR4 peptide antagonists endowed with flanking binding sites.
PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations.
Trifluoroacetic Acid Mediated Additive-Free Late-Stage Native Peptide Cyclization to Form Disulfide Mimetics via Thioketalization with Ketones.
Chiral inversion induced by aromatic interactions in short peptide assembly.
Quaternized antimicrobial peptide mimics based on harmane as potent anti-MRSA agents by multi-target mechanism covering cell wall, cell membrane and intracellular targets.

Pharmacol Res. 2024 Jul 18. pii: S1043-6618(24)00243-3. [Epub ahead of print]207 107298

Cyclic tachyplesin I kills proliferative, non-proliferative and drug-resistant melanoma cells without inducing resistance.

Aurélie H Benfield, Felicitas Vernen, Reuben S E Young, Ferran Nadal-Bufí, Henry Lamb, Heinz Hammerlindl, David J Craik, Helmut Schaider, Nicole Lawrence, Stephen J Blanksby, Sónia Troeira Henriques.

  Acquired drug resistance is the major cause for disease recurrence in cancer patients, and this is particularly true for patients with metastatic melanoma that carry a BRAF V600E mutation. To address this problem, we investigated cyclic membrane-active peptides as an alternative therapeutic modality to kill drug-tolerant and resistant melanoma cells to avoid acquired drug resistance. We selected two stable cyclic peptides (cTI and cGm), previously shown to have anti-melanoma properties, and compared them with dabrafenib, a drug used to treat cancer patients with the BRAF V600E mutation. The peptides act via a fast membrane-permeabilizing mechanism and kill metastatic melanoma cells that are sensitive, tolerant, or resistant to dabrafenib. Melanoma cells do not become resistant to long-term treatment with cTI, nor do they evolve their lipid membrane composition, as measured by lipidomic and proteomic studies. In vivo studies in mice demonstrated that the combination treatment of cTI and dabrafenib resulted in fewer metastases and improved overall survival. Such cyclic membrane-active peptides are thus well suited as templates to design new anticancer therapeutic strategies.

Keywords:  Anticancer peptides; Antimicrobial peptides; Drug resistance; Lipid metabolism; Membrane lipids

DOI:  https://doi.org/10.1016/j.phrs.2024.107298
Pharmaceuticals (Basel). 2024 Jun 27. pii: 845. [Epub ahead of print]17(7):

Small Natural Cyclic Peptides from DBAASP Database.

Evgenia Alimbarashvili, Natia Samsonidze, Maia Grigolava, Malak Pirtskhalava.

  Antimicrobial peptides (AMPs) are promising tools for combating microbial resistance. However, their therapeutic potential is hindered by two intrinsic drawbacks-low target affinity and poor in vivo stability. Macrocyclization, a process that improves the pharmacological properties and bioactivity of peptides, can address these limitations. As a result, macrocyclic peptides represent attractive drug candidates. Moreover, many drugs are macrocycles that originated from natural product scaffolds, suggesting that nature offers solutions to the challenges faced by AMPs. In this review, we explore natural cyclic peptides from the DBAASP database. DBAASP is a comprehensive repository of data on antimicrobial/cytotoxic activities and structures of peptides. We analyze the data on small (≤25 AA) ribosomal and non-ribosomal cyclic peptides from DBAASP according to their amino acid composition, bonds used for cyclization, targets they act on, and mechanisms of action. This analysis will enhance our understanding of the small cyclic peptides that nature has provided to defend living organisms.

Keywords:  AMPs; antimicrobial peptides; cyclic peptides; macrocyclization

DOI:  https://doi.org/10.3390/ph17070845
Molecules. 2024 Jul 16. pii: 3339. [Epub ahead of print]29(14):

Cell-Penetrating Peptide-Mediated Biomolecule Transportation in Artificial Lipid Vesicles and Living Cells.

Akari Miwa, Koki Kamiya.

  Signal transduction and homeostasis are regulated by complex protein interactions in the intracellular environment. Therefore, the transportation of impermeable macromolecules (nucleic acids, proteins, and drugs) that control protein interactions is essential for modulating cell functions and therapeutic applications. However, macromolecule transportation across the cell membrane is not easy because the cell membrane separates the intra/extracellular environments, and the types of molecular transportation are regulated by membrane proteins. Cell-penetrating peptides (CPPs) are expected to be carriers for molecular transport. CPPs can transport macromolecules into cells through endocytosis and direct translocation. The transport mechanism remains largely unclear owing to several possibilities. In this review, we describe the methods for investigating CPP conformation, translocation, and cargo transportation using artificial membranes. We also investigated biomolecular transport across living cell membranes via CPPs. Subsequently, we show not only the biochemical applications but also the synthetic biological applications of CPPs. Finally, recent progress in biomolecule and nanoparticle transportation via CPPs into specific tissues is described from the viewpoint of drug delivery. This review provides the opportunity to discuss the mechanism of biomolecule transportation through these two platforms.

Keywords:  artificial cell model; biomolecule transport; cell-penetrating peptide; lipid vesicle; membrane-active peptide; protein transport; therapy

DOI:  https://doi.org/10.3390/molecules29143339
Bioorg Med Chem. 2024 Jul 24. pii: S0968-0896(24)00249-9. [Epub ahead of print]111 117835

An approach for the intracellular delivery of IgG via enzymatic ligation with a cell-permeable attenuated cationic amphiphilic lytic peptide.

Yoshimasa Kawaguchi, Sakahiro Terada, Shiroh Futaki.

  Achieving effective intracellular delivery of therapeutic molecules such as antibodies (IgG) is a challenge in biomedical research and pharmaceutical development. Conjugation of IgG with a cell-penetrating peptide is a rational approach. Here, not only the efficacy of the conjugates in internalizing into cells, but also the physicochemical property of the conjugates allowing their solubilized states in solution without forming aggregates are critical. In this study, we have shown that the first requirement can be addressed using a cell-permeable attenuated cationic amphiphilic lytic (CP-ACAL) peptide, L17ER4. The second requirement can be addressed by ligation of IgG to L17ER4 using sortase A, where the use of a linker of appropriate chain length is also important. For evaluation, the intracellular delivery efficacy was studied using conjugate structures with different orientations and conjugation modes of L17ER4 in ligation to a model protein, green fluorescent protein fused to a nuclear localization signal (NLS-EGFP). The effect of tetraarginine positioning in the L17ER4 sequence was also investigated. Following these studies, an optimized peptide sequence containing L17ER4 was ligated to an anti-green fluorescent protein (GFP) IgG bearing a sortase A recognition sequence. Treatment of the cells with the conjugate of anti-GFP IgG and L17ER4 resulted in a high efficiency of cytosolic translocation of the conjugate and the binding to the target protein in the cell without significant aggregate formation. The feasibility of the d-form of L17ER4 as a CP-ACAL was also confirmed.

Keywords:  Antibody; Cell-permeable attenuated amphiphilic lytic peptide; Conjugate; Cytosolic protein delivery; L17ER4; sortase A

DOI:  https://doi.org/10.1016/j.bmc.2024.117835
Mol Pharm. 2024 Jul 20.

Predicting Peptide Permeability Across Diverse Barriers: A Systematic Investigation.

Xiaorong Tan, Qianhui Liu, Yanpeng Fang, Yingli Zhu, Fei Chen, Wenbin Zeng, Defang Ouyang, Jie Dong.

  Peptide-based therapeutics hold immense promise for the treatment of various diseases. However, their effectiveness is often hampered by poor cell membrane permeability, hindering targeted intracellular delivery and oral drug development. This study addressed this challenge by introducing a novel graph neural network (GNN) framework and advanced machine learning algorithms to build predictive models for peptide permeability. Our models offer systematic evaluation across diverse peptides (natural, modified, linear and cyclic) and cell lines [Caco-2, Ralph Russ canine kidney (RRCK) and parallel artificial membrane permeability assay (PAMPA)]. The predictive models for linear and cyclic peptides in Caco-2 and RRCK cell lines were constructed for the first time, with an impressive coefficient of determination (R2) of 0.708, 0.484, 0.553, and 0.528 in the test set, respectively. Notably, the GNN framework behaved better in permeability prediction with larger data sets and improved the accuracy of cyclic peptide prediction in the PAMPA cell line. The R2 increased by about 0.32 compared with the reported models. Furthermore, the important molecular structural features that contribute to good permeability were interpreted; the influence of cell lines, peptide modification, and cyclization on permeability were successfully revealed. To facilitate broader use, we deployed these models on the user-friendly KNIME platform (https://github.com/ifyoungnet/PharmPapp). This work provides a rapid and reliable strategy for systematically assessing peptide permeability, aiding researchers in drug delivery optimization, peptide preselection during drug discovery, and potentially the design of targeted peptide-based materials.

Keywords:  cell permeability; drug delivery; graph neural network; machine learning; peptide; permeability prediction

DOI:  https://doi.org/10.1021/acs.molpharmaceut.4c00478
Bioorg Chem. 2024 Jul 15. pii: S0045-2068(24)00550-9. [Epub ahead of print]151 107645

Development and biological evaluation of 68Ga-labeled peptides for potential application in HER2-positive colorectal cancer.

Jinglin Zhang, Yixiang Lin, Jingyue Gao, Yuan Pan, Guihua Hou, Chun Guo, Feng Gao.

  Colorectal cancer (CRC) is among the most lethal and prevalent malignancies in the world. Human epidermal growth factor receptor 2 (HER2) is a promising target for the diagnosis and treatment of CRC. In this study, we aimed to design, synthesize and label peptide-based positron emission tomography (PET) tracers targeting HER2-positive CRC, namely [68Ga]Ga-ES-01 and [68Ga]Ga-ES-02. The results show that [68Ga]Ga-ES-01 and [68Ga]Ga-ES-02 possessed hydrophilicity, rapid pharmacokinetic properties and excellent stabilities. [68Ga]Ga-ES-02 demonstrated higher binding affinity (Kd = 24.29 ± 4.95 nM) toward the HER2 in CRC. In HER2-positive HT-29 CRC xenograft mouse model, PET study showed specific tumor uptake after injection of [68Ga]Ga-ES-02 (SUV15min max = 0.87 ± 0.03; SUV30min max = 0.64 ± 0.02). In biodistribution study, the T/M ratios of 68Ga-ES-02 at 30 min after injection reached a maximum of 4.07 ± 0.34. In summary, we successfully synthesized and evaluated two novel peptide-based PET tracers. Our data demonstrate that [68Ga]Ga-ES-01/02 is capable of HER2-positive colorectal cancer, with [68Ga]Ga-ES-02 showing superior imaging effect, enhanced targeting, and increased specificity.

Keywords:  (68)Ga; Colorectal cancer (CRC); Human epidermal growth factor receptor 2 (HER2); Labelling; Positron emission tomography (PET); Radiotracer

DOI:  https://doi.org/10.1016/j.bioorg.2024.107645
Chem Sci. 2024 Jul 24. 15(29): 11272-11278

Macrophage-engaging peptidic bispecific antibodies (pBsAbs) for immunotherapy via a facile bioconjugation strategy.

Chihao Shao, Bo Tang, Jacky C H Chu, Kwai Man Lau, Wai-Ting Wong, Chi-Ming Che, William C S Tai, Wing-Tak Wong, Clarence T T Wong.

Bispecific antibodies are artificial molecules that fuse two different antigen-binding sites of monoclonal antibodies into one single entity. They have emerged as a promising next-generation anticancer treatment. Despite the fascinating applications of bispecific antibodies, the design and production of bispecific antibodies remain tedious and challenging, leading to a long R&D process and high production costs. We herein report an unprecedented strategy to cyclise and conjugate tumour-targeting peptides on the surface of a monoclonal antibody to form a novel type of bispecific antibody, namely the peptidic bispecific antibody (pBsAb). Such design combines the merits of highly specific monoclonal antibodies and serum-stable cyclic peptides that endows an additional tumour-targeting ability to the monoclonal antibody for binding with two different antigens. Our results show that the novel pBsAb, which comprises EGFR-binding cyclic peptides and an anti-SIRP-α monoclonal antibody, could serve as a macrophage-engaging bispecific antibody to initiate enhanced macrophage-cancer cell interaction and block the "don't eat me" signal between CD47-SIRP-α, as well as promoting antibody-dependent cellular phagocytosis and 3D cell spheroid infiltration. These findings give rise to a new type of bispecific antibody and a new platform for the rapid generation of new bispecific antibodies for research and potential therapeutic uses.

DOI: https://doi.org/10.1039/d4sc00851k
J Med Chem. 2024 Jul 25.

Structure of Designer Antibody-like Peptides Binding to the Human C5a with Potential to Modulate the C5a Receptor Signaling.

Manaswini Ghosh, Pulkit Kr Gupta, Lalita Mohan Behera, Soumendra Rana.

C5a is an integral glycoprotein of the complement system that plays an important role in inflammation and immunity. The physiological concentration of C5a is observed to be elevated under various immunoinflammatory pathophysiological conditions in humans. The pathophysiology of C5a is linked to the "two-site" protein-protein interactions (PPIs) with two genomically related receptors, such as C5aR1 and C5aR2. Therefore, pharmacophores that can potentially block the PPIs between C5a-C5aR1 and C5a-C5aR2 have tremendous potential for development as future therapeutics. Notably, the FDA has already approved antibodies that target the precursors of C5a (Eculizumab, 148 kDa) and C5a (Vilobelimab, 149 kDa) for marketing as complement-targeted therapeutics. In this context, the current study reports the structural characterization of a pair of synthetic designer antibody-like peptides (DePA and DePA1; ≤3.8 kDa) that bind to hotspot regions on C5a and also demonstrates potential traits to neutralize the function of C5a under pathophysiological conditions.

DOI: https://doi.org/10.1021/acs.jmedchem.4c00961
Eur J Med Chem. 2024 Jul 14. pii: S0223-5234(24)00549-X. [Epub ahead of print]276 116669

Disulfide bond replacement with non-reducible side chain to tail macrolactamization for the development of potent and selective CXCR4 peptide antagonists endowed with flanking binding sites.

Anna Maria Trotta, Stefano Tomassi, Gaetana Di Maiolo, Caterina Ieranò, Cinzia Vetrei, Crescenzo D'Alterio, Francesco Merlino, Anna Messere, Antonia D'Aniello, Alessandra Del Bene, Vincenzo Mazzarella, Michele Roggia, Benito Natale, Roberto Cutolo, Erica Campagna, Salvatore Mottola, Rosita Russo, Angela Chambery, Rosaria Benedetti, Lucia Altucci, Sandro Cosconati, Stefania Scala, Salvatore Di Maro.

The present study describes a small library of peptides derived from a potent and selective CXCR4 antagonist (3), wherein the native disulfide bond is replaced using a side-chain to tail macrolactamization technique to vary ring size and amino acid composition. The peptides were preliminary assessed for their ability to interfere with the interaction between the receptor and anti-CXCR4 PE-conjugated antibody clone 12G5. Two promising candidates (13 and 17) were identified and further evaluated in a125I-CXCL12 competition binding assay, exhibiting IC50 in the low-nanomolar range. Furthermore, both candidates displayed high selectivity towards CXCR4 with respect to the cognate receptor CXCR7, ability to block CXCL12-dependent cancer cell migration, and receptor internalization, albeit at a higher concentration compared to 3. Molecular modeling studies on 13 and 17 produced a theoretical model that may serve as a guide for future modifications, aiding in the development of analogs with improved affinity. Finally, the study provides valuable insights into developing therapeutic agents targeting CXCR4-mediated processes, demonstrating the adaptability of our lead peptide 3 to alternative cyclization approaches and offering prospects for comprehensive investigations into the receptor region's interaction with its C-terminal region.

DOI: https://doi.org/10.1016/j.ejmech.2024.116669
J Phys Chem B. 2024 Jul 23.

PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations.

Jinan Wang, Kushal Koirala, Hung N Do, Yinglong Miao.

Predicting protein-peptide interactions is crucial for understanding peptide binding processes and designing peptide drugs. However, traditional computational modeling approaches face challenges in accurately predicting peptide-protein binding structures due to the slow dynamics and high flexibility of the peptides. Here, we introduce a new workflow termed "PepBinding" for predicting peptide binding structures, which combines peptide docking, all-atom enhanced sampling simulations using the Peptide Gaussian accelerated Molecular Dynamics (Pep-GaMD) method, and structural clustering. PepBinding has been demonstrated on seven distinct model peptides. In peptide docking using HPEPDOCK, the peptide backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures ranged from 3.8 to 16.0 Å, corresponding to the medium to inaccurate quality models according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. The Pep-GaMD simulations performed for only 200 ns significantly improved the docking models, resulting in five medium and two acceptable quality models. Therefore, PepBinding is an efficient workflow for predicting peptide binding structures and is publicly available at https://github.com/MiaoLab20/PepBinding.

DOI: https://doi.org/10.1021/acs.jpcb.4c02047
Org Lett. 2024 Jul 24.

Trifluoroacetic Acid Mediated Additive-Free Late-Stage Native Peptide Cyclization to Form Disulfide Mimetics via Thioketalization with Ketones.

Yisa Xiao, Haiyan Zhou, Han Liu, Xuechen Li.

Peptide cyclization is often used to introduce conformational rigidity and to enhance the physiological stability of the peptide. This study presents a novel late-stage cyclization method for creating thioketal cyclic peptides from bis-cysteine peptides and drugs. Symmetrical cyclic ketones and acetone were found to react with bis-cysteine unprotected peptides efficiently to form thioketal linkages in trifluoroacetic acid (TFA) without any other additive. The attractive features of this method include high chemoselectivity, operational simplicity, and robustness. In addition, TFA as the reaction solvent can dissolve any unprotected peptide. As a showcase, the dimethyl thioketal versions of lanreotide and octreotide were prepared and evaluated, both of which showed much improved reductive stability and comparable activity.

DOI: https://doi.org/10.1021/acs.orglett.4c02464
Nat Commun. 2024 Jul 23. 15(1): 6186

Chiral inversion induced by aromatic interactions in short peptide assembly.

Kai Qi, Hao Qi, Muhan Wang, Xiaoyue Ma, Yan Wang, Qiang Yao, Wenliang Liu, Yurong Zhao, Jiqian Wang, Yuefei Wang, Wei Qi, Jun Zhang, Jian R Lu, Hai Xu.

Although hydrophobic interactions provide the main driving force for initial peptide aggregation, their role in regulating suprastructure handedness of higher-order architectures remains largely unknown. We here interrogate the effects of hydrophobic amino acids on handedness at various assembly stages of peptide amphiphiles. Our studies reveal that relative to aliphatic side chains, aromatic side chains set the twisting directions of single β-strands due to their strong steric repulsion to the backbone, and upon packing into multi-stranded β-sheets, the side-chain aromatic interactions between strands form the aromatic ladders with a directional preference. This ordering not only leads to parallel β-sheet arrangements but also induces the chiral flipping over of single β-strands within a β-sheet. In contrast, the lack of orientational hydrophobic interactions in the assembly of aliphatic peptides implies no chiral inversion upon packing into β-sheets. This study opens an avenue to harness peptide aggregates with targeted handedness via aromatic side-chain interactions.

DOI: https://doi.org/10.1038/s41467-024-50448-0
Eur J Med Chem. 2024 Jul 04. pii: S0223-5234(24)00537-3. [Epub ahead of print]276 116657

Quaternized antimicrobial peptide mimics based on harmane as potent anti-MRSA agents by multi-target mechanism covering cell wall, cell membrane and intracellular targets.

Jinyi Liu, Yidan Cao, Chenggong Xu, Runchu Li, Yingyan Xiong, Yi Wei, Xianghui Meng, Wenjia Dan, Chunbo Lu, Jiangkun Dai.

  Infectious disease caused by methicillin-resistant Staphylococcus aureus (MRSA) seriously threatens public health. The design of antimicrobial peptide mimics (AMPMs) based on natural products (NPs) is a new strategy to kill MRSA and slow the development of drug resistance recently. Here, we reported the design and synthesis of novel AMPMs based on harmane skeleton. Notably, compound 9b exhibited comparable or even better anti-MRSA activity in vitro and in vivo with minimum inhibitory concentration (MIC) of 0.5-2 μg/mL than the positive drug vancomycin. The highly active compound 9b not only showed low cytotoxicity, no obvious hemolysis and good plasma stability, but also presented low tendency of developing resistance. Anti-MRSA mechanism revealed that compound 9b could destroy cell wall structure by interacting with lipoteichoic acid and peptidoglycan, cause membrane damage by depolarization, increased permeability and destructed integrity, reduce cell metabolic activity by binding to lactate dehydrogenase (LDH), interfere cellular redox homeostasis, and bind to DNA. Overall, compound 9b killed the MRSA by multi-target mechanism, which provide a promising light for combating the growing MRSA resistance.

Keywords:  Antimicrobial peptide mimics; Harmane; MRSA; Multi-target mechanism; Quaternization

DOI:  https://doi.org/10.1016/j.ejmech.2024.116657