bims-cepepe 2024-09-22 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2024‒09‒22
ten papers selected by
Henry Lamb, Queensland University of Technology

Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery.
Beware of extreme calculated lipophilicity when designing cyclic peptides.
Venom exaptation and adaptation during the trophic switch to blood-feeding by kissing bugs.
Design, Synthesis, and Biological Evaluation of Lysine-Stapled Peptide Inhibitors of p53-MDM2/MDMX Interactions with Potent Antitumor Activity In Vivo.
Lipid Metabolism Modulatory Cisplatin Prodrug Sensitizes Resistant Prostate Cancer toward Androgen Deprivation Therapy.
AutoPeptideML: A study on how to build more trustworthy peptide bioactivity predictors.
Comparison of in vitro screening methods for evaluating the effects of pharmaceutical excipients on membrane permeability.
Multi-site esterification: a tunable, reversible strategy to tailor therapeutic peptides for delivery.
Peptide nucleic acids can form hairpins and bind RNA-binding proteins.
Impact of lipidation site on the activity of α-helical antimicrobial peptides.

J Pharm Biomed Anal. 2024 Sep 16. pii: S0731-7085(24)00516-8. [Epub ahead of print]252 116476

Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery.

Wen Guo, Alexey A Makarov, Alexei V Buevich, Yuan Jiang.

  Peptide therapeutics have emerged as an appealing modality in the pharmaceutical industry. Understanding peptide conformation in solution remains one of the most critical areas for peptide drug development. Circular dichroism (CD) spectroscopy is a useful technique to study the secondary structure of proteins and peptides, but the current approaches are limited to protein-focused models to predict high-order structures of peptides, and the models were built based on X-ray crystallography instead of solution-based technique, as a result, such models may have poor predictions for peptides. In this study, we present a novel CD deconvolution model to determine peptide conformation in solution. To quantitatively obtain secondary structure information using CD, a calibration model is needed beforehand to establish the relationship between each secondary structure feature and the corresponding CD response. A reference set containing the majority of cyclic peptides with known structures from solution-state NMR spectroscopy was used to build the calibration model for CD deconvolution. Improved prediction accuracy on the secondary structure determination for cyclic peptides was achieved by this model compared to the commercial standard model using commercially available platforms. This new CD deconvolution method is crucial for peptide conformational analysis in solution, and has the potential to greatly accelerate peptide drug candidate optimization in the pharmaceutical drug discovery field.

Keywords:  Circular dichroism deconvolution; Macrocyclic peptides; Secondary structure

DOI:  https://doi.org/10.1016/j.jpba.2024.116476
Nat Chem Biol. 2024 Sep 19.

Beware of extreme calculated lipophilicity when designing cyclic peptides.

Vasanthanathan Poongavanam, Duc Duy Vo, Jan Kihlberg.

DOI: https://doi.org/10.1038/s41589-024-01715-0
iScience. 2024 Sep 20. 27(9): 110723

Venom exaptation and adaptation during the trophic switch to blood-feeding by kissing bugs.

Christina N Zdenek, Fernanda C Cardoso, Samuel D Robinson, Raine S Mercedes, Enriko R Raidjõe, María José Hernandez-Vargas, Jiayi Jin, Gerardo Corzo, Irina Vetter, Glenn F King, Bryan G Fry, Andrew A Walker.

  Kissing bugs are known to produce anticoagulant venom that facilitates blood-feeding. However, it is unknown how this saliva evolved and if the venom produced by the entomophagous ancestors of kissing bugs would have helped or hindered the trophic shift. In this study, we show that venoms produced by extant predatory assassin bugs have strong anticoagulant properties mediated chiefly by proteolytic degradation of fibrinogen, and additionally contain anticoagulant disulfide-rich peptides. However, venom produced by predatory species also has pain-inducing and membrane-permeabilizing activities that would be maladaptive for blood-feeding, and which venom of the blood-feeding species lack. This study demonstrates that venom produced by the predatory ancestors of kissing bugs was exapted for the trophic switch to blood-feeding by virtue of its anticoagulant properties. Further adaptation to blood-feeding occurred by downregulation of venom toxins with proteolytic, cytolytic, and pain-inducing activities, and upregulation and neofunctionalization of toxins with anticoagulant activity independent of proteolysis.

Keywords:  Biochemistry; Entomology; Evolutionary biology; Pharmacology

DOI:  https://doi.org/10.1016/j.isci.2024.110723
J Med Chem. 2024 Sep 19.

Design, Synthesis, and Biological Evaluation of Lysine-Stapled Peptide Inhibitors of p53-MDM2/MDMX Interactions with Potent Antitumor Activity In Vivo.

Lei Xu, Xin Fan, Yi He, Xuefeng Xia, Jinqiang Zhang.

We introduce novel lysine-stapled peptide inhibitors targeting p53-MDM2/MDMX interactions. Leveraging the model peptides pDI (LTFEHYWAQLTS) and PMI-M3 (LTFLEYWAQLMQ) as starting points, a series of lysine-stapled analogues were designed and synthesized. Through in vitro cell assay screening, two lead compounds, SPDI-48-T1 and SPMI-48-T3, were identified for their excellent antiproliferation activity. Fluorescence polarization assays revealed that both compounds exhibited strong binding affinities against MDM2 and MDMX, ascertained by Kd values within the low micromolar spectrum. Further characterization of SPDI-48-T1 and SPMI-48-T3 demonstrated that SPDI-48-T1 possessed superior cell permeability and serum stability. Notably, SPDI-48-T1 displayed a dose-dependent suppression of tumor growth in an HCT116 xenograft mouse model. Our findings indicate that SPDI-48-T1 holds promise as a lead compound for further development as an anticancer agent by modulating p53-MDM2/MDMX interactions. Additionally, this study also proved that the lysine stapling strategy may serve as a robust approach for generating peptide ligands targeting other protein-protein interactions.

DOI: https://doi.org/10.1021/acs.jmedchem.4c01939
ACS Pharmacol Transl Sci. 2024 Sep 13. 7(9): 2820-2826

Lipid Metabolism Modulatory Cisplatin Prodrug Sensitizes Resistant Prostate Cancer toward Androgen Deprivation Therapy.

Subham Guin, Akash Ashokan, Alan Pollack, Shanta Dhar.

Mainstream treatment modalities which dominate the therapeutic landscape of prostate cancer (PCa) are prostatectomy, radiation therapy, and androgen deprivation therapy (ADT) or castration. These therapeutic options can extend the life expectancy of the patients but eventually fail to completely cure the disease. Despite undergoing ADT, patients still experience disease recurrence. One of the reasons for this recurrence is the binding of the basal androgens present in blood plasma to the androgen receptor (AR). At this stage, the disease becomes castration-resistant prostate cancer (CRPC) showing resistance to ADT promoting progression, and there is no effective treatment available. Although another male cancer such as testicular cancer responds to cisplatin-based therapy very well, PCa is resistant to cisplatin. In our continued effort to find the pathways that are important for such resistance, we link in this report, tumor metabolism driven androgen regulation and PCa resistance toward cisplatin-based therapy. To delve deeper into understanding how metabolic modulatory cisplatin prodrugs can be used to target the ADT resistant population, we demonstrate that metabolic inhibition by a cisplatin prodrug, Platin-L has the potential to modulate AR activity and resensitize ADT resistant cells toward cisplatin-based chemotherapy as well as ADT. The mode of action for Platin-L is inhibition of fatty acid oxidation (FAO) of prostate cancer cells. We demonstrated that FAO inhibition by Platin-L in PCa cells contribute to AR regulation resulting in altered tumorigenicity of androgen sensitive prostate cancer.

DOI: https://doi.org/10.1021/acsptsci.4c00301
Bioinformatics. 2024 Sep 18. pii: btae555. [Epub ahead of print]

AutoPeptideML: A study on how to build more trustworthy peptide bioactivity predictors.

Raúl Fernández-Díaz, Rodrigo Cossio-Pérez, Clement Agoni, Thanh Lam Hoang, Vanessa Lopez, Denis C Shields.

MOTIVATION: Automated machine learning (AutoML) solutions can bridge the gap between new computational advances and their real-world applications by enabling experimental scientists to build their own custom models. We examine different steps in the development life-cycle of peptide bioactivity binary predictors and identify key steps where automation can not only result in a more accessible method, but also more robust and interpretable evaluation leading to more trustworthy models.RESULTS: We present a new automated method for drawing negative peptides that achieves better balance between specificity and generalisation than current alternatives. We study the effect of homology-based partitioning for generating the training and testing data subsets and demonstrate that model performance is overestimated when no such homology correction is used, which indicates that prior studies may have overestimated their performance when applied to new peptide sequences. We also conduct a systematic analysis of different protein language models as peptide representation methods and find that they can serve as better descriptors than a naive alternative, but that there is no significant difference across models with different sizes or algorithms. Finally, we demonstrate that an ensemble of optimised traditional machine learning algorithms can compete with more complex neural network models, while being more computationally efficient. We integrate these findings into AutoPeptideML, an easy-to-use AutoML tool to allow researchers without a computational background to build new predictive models for peptide bioactivity in a matter of minutes.
AVAILABILITY AND IMPLEMENTATION: Source code, documentation, and data are available at https://github.com/IBM/AutoPeptideML and a dedicated web-server at http://peptide.ucd.ie/AutoPeptideML.
CONTACT AND SUPPLEMENTARY INFORMATION: Raul.fernandezdiaz@ucdconnect.ie or denis.shields@ucd.ie. Supplementary Information can be accessed from Zenodo: Https://zenodo.org/records/13363975.

DOI: https://doi.org/10.1093/bioinformatics/btae555
Int J Pharm. 2024 Sep 16. pii: S0378-5173(24)00961-X. [Epub ahead of print] 124727

Comparison of in vitro screening methods for evaluating the effects of pharmaceutical excipients on membrane permeability.

Tokio Morita, Hiroyuki Yoshida, Naomi Tomita, Yoji Sato.

  The effects of pharmaceutical excipients on intestinal drug absorption have been highlighted and careful excipient selection is required to develop biologically equivalent formulations. This study aimed to evaluate the effects of excipients on drug permeability and compare the characteristics of in vitro screening methods. Three in vitro models, the commercial precoated parallel artificial membrane permeability assay (PAMPA), PermeaPadTM, and Caco-2 monolayer, were used to evaluate the effects of 14 excipients on the permeability of several drugs with different biopharmaceutical classification system classes. Concentration-dependent effects were analyzed to distinguish non-specific effects. The permeability of low-permeability drugs was increased by excipients such as hydroxypropyl cellulose and povidone K30 in the precoated PAMPA model, whereas PermeaPadTM maintained membrane integrity at higher concentrations. Conversely, croscarmellose sodium and sodium lauryl sulfate (SLS) decreased the permeability of highly permeable drugs in both precoated PAMPA and PermeaPadTM assays in a concentration-dependent manner. In Caco-2 monolayer assays, most excipients showed minimal effects on drug permeability. However, SLS significantly reduces the permeability of highly permeable drugs at concentrations above the critical micelle concentration, thereby compromising the integrity of the cell monolayer. Our results suggested that most of excipients, except SLS, did not affect the membrane permeation of drugs at clinically used concentrations. The pre-coated PAMPA model demonstrated high sensitivity to excipient effects, making it suitable for conservative evaluation. The PermeaPadTM and Caco-2 models allowed assessment at higher excipient concentrations, with PermeaPadTM being particularly useful for excipients that cause toxicity in Caco-2 cells.

Keywords:  Drug interaction; Membrane permeability; Pharmaceutical excipient; Screening method

DOI:  https://doi.org/10.1016/j.ijpharm.2024.124727
Mol Syst Des Eng. 2024 Sep 13.

Multi-site esterification: a tunable, reversible strategy to tailor therapeutic peptides for delivery.

Mark S Bannon, Jeffrey F Ellena, Aditi S Gourishankar, Spencer R Marsh, Dilza Trevisan-Silva, Nicholas E Sherman, L Jane Jourdan, Robert G Gourdie, Rachel A Letteri.

Peptides are naturally potent and selective therapeutics with massive potential; however, low cell membrane permeability limits their clinical implementation, particularly for hydrophilic, anionic peptides with intracellular targets. To overcome this limitation, esterification of anionic carboxylic acids on therapeutic peptides can simultaneously increase hydrophobicity and net charge to facilitate cell internalization, whereafter installed esters can be cleaved hydrolytically to restore activity. To date, however, most esterified therapeutics contain either a single esterification site or multiple esters randomly incorporated on multiple sites. This investigation provides molecular engineering insight into how the number and position of esters installed onto the therapeutic peptide α carboxyl terminus 11 (αCT11, RPRPDDLEI) with 4 esterification sites affect hydrophobicity and the hydrolysis process that reverts the peptide to its original form. After installing methyl esters onto αCT11 using Fischer esterification, we isolated 5 distinct products and used 2D nuclear magnetic resonance spectroscopy, reverse-phase high performance liquid chromatography, and mass spectrometry to determine which residues were esterified in each and the resulting increase in hydrophobicity. We found esterifying the C-terminal isoleucine to impart the largest increase in hydrophobicity. Monitoring ester hydrolysis showed the C-terminal isoleucine ester to be the most hydrolytically stable, followed by the glutamic acid, whereas esters on aspartic acids hydrolyze rapidly. LC-MS revealed the formation of transient intramolecular aspartimides prior to hydrolysis to carboxylic acids. In vitro proof-of-concept experiments showed esterifying αCT11 to increase cell migration into a scratch, highlighting the potential of multi-site esterification as a tunable, reversible strategy to enable the delivery of therapeutic peptides.

DOI: https://doi.org/10.1039/d4me00072b
PLoS One. 2024 ;19(9): e0310565

Peptide nucleic acids can form hairpins and bind RNA-binding proteins.

Yichen Zhong, Lorna Wilkinson-White, Esther Zhang, Biswaranjan Mohanty, Belinda B Zhang, Madeline S McRae, Rachel Luo, Thomas A Allport, Anthony P Duff, Jennifer Zhao, Serene El-Kamand, Mar-Dean Du Plessis, Liza Cubeddu, Roland Gamsjaeger, Sandro F Ataide, Ann H Kwan.

RNA-binding proteins (RBPs) are a major class of proteins that interact with RNAs to change their fate or function. RBPs and the ribonucleoprotein complexes they constitute are involved in many essential cellular processes. In many cases, the molecular details of RBP:RNA interactions differ between viruses, prokaryotes and eukaryotes, making prokaryotic and viral RBPs good potential drug targets. However, targeting RBPs with small molecules has so far been met with limited success as RNA-binding sites tend to be extended, shallow and dynamic with a mixture of charged, polar and hydrophobic interactions. Here, we show that peptide nucleic acids (PNAs) with nucleic acid-like binding properties and a highly stable peptide-like backbone can be used to target some RBPs. We have designed PNAs to mimic the short RNA stem-loop sequence required for the initiation of prokaryotic signal recognition particle (SRP) assembly, a target for antibiotics development. Using a range of biophysical and biochemical assays, the designed PNAs were demonstrated to fold into a hairpin structure, bind the targeted protein and compete with the native RNA hairpin to inhibit SRP formation. To show the applicability of PNAs against other RBPs, a PNA was also shown to bind Nsp9 from SARS-CoV-2, a protein that exhibits non-sequence-specific RNA binding but preferentially binds hairpin structures. Taken together, our results support that PNAs can be a promising class of compounds for targeting RNA-binding activities in RBPs.

DOI: https://doi.org/10.1371/journal.pone.0310565
Bioorg Chem. 2024 Sep 13. pii: S0045-2068(24)00726-0. [Epub ahead of print]153 107821

Impact of lipidation site on the activity of α-helical antimicrobial peptides.

Marta Makowska, Anna Wardowska, Marta Bauer, Dariusz Wyrzykowski, Izabela Małuch, Emilia Sikorska.

  Antimicrobial peptides (AMPs) display advantages over traditional antibiotics due to their broad spectrum of activity against various pathogens, and may even overcome bacterial drug resistance. However, despite their potential therapeutic benefits, widespread application of AMPs is limited by their instability, sensitivity to high salt concentrations, toxicity, and immunogenicity. Lipidation is a promising strategy in overcoming these drawbacks and potential problems for drug candidates. While N-terminal lipidation is a well-studied form of acylation of biologically active peptides, fatty acylation of the lysine side chain has still been poorly explored. In this study, we examined systematic introduction of octanoic (C8) or decanoic (C10) acid into the sequences of three antimicrobial α-helical peptides, namely LL-I, LK6, and ATRA-1, by acylation of subsequent lysine residues, resulting in 17 lipopeptides. Fatty acid lengths optimal for antimicrobial activity were selected based on a previous study on the N-terminal lipidated counterparts of these peptides. Shuffling the position of the fatty acid tails in the sequences of the peptides preserved high activity against Gram-positive bacteria, increased activity against Gram-negative strains and reduced cytotoxicity, compared to the N-terminal acylated counterparts. In the case of the LL-I and LK6 conjugates, the interactions with artificial negatively charged membranes induced formation of an α-helical structure but without a direct correlation between helicity and amphipathicity. Unexpectedly, the ATRA-1 derivatives showed only a small tendency, if any, to adopt a helical structure upon binding to POPG vesicles, which may indicate a non-helical active conformation. A more detailed study of the selected analogues, namely LL-I-4C8, LK6-7C8, and ATRA-1-11C10, provided evidence of a tendency to self-assemble into clumped and/or isolated fibrils, micelles or clusters of micelles, and proved that the lipid bilayer is the main target of action of the tested lipopeptides. In summary, the results of the present study highlight that alternative conjugation sites for lipid modification of AMPs, rather than the commonly applied N-terminal conjugation site, may improve the selectivity of action and be feasible in testing for the development of new lipid-peptide conjugates.

Keywords:  Antimicrobial peptides; Fatty acids; Lipopeptides; Peptide-membrane interactions; Self-assembly; Structure–activity relationship

DOI:  https://doi.org/10.1016/j.bioorg.2024.107821