bims-cepepe 2024-10-27 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2024–10–27
twelve papers selected by
Henry Lamb, Queensland University of Technology

Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets.
Total Synthesis of Talarolide A and atrop-Talarolide A: Hydroxamate H-Bond Bridge Stabilization of Cyclic Peptide Conformers Invokes Non-Canonical Atropisomerism.
Chromatographic Determination of Permeability-Relevant Lipophilicity Facilitates Rapid Analysis of Macrocyclic Peptide Scaffolds.
Discovery of Truncated Cyclic Peptides Targeting an Induced-Fit Pocket on PCSK9.
Evaluating delivery of peptide nucleic acids to Gram-negative bacteria using differently linked membrane-active peptides and their stapled analogs.
Insights into Translocation of Arginine-Rich Cell-Penetrating Peptides across a Model Membrane.
Peptide-Oligonucleotide Conjugation: Chemistry and Therapeutic Applications.
A High-Throughput Screen for Antiproliferative Peptides in Mammalian Cells Identifies Key Transcription Factor Families.
The Influence of Cholesterol on Membrane Targeted Bioactive Peptides: Modulating Peptide Activity Through Changes in Bilayer Biophysical Properties.
Comparative Properties of Helical and Linear Amphipathicity of Peptides Composed of Arginine, Tryptophan, and Valine.
Development and preclinical evaluation of a cyclic PET tracer targeting integrin-α6 on colorectal cancer models.
Electrochemiluminescence microscopy for the investigation of peptide interactions within planar lipid membranes.

Chem Rev. 2024 Oct 25.

Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets.

Kilian Colas, Daniel Bindl, Hiroaki Suga.

Technological advances and breakthrough developments in the pharmaceutical field are knocking at the door of the "undruggable" fortress with increasing insistence. Notably, the 21st century has seen the emergence of macrocyclic compounds, among which cyclic peptides are of particular interest. This new class of potential drug candidates occupies the vast chemical space between classic small-molecule drugs and larger protein-based therapeutics, such as antibodies. As research advances toward clinical targets that have long been considered inaccessible, macrocyclic peptides are well-suited to tackle these challenges in a post-rule of 5 pharmaceutical landscape. Facilitating their discovery is an arsenal of high-throughput screening methods that exploit massive randomized libraries of genetically encoded compounds. These techniques benefit from the incorporation of non-natural moieties, such as non- proteinogenic amino acids or stabilizing hydrocarbon staples. Exploiting these features for the strategic architectural design of macrocyclic peptides has the potential to tackle challenging targets such as protein-protein interactions, which have long resisted research efforts. This Review summarizes the basic principles and recent developments of the main high-throughput techniques for the discovery of macrocyclic peptides and focuses on their specific deployment for targeting undruggable space. A particular focus is placed on the development of new design guidelines and principles for the cyclization and structural stabilization of cyclic peptides and the resulting success stories achieved against well-known inaccessible drug targets.

DOI: https://doi.org/10.1021/acs.chemrev.4c00422
Mar Drugs. 2024 Oct 03. pii: 454. [Epub ahead of print]22(10):

Total Synthesis of Talarolide A and atrop-Talarolide A: Hydroxamate H-Bond Bridge Stabilization of Cyclic Peptide Conformers Invokes Non-Canonical Atropisomerism.

Waleed M Hussein, Yuxuan Zhu, Angela A Salim, Robert J Capon.

  The first total synthesis of the Australian marine tunicate fungus-derived cyclic peptide talarolide A (1) has confirmed the structure previously proposed on the basis of spectroscopic and chemical analyses and re-affirmed the importance of the unique hydroxamate H-bond bridge in ring conformer stabilization. The unexpected co-synthesis of atrop-talarolide A (8) revealed, for the first time, that hydroxamate H-bond bridging in the talarolide framework invokes non-canonical atropisomerism and that talarolides A (1), C (3), and D (4) all exist naturally as atropisomers. These discoveries raise the intriguing prospect that comparable functionalisation of other cyclic peptides, including those with commercial value, could provide ready access to new "unnatural atropisomeric" chemical space, with new and/or improved chemical and biological properties.

Keywords:  Talaromyces; atropisomerism; conformer stabilization; cyclic peptide; hydroxamate H-bond bridge; marine-derived fungus; natural product; talarolide A; total synthesis

DOI:  https://doi.org/10.3390/md22100454
J Med Chem. 2024 Oct 25.

Chromatographic Determination of Permeability-Relevant Lipophilicity Facilitates Rapid Analysis of Macrocyclic Peptide Scaffolds.

Grant Koch, Alexander Engstrom, Jaru Taechalertpaisarn, Justin Faris, Satoshi Ono, Matthew R Naylor, R Scott Lokey.

Hydrocarbon-determined shake-flask measurements have demonstrated great utility for optimizing lipophilicity during early drug discovery. Alternatively, chromatographic methods confer reduced experimental error and improved handling of complex mixtures. In this study, we developed a chromatographic approach for estimating hydrocarbon-water shake-flask partition coefficients for a variety of macrocyclic peptides and other bRo5 molecules including PROTACs. The model accurately predicts experimental shake-flask measurements with high reproducibility across a wide range of lipophilicities. The chromatographic retention times revealed subtle conformational effects and correlated with the ability to sequester hydrogen bond donors in low dielectric media. Estimations of shake-flask lipophilicity from our model also accurately predicted trends in MDCK passive cell permeability for a variety of thioether-cyclized decapeptides. This method provides a convenient, high-throughput approach for measuring lipophilic permeability efficiency and predicting passive cell permeability in bRo5 compounds that is suitable for multiplexing pure compounds or investigating the properties of complex library mixtures.

DOI: https://doi.org/10.1021/acs.jmedchem.4c01956
ChemMedChem. 2024 Oct 22. e202400208

Discovery of Truncated Cyclic Peptides Targeting an Induced-Fit Pocket on PCSK9.

Philipp Grosche, Alec N Flyer, Raphael Gattlen, Mei Xu, Andrei A Golosov, Victoria Vera, Stephanie Pickett, Margaret E Brousseau, Rajiv Chopra, Kevin B Clairmont, Alexander Koch, Eugene Liu, Patrick Reid, Lauren Perry, Lihua Yang, Qing Yang, Lauren G Monovich.

  Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma low-density lipoprotein cholesterol (LDL-C) levels by promoting hepatic LDL receptor (LDL-R) degradation. We previously identified and optimized 13-mer cyclic peptides that bind to a novel, induced-fit pocket adjacent to the binding interface of PCSK9 and LDL-R and effectively disrupted the PCSK9/LDL-R protein-protein interaction (PPI) both in vitro and in vivo. However this series of large cyclic peptides required charged groups for function and lacked oral bioavailability in rodents. We describe herein multiple structure-based modifications to these original peptides to yield truncated, neutral molecules with full PPI function in both biochemical and cellular assays. In parallel, new mRNA-peptide display screens identified non-functional 8- and 9-mer compounds which ligand the induced-fit pocket in a distinct manner. Taken together, these studies indicate multiple directions to reduce the size and complexity of this peptide class toward a true small molecule oral agent.

Keywords:  Cyclic peptide; LDL−C; LDL−R; PCSK9; PPI disruption; Peptide structure-based drug design

DOI:  https://doi.org/10.1002/cmdc.202400208
Bioorg Med Chem Lett. 2024 Oct 18. pii: S0960-894X(24)00395-0. [Epub ahead of print]114 129993

Evaluating delivery of peptide nucleic acids to Gram-negative bacteria using differently linked membrane-active peptides and their stapled analogs.

Izabela Siekierska, Michał Burmistrz, Joanna Trylska.

  Antisense oligonucleotides have been developed as therapeutic compounds, with peptide nucleic acid (PNA) emerging as a promising nucleic acid mimic for antimicrobial applications. To be effective, PNAs must be internalized into bacterial cells, as they are not naturally absorbed. A strategy to improve PNA membrane penetration and cellular uptake involves covalently conjugating them to cell-penetrating peptides. However, these membrane-active peptides can exhibit cytotoxicity, and their efficiency as PNA carriers needs to be enhanced. Therefore, we explored new peptide-PNA conjugates and their linkers to understand how they affect PNA uptake into bacteria. We conjugated PNA to two peptides, anoplin and (KFF)3K, along with their structurally stabilized hydrocarbon-stapled derivatives, and evaluated their transport into various bacterial strains. The PNA sequence targeted bacterial mRNA encoding the essential acyl carrier protein. As linkages, we used either a non-cleavable 8-amino-2,6-dioxaoctanoyl (ethylene glycol, eg1) linker or a reducible disulfide bridge. We found that the hydrocarbon-stapled peptides did not enhance PNA delivery, despite the strong inner- and outer-membrane-penetrating capabilities of the standalone peptides. Additionally, the disulfide bridge linkage, which is cleavable in the bacterial cytoplasm, decreased the antimicrobial activity of the peptide-PNA conjugates. Notably, we identified anoplin as a new potent PNA carrier peptide, with the anoplin-eg1-PNA conjugate demonstrating antibacterial activity against E. coli and S. Typhimurium strains in the 2-4 µM range.

Keywords:  Anoplin; Disulfide bridge; Gram-negative bacteria; Hydrocarbon stapling; Membrane-active peptides; Peptide nucleic acid (PNA); Peptide–PNA conjugates

DOI:  https://doi.org/10.1016/j.bmcl.2024.129993
J Phys Chem B. 2024 Oct 24.

Insights into Translocation of Arginine-Rich Cell-Penetrating Peptides across a Model Membrane.

Seungho Choe.

It is well-known that membrane deformation and water pores contribute to the spontaneous translocation of arginine-rich cell-penetrating peptides (CPPs). We confirm this through the observation of the spontaneous translocation of single R9 (nona-arginine) and Tat (48-60) peptides across a model membrane using the weighted ensemble (WE) method within all-atom molecular dynamics (MD) simulations. Furthermore, we demonstrate that membrane deformation and the presence of a water pore reduce the effective charge of the CPP and the bending rigidity of the model membrane during translocation. We find that R9 disturbs the model membrane more than Tat (48-60), leading to more efficient translocation of R9 across the model membrane.

DOI: https://doi.org/10.1021/acs.jpcb.4c04266
Curr Issues Mol Biol. 2024 Sep 30. 46(10): 11031-11047

Peptide-Oligonucleotide Conjugation: Chemistry and Therapeutic Applications.

Anna L Malinowska, Harley L Huynh, Sritama Bose.

  Oligonucleotides have been identified as powerful therapeutics for treating genetic disorders and diseases related to epigenetic factors such as metabolic and immunological dysfunctions. However, they face certain obstacles in terms of limited delivery to tissues and poor cellular uptake due to their large size and often highly charged nature. Peptide-oligonucleotide conjugation is an extensively utilized approach for addressing the challenges associated with oligonucleotide-based therapeutics by improving their delivery, cellular uptake and bioavailability, consequently enhancing their overall therapeutic efficiency. In this review, we present an overview of the conjugation of oligonucleotides to peptides, covering the different strategies associated with the synthesis of peptide-oligonucleotide conjugates (POC), the commonly used peptides employed to generate POCs, with the aim to develop oligonucleotides with favourable pharmacokinetic (PK) or pharmacodynamic (PD) properties for therapeutic applications. The advantages and drawbacks of the synthetic methods and applications of POCs are also described.

Keywords:  cell-penetrating peptides; cellular uptake; conjugation chemistry; drug delivery; nucleic acid therapeutics; peptide–oligonucleotide conjugates; receptor-mediated oligonucleotide delivery

DOI:  https://doi.org/10.3390/cimb46100655
ACS Synth Biol. 2024 Oct 19.

A High-Throughput Screen for Antiproliferative Peptides in Mammalian Cells Identifies Key Transcription Factor Families.

Shane M Liila-Fogarty, Grace E Boyum, Claire L Schwabe, Gaelen T Hess.

  Transcription factors (TFs) are a promising therapeutic target for a multitude of diseases. TFs perform their cellular roles by participating in multiple specific protein-protein interactions. For example, homo- or heterodimerization of some TFs controls DNA binding, while interactions between TFs and components of basal transcriptional machinery or chromatin modifiers can also be critical. While, in theory, small molecules could be used to disrupt specific protein-protein interfaces required for TF function, in practice, it is difficult to identify small molecules with the necessary specificity and efficacy, likely due to the extensive protein-protein interfaces that often underlie TF function. However, in contrast to small molecules, peptides have the potential to provide both the specificity and efficacy required to disrupt such interfaces. Here, we identified ∼15 peptides that inhibit the proliferation of leukemia cells using a high-throughput pooled screen of a library of 80-mer protein regions (peptides) derived from human nuclear-localized proteins. The antiproliferative peptides were enriched for regions known to be involved in specific TF dimerization, including the basic leucine zipper (bZIP) domain family. One of these bZIP domains, JDP2;bZIP_1, from the TF JDP2, was the top antiproliferative peptide, reducing the proliferation of K562 cells by 2-fold. JDP2;bZIP_1 inhibited AP-1 transcriptional activity and phenocopied JDP2 overexpression, suggesting that the peptide affected proliferation through a native JDP2 mechanism. Unexpectedly, given the strong conservation of the bZIP domain, residues outside of the annotated dimerization domain were critical for the peptide's antiproliferative potency. The peptide-mediated antiproliferative effect initiated erythrocyte differentiation in K562 cells and increased G0/G1 cells across multiple cell line models. We also found that many of the antiproliferative peptides identified in this study, including JDP2;bZIP_1, did not require a nuclear localization signal to function, a potential benefit for delivering these peptides in therapeutic applications.

Keywords:  high-throughput screening; peptide therapeutics; transcription factors

DOI:  https://doi.org/10.1021/acssynbio.4c00337
Membranes (Basel). 2024 Oct 17. pii: 220. [Epub ahead of print]14(10):

The Influence of Cholesterol on Membrane Targeted Bioactive Peptides: Modulating Peptide Activity Through Changes in Bilayer Biophysical Properties.

Juan M Giraldo-Lorza, Chad Leidy, Marcela Manrique-Moreno.

  Cholesterol is a biological molecule that is essential for cellular life. It has unique features in terms of molecular structure and function, and plays an important role in determining the structure and properties of cell membranes. One of the most recognized functions of cholesterol is its ability to increase the level of lipid packing and rigidity of biological membranes while maintaining high levels of lateral mobility of the bulk lipids, which is necessary to sustain biochemical signaling events. There is increased interest in designing bioactive peptides that can act as effective antimicrobial agents without causing harm to human cells. For this reason, it becomes relevant to understand how cholesterol can affect the interaction between bioactive peptides and lipid membranes, in particular by modulating the peptides' ability to penetrate and disrupt the membranes through these changes in membrane rigidity. Here we discuss cholesterol and its role in modulating lipid bilayer properties and discuss recent evidence showing how cholesterol modulates bioactive peptides to different degrees.

Keywords:  bioactive peptides; cholesterol; cholesterol–peptide interactions; membrane fluidity

DOI:  https://doi.org/10.3390/membranes14100220
Antibiotics (Basel). 2024 Oct 11. pii: 954. [Epub ahead of print]13(10):

Comparative Properties of Helical and Linear Amphipathicity of Peptides Composed of Arginine, Tryptophan, and Valine.

Jessie Klousnitzer, Wenyu Xiang, Vania M Polynice, Berthony Deslouches.

   BACKGROUND: The persistence of antibiotic resistance has incited a strong interest in the discovery of agents with novel antimicrobial mechanisms. The direct killing of multidrug-resistant bacteria by cationic antimicrobial peptides (AMPs) underscores their importance in the fight against infections associated with antibiotic resistance. Despite a vast body of AMP literature demonstrating a plurality in structural classes, AMP engineering has been largely skewed toward peptides with idealized amphipathic helices (H-amphipathic). In contrast to helical amphipathicity, we designed a series of peptides that display the amphipathic motifs in the primary structure. We previously developed a rational framework for designing AMP libraries of H-amphipathic peptides consisting of Arg, Trp, and Val (H-RWV, with a confirmed helicity up to 88% in the presence of membrane lipids) tested against the most common MDR organisms.
METHODS: In this study, we re-engineered one of the series of the H-RWV peptides (8, 10, 12, 14, and 16 residues in length) to display the amphipathicity in the primary structure by side-by-side (linear) alignment of the cationic and hydrophobic residues into the 2 separate linear amphipathic (L-amphipathic) motifs. We compared the 2 series of peptides for antibacterial activity, red blood cell (RBC) lysis, killing and membrane-perturbation properties.
RESULTS: The L-RWV peptides achieved the highest antibacterial activity at a minimum length of 12 residues (L-RWV12, minimum optimal length or MOL) with the lowest mean MIC of 3-4 µM, whereas the MOL for the H-RWV series was reached at 16 residues (H-RWV16). Overall, H-RWV16 displayed the lowest mean MIC at 2 µM but higher levels of RBC lysis (25-30%), while the L-RWV series displayed minor RBC lytic effects at the test concentrations. Interestingly, when the S. aureus strain SA719 was chosen because of its susceptibility to most of the peptides, none of the L-RWV peptides demonstrated a high level of membrane perturbation determined by propidium iodide incorporation measured by flow cytometry, with <50% PI incorporation for the L-RWV peptides. By contrast, most H-RWV peptides displayed almost up to 100% PI incorporation. The results suggest that membrane perturbation is not the primary killing mechanism of the L-amphipathic RWV peptides, in contrast to the H-RWV peptides.
CONCLUSIONS: Taken together, the data indicate that both types of amphipathicity may provide different ideal pharmacological properties that deserve further investigation.

Keywords:  ESKAPE pathogens; antibiotic resistance; antimicrobial agents; antimicrobial peptides; cationic amphipathic peptides; cationic polymers; engineered AMPs; helical amphipathicity; linear amphipathicity; multidrug resistance; peptide antibiotics

DOI:  https://doi.org/10.3390/antibiotics13100954
Bioorg Chem. 2024 Oct 17. pii: S0045-2068(24)00797-1. [Epub ahead of print]153 107892

Development and preclinical evaluation of a cyclic PET tracer targeting integrin-α6 on colorectal cancer models.

Liping Chen, Haitian Fu, Wenjin Li, Qiaolin Shen, Yihui Luo, Junjie Fu, Chong Shao, Huihui He, Kequan Lou, Jialiang Wang, Guokai Feng, Chunjing Yu.

  Integrin-α6 is an attractive diagnostic and therapeutic biomarker in cancer, because it is highly expressed in several types of malignancies. Based on our previous findings, we designed a cyclic peptide, NOTA-A6P, to enhancing affinity, tumor uptake and serum stability, and then developed a cyclic radiotracer, [18F]AlF-NOTA-A6P, for the specific detection of early colorectal cancer by PET/CT imaging. [18F] AlF-NOTA-A6P was automatically labeled for colorectal cancer imaging in a novel synthesis module. The affinity, stability, radiochemical yield (RCY), radiochemical purity (RCP), molar activity (Am), and octanol-water partition coefficient of [18F]AlF-NOTA-A6P were investigated. Results demonstrated that the tracer exhibited high serum stability, high RCY (58.1 ± 4.1 %) (undecay-corrected, n = 5) and hydrophilicity. In vivo microPET/CT imaging of LS174T and HT29 xenograft tumor models with high integrin-α6 expression indicated that [18F]AlF-NOTA-A6P exhibited higher tumor uptake and tumor-to-muscle ratio than SW620, which has low integrin-α6 expression. Moreover, the specificity of [18F]AlF-NOTA-A6P for integrin-α6 was confirmed by additional methods, including autoradiography, hematoxylin and eosin staining, and immunohistochemical staining. In conclusion, a cyclic peptide NOTA-A6P targeting integrin-α6 was designed and a promising PET tracer [18F]AlF-NOTA-A6P was synthesized in a novel cassette-type synthesis module. The tracer demonstrated a favorable binding affinity with integrin-α6, stability in human serum and specificity for colorectal cancer xenograft mice. These properties render it a promising non-invasive PET radiotracer for the detection of integrin-α6-overexpressing cancers, including colorectal cancer.

Keywords:  Automated synthesis; Colorectal cancer; Cyclic peptide; Integrin-α6; Positron emission tomography; [(18)F]AlF-NOTA-A6P

DOI:  https://doi.org/10.1016/j.bioorg.2024.107892
Faraday Discuss. 2024 Oct 23.

Electrochemiluminescence microscopy for the investigation of peptide interactions within planar lipid membranes.

Kaoru Hiramoto, Kosuke Ino, Ibuki Takahashi, Ayumi Hirano-Iwata, Hitoshi Shiku.

Understanding the interactions between lipid membranes and peptides is crucial for controlling bacterial and viral infections, and developing effective drugs. In this study, we proposed the use of electrochemiluminescence (ECL) microscopy in a solution of [Ru(bpy)3]2+ and tri-n-propylamine to monitor alterations in the lipid membranes due to peptide action. A planar artificial lipid membrane served as a model platform, and its surface was observed using ECL microscopy during exposure to melittin, a representative membrane lytic peptide. Upon exposure to melittin, the light-emitting process of the [Ru(bpy)3]2+/tri-n-propylamine system through the lipid membrane exhibited complex changes, suggesting that stepwise peptide actions can be monitored through the system. Furthermore, wide-field imaging with ECL microscopy provided an effective means of elucidating the membrane surface at the submicron level and revealing heterogeneous changes upon exposure to melittin. This complemented the spatiotemporal information that could not be obtained using conventional electrochemical measurements.

DOI: https://doi.org/10.1039/d4fd00137k