bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2024–04–28
thirteen papers selected by
Henry Lamb, Queensland University of Technology
  1. An efficient mRNA display protocol yields potent bicyclic peptide inhibitors for FGFR3c: outperforming linear and monocyclic formats in affinity and stability.
  2. Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides.
  3. Investigating the impact of thiol reactivity and disulfide formation on cellular uptake of cell-permeable peptides.
  4. Development of a Decafluorobiphenyl Cyclized Peptide Targeting the NEMO-IKKα/β Interaction that Enhances Cell Penetration and Attenuates Lipopolysaccharide-Induced Acute Lung Injury.
  5. 68Ga labeled EphA2-targeted cyclic peptide: a novel positron imaging tracer for triple-negative breast cancer?
  6. Process Development of a Macrocyclic Peptide Inhibitor of PD-L1.
  7. Expansive discovery of chemically diverse structured macrocyclic oligoamides.
  8. mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B.
  9. Discovery of Novel Dual Inhibitors Targeting Mutant IDH1 and NAMPT for the Treatment of Glioma with IDH1Mutation.
  10. Organelle-targeted Laurdans measure heterogeneity in subcellular membranes and their responses to saturated lipid stress.
  11. Prospective de novo drug design with deep interactome learning.
  12. Alpha-emitter Peptide Receptor Radionuclide Therapy in Neuroendocrine Tumors.
  13. Synergistic Activity of DNA Damage Response Inhibitors in Combination with Radium-223 in Prostate Cancer.
  1. Chem Sci. 2024 Apr 24. 15(16): 6122-6129
    An efficient mRNA display protocol yields potent bicyclic peptide inhibitors for FGFR3c: outperforming linear and monocyclic formats in affinity and stability.
    Camille Villequey, Silvana S Zurmühl, Christian N Cramer, Bhaskar Bhusan, Birgitte Andersen, Qianshen Ren, Haimo Liu, Xinping Qu, Yang Yang, Jia Pan, Qiujia Chen, Martin Münzel.
      Macrocyclization has positioned itself as a powerful method for engineering potent peptide drug candidates. Introducing one or multiple cyclizations is a common strategy to improve properties such as affinity, bioavailability and proteolytic stability. Consequently, methodologies to create large libraries of polycyclic peptides by phage or mRNA display have emerged, allowing the rapid identification of binders to virtually any target. Yet, within those libraries, the performance of linear vs. mono- or bicyclic peptides has rarely been studied. Indeed, a key parameter to perform such a comparison is to use a display protocol and cyclization chemistry that enables the formation of all 3 formats in equal quality and diversity. Here, we developed a simple, efficient and fast mRNA display protocol which meets these criteria and can be used to generate highly diverse libraries of thioether cyclized polycyclic peptides. As a proof of concept, we selected peptides against fibroblast growth factor receptor 3c (FGFR3c) and compared the different formats regarding affinity, specificity, and human plasma stability. The peptides with the best KD's and stability were identified among bicyclic peptide hits, further strengthening the body of evidence pointing at the superiority of this class of molecules and providing functional and selective inhibitors of FGFR3c.
    DOI:  https://doi.org/10.1039/d3sc04763f
  2. PLoS One. 2024 ;19(4): e0300688
    Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides.
    Nicolas Frazee, Kyle R Billlings, Blake Mertz.
      Despite their widespread use as therapeutics, clinical development of small molecule drugs remains challenging. Among the many parameters that undergo optimization during the drug development process, increasing passive cell permeability (i.e., log(P)) can have some of the largest impact on potency. Cyclic peptides (CPs) have emerged as a viable alternative to small molecules, as they retain many of the advantages of small molecules (oral availability, target specificity) while being highly effective at traversing the plasma membrane. However, the relationship between the dominant conformations that typify CPs in an aqueous versus a membrane environment and cell permeability remain poorly characterized. In this study, we have used Gaussian accelerated molecular dynamics (GaMD) simulations to characterize the effect of solvent on the free energy landscape of lariat peptides, a subset of CPs that have recently shown potential for drug development (Kelly et al., JACS 2021). Differences in the free energy of lariat peptides as a function of solvent can be used to predict permeability of these molecules, and our results show that permeability is most greatly influenced by N-methylation and exposure to solvent. Our approach lays the groundwork for using GaMD as a way to virtually screen large libraries of CPs and drive forward development of CP-based therapeutics.
    DOI:  https://doi.org/10.1371/journal.pone.0300688
  3. J Pept Sci. 2024 Apr 23. e3604
    Investigating the impact of thiol reactivity and disulfide formation on cellular uptake of cell-permeable peptides.
    Merlin Klußmann, Katharina Stillger, Melina Ruppel, Coco-Louisa Sticker, Ines Neundorf.
      Cell-penetrating peptides (CPPs) have been explored as versatile tools to transport various molecules into cells. The uptake mechanism of CPPs is still not clearly understood and most probably depends on several factors like the nature of the CPP itself, the attached cargo, the investigated cell system, and other experimental conditions, such as temperature and concentration. One of the first steps of internalization involves the interaction of CPPs with negatively charged molecules present at the outer layer of the cell membrane. Recently, thiol-mediated uptake has been found to support the effective translocation of sulfhydryl-bearing substances that would actually not be cell-permeable. Within this work, we aimed to understand the relevance of thiol reactivity for the uptake mechanism of cysteine-containing CPPs that we have developed previously in our group. Therefore, we compared the two peptides, sC18-Cys and CaaX-1, in their single reduced and dimeric disulfide versions. Cytotoxicity, intracellular accumulation, and impact on the internalization process of the disulfides were investigated in HeLa cells. Both disulfide CPPs demonstrated significantly stronger cytotoxic effects and membrane activity compared with their reduced counterparts. Notably, thiol-mediated uptake could be excluded as a main driver for translocation, showing that peptides like CaaX-1 are most likely taken up by other mechanisms.
    Keywords:  cellular uptake; cell‐penetrating peptides; disulfide exchange; thiol reactivity
    DOI:  https://doi.org/10.1002/psc.3604
  4. Bioconjug Chem. 2024 Apr 26.
    Development of a Decafluorobiphenyl Cyclized Peptide Targeting the NEMO-IKKα/β Interaction that Enhances Cell Penetration and Attenuates Lipopolysaccharide-Induced Acute Lung Injury.
    Shu Li, Shibo Song, Xiaojing Liu, Xingjiao Zhang, Xueya Liang, Xin Chang, Daijun Zhou, Jianting Han, Yaoyan Nie, Chen Guo, Xiaojun Yao, Min Chang, Yali Peng.
      Aberrant canonical NF-κB signaling has been implicated in diseases, such as autoimmune disorders and cancer. Direct disruption of the interaction of NEMO and IKKα/β has been developed as a novel way to inhibit the overactivation of NF-κB. Peptides are a potential solution for disrupting protein-protein interactions (PPIs); however, they typically suffer from poor stability in vivo and limited tissue penetration permeability, hampering their widespread use as new chemical biology tools and potential therapeutics. In this work, decafluorobiphenyl-cysteine SNAr chemistry, molecular modeling, and biological validation allowed the development of peptide PPI inhibitors. The resulting cyclic peptide specifically inhibited canonical NF-κB signaling in vitro and in vivo, and presented positive metabolic stability, anti-inflammatory effects, and low cytotoxicity. Importantly, our results also revealed that cyclic peptides had huge potential in acute lung injury (ALI) treatment, and confirmed the role of the decafluorobiphenyl-based cyclization strategy in enhancing the biological activity of peptide NEMO-IKKα/β inhibitors. Moreover, it provided a promising method for the development of peptide-PPI inhibitors.
    DOI:  https://doi.org/10.1021/acs.bioconjchem.4c00122
  5. Dalton Trans. 2024 Apr 22.
    68Ga labeled EphA2-targeted cyclic peptide: a novel positron imaging tracer for triple-negative breast cancer?
    Bin Qu, Xianjun Li, Yuze Ma, Yanzhi Wang, Yeming Han, Guihua Hou, Feng Gao.
      The absence of better biomarkers currently limits early diagnosis and treatment of triple-negative breast cancer (TNBC). Our previously published study reported that the cyclic-peptide SD01 exhibited specific binding to EphA2 (Ephrin type-A receptor 2) on TNBC. To develop a novel PET imaging agent, we prepared gallium-68 (68Ga) labeled-DOTA-SD01 and evaluated its specificity and effectiveness through micro PET/CT imaging in a TNBC-bearing mouse model. SD01 and a control linear peptide YSA were conjugated to DOTA and subsequently labeled with 68Ga, obtaining 68Ga-DOTA-SD01 and 68Ga-DOTA-YSA. Both showed high radiochemical purity, stability, good hydrophilicity, and high binding affinity to 4T1 cells. Micro PET/CT imaging showed high radioactivity accumulation in tumors; SUVmean (mean standardized uptake value) of tumors in the group of 68Ga-DOTA-SD01 was 3.34 ± 0.25 and 2.65 ± 0.32 in the group of 68Ga-DOTA-YSA; T/NT ratios (target to non-target, SUVmean ratios of tumor to muscle) were 3.12 ± 0.06 and 2.77 ± 0.11 at 30 min, respectively (p < 0.05). The biodistribution study showed that tumor uptake % ID per g (percentage of injected dose per gram of tissue) in the group of 68Ga-DOTA-SD01 was 2.73 ± 0.34, and 1.77 ± 0.38 in the group of 68Ga-DOTA-YSA; T/NT ratios (radioactivity of tumor to muscle) were 3.55 ± 0.12 and 3.05 ± 0.10 for both groups at 30 min, respectively (p < 0.05). All these suggest that 68Ga-DOTA-SD01 may act as a better novel PET imaging agent for EphA2 positive tumors, such as TNBC.
    DOI:  https://doi.org/10.1039/d4dt00837e
  6. J Org Chem. 2024 Apr 25.
    Process Development of a Macrocyclic Peptide Inhibitor of PD-L1.
    Subha Mukherjee, Amanda Rogers, Gardner Creech, Chao Hang, Antonio Ramirez, Michael Dummeldinger, Shawn Brueggemeier, Claudio Mapelli, Serge Zaretsky, Masano Huang, Regina Black, Michael B Peddicord, Nicolas Cuniere, James Kempson, Joseph Pawluczyk, Martin Allen, Rodney Parsons, Chris Sfouggatakis.
      This article outlines the process development leading to the manufacture of 800 g of BMS-986189, a macrocyclic peptide active pharmaceutical ingredient. Multiple N-methylated unnatural amino acids posed challenges to manufacturing due to the lability of the peptide to cleavage during global side chain deprotection and precipitation steps. These issues were exacerbated upon scale-up, resulting in severe yield loss and necessitating careful impurity identification, understanding the root cause of impurity formation, and process optimization to deliver a scalable synthesis. A systematic study of macrocyclization with its dependence on concentration and pH is presented. In addition, a side chain protected peptide synthesis is discussed where the macrocyclic protected peptide is extremely labile to hydrolysis. A computational study explains the root cause of the increased lability of macrocyclic peptide over linear peptide to hydrolysis. A process solution involving the use of labile protecting groups is discussed. Overall, the article highlights the advancements achieved to enable scalable synthesis of an unusually labile macrocyclic peptide by solid-phase peptide synthesis. The sustainability metric indicates the final preparative chromatography drives a significant fraction of a high process mass intensity (PMI).
    DOI:  https://doi.org/10.1021/acs.joc.4c00430
  7. Science. 2024 Apr 26. 384(6694): 420-428
    Expansive discovery of chemically diverse structured macrocyclic oligoamides.
    Patrick J Salveson, Adam P Moyer, Meerit Y Said, Gizem Gӧkçe, Xinting Li, Alex Kang, Hannah Nguyen, Asim K Bera, Paul M Levine, Gaurav Bhardwaj, David Baker.
      Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug design.
    DOI:  https://doi.org/10.1126/science.adk1687
  8. ACS Chem Biol. 2024 Apr 24.
    mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B.
    Gregor S Cremosnik, Yannick Mesrouze, Patrik Zueger, David Furkert, Frédéric Grandjean, Dayana Argoti, Fanny Mermet-Meillon, Matthias R Bauer, Scott Brittain, Phuong Rogemoser, Winnie Yang, Jerome Giovannoni, Lynn McGregor, Jenny Tang, Mark Knapp, Sandra Holzinger, Sylvia Buhr, Lionel Muller, Lukas Leder, Lili Xie, Cesar Fernandez, Cristina Nieto-Oberhuber, Patrick Chène, Giorgio G Galli, Fabian Sesterhenn.
      The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.
    DOI:  https://doi.org/10.1021/acschembio.4c00083
  9. J Med Chem. 2024 Apr 23.
    Discovery of Novel Dual Inhibitors Targeting Mutant IDH1 and NAMPT for the Treatment of Glioma with IDH1Mutation.
    Fei Wen, Gang Gui, Xiaoyu Wang, Anqi Qin, Tianfang Ma, Hui Chen, Chunzheng Li, Xiaoming Zha.
      The targeting of cancer cell intrinsic metabolism has emerged as a promising strategy for antitumor intervention. In the study, we identified the first-in-class small molecules that effectively inhibit both mutant isocitrate dehydrogenase 1 (mIDH1) and nicotinamide phosphoribosyltransferase (NAMPT), two crucial targets in cancer metabolism, through structure-based drug design. Notably, compound 23h exhibits excellent and balanced inhibitory activities against both mIDH1 (IC50 = 14.93 nM) and NAMPT (IC50 = 12.56 nM), leading to significant suppression of IDH1-mutated glioma cell (U87 MG-IDH1R132H) proliferation. Significantly, compound 23h has the ability to cross the blood-brain barrier (B/P ratio, 0.76) and demonstrates remarkable in vivo antitumor efficacy (20 mg/kg) in the U87 MG-IDH1R132H orthotopic transplantation mouse models without any notable toxicity. This proof-of-concept investigation substantiates the viability of discovering small molecules that concurrently target mIDH1 and NAMPT, providing valuable leads for the treatment of glioma and an efficient approach for the discovery of multitarget antitumor drugs.
    DOI:  https://doi.org/10.1021/acs.jmedchem.3c02482
  10. bioRxiv. 2024 Apr 20. pii: 2024.04.16.589828. [Epub ahead of print]
    Organelle-targeted Laurdans measure heterogeneity in subcellular membranes and their responses to saturated lipid stress.
    Adrian M Wong, Itay Budin.
      Cell organelles feature characteristic lipid compositions that lead to differences in membrane properties. In living cells, membrane ordering and fluidity are commonly measured using the solvatochromic dye Laurdan, whose fluorescence is sensitive to membrane packing. As a general lipophilic dye, Laurdan stains all hydrophobic environments in cells, so it is challenging to characterize membrane properties in specific organelles or assess their responses to pharmacological treatments in intact cells. Here, we describe the synthesis and application of Laurdan-derived probes that read out membrane packing of individual cellular organelles. The set of Organelle-targeted Laurdans (OTL) localizes to the ER, mitochondria, lysosomes and Golgi compartments with high specificity, while retaining the spectral resolution needed to detect biological changes in membrane packing. We show that ratiometric imaging with OTL can resolve membrane heterogeneity within organelles, as well as changes in membrane packing resulting from inhibition of lipid trafficking or bioenergetic processes. We apply these probes to characterize organelle-specific responses to saturated lipid stress. While ER and lysosomal membrane fluidity is sensitive to exogenous saturated fatty acids, that of mitochondrial membranes is protected. We then use differences in ER membrane fluidity to sort populations of cells based on their fatty acid diet, highlighting the ability of organelle-localized solvatochromic probes to distinguish between cells based on their metabolic state. These results expand the repertoire of targeted membrane probes and demonstrate their application to interrogating lipid dysregulation.
    DOI:  https://doi.org/10.1101/2024.04.16.589828
  11. Nat Commun. 2024 Apr 22. 15(1): 3408
    Prospective de novo drug design with deep interactome learning.
    Kenneth Atz, Leandro Cotos, Clemens Isert, Maria Håkansson, Dorota Focht, Mattis Hilleke, David F Nippa, Michael Iff, Jann Ledergerber, Carl C G Schiebroek, Valentina Romeo, Jan A Hiss, Daniel Merk, Petra Schneider, Bernd Kuhn, Uwe Grether, Gisbert Schneider.
      De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the "zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.
    DOI:  https://doi.org/10.1038/s41467-024-47613-w
  12. PET Clin. 2024 Apr 23. pii: S1556-8598(24)00020-8. [Epub ahead of print]
    Alpha-emitter Peptide Receptor Radionuclide Therapy in Neuroendocrine Tumors.
    Sudhir Bhimaniya, Hina Shah, Heather Jacene.
      Peptide receptor radionuclide therapy (PRRT) has become mainstream therapy of metastatic neuroendocrine tumors not controlled by somatostatin analog therapy. Currently, beta particle-emitting radiopharmaceuticals are the mainstay of PRRT. Alpha particle-emitting radiopharmaceuticals have a theoretic advantage over beta emitters in terms of improved therapeutic efficacy due to higher cancer cell death and lower nontarget tissue radiation-induced adverse events due to shorter path length of alpha particles. We discuss the available evidence for and the role of alpha particle PRRT.
    Keywords:  Alpha particles; Beta particles; Neuroendocrine tumors; Peptide receptor radiopharmaceutical therapy (PRRT); Somatostatin receptors
    DOI:  https://doi.org/10.1016/j.cpet.2024.03.005
  13. Cancers (Basel). 2024 Apr 15. pii: 1510. [Epub ahead of print]16(8):
    Synergistic Activity of DNA Damage Response Inhibitors in Combination with Radium-223 in Prostate Cancer.
    Victoria L Dunne, Timothy C Wright, Francisco D C Guerra Liberal, Joe M O'Sullivan, Kevin M Prise.
      Radium-223 (223Ra) and Lutetium-177-labelled-PSMA-617 (177Lu-PSMA) are currently the only radiopharmaceutical treatments to prolong survival for patients with metastatic-castration-resistant prostate cancer (mCRPC); however, mCRPC remains an aggressive disease. Recent clinical evidence suggests patients with mutations in DNA repair genes associated with homologous recombination have a greater clinical benefit from 223Ra. In this study, we aimed to determine the utility of combining DNA damage response (DDR) inhibitors to increase the therapeutic efficacy of X-rays, or 223Ra. Radiobiological responses were characterised by in vitro assessment of clonogenic survival, repair of double strand breaks, cell cycle distribution, and apoptosis via PARP-1 cleavage. Here, we show that DDR inhibitors increase the therapeutic efficacy of both radiation qualities examined, which is associated with greater levels of residual DNA damage. Co-treatment of ATM or PARP inhibition with 223Ra increased cell cycle arrest in the G2/M phase. In comparison, combined ATR inhibition and radiation qualities caused G2/M checkpoint abrogation. Additionally, greater levels of apoptosis were observed after the combination of DDR inhibitors with 223Ra. This study identified the ATR inhibitor as the most synergistic inhibitor for both radiation qualities, supporting further pre-clinical evaluation of DDR inhibitors in combination with 223Ra for the treatment of prostate cancer.
    Keywords:  ATM inhibition; ATR inhibition; DNA damage; PARP inhibition; X-rays; cell cycle checkpoints; prostate cancer; radium-223
    DOI:  https://doi.org/10.3390/cancers16081510
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