bims-cepepe 2024-08-11 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2024‒08‒11
eighteen papers selected by
Henry Lamb, Queensland University of Technology

Molecular Mechanism of P53 Peptide Permeation through Lipid Membranes from Solid-State NMR Spectroscopy and Molecular Dynamics Simulations.
De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure.
Development of Macrocyclic Neurotensin Receptor Type 2 (NTS2) Opioid-Free Analgesics.
Exocyclic and Linker Editing of Lys63-linked Ubiquitin Chains Modulators Specifically Inhibits Non-homologous End-joining Repair.
An N-ortho-nitrobenzylated benzanilide amino acid enables control of the conformation and membrane permeability of cyclic peptides.
Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities.
68Ga Radiolabeling of NODASA-Functionalized Phage Display-Derived Peptides for Prospective Assessment as Tuberculosis-Specific PET Radiotracers.
Cyclization increases bactericidal activity of arginine-rich cationic cell-penetrating peptide for Neisseria gonorrhoeae.
DeepB3P: A transformer-based model for identifying blood-brain barrier penetrating peptides with data augmentation using feedback GAN.
Regulated induced proximity targeting chimeras-RIPTACs-A heterobifunctional small molecule strategy for cancer selective therapies.
Macrocyclic-based strategy in drug design: From lab to the clinic.
Mechanism of the blood-brain barrier modulation by cadherin peptides.
Structurally decoupled hyaluronic acid hydrogels for studying matrix metalloproteinase-mediated invasion of metastatic breast cancer cells.
A cyclic peptide-grafted Fc with hepatocyte growth factor functionality ameliorates hepatic fibrosis in a non-alcoholic steatohepatitis mouse model.
Inhibition of Lysosomal Cathepsin A and Neuraminidase 1 Interaction by Anti-obesity Cyclic Peptide.
Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.
The peptide-based bispecific CAR T cells target EGFR and tumor stroma for effective cancer therapy.
Diverse Proteomimetic Frameworks via Rational Design of π-Stacking Peptide Tectons.

J Am Chem Soc. 2024 Aug 07.

Molecular Mechanism of P53 Peptide Permeation through Lipid Membranes from Solid-State NMR Spectroscopy and Molecular Dynamics Simulations.

Mingyue Li, Jianguo Li, Xingyu Lu, Ryan Schroder, Arun Chandramohan, W Peter Wuelfing, Allen C Templeton, Wei Xu, Marian Gindy, Filippos Kesisoglou, Jing Ling, Tomi Sawyer, Chandra S Verma, Anthony W Partridge, Yongchao Su.

Macrocyclic peptides show promise in targeting high-value therapeutically relevant binding sites due to their high affinity and specificity. However, their clinical application is often hindered by low membrane permeability, which limits their effectiveness against intracellular targets. Previous studies focused on peptide conformations in various solvents, leaving a gap in understanding their interactions with and translocation through lipid bilayers. Addressing this, our study explores the membrane interactions of stapled peptides, a subclass of macrocyclic peptides, using solid-state nuclear magnetic resonance (ssNMR) spectroscopy and molecular dynamics (MD) simulations. We conducted ssNMR measurements on ATSP-7041M, a prototypical stapled peptide, to understand its interaction with lipid membranes, leading to an MD-informed model for peptide membrane permeation. Our findings reveal that ATSP-7041M adopts a stable α-helical structure upon membrane binding, facilitated by a cation-π interaction between its phenylalanine side chain and the lipid headgroup. This interaction makes the membrane-bound state energetically favorable, facilitating membrane affinity and insertion. The bound peptide displayed asymmetric insertion depths, with the C-terminus penetrating deeper (approximately 9 Å) than the N-terminus (approximately 4.3 Å) relative to the lipid headgroups. Contrary to expectations, peptide dynamics was not hindered by membrane binding and exhibited rapid motions similar to cell-penetrating peptides. These dynamic interactions and peptide-lipid affinity appear to be crucial for membrane permeation. MD simulations indicated a thermodynamically stable transmembrane conformation of ATSP-7041M, reducing the energy barrier for translocation. Our study offers an in silico view of ATSP-7041M's translocation from the extracellular to the intracellular region, highlighting the significance of peptide-lipid interactions and dynamics in enabling peptide transit through membranes.

DOI: https://doi.org/10.1021/jacs.4c04230
ACS Omega. 2024 Jul 30. 9(30): 32991-32999

De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure.

Jaehui Park, Eiki Yamashita, Jaehoon Yu, Soo Jae Lee, Soonsil Hyun.

Recent attention has focused on the de novo design of proteins, paralleling advancements in biopharmaceuticals. Achieving protein designs with both structure and function poses a significant challenge, particularly considering the importance of quaternary structures, such as oligomers, in protein function. The cell penetration properties of peptides are of particular interest as they involve the penetration of large molecules into cells. We previously suggested a link between the oligomerization propensity of amphipathic peptides and their cell penetration abilities, yet concrete evidence at cellular-relevant concentrations was lacking due to oligomers' instability. In this study, we sought to characterize oligomerization states using various techniques, including X-ray crystallography, acceptor photobleaching Förster resonance energy transfer (FRET), native mass spectrometry (MS), and differential scanning calorimetry (DSC), while exploring the function related to oligomer status. X-ray crystallography revealed the atomic structures of oligomers formed by LK-3, a bis-disulfide bridged dimer with amino acid sequence LKKLCLKLKKLCKLAG, and its derivatives, highlighting the formation of hexamers, specifically the trimer of dimers, which exhibited a stable hydrophobic core. FRET experiments showed that LK-3 oligomer formation was associated with cell penetration. Native MS confirmed higher-order oligomers of LK-3, while an intriguing finding was the enhanced cell-penetrating capability of a 1:1 mixture of l/d-peptide dimers compared to pure enantiomers. DSC analysis supported the notion that this enantiomeric mixture promotes the formation of functional oligomers, crucial for cell penetration. In conclusion, our study provides direct evidence that amphipathic peptide LK-3 forms oligomers at low nanomolar concentrations, underscoring their significance in cell penetration behavior.

DOI: https://doi.org/10.1021/acsomega.4c04004
Angew Chem Int Ed Engl. 2024 Aug 07. e202405941

Development of Macrocyclic Neurotensin Receptor Type 2 (NTS2) Opioid-Free Analgesics.

Michael Desgagné, Magali Chartier, Camille Lagard, Sára Ferková, Mathieu Choquette, Jean-Michel Longpré, Jérôme Côté, Pierre-Luc Boudreault, Philippe Sarret.

  The opioid crisis has highlighted the urgent need to develop non-opioid alternatives for managing pain, with an effective, safe, and non-addictive pharmacotherapeutic profile. Using an extensive structure-activity relationship approach, here we have identified a new series of highly selective neurotensin receptor type 2 (NTS2) macrocyclic compounds that exert potent, opioid-independent analgesia in various experimental pain models. To our knowledge, the constrained macrocycle in which the Ile12 residue of NT(7-12) was substituted by cyclopentylalanine, Pro7 and Pro10 were replaced by allyl-glycine followed by side-chain to side-chain cyclization is the most selective analog targeting NTS2 identified to date (Ki 2.9 nM), showing 30,000-fold selectivity over NTS1. Of particular importance, this macrocyclic analog is also able to potentiate the analgesic effects of morphine in a dose- and time-dependent manner. Exerting complementary analgesic actions via distinct mechanisms of nociceptive transmission, NTS2-selective macrocycles can therefore be exploited as opioid-free analgesics or as opioid-sparing therapeutics, offering superior pain relief with reduced adverse effects to pain patients.

Keywords:  Cyclic peptides; NTS2 G-protein coupled receptor; analgesia and pain; opioid-sparing; structure-activity relationship

DOI:  https://doi.org/10.1002/anie.202405941
Angew Chem Int Ed Engl. 2024 Aug 08. e202409012

Exocyclic and Linker Editing of Lys63-linked Ubiquitin Chains Modulators Specifically Inhibits Non-homologous End-joining Repair.

Ashraf Brik, Abhishek Saha, Laila A Bishara, Yakop Saed, Ganga B Vamisetti, Shaswati Mandal, Hiroaki Suga, Nabieh Ayoub.

  Despite the great advances in discovering cyclic peptides against protein targets, their reduced aqueous solubility, cell permeability, and activity of the cyclic peptide restrict its utilization in advanced biological research and therapeutic applications. Here we report on a novel approach of structural alternation of the exocyclic and linker parts that led to a new derivative with significantly improved cell activity allowing us to dissect its mode of action in detail. We have identified an effective cyclic peptide (CP7) that induces approximately a 9-fold increase in DNA damage accumulation and a remarkable increase in apoptotic cancer cell death compared to the reported molecule. Notably, treating cells with CP7 leads to a dramatic decrease in the efficiency of non-homologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs), which is accompanied by an increase in homologous recombination (HR) repair. Interestingly, treating BRCA1-deficient cells with CP7 restores HR integrity, which is accompanied by increased resistance to CP7. Additionally, CP7 treatment increases the sensitivity of cancer cells to ionizing radiation. Collectively, our findings demonstrate that CP7 is a selective inhibitor of NHEJ, offering a potential strategy to enhance the effectiveness of radiation therapy.

Keywords:  cyclic peptide * DNA damage repair * non-homologous end joining * apoptosis * reporter assay * radiotherapy

DOI:  https://doi.org/10.1002/anie.202409012
Chem Commun (Camb). 2024 Aug 08.

An N-ortho-nitrobenzylated benzanilide amino acid enables control of the conformation and membrane permeability of cyclic peptides.

Yuko Otani, Asami Ichinose, Xihong Wang, Zhihan Huang, Akitomo Kasahara, Mayumi Ishii, Eri Watanabe, Kayoko Kanamitsu, Kempei Tai, Hiroyuki Kusuhara, Takumi Ueda, Koh Takeuchi, Tomohiko Ohwada.

We designed and synthesized an N-ortho-nitrobenzylated benzanilide-based amino acid having a cis-amide structure that facilitates cyclization of peptides containing it. Photo-induced removal of the nitrobenzyl group from this residue in the resulting cyclized peptides dramatically alters their conformation and passive membrane permeability via complete cis-amide to trans-amide conversion.

DOI: https://doi.org/10.1039/d4cc02738h
J Med Chem. 2024 Aug 08.

Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities.

Rahul Deb, Marcelo D T Torres, Miroslav Boudný, Markéta Koběrská, Floriana Cappiello, Miroslav Popper, Kateřina Dvořáková Bendová, Martina Drabinová, Adelheid Hanáčková, Katy Jeannot, Miloš Petřík, Maria Luisa Mangoni, Gabriela Balíková Novotná, Marek Mráz, Cesar de la Fuente-Nunez, Robert Vácha.

Peptides that form transmembrane barrel-stave pores are potential alternative therapeutics for bacterial infections and cancer. However, their optimization for clinical translation is hampered by a lack of sequence-function understanding. Recently, we have de novo designed the first synthetic barrel-stave pore-forming antimicrobial peptide with an identified function of all residues. Here, we systematically mutate the peptide to improve pore-forming ability in anticipation of enhanced activity. Using computer simulations, supported by liposome leakage and atomic force microscopy experiments, we find that pore-forming ability, while critical, is not the limiting factor for improving activity in the submicromolar range. Affinity for bacterial and cancer cell membranes needs to be optimized simultaneously. Optimized peptides more effectively killed antibiotic-resistant ESKAPEE bacteria at submicromolar concentrations, showing low cytotoxicity to human cells and skin model. Peptides showed systemic anti-infective activity in a preclinical mouse model of Acinetobacter baumannii infection. We also demonstrate peptide optimization for pH-dependent antimicrobial and anticancer activity.

DOI: https://doi.org/10.1021/acs.jmedchem.4c00912
J Labelled Comp Radiopharm. 2024 Aug 08.

68Ga Radiolabeling of NODASA-Functionalized Phage Display-Derived Peptides for Prospective Assessment as Tuberculosis-Specific PET Radiotracers.

Christiaan A Gouws, Tricia Naicker, Beatriz G de la Torre, Fernando Albericio, Janie Duvenhage, Hendrik G Kruger, Biljana Marjanovic-Painter, Sipho Mdanda, Jan R Zeevaart, Thomas Ebenhan, Thavendran Govender.

  This research presents the development of positron emission tomography (PET) radiotracers for detecting Mycobacterium tuberculosis (MTB) for the diagnosis and monitoring of tuberculosis. Two phage display-derived peptides with proven selective binding to MTB were identified for development into PET radiopharmaceuticals: H8 (linear peptide) and PH1 (cyclic peptide). We sought to functionalize H8/PH1 with NODASA, a bifunctional chelator that allows complexation of PET-compatible radiometals such as gallium-68. Herein, we report on the chelator functionalization, optimized radiosynthesis, and assessment of the radiopharmaceutical properties of [68Ga]Ga-NODASA-H8 and [68Ga]Ga-NODASA-PH1. Robust radiolabeling was achieved using the established routine method, indicating consistent production of a radiochemically pure product (RCP ≥ 99.6%). For respective [68Ga]Ga-NODASA-H8 and [68Ga]Ga-NODASA-PH1, relatively high levels of decay-corrected radiochemical yield (91.2% ± 2.3%, 86.7% ± 4.0%) and apparent molar activity (Am, 3.9 ± 0.8 and 34.0 ± 5.3 GBq/μmol) were reliably achieved within 42 min, suitable for imaging purposes. Notably, [68Ga]Ga-NODASA-PH1 remained stable in blood plasma for up to 2 h, while [68Ga]Ga-NODASA-H8 degraded within 30 min. For both 68Ga peptides, minimal whole-blood cell binding and plasma protein binding were observed, indicating a favorable pharmaceutical behavior. [68Ga]Ga-NODASA-PH1 is a promising candidate for further in vitro/in vivo evaluation as a tuberculosis-specific infection imaging agent.

Keywords:   Mycobacterium tuberculosis ; imaging of infection; phage display; positron emission tomography; radiochemical characterization; radiolabeling

DOI:  https://doi.org/10.1002/jlcr.4120
Microbiol Spectr. 2024 Aug 06. e0099724

Cyclization increases bactericidal activity of arginine-rich cationic cell-penetrating peptide for Neisseria gonorrhoeae.

Constance M John, Suzanne A Otala, Gary A Jarvis.

  We previously reported that a linear cationic 12-amino acid cell-penetrating peptide (CPP) was bactericidal for Neisseria gonorrhoeae. In this study, our objectives were to determine the effect of cyclization of the linear CPP on its antibacterial activity for N. gonorrhoeae and cytotoxicity for human cells. We compared the bactericidal effect of 4-hour treatment with the linear CPP to that of CPPs cyclized by a thioether or a disulfide bond on human challenge and multi-drug resistant (MDR) strains of N. gonorrhoeae grown in cell culture media with 10% fetal bovine serum (FBS). The effect of lipooligosaccharide (LOS) sialylation on bactericidal activity was analyzed. We determined the ability of the CPPs to treat human cells infected in vitro with N. gonorrhoeae, to reduce the inflammatory response of human monocytic cells to gonococci, to kill strains of three commensal Neisseria species, and to inhibit gonococcal biofilms. The cyclized CPPs killed 100% of gonococci from all strains at 100 µM and >90% at 20 µM and were more potent than the linear form. The thioether-linked but not the disulfide-linked CPP was less cytotoxic for human cervical cells compared to the linear CPP. LOS sialylation had minimal effect on bactericidal activity. In treating infected human cells, the thioether-linked CPP at 20 µM killed >60% of extra- and intracellular bacteria and reduced TNF-α expression by THP-1 cells. The potency of the CPPs for the pathogenic and the commensal Neisseria was similar. The thioether-linked CPP partially eradicated gonococcal biofilms. Future studies will focus on determining efficacy in the female mouse model of gonorrhea.IMPORTANCENeisseria gonorrhoeae remains a major cause of sexually transmitted infections with 82 million cases worldwide in 2020, and 710,151 confirmed cases in the US in 2021, up 25% from 2017. N. gonorrhoeae can infect multiple tissues including the urethra, cervix, rectum, pharynx, and conjunctiva. The most serious sequelae are suffered by infected women as gonococci ascend to the upper reproductive tract and cause pelvic inflammatory disease, chronic pelvic pain, and infertility in 10%-20% of women. Control of gonococcal infection is widely recognized as increasingly challenging due to the lack of any vaccine. N. gonorrhoeae has quickly developed resistance to all but one class of antibiotics and the emergence of multidrug-resistant strains could result in untreatable infections. As such, gonorrhea is classified by the Center for Disease Control (CDC) as an urgent public health threat. The research presented herein on new therapeutics for gonorrhea has identified a cyclic cell-penetrating peptide (CPP) as a potent molecule targeting N. gonorrhoeae.

Keywords:  Neisseria gonorrhoeae; bactericidal activity; cell-penetrating peptides; gonorrhea; lipooligosaccharide; sialic acid

DOI:  https://doi.org/10.1128/spectrum.00997-24
J Adv Res. 2024 Aug 05. pii: S2090-1232(24)00325-4. [Epub ahead of print]

DeepB3P: A transformer-based model for identifying blood-brain barrier penetrating peptides with data augmentation using feedback GAN.

Qiang Tang, Wei Chen.

  INTRODUCTION: The blood-brain barrier (BBB) serves as a critical structural barrier and impedes the entry of most neurotherapeutic drugs into the brain. This poses substantial challenges for central nervous system (CNS) drug development, as there is a lack of efficient drug delivery technologies to overcome this obstacle. BBB penetrating peptides (BBBPs) hold promise in overcoming the BBB and facilitating the delivery of drug molecules to the brain. Therefore, precise identification of BBBPs has become a crucial step in CNS drug development. However, most computational methods are designed based on conventional models that inadequately capture the intricate interaction between BBBPs and the BBB. Moreover, the performance of these methods was further hampered by unbalanced datasets.OBJECTIVES: This study addresses the problem of unbalanced datasets in BBBP prediction and proposes a powerful predictor for efficiently and accurately identifying BBBPs, as well as generating analogous BBBPs.
METHODS: A transformer-based deep learning model, DeepB3P, was proposed for predicting BBBP. The feedback generative adversarial network (FBGAN) model was employed to effectively generate analogous BBBPs, addressing data imbalance.
RESULTS: The FBGAN model possesses the ability to generate novel BBBP-like peptides, effectively mitigating the data imbalance in BBBP prediction. Extensive experiments on benchmarking datasets demonstrated that DeepB3P outperforms other BBBP prediction models by approximately 9.09%, 4.55% and 9.41% in terms of specificity, accuracy, and Matthew's correlation coefficient, respectively. For accelerating the progress in BBBP identification and CNS drug design, the proposed DeepB3P was implemented as a webserver, which is accessible at http://cbcb.cdutcm.edu.cn/deepb3p/.
CONCLUSION: The interpretable analyses provided by DeepB3P offer valuable insights and enhance downstream analyses for BBBP identification. Moreover, the BBBP-like peptides generated by FBGAN hold potential as candidates for CNS drug development.

Keywords:  Blood–brain barrier penetrating peptides; Deep learning; Generative adversarial networks; Transformer

DOI:  https://doi.org/10.1016/j.jare.2024.08.002
Cell Chem Biol. 2024 Aug 01. pii: S2451-9456(24)00307-6. [Epub ahead of print]

Regulated induced proximity targeting chimeras-RIPTACs-A heterobifunctional small molecule strategy for cancer selective therapies.

Kanak Raina, Chris D Forbes, Rebecca Stronk, Jonathan P Rappi, Kyle J Eastman, Nilesh Zaware, Xinheng Yu, Hao Li, Amit Bhardwaj, Samuel W Gerritz, Mia Forgione, Abigail Hundt, Madeline P King, Zoe M Posner, Allison D Correia, Andrew McGovern, David E Puleo, Rebekka Chenard, James J Mousseau, J Ignacio Vergara, Ethan Garvin, Jennifer Macaluso, Michael Martin, Kyle Bassoli, Kelli Jones, Marco Garcia, Katia Howard, Madeleine Yaggi, Levi M Smith, Jinshan M Chen, Andrew B Mayfield, Cesar A De Leon, John Hines, Katherine J Kayser-Bricker, Craig M Crews.

  We describe a protein proximity inducing therapeutic modality called Regulated Induced Proximity Targeting Chimeras or RIPTACs: heterobifunctional small molecules that elicit a stable ternary complex between a target protein (TP) selectively expressed in tumor cells and a pan-expressed protein essential for cell survival. The resulting co-operative protein-protein interaction (PPI) abrogates the function of the essential protein, thus leading to death selectively in cells expressing the TP. This approach leverages differentially expressed intracellular proteins as novel cancer targets, with the advantage of not requiring the target to be a disease driver. In this chemical biology study, we design RIPTACs that incorporate a ligand against a model TP connected via a linker to effector ligands such as JQ1 (BRD4) or BI2536 (PLK1) or CDK inhibitors such as TMX3013 or dinaciclib. RIPTACs accumulate selectively in cells expressing the HaloTag-FKBP target, form co-operative intracellular ternary complexes, and induce an anti-proliferative response in target-expressing cells.

Keywords:  Halda Therapeutics; RIPTAC; anticancer drugs; biotechnology; chemical biology; drug discovery; heterobifunctional molecules; oncology; protein proximity; ternary complex

DOI:  https://doi.org/10.1016/j.chembiol.2024.07.005
Eur J Med Chem. 2024 Aug 02. pii: S0223-5234(24)00614-7. [Epub ahead of print]277 116733

Macrocyclic-based strategy in drug design: From lab to the clinic.

Xin Jin, Ning Ding, Hong-Yu Guo, Qing Hu.

  Macrocyclic compounds have emerged as potent tools in the field of drug design, offering unique advantages for enhancing molecular recognition, improving pharmacokinetic properties, and expanding the chemical space accessible to medicinal chemists. This review delves into the evolutionary trajectory of macrocyclic-based strategies, tracing their journey from laboratory innovations to clinical applications. Beginning with an exploration of the defining structural features of macrocycles and their impact on drug-like characteristics, this discussion progresses to highlight key design principles that have facilitated the development of diverse macrocyclic drug candidates. Through a series of illustrative representative case studies from approved macrocyclic drugs and candidates spanning various therapeutic areas, particular emphasis is placed on their efficacy in targeting challenging protein-protein interactions, enzymes, and receptors. Additionally, this review thoroughly examines how macrocycles effectively address critical issues such as metabolic stability, oral bioavailability and selectivity. Valuable insights into optimization strategies employed during both approved and clinical phases underscore successful translation of promising leads into efficacious therapies while providing valuable perspectives on harnessing the full potential of macrocycles in drug discovery and development endeavors.

Keywords:  Clinical translation; Drug candidates; Drug design; Macrocycles; Pharmacokinetics

DOI:  https://doi.org/10.1016/j.ejmech.2024.116733
Explor Drug Sci. 2024 ;2(3): 322-338

Mechanism of the blood-brain barrier modulation by cadherin peptides.

Elinaz Farokhi, Ahmed L Alaofi, Vivitri D Prasasty, Filia Stephanie, Marlyn D Laksitorini, Krzysztof Kuczera, Teruna J Siahaan.

  Aim: This study was aimed at finding the binding site on the human E-cadherin for Ala-Asp-Thr Cyclic 5 (ADTC5), ADTC7, and ADTC9 peptides as blood-brain barrier modulator (BBBM) for determining their mechanism of action in modulating the blood-brain barrier (BBB).Methods: ADTC7 and ADTC9 were derivatives of ADTC5 where the Val6 residue in ADTC5 was replaced by Glu6 and Tyr6 residues, respectively. The binding properties of ADTC5, ADTC7, and ADTC9 to the extracellular-1 (EC1) domain of E-cadherin were evaluated using chemical shift perturbation (CSP) method in the two dimensional (2D) 1H-15N-heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy. Molecular docking experiments were used to determine the binding sites of these peptides to the EC1 domain of E-cadherin.
Results: This study indicates that ADTC5 has the highest binding affinity to the EC1 domain of E-cadherin compared to ADTC7 and ADTC9, suggesting the importance of the Val6 residue as shown in our previous in vitro study. All three peptides have a similar binding site at the hydrophobic binding pocket where the domain swapping occurs. ADTC5 has a higher overlapping binding site with ADTC7 than that of ADTC9. Binding of ADTC5 on the EC1 domain influences the conformation of the EC1 C-terminal tail.
Conclusions: These peptides bind the domain swapping region of the EC1 domain to inhibit the trans-cadherin interaction that creates intercellular junction modulation to increase the BBB paracellular porosity.

Keywords:  Ala-Asp-Thr peptides; NMR; blood-brain barrier; blood-brain barrier modulator; cadherin peptides; molecular docking; trans-cadherin interaction

DOI:  https://doi.org/10.37349/eds.2024.00049
Int J Biol Macromol. 2024 Aug 05. pii: S0141-8130(24)05298-X. [Epub ahead of print] 134493

Structurally decoupled hyaluronic acid hydrogels for studying matrix metalloproteinase-mediated invasion of metastatic breast cancer cells.

Kasra Goodarzi, Shreyas S Rao.

  In recent years, polymeric hydrogels have been employed to investigate cancer cell-extracellular matrix (ECM) interactions in vitro. In the context of breast cancer, cancer cells are known to degrade the ECM using matrix-metalloproteinases (MMPs) to support invasion resulting in disease progression. Polymeric hydrogels incorporating MMP-cleavable peptides have been employed to study cancer cell invasion, however, the approaches employed to incorporate these peptides often change other hydrogel properties. This underscores the need for decoupling hydrogel properties while incorporating MMP-cleavable peptides. Herein, we report structurally decoupled hyaluronic acid (HA) hydrogels formulated using varying ratios of a biologically sensitive MMP-cleavable peptide and an insensitive counterpart (Dithiothreitol (DTT) or polyethylene glycol dithiol (PEGDT)) to study MMP-mediated metastatic breast cancer cell invasion. Rheological, swelling ratio, estimated mesh size, and permeability measurements showed similar mechanical and physical properties for hydrogels crosslinked with different DTT (or PEGDT)/MMP ratios. However, their degradation rate in the presence of collagenase correlated with the ratio of MMP-cleavable peptide. Encapsulated metastatic breast cancer spheroids in HA hydrogels with MMP sensitivity exhibited increased invasiveness compared to those without MMP sensitivity after 14 days of culture. Overall, such structurally decoupled HA hydrogels provide a platform to study MMP-mediated breast cancer cell invasion in vitro.

Keywords:  Breast cancer metastasis; Crosslinking; Hyaluronic acid; Hydrogel; Invasion; Spheroids

DOI:  https://doi.org/10.1016/j.ijbiomac.2024.134493
iScience. 2024 Aug 16. 27(8): 110426

A cyclic peptide-grafted Fc with hepatocyte growth factor functionality ameliorates hepatic fibrosis in a non-alcoholic steatohepatitis mouse model.

Nichole Marcela Rojas-Chaverra, Ryu Imamura, Hiroki Sato, Toby Passioura, Emiko Mihara, Tatsunori Nishimura, Junichi Takagi, Hiroaki Suga, Kunio Matsumoto, Katsuya Sakai.

  The regenerative functions associated with cytokines and growth factors have immense therapeutic potential; however, their poor pharmacokinetics, resulting from structural features, hinder their effectiveness. In this study, we aimed to enhance the pharmacokinetics of growth factors by designing receptor-binding macrocyclic peptides through in vitro mRNA display and grafting them into loops of immunoglobulin's crystallizable region (Fc). As a model, we developed peptide-grafted Fc proteins with hepatocyte growth factor (HGF) functionality that exhibited a prolonged circulation half-life and could be administered subcutaneously. The Fc-based HGF mimetic alleviated liver fibrosis in a mouse model fed a choline-deficient high-fat diet, which induces hepatic features of non-alcoholic steatohepatitis, including fibrosis, showcasing its potential as a therapeutic intervention. This study provides a basis for developing growth factor and cytokine mimetics with improved pharmacokinetics, expanding their therapeutic applications.

Keywords:  Biomimetics; Fibrosis; Model organism; Peptides

DOI:  https://doi.org/10.1016/j.isci.2024.110426
Chemistry. 2024 Aug 08. e202402049

Inhibition of Lysosomal Cathepsin A and Neuraminidase 1 Interaction by Anti-obesity Cyclic Peptide.

Masaki Kita, Yiting Sun, Ayumi Dakiiwa, Menghua Zhang, Takahiro Shibata.

  Chronic inflammation in adipose tissue is associated with metabolic disorders such as obesity and type 2 diabetes. Novel small molecules targeting adipocyte differentiation and fat accumulation offer potential for new anti-inflammatory and anti-obesity drugs. Here we show that the marine cyclic heptapeptide stylissatin A and its analogs (SAs) inhibit membranous neuraminidase 1 (Neu1) function by interacting with lysosomal protective protein cathepsin A (PPCA). Neu1 has been less explored as a therapeutic target due to the genetic defects leading to neurodegenerative disorders. However, unlike traditional neuraminidase inhibitors, SAs don't directly bind to Neu1 but modulate the molecular chaperone activity of PPCA. SAs caused degradation of perilipin 1 around lipid droplets and inhibited fat accumulation, along with decrease in membranous Neu1. Molecular docking and molecular dynamics simulations revealed that SAs interacted with activated PPCA at the Neu1 binding site. Focusing on this newfound protein-protein interaction inhibition mechanism could lead to the development of pharmaceuticals with fewer side effects.

Keywords:  Bioactive Natural Products; Molecular Dynamics Simulation; PPI inhibitor; Protective Protein Cathepsin A; chemical probe

DOI:  https://doi.org/10.1002/chem.202402049
Nat Commun. 2024 Aug 05. 15(1): 6645

Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.

F Emil Thomasen, Tórur Skaalum, Ashutosh Kumar, Sriraksha Srinivasan, Stefano Vanni, Kresten Lindorff-Larsen.

Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is difficult. We have previously shown that the coarse-grained model, Martini 3, produces too compact ensembles in solution, that may in part be remedied by strengthening protein-water interactions. Here, we show that decreasing the strength of protein-protein interactions leads to improved agreement with experimental data on a wide set of systems. We show that the 'symmetry' between rescaling protein-water and protein-protein interactions breaks down when studying interactions with or within membranes; rescaling protein-protein interactions better preserves the binding specificity of proteins with lipid membranes, whereas rescaling protein-water interactions preserves oligomerization of transmembrane helices. We conclude that decreasing the strength of protein-protein interactions improves the accuracy of Martini 3 for IDPs and multidomain proteins, both in solution and in the presence of a lipid membrane.

DOI: https://doi.org/10.1038/s41467-024-50647-9
Int J Pharm. 2024 Aug 05. pii: S0378-5173(24)00792-0. [Epub ahead of print] 124558

The peptide-based bispecific CAR T cells target EGFR and tumor stroma for effective cancer therapy.

Cuijuan Liu, Qianqian Wang, Lin Li, Fan Gao, Yuanyue Zhang, Yimin Zhu.

  BACKGROUND AND PURPOSE: The efficacy of chimeric antigen receptor (CAR)-T cell for solid tumors is limited partially because of the lack of tumor-specific antigens and off-target effects. Low molecular weight peptides allowed CAR T cell to display several antigen receptors to reduce off-target effects. Here, we develop a peptide-based bispecific CAR for EGFR and tumor stroma, which are expressed in a variety of tumor types.EXPERIMENTAL APPROACH AND KEY RESULTS: The peptide-based CAR T cells show excellent proliferation, cytotoxicity activity and are only activated by tumor cells overexpressing EGFR instead of normal cells with low EGFR expressing. In mouse xenograft models, the peptide bispecific CAR T cells can be delivered into the inner of tumor masses and thus are effective in inhibiting tumor growth. Meanwhile, they show strong expansion capacity and the property of maintaining long-term function in vivo. During treatment, no off-tumor toxicity is observed on healthy organs expressing lower levels of EGFR.
CONCLUSIONS & IMPLICATIONS: Our findings demonstrate that peptide-based bispecific CAR T holds great potential in solid tumor therapy due to an excellent targeting ability towards tumors and tumor microenvironment.

Keywords:  Affinity; Chimeric antigen receptor; Off-target effect; Peptide; TAA

DOI:  https://doi.org/10.1016/j.ijpharm.2024.124558
J Am Chem Soc. 2024 Aug 03.

Diverse Proteomimetic Frameworks via Rational Design of π-Stacking Peptide Tectons.

Pragati Ganatra, Daniel F Wang, Vaibhav Ganatra, Viet Thuc Dang, Andy I Nguyen.

Peptide-based frameworks aim to integrate protein architecture into solid-state materials using simpler building blocks. Despite the growing number of peptide frameworks, there are few strategies to rationally engineer essential properties like pore size and shape. Designing peptide assemblies is generally hindered by the difficulty of predicting complex networks of weak intermolecular interactions. Peptides conjugated to polyaromatic groups are a unique case where assembly appears to be strongly driven by π-π interactions, suggesting that rationally adjusting the geometry of the π-stackers could create novel structures. Here, we report peptide elongation as a simple mechanism to predictably tune the angle between the π-stacking groups to produce a remarkable diversity of pore shapes and sizes, including some that are mesoporous. Notably, rapid jumps in pore size and shape can occur with just a single amino acid insertion. The geometry of the π-stacking residues also significantly influences framework structure, representing an additional dimension for tuning. Lastly, sequence identity can also indirectly modulate the π-π interactions. By correlating each of these factors with detailed crystallographic data, we find that, despite the complexity of peptide structure, the shape and polarity of the tectons are straightforward predictors of framework structure. These guidelines are expected to accelerate the development of advanced porous materials with protein-like capabilities.

DOI: https://doi.org/10.1021/jacs.4c03094